J. Crop Sci. Biotech.

2015 (December) 18 (5) : 293 ~ 308

DOI No. 10.1007/s 12892-015-0037-5
REVIEW ARTICLE

Recent Advances in Molecular Marker Techniques: Insight into QTL

Mapping, GWAS and Genomic Selection in Plants
Sajad Majeed Zargar1*, Bodo Raatz2, Humira Sonah3, MuslimaNazir4, Javid A Bhat5, Zahoor Ahmad Dar6,
Ganesh Kumar Agrawal7, Randeep Rakwal7,8
Centre for Plant Biotechnology, Division of Biotechnology, S K University of Agricultural Sciences and Technology of
Kashmir, Shalimar, Srinagar, Jammu & Kashmir-190025, India
2
International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
3
Dpartement de phytologie-FSAA, Universit Laval, Qubec, Qc G1V 0A6
4
Department of Botany, Faculty of Science, Jamia Hamdard University, New Delhi-110062, India
5
Division of Plant Breeding & Genetics, S K University of Agricultural Sciences and Technology of Jammu, Chatha, Jammu,
Jammu & Kashmir-180009, India
6
Division of Plant Breeding & Genetics, S K University of Agricultural Sciences and Technology of Kashmir, Shalimar,
Srinagar, Jammu & Kashmir-190025,
7
IndiaResearch Laboratory for Biotechnology and Biochemistry (RLABB), P.O. Box 13265, Kathmandu, Nepal
8
Organization for Educational Initiatives, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba 305-8577, Ibaraki, Japan
1

Received: April 19, 2015 / Revised: August13, 2015 / Accepted: October 4, 2015
Korean Society of Crop Science and Springer 2015

Abstract
Recent advances in sequencing technology have brought several novel platforms for marker development and subsequent
genotyping. The high-throughput and cost effective marker techniques have changed the entire scenario of marker applications. The huge genotypic data obtained with next generation sequencing (NGS) also demands analytical tools, statistical
advances, and comprehensive understanding to cope with breeding applications. In the present review, we discussed different
available marker techniques, their strengths, and limitations. Emphasis was given on software tools, analytical pipelines, workbenches, and online resources available for marker development. Comparison of SNP genotyping involving complexity reduction techniques like GBS, RRL, RAD, and array-based platforms were presented in a view to describe suitability for specific
purposes. We found that genotyping by whole genome re-sequencing has great potential, and could be a routine application in
the near future with continuously decreasing cost of sequencing. Microsatellites, still a valuable option for breeders, have also
advanced with NGS. Here a catalogue of tools for microsatellite evaluation in short sequence reads was provided. The most
common applications of molecular marker like QTL mapping, genome-wide association mapping (GWAS), and genomic
selection were highlighted. The present review will be helpful for the effective utilization of available resources and for the
planning of crop improvement programs employing molecular marker techniques.
Key words : Molecular marker, GBS, NGS, RNA-seq, RAD, QTL, SNP
Abbreviations
AFLP: amplified fragment length polymorphism; CRoPS: complexity reduction of polymorphic sequences; DArT: diversity
array technology; EST: expressed sequence tag; GBS: genotyping by sequencing; GS: genomic selection; GWAS: genomewide association studies; MAS: marker-assisted selection; NGS: next generation sequencing; PCR: polymerase chain reaction;
QTL: quantitative trait loci; RAD: restriction site-associated DNA; RFLP: restriction fragment length polymorphism; RRLs:
reduced-representation libraries; RRS: reduced representation sequencing; SCAR: sequence characterized amplified region;
SGS: second generation sequencing; STS: sequence tagged site; TILLING: targeting induced local lesions in genomes WGS:
whole genome sequencing
Dr. Sajad Majeed Zargar (

)
Tel: +91-7298410126 / Fax: +82-31-695-4095
Email: smzargar@gmail.com

The Korean Society of Crop Science

293

294

Advances in Molecular Marker Techniques

Introduction
The main objective of plant breeding is to attain sustainability in agriculture. This can only be achieved by enhancing crop yield, keeping yield stability, and improving the
quality by crossing elite cultivars of choice with lines that
possess desired new traits. Conventional plant breeding
involves crossing of the elite cultivar with the donor followed
by selection of superior recombinants. The process involves
several crosses and several generations, requiring a careful
phenotypic selection. Moreover, the whole process is time
consuming and laborious. Additionally, there is a threat of
transferring undesirable traits along with the traits of interest.
These drawbacks are major hindrances in enhancing agricultural production (Collard et al. 2005). The availability of
molecular marker technology provides solutions to problems
associated with conventional breeding. Utilization of molecular markers by tagging the desired genes or chromosome
regions during breeding makes the process more efficient and
faster (Collard et al. 2005). Using molecular tools to select
favorable alleles and selection against undesirable background regions also helps the breeder concentrate his/her
work on improved populations.
Genetic markers have evolved from traditional morphological markers to biochemical and currently to molecular
markers. Traditional morphological markers are limited in
number and highly influenced by the environment, which in
turn limits their usefulness. On the other hand, biochemical
markers although more in numbers, are also influenced by
the environment, at times difficult to measure and hence lead
to false positives and negatives in gene-mapping studies.
Using a molecular marker means employing a method to
investigate a certain polymorphic positions on the DNA and
to identify the genotype. Thus, a molecular marker allows
tracing for a genomic region in genetic populations, giving
information from which parent it originated. Molecular
markers detect polymorphisms at the DNA level such as
nucleotide changes: deletion, duplication, inversion, and/or
insertion, transition, and transversion. The evolution of
molecular markers dates back to the use of restriction fragment length polymorphism (RFLP). Due to various limitations of this technique and with coincidence of PCR
(Polymerase Chain Reaction) discovery, PCR-based markers
were developed, which includes a large number of techniques. The discovery of SSR and SNP markers usually
requires DNA sequence information, and is therefore expensive. However, with the emergence of next-generation
sequencing (NGS), the cost of sequencing has dropped dramatically so that it is being routinely used for development of
molecular marker and genotyping (Elshire et al. 2011; Sonah
et al. 2013; Wetterstrand 2014).
Reduced-representation sequencing includes reduced-representation libraries (RRLs), complexity reduction of polymorphic sequences (CRoPS), restriction site-associated DNA
(RAD)-seq, low coverage genotyping, including multiplexed
shotgun genotyping (MSG) and genotyping by sequencing

Fig. 1. Evolution of marker technologies from primitive morphological

markers through restriction fragment length polymorphisms (RFLPs) to
present-day, next-generation sequencing (NGS) based markers.

(GBS), and RNAseq.

NGS data can be used to either identify polymorphisms to
genotype these with other methods or to directly genotype a
large number of lines. These markers have wide application
in plant breeding research including development of dense
genetic and physical maps, trait-maker association either by
QTL mapping or Genome-wide association study (GWAS)
and subsequent utilization through marker-assisted breeding
(MAB) (Koebner 2005; Korzun 2002). Other applications of
molecular markers include genetic diversity analysis, genome
mapping, haplotype determination, harnessing heterosis,
germplasm characterization, genetic diagnostics, characterization of transformants, and the study of genome organization (Jain et al. 2010); these are also used intensively for
quality control in large breeding programs.

Molecular Marker Technology: Technological

advances
Genetic marker technology has evolved rapidly from the
early morphological marker (Fig.1). This molecular marker
technology basically evolved in several phases. The earlier
non-DNA-based markers were laborious, time consuming,
limited in number, and highly influenced by environment,
and subsequently were replaced by DNA-based markers. The
development of DNA-based methods has provided an opportunity to directly analyze differences in the genome of the
organism rather than rely on inferences from analysis of
expressed proteins, i.e. as in isozyme analysis. Early DNAbased methods, i.e. RFLP initiated the era of molecular
marker technology during the 1980s, and is also referred to
as First generation molecular markers (Jones et al. 2009).
RFLP uses hybridization of DNA to detect variation in the
DNA samples and became the standard approach until it was
replaced by PCR-based methods in the 1990s. PCR-based
methods greatly increased the feasibility of high-throughput
marker screening. RAPDs (Random Amplified Polymorphic
DNA) are probably the first PCR-based genetic markers that
were easy to use and inexpensive (Williams et al. 1990).

JCSB 2015 (December) 18 (5) : 293 ~ 308

Table 1. Marker diversity and their characteristics.

Markers

Throughput

Status

DNA quantity
/reaction

Restriction
enzyme needed

PCR
needed

Sequence
information

Multiplexing

Morphological
Biochemical
RFLPs
RAPDs
AFLPs
SSRs
SNPs
SFPs
DArT
RRLs
RAD-seq
CRoPs
GBS
MSG

Low-throughput
Low-throughput
Low-throughput
Medium-throughput
Medium-throughput
Medium-throughput
High-throughput
High-throughput
High-throughput
Ultra high-throughput
Ultra high-throughput
Ultra high-throughput
Ultra high-throughput
Ultra high-throughput

Past
Past
Past
Past
Past
Present
Present
Present
Present
Future
Future
Future
Future
Future

Phenotypic based
Protein based
2-10 g
5-10 g
~1 g
10-20 ng
5ng
50-100 ng
50-100 ng
25 ng
300 ng
300 ng
100 ng
10 ng

No
No
Yes
No
Yes
No
No
Yes
Yes
Yes
Yes
Yes
Yes
Yes

No
No
No
Yes
Yes
Yes
Yes
No
No
Yes
Yes
Yes
Yes
Yes

No
No
No
No
No
Yes
Yes
No
No
Yes
Yes
Yes
Yes
Yes

No
No
Difficult
Difficult
Possible
Possible
Possible
No
No
Possible
Possible
Possible
Possible
Possible

RAPD technology relied upon arbitrary primers because of a

lack of sequence information and also these markers do not
exhibit reliable amplification patterns and have a low reproducibility as results vary with the experimental conditions
(Ellsworth et al. 1993; Heun and Helentjaris 1993).
Amplified fragment length polymorphism (AFLP) was
developed to combine the advantages of both RFLP and
RAPD (Vos et al. 1995). AFLP have been used for trait mapping in many instances, but the conversion of associated
AFLP markers into locus-specific and user-friendly markers
such as a sequence tagged site (STS) or sequence characterized amplified region (SCAR) has not always been straightforward. Therefore, the use of AFLP markers has not been
common for molecular breeding applications (Xu and Ban
2004). However, they have been used extensively in genetic
diversity studies (Geleta et al. 2006; Kondetti et al. 2012;
Murtaza 2006). SSRs are simple repeats that are generated in
the genome mostly due to replication slippage that causes a
difference in the number of repeats, and in SSR length hence
causing the polymorphism. Development of SSR markers is
expensive and laborious. In recent years however, due to the
availability of NGS technologies large-scale sequence information became available for both model and non-model
species, SSR markers have been developed from
gene/expressed sequence tag (EST) sequencing or WGS
(Blair et al. 2011, Singh et al. 2010, Sonah et al. 2011). SSRs
show a high level of polymorphism as compared to RFLPs
and RAPDs, and their locus-specific and co-dominant nature
makes them the marker of choice for a variety of purposes
including MAS in practical plant breeding (Gupta and
Varshney 2000) where they are still used in many programs.
SSR markers are the only class of markers that have been
used for almost all aspects of genetic research and breeding
in a majority of the plant species (Gupta and Varshney 2000;
Varshney et al. 2005). However, in recent years, the domination of medium-throughput SSRs was eventually broken by
SNP markers whose discovery also requires sequence information. First discovered in the human genome (Wang et al.
1998), SNPs proved to be universal, and are the most abundant forms of genetic variation among individuals of the

Sample
size
Cost
Variable
Variable
<50-100
<100
<100
48-384
Variable
100-500
100-500
>1000
>1000
>1000
>1000
>1000

Variable
Less
High
Less
High
High
Variable
Cheapest
Cheapest
Moderate
Moderate
Moderate
Moderate
Moderate

same species. Although SNPs are less polymorphic than SSR

markers because of their biallelic nature, they easily compensate this drawback by being abundant, ubiquitous, and
amenable to high- and ultra-high-throughput automation.
Among all these markers, SSR markers were for a long time
the markers of choice because of their various desirable
attributes (Gupta and Varshney 2000) but are now being
replaced by SNP-based markers due to their high abundance,
uniform distribution and compatibility with automated genotyping platforms. The characteristic of the above marker
classes is given in Table 1.

SNP Genotyping Technologies

SNPs are the most abundant sequence polymorphism in
nature (Rafalski 2002) and are mostly bi-allelic. Work with
SNPs can be divided into SNP discovery and SNP genotyping, required for the various applications. Genome-wide
SNPs discovery was expensive when based on Sanger
sequencing, however, it has become cost effective with the
use of various NGS technologies (Metzker 2010; Varshney at
al. 2009). The other SNP genotyping technologies such as
genotyping by sequencing (GBS) (Elshire et al. 2011; Sonah
et al. 2013) can simultaneously identify and genotype the
SNP markers or the identified markers can be used to add
more markers to genotyping assay (Davey et al. 2011). For
genotyping SNP markers in low- to medium-throughput,
more than 30 assays types have been reported that can be
classified into different reaction principles/chemistries:
hybridization with allele-specific oligonucleotide probes like
TaqMan (lifetechnologies.com), oligonucleotide ligation, single nucleotide primer extension and subsequent sequencing,
enzymatic cleavage, Competitive Allele-Specific PCR like
(KASPar) Assays (http://www.kbioscience.co.uk/), Illumina
Golden Gate (Thomson et al. 2011), and Tm-shift (Gupta et
al. 2001; Kwok 2001; Steemers et al. 2006; Syvanen 2005;
Wang et al. 2005). Some low-throughput technologies can
combine SNP discovery and genotyping like high resolution
melting (HRM) analysis (Studeret al. 2009), CELI assays
(Galeano et al. 2009), or Sanger sequencing of PCR ampli-

295

296

Advances in Molecular Marker Techniques

Table 2. Genome-wide marker discovery in model and non-model crop species.

S.No.

Crop

Marker class

NGS Platform

No. of markers
identified

References

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22

Sunflower
Flax
Lupinus angustifolius L.
Linseed
Soybean
Soybean
Peach
Brassica napus
Aegilops tauschii
Durum wheat
Amaranth
Barley
Maize
Soybean
Rice
Globe artichoke
Cotton
Rice
Rice
Brassica napus
Arabidopsis
Lettuce

SNP
SNP
SNP
SSR
SNP
SNP
SNP
SNP, INDELs
SNP
SNP
SNP
SNP
SNP
SNP
SNP
SNP, INDELs
SNP
SNP
SNP, INDELs
SNP
SNP
SNP

Solexa Illumina
Solexa Illumina
Solexa Illumina
454 Roche
Solexa Illumina
Solexa Illumina
Solexaillumina /454 Roche
Solexa Illumina
Solexa Illumina /454Roche
Solexa Illumina
454 Roche
Solexa Illumina
SolexaIllumina
Solexa Illumina
Solexa Illumina
Solexa Illumina
Solexa Illumina
Solexa Illumina
Solexa Illumina
Solexa Illumina
Solexa Illumina
Solexa Illumina

16,467
55,465
8,207
1,842
25,047
39,022
6,654
20,000; 125
1,95,631
2,659
27,658
530
1,123
1,682
2,618
34,000; 800
13,513
67,051
1,32,462; 16,448
8,92,536
1,409
5,583

(Pegadaraju et al. 2013)

(Kumar et al. 2012)
(Yang et al. 2012)
(Kale et al. 2012)
(Hyten et al. 2010)
(Wu et al. 2010)
(Ahmad et al. 2011)
(Bus et al. 2012)
(You et al. 2011)
(Trebbi et al. 2011)
(Maughan et al. 2009)
(Chutimanitsakun et al. 2011)
(Mammadov et al. 2010)
(Deschamps et al. 2010)
(Deschamps et al. 2010)
(Scaglione et al. 2012)
(Byers et al. 2012)
(Yamamoto et al. 2010)
(Arai-kichise et al. 2011)
(Huang et al. 2013)
(Truong et al. 2012)
(Truong et al. 2012)

cons. Agricultural biotechnology-based companies currently

employ single data point analysis by PCR-based TaqMan
assays and high throughput and turnaround time is achieved
by highly automated genotyping process. Initial identification
of polymorphisms on which to design individual SNP assays
is nowadays usually achieved by NGS.
Presently, it is unclear to decide which SNP genotyping
technologies will prevail in the future because each technology has its advantages and disadvantages (Ganal et al. 2012).

Microarray-based genotyping
The problem of expensive and laborious scoring of marker
panels across target populations in gel-based marker systems
(Gupta et al. 2013) was first overcome by the development of
high-throughput array-based markers (e.g. DArT, SFPs).
These microarray-based markers have been used for the construction of high-density maps, quantitative trait loci (QTL)
mapping (including expression QTLs), and genetic diversity
analysis with a limited expense in terms of time and money
(Colasuonno et al. 2013; King et al. 2013; Mace et al. 2008;
Raman et al. 2012; Sansaloni et al. 2010). Diversity array
technology (DArT) (diversityarrays.com) allows simultaneous typing of several hundred polymorphic loci spread over a
genome without any previous sequence information about
these loci. This technique has shown to be reproducible and
cost-effective (Gupta et al. 2013). Arrays are greatly used,
e.g. a 4 44 K chip in rice (Zhao et al. 2011), common bean
768 SNPs, Illumina chip (Blair et al. 2013), a 5 K chip was
developed for common bean (Bean CAP, unpublished data),
and still further arrays are in the pipeline, such as for cowpea.
These SNP arrays are limited to known SNPs, which are usually identified via NGS, also they are comparatively inflexi-

ble as the SNP number cannot be modified and is not costeffective compared to latest developments in reduced-representation sequencing. Several platforms for high-throughput
genotyping are provided by different universities and institutes at a very reasonable cost (Table 3). Therefore, for the
breeder community, it is easy to get work done with outsourcing rather than development in their own-facility.

Next Generation Sequencing (NGS) Technology

The ultimate approach for the study of polymorphism in
any crop would be to sequence/re-sequence the entire
genome (or a part of it) of a large number of accessions. This
was unimaginable a few decades back. Availability of the
NGS platform has revolutionized genomics approaches to
biology drastically increasing the speed at which DNA
sequence can be acquired while reducing the costs by several
orders of magnitude (Supplementary Figure 1). NGS, also
known as massive parallel sequencing, second generation
sequencing (SGS), deep sequencing, or ultra-high throughput
sequencing is based on sequencing a large number (currently
up to ~21,000,000,000, Illumina HiSeqX) of DNA fragments
at the same time in a single run. Fragments are usually shorter and sequencing data is of lesser quality compared to
Sanger sequencing. Main platforms and offering companies
are: Solexa by Illumina, 454 by Roche, Solid and Ion Torrent
by Life technologies. Readers are referred to the work of
Deschamps et al. (2012) for further details. In the US and
Europe, a survey was conducted in both private and public
sequencing laboratories revealing an increase in utilization of
SGS technologies from ~37 - 56% within 2 years. Third-generation DNA-sequencing technologies refers to a number of
newly developing technologies that promise a number of different advances, lower cost per analysis, longer reads, direct

JCSB 2015 (December) 18 (5) : 293 ~ 308

Table 3. Details of different SNP genotyping platform along with cost and time required
Genotyping
Platform/Method

Number of SNP

Cost/sample

Facility available

Time*

GBS (Hi-seq)-96 plex

GBS (Hi-seq)-384 plex
GBS (Ion-torent)-96 plex
GBS (Hi-seq) 0.2x
nextRAD (3x)
Infinium 6K
BeadXpress
iScan
Fluidigm 96x96

30-80K
10-40K
10-20K
1M
60K
6K
384
1536
96

$38
$25
$35
$65
$55
$80
$40
$80
$20

Cornell University, Laval University

Cornell University, Laval University
Laval University
BGI
snpsaurus (nextrad-services)
IRRI
UC Davis
UC Davis
IRRI

2-6 months
2-6 months
1-month
2-months
1-month
1-month
1-month
1-month
1-month

http://www.igd.cornell.edu/index.cfm/page/GBS/GBSpricing.htm
http://www.ibis.ulaval.ca/?pg=sequencage_genotypageSequencage
http://gsl.irri.org/services/prices-and-sample-submission/prices
http://dnatech.genomecenter.ucdavis.edu/wp-content/uploads/2013/06/Golden_Gate_Genotyping_Prices_Dec2012.pdf
http://www.ibis.ulaval.ca/?pg=sequencage_genotypageSequencage
*as per service providers

RNA sequencing, and direct analysis of methylation. Thirdgeneration DNA-sequencing is mostly distinguished by
direct inspection of single molecules with methods that do
not require the repetitive wash and scan steps during DNA
synthesis, synchronization of multiple reactions, or problems
associated with PCR amplifications or phasing (Thudi et al.
2012). It has been predicted that the third-generation
sequencing platform will replace the SGS by 47% in the next
three years (Peterson et al. 2010). These technologies are also
expected to increase the accuracy of SNP discovery, and
reduce the chances of wrong base calling.
A major issue when dealing with NGS data is the bioinformatics analysis of huge amounts of data generated, involving
trimming, deconvolution and filtering of reads, alignment to
a reference sequence or de novo alignment, and SNP calling
for polymorphism identification or genotyping. The analysis
is much more resource-dependent requiring more than previous technologies the bioinformatics support. A plethora of
commercial and non-commercial software solutions are
available; various reviews cover the available tools (Horner
et al. 2009) or specific topics like alignment (Li and Homer
2010), de novo assembly (Zhang et al. 2011), and SNP calling (Nielsen et al. 2011).
Target enrichment followed by massively parallel
sequencing is the less expensive method over whole genome
sequencing for exploring variations in specific sub-regions of
the genome such as exomes or regions associated with QTLs
(Kiialainen et al. 2011). This method requires a priori availability of sequence data to design DNA capture probes. The
protocol involves design of complementary biotinylated
RNA baits for regions of interest, and the baits are hybridized
onto the targets followed by hybrid capture and NGS. The
popular capture methods are SureSelect, Nimblegen, and
Raindance (Davey et al. 2011). This in-solution-based
genome complexity reduction technology is a simplified
method for identifying genetic diversity between plant varieties. This method has been employed successfully in recent
times on various crops (Uitdewilligen et al. 2013; Zhou and

Holliday 2012). Another advantage of this technique is that it

can be used for capturing homologus loci using the same
oligonucleotides and resolved later based on inter locus polymorphisms in polyploidy crops (Snowdon and Luy 2012).

NGS for Marker Discovery

Developments in the field of bioinformatics for alignment,
assembly, and polymorphism calling using the short DNA
reads produced through NGS technologies, enabled the discovery of millions of DNA polymorphisms such as SNPs and
small InDels by comparing the whole genome sequences of
several individuals within a species. Further, the WGS has
been used for a wide array of crops having reference genome
available for the discovery of molecular markers such as
Brassica napus (Bus et al. 2012; Huang et al. 2013), rice
(Arai-Kichise et al. 2011; Yamamoto et al. 2010), maize
(Yan et al. 2010), and soybean (Kim et al. 2010). For genetic
studies WGS of various genotypes can be used, e.g. to evaluate recombinant inbred line (RIL) parents that are used for
most QTL studies. Comparison of complete resequenced
genomes (10) may yield, depending on the crop and kinship, ~10,000 - 1,000,000 SNPs. Out of these, markers can be
selected to genotype the whole RIL population by other SNP
platforms or by low-coverage resequencing (0.26) as shown
by Yu et al. (2013). The large number of polymorphisms
allows selection of perfectly located markers (e.g. every 10
cM is considered sufficient for a 2-parental population)
(Darvasi et al. 1993). The huge amount of markers also
allows for fine mapping projects, which require a large number of markers in specific regions, and the complete parental
sequences may allow identification of polymorphisms underlying QTLs. Low-coverage sequencing of segregating populations or resequencing of bulk segregants allows genotyping
and mapping, and possibly gene identification in one experiment, first shown by (Schneeberger et al. 2009). Sequencing
of phenotypically selected bulks by WGS is used to detect
markers, identify QTL regions, and as the mutant allele in
one of the parents is sequenced in the same experiment can-

297

298

Advances in Molecular Marker Techniques

Table 4. Crop species were transcriptome sequencing have been used for marker discovery
S.No.

Crop

Marker class

NGS platform

1
2

Eucalyptus
Maize

3
4
5

Wheat
Watermelon
Pepper

454 Roche
454 Roche
454 Roche
__
454 Roche
454 Roche

6
7
8
9

Lentil
Rubber tree
Sweet potato
Blackcurrant

10
11
12
13

Brassica napus
Pigeonpea
Sesame
Cucurbita pepo

14

Carrot

15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32

Lentil
Olive
Blackberry
A. mongolicus
C. nankingense
Camelina sativa L.
Oil palm
Tea
Amorphophallus
Sesame
Chickpea
Field pea
Faba bean
Chickpea
Chickpea
Silene vulgaris
Silene vulgaris
Tomato

SNP
SNP
SNP
SNP
SSR
SNP
SSR
SSR
SSR
SSR
SNP
SSR
SNP
SSR
SSR
SNP
SSR
SNP
SSR
SSR
SNP
SSR
SSR
SSR
SSR
SNP
SNP
SSR
SSR
SSR
SSR
SSR
SSR
SNP
SSR
SNP
SNP

454 Roche
Solexa Illumina
Solexa Illumina
454 Roche
Solexa Illumina
454 Roche
Solexa Illumina
454 Roche
Solexa Illumina
454 Roche
Solexa Illumina
454 Roche
454 Roche
Solexa Illumina
Solexa Illumina
454 Roche
454 Roche
Solexa Illumina
Solexa Illumina
454 Roche
454 Roche
454 Roche
454 Roche
454 Roche
454 Roche
454 Roche
-

didate polymorphisms explaining the phenotype can be

detected. Specific markers for MAS can also be taken from
the same dataset. This technology can greatly enhance the
speed of QTL detection and identification of associated
markers.
A simple application of WGS/resequencing in breeding is
for example, the conversion of known SSR markers. As SSR
markers are difficult to use in automated workflows and are
usually identified in bi-parental study populations, leading to
SSR polymorphisms that are polymorphic between these parents, but not necessarily specific to the donor parent.
Knowing the genomic position of a QTL/SSR marker makes
it easier to select a SNP in this region, e.g. of a resequenced
resistance donor source. The more parental lines are
sequenced, the easier it is to select a SNP that is highly specific for an individual donor parent. These can then be used
to design gel-free SNP assays and applied in automated
processes in MAS to support breeding.

No. of markers
identified
23,742
36,000
7,000
5,471
5,000
11,849
853
192
39,257
4,114
7,000
3,000
41,593
3,771
7,702
9,043
1,882
20,058
114
192
2,987
15,886
1,827
1,788
19,379
823
3,767
19,596
7,702
4,000
2,397
802
4,072
36,446
1,320
13,432
8,784

Reference
(Novaes et al. 2008)
(Barbazuk and Schnable 2007)
(Barbazuk and Schnable 2011)
(Akhunov et al. 2010)
(Guo et al. 2011)
(Nicolai et al. 2013)
(Kaur et al. 2011)
(Li et al. 2012)
(Wang et al. 2010)
(Russell et al. 2011)
(Trick et al. 2009)
(Dutta et al. 2011)
(Wei et al. 2011)
(Blanca et al. 2011)
(Iorizzo et al. 2011
(Kaur et al. 2011)
(Kaya et al. 2013)
(Rowland et al. 2012)
(Zhou et al. 2012)
(Wang et al. 2013)
(Mudalkar et al. 2014)
(Pootakham et al. 2013)
(Wu et al. 2013)
(Zheng et al. 2013)
(Wei et al. 2011)
(Garg et al. 2011)
(Kaur et al. 2012)
(Kaur et al. 2012)
(Jhanwar et al. 2012)
(Jhanwar et al. 2012)
(Sloan et al. 2012)
(Sloan et al. 2012)
(Sim et al. 2012)

Reduced Representation Libraries

WGS is the most informative method extracting nearly all
information from a genome, which is an excess of information for most genetic studies. Unfortunately, it is still costprohibitive to apply saturated WGS to a larger number of
genotypes. For these reasons, the reduced representation
sequencing (RRS) methods have been developed which
allow the sequencing of a small, reproducible fraction of the
complete genome, at a fraction of the cost while still supplying more information than most other genotyping platforms.
RRS is used to identify SNPs and increasingly also genotype
whole populations, leading to a new era of applied genomics.
RRS is based on the production of reduced representation
libraries (RRL), first reported in humans (Altshuler et al.
2000) to find SNPs using Sanger sequencing, since then
modified in many ways. There are different methods to
achieve genomic complexity reduction involving the use of

JCSB 2015 (December) 18 (5) : 293 ~ 308

Table 5. Details of some of the important platforms and severs available for next generation sequencing data analysis
NGS Platform/ Server

Website

Features and specifications

Galaxy

https://usegalaxy.org/

Online server provides variety of tools for NGS data analysis including SNP identification
and RNA-seq

Goldenhelix

www.goldenhelix.com

Software package provide comprehensive tools for NGS data analysis and visualization

CASAVA (Illumina)

www.support.illumina.com

Read processing and alignment, SNP and InDel calling, Expression analysis, splice junction
detection RNA-Seq analysis.

CLC Genomics Workbench

www.clcbio.com

All-inclusive and user-friendly software package for NGS analysis, SNP calling, read-pro
cessing, RNA-seq analysis, Data visualization

DNASTAR

www.dnastar.com

Provides all the software needed for next-gen sequence assembly and analysis, in a single
integrated package. It support all major NGS technologies, making it easy to work with
data form any type of NGS project.

GenomicTools

http://code.google.com/p/ibm-cbc-genomic-tools

GenomicTools is a flexible computational platform for the analysis and manipulation of

high-throughput sequencing data such as RNA-seq and ChIP-seq

GenoMiner

http://astridbio.com/genominer-genome-analyzer/

GenoMiner is a next generation sequencing data analysis computer for life science
researchers with or without IT background. With GenoMiners easy to-use graphical interface you can analyze your sequencing data in your own lab with only 15 clicks!

HiPipe

http://hipipe.ncgm.sinica.edu.tw/

HiPipe provides high performance NGS data analysis pipelines with intuitive user interface
to the community so that researchers with minimum IT or bioinformatics knowledge can
perform common analyses on NGS data.

JMP Genomics

http://www.jmp.com/

JMP Genomics provides comprehensive tools to analyze rare and common variants, detect
differential expression patterns, understand NGS data, discover reliable biomarker profiles,
and incorporate pathway information into your analysis workflows

Omics Pipe

http://sulab.scripps.edu/omicspipe/

Omics Pipe provides two RNA sequencing (RNA-seq) pipelines, variant calling from whole
exome sequencing (WES) and whole genome sequencing (WGS), and two ChIP-seq
pipelines

NGS for genome-wide marker discovery (Davey et al. 2011).

The most popular restriction fragment ligation methods
involve the following key steps: the digestion of multiple
samples of genomic DNA (from individuals or populations)
with one or more restriction enzymes; ligation of adapters to
the resulting restriction fragments; and NGS of the final set
of fragments. Polymorphisms in the resulting sequenced
fragments can be used to design genetic markers (Fig.2).
These approaches allow large-scale SNP detection without
any previous knowledge of the genome, thereby had made
possible for orphan crops to enter into the genomic phase,
and made available large number of markers either directly
by GBS or polymorphism for other genotyping platforms.
These markers have been used for the preparation of saturated linkage map (Zhang et al. 2013), QTL mapping
(Leonforte et al. 2013; Wu et al. 2010; Zou et al. 2013), high
quality linkage maps for scaffold orientation (Hyten et al.
2010), association mapping (Rabbi et al. 2014), markerassisted breeding (Yang et al. 2012), genetic diversity analysis (Bus et al. 2012), and so on (Table 2).

Amplicon Sequencing: Marker Discovery

In some genomic studies like candidate gene approach for
association mapping, allele mining, TILLING (Targeting
Induced Local Lesions in Genomes), and marker development at specific loci, the variation at the specific region of
the genome and their association with the trait phenotype is
investigated. The amplicon sequencing is an ideal method for
the discovery of SNPs and InDels in those cases (Sexton et
al. 2012). It involves the development of primers for the
amplincation of DNA fragments of candidate genes, ESTs, or
other single copy genomic sequences. The amplincation
products from a number of representative lines are fully
sequenced and the obtained sequences are subsequently compared with one another using sequence alignment tools in
bioinformatics pipelines (Fig.2). Hence, this approach utilizes the power of PCR to isolate and restrict the analysis to
genomic regions of interest (Sexton et al. 2012).
The amplicon sequencing is the best alternative in polyploid species where identification and discovery of SNP is
more complicated since it has to be discriminated between
SNPs that are present between the genomes and within
genomes (Ganal et al. 2009). For example, in hexaploid

299

300

Advances in Molecular Marker Techniques

Fig. 2. Illustration of reduced representation sequencing, amplicon

sequencing and transcriptome sequencing involving NGS-sequencing
technologies for marker discovery.

wheat, direct sequencing of amplicons derived from all three

genomes is not efficient since the three genomes differ frequently through insertions/deletions making the analysis of
the resulting sequences difficult or impossible. An alternative
approach that requires considerable efforts is amplicon
sequencing using genome-specific primers (i.e. the sequence
is amplified from only one of the genomes). This approach
has been used in several projects for the identification of
SNPs in wheat where thousands of genome-specific primers
(URL: http:// wheat.pw.usda.gov/SNP) have been developed
for amplicon sequencing and SNP analysis in wheat varieties.
Similarly, in oilseed rape (Brassica napus) 604 SNPs were
identified through amplicon sequencing (Deschamps et al.
2010). Therefore, for those crop species with complex
genomes and allopolyploidy amplicon sequencing using
genome specific primers might be the best alternative for
marker discovery. Tewhey and co-workers in 2009 reported
sequencing PCR amplicons from primers targeting 435 exons
of 47 genes in six samples simultaneously using a microdroplet PCR platform from RainDance Technologies
(Lexington, USA) (Tewhey et al. 2009). This allows
sequencing and SNP detection in desired parts of the
genome, like gene families or chromosome regions of choice.

Marker Discovery through RNA-seq

The genomic resource for most of the non-model crop
species are limited and simple de novo assembly from WGS
is not very successful in plants. Transcriptome sequencing is
the one path for non-model crop species to develop functional genomic level data. RNA-seq provides advantages like
RRS in which only expressed genes are sequenced (Fig.2).
However, the represented fragment is heavily dependent on
the level of gene expression which differs with tissues and
developmental states. Accordingly, transcriptome data generated for gene expression analysis can be easily utilized for
marker development. Thousands of transcriptomes of plant

species have been sequenced and available in public repositories (www.ncbi.nlm.nih.gov/sra). Regarding marker development, the RNA-seq data are being used for SSR and SNP
mining in less-studied plant species. The usage of transcriptome sequencing for marker discovery is rapidly expanding
(Table 4). A significant technical advantage of the use of
transcript data for marker discovery is that transcripts rarely
contain large stretches of repetitive DNA, which interferes
with SNP detection in large and complex genomes of many
crop plants. This allows for increased confidence in base
calling and correct assignment to individual alleles.
Disadvantages are the lower number of SNPs compared to
other techniques and a lower reproducibility due to the
changing transcript expression patterns.
A particularly elegant example of application of RNA-seq
in genomic studies is bulk segregant analysis (BSA), RNAseq for mutant mapping and detection (Liu et al. 2012).
Mutants and non-mutants out of a segregating population
were bulked and the bulks subjected to RNA-seq. SNPs were
identified and based on marker distortions between the bulks
the mutated locus and associated markers were found. As all
the expressed genes are sequenced, it will also be possible to
identify the underlying mutation. Applying this to breeding
traits will allow mapping and identification of major QTL
and possibly the underlying gene in one experiment which
will also produce specific markers for MAS. At a low cost of
only two sequenced mRNA bulks this is likely to impact
marker development in future.

Future Applications of NGS

Although the initial aim of NGS technologies was resequencing, they are currently being used to explore de novo
genome sequencing in several crop species, including castor,
cocoa, rubber, wheat, chickpea, pigeonpea, and common
bean. If the ongoing revolution in NGS technologies can
reduce the cost for resequencing the genome to only a few
hundred US dollars, WGS/resequencing will not be limited to
model plant and major crop species and could be extended to
parental and progeny lines of mapping populations and of
germplasm lines currently present in different germplasm
repositories (Supplementary Fig.1). In the future, we will
also see more and more NGS applications, which will probably replace array technologies and the current medium
throughput SNP genotyping platforms. Development is
required in bioinformatic analysis and turnaround time,
which is currently a weak point.
The genome-wide sequence data should greatly facilitate
our understanding of complex phenomena, such as heterosis
and epigenetics which have implications for crop genetics
and breeding. High-throughput information of variation will
help to precisely locate recombination events on chromosomes and eventually it will increase mapping resolution
many times. Therefore, it can be anticipated that NGS technologies will be particularly useful for developing and confirming introgression lines for a trait of interest. In addition

JCSB 2015 (December) 18 (5) : 293 ~ 308

to facilitating genomics assisted breeding, NGS can also

accelerate the development of transformation technologies
for crops because it will become easier to modify genes with
the increasing availability of genomic data. Although largescale NGS data analysis remains a challenge at present, significant progress is being made in improving existing tools
and in developing new approaches for this task. In summary,
we envisage an exponential increase in the use of NGS technologies, not only for major crop species, but also for socalled orphan crops. The results of these efforts will undoubtedly have a profound impact on crop breeding.

QTL Mapping with High-throughput Marker

Genotyping
QTL mapping is powerful tool to identify genetic loci
governing traits of interest by using the principle of genetic
linkage. The success of QTL mapping depends on molecular
markers and mapping populations. Therefore, QTL mapping
has become more sophisticated with the recent availability of
several NGS-based novel genotyping platforms (Table 5).
High-throughput marker genotyping has increased the power
of QTL mapping many times but it has also brought challenges for an effective analysis. Most of the earlier QTL
mapping software has limitations for the number of markers
since there is a need for advancement in analytical tools. The
common problem with high-throughput SNP data in QTL
mapping is redundancy since closely placed markers segregate together and there may be no crossing-over between
thousands of marker pairs. Such marker pairs can be eliminated by a bin mapping approach. Errors in genotyping data
are most challenging for a correct interpretation of the results
analysis. Such errors can happen during the handling of the
samples prior to their genotyping and will increase the length
of genetic maps and affect the correct marker order (Deokar
et al. 2014). To address these problems, several software
tools like IciMapping (Meng et al. 2015), SEG-Map (Zhao et
al. 2010), Lep-MAP (http://sourceforge.net/projects/lepmap),CARTHAGENE (www7.inra.fr/mia/T/CarthaGene/),
MSTMAP (http://alumni.cs.ucr.edu), and AntMap
(http://lbm.ab.a.u-tokyo.ac.jp/) have been developed.
Recently, QTL mapping performed with WGS of mapping
populations has succeeded to precisely pinpoint the gene
responsible for nematode resistance in soybean (Xu et al.
2013). This study has shown the improved precision of QTL
mapping with the availability of NGS-derived markers.

Genome-wide Association Mapping and Genomic

Selection with NGS Derived Markers
GWAS and GS are not new to the plant breeder community and have been used for decades for crop improvement
(Aranzana et al. 2005; Hillel et al. 1990;). Effectivity of
GWAS and GS has increased with the arrival of NGS-based
genotyping techniques. Several GWAS studies have been
completed using SNP genotyping of vast germplasm collections. Recently, GWAS for sclerotinia stem rot resistance in

soybean have been performed using GBS approach (Bastien

et al. 2014, Iquira et al. 2015). In this effort, the number of
SNPs required for effective GWAS have been estimated
based on the LD-decay which justifies the use of complexity
reduction techniques to identify SNP for GWAS. A similar
approach has been used to locally associate allelic variation
in genes with the phenotypic trait (Tardivel et al. 2014).
However, as discussed above, WGS will soon replace the
complexity reduction techniques, therefore advances in analytical tools for GWAS and GS will be needed. Therefore,
driven by technological advances several servers and analytical pipelines have been developed which facilitate SNP identification, genotyping, and subsequent GWAS and GS analysis (Table 5). The number of reports for GS has increased
several fold during the last few years which suggest its applicability and promising future for crop improvement
(Supplementary Fig.2).
Molecular markers and genetic variation are the common
factors among QTL mapping, GWAS, and GS. This can be
the basis to combine these approaches together (Deshmukh et
al 2014). Recently, an integrated approach of GWAS and
QTL mapping has been used to identify genomic loci governing high oil and protein content in soybean (Sonah et al.
2014). Similarly, several GS studies have been performed
using mapping populations like F2, RIL, and backcross
inbred lines (Supplementary Table 1). Therefore, it will be
more effective to perform GS along with QTL mapping for
effective utilization of resources.

Conclusions
The whole genome sequence is available for only a few
select crop species and most of the non-model species have
limited/poor genomic resources. Also, most of the crop
species are orphans as far as genomic resource are considered
that limits their improvement. Molecular markers evolved
continuously from low-throughput hybridization-based platforms (e.g. RFLP) to medium-throughput PCR-based platforms (e.g. SSR),high-throughput SNP-based platforms and
finally ultra-high-throughput NGS-based markers. With a
decreasein cost and increase in throughput of NGS, these
ultra-high-throughput NGS-based molecular markers will
definitely replace most marker systems in the coming future.
The NGS-based molecular markers have been already developed in both model and non-model crop species and hence
have made it possible for a large number of markers available in non-model crop species. Thus, allowing the orphan
crop species to enter into the genomic phase will make it possible for the genomic-assisted crop improvement therein. The
modern genomic and breeding approaches like GWAS and
GS have not been fully exploited for crop improvement, but
can be increasingly deployed in both model and non-model
crop species with the availability of these NGS-based markers. Thus, reduced representation sequencing, amplicon
sequencing, and transcriptome sequencing using NGS-

301

302

Advances in Molecular Marker Techniques

sequencing technologies have paved the way for marker discoveries which are ultra-high-throughput, cost-effective, and
available in both model and non-model crop species. Hence,
these approaches will revolutionize genomic-assisted crop
improvement.

Acknowledgements
SMZ acknowledges the financial support of SERB-DST,
New Delhi (Government of India) for performing genetic
diversity studies in the common bean using molecular markers.

References
Ahmad R, Parfitt DE, Fass J, Ogundiwin E, Dhingra A,
Gradziel TM, et al. 2011. Whole genome sequencing of
peach (Prunus persica L.) for SNP identification and
selection. BMC genomics 12: 569
Akhunov ED, Akhunova AR, Anderson OD, Anderson JA,
Blake N, Clegg MT, Coleman-Derr D. 2010. Nucleotide
diversity maps reveal variation in diversity among wheat
genomes and chromosomes. BMC Genomics 11: 702
Altshuler D, Pollara VJ, Cowles CR, Van Etten WJ, Baldwin
J, Linton L, Lander ES. 2000. An SNP map of the human
genome generated by reduced representation shotgun
sequencing. Nature 40: 513-516
Arai-Kichise Y, Shiwa Y, Nagasaki H, Ebana K, Yoshikawa
H, Yano M, Wakasa K. 2011. Discovery of genome-wide
DNA polymorphism in a landrace cultivar of japonica rice
by whole genome sequencing. Plant Cell Physiol. 52: 274282
Aranzana MJ, Kim S, Zhao K, Bakker E, Horton M, Jakob
K, Lister C, Molitor J, Shindo C, Tang C. 2005. Genomewide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance
genes. PLoS Genet. 1: e60
Barbazuk WB, Schnable PS. 2011. SNP discovery by transcriptome pyrosequencing. Methods Mol. Biol. 729: 225246
Bastien M, Sonah H, Belzile F. 2014. Genome-wide association mapping of resistance in soybean with a genotypingby-sequencing approach. Plant Genome 7: 1-13
Beyene Y, Semagn K, Mugo S, Tarekegne A, Babu R,
Meisel B, Sehabiague P, Makumbi D, Magorokosho C,
Oikeh S. 2015. Genetic gains in grain yield through
genomic selection in eight bi-parental maize populations
under drought stress. Crop Sci. 55: 154-163
Blair MW, Corts AJ, Penmetsa RV. 2013. A high-throughput SNP marker system for parental polymorphism
screening, and diversity analysis in common bean
(Phaseolus vulgaris L.). Theor. Appl. Genet. 126: 535-548
Blair MW, Hurtado N, Chavarro CM, Muoz Torres MC,
Giraldo MC, Pedraza F, Tomkins J, Wing RA. 2011.
Gene-based SSR markers for common bean (Phaseolus

vulgaris L.) derived from root and leaf tissue ESTs: an

integration of the BMc series. BMC Plant Biol. 11: 50
Blanca J, Caizares J, Roig C, Ziarsolo P, Nuez F, Pic B.
2011. Transcriptome characterization and high throughput
SSRs and SNPs discovery in Cucurbitapepo (Cucurbitaceae). BMC Genomics 12: 104
Bus A, Hecht J, Huettel B, Reinhardt R, Stich B. 2012. Highthroughput polymorphism detection and genotyping in
Brassica napus using next-generation RAD sequencing.
BMC Genomics 13: 281
Byers RL, David B, Yourstone HSM, Maughan PJ, Udall JA.
2012. Development and mapping of SNP assays in allotetraploid cotton. Theor. Appl. Genet. 124: 1201-1214
Chutimanitsakun Y, Nipper RW, Cuesta-Marcos A, Cistu L,
Corey A, Filichkina T, Johnson EA, Hayes PM. 2011.
Construction and application for QTL analysis of a
Restriction Site Associated DNA (RAD) linkage map in
barley. BMC Genomics 12: 4
ColasuonnoP, Maria MA, Blanco A, Gadaleta A. 2013.
Description of durum wheat linkage map and comparative
sequence analysis of wheat mapped DArT markers with
rice and Brachypodium genomes. BMC Genet.14: 114
Collard BCY, Jahufer MZZ, Brouwer JB, Pang ECK. 2005.
An introduction to markers, quantitative trait loci (QTL)
mapping and marker-assisted selection for crop improvement: The basic concepts. Euphytica 142: 169-196
Crossa J, de Los Campos G, Prez P, Gianola D, Burgueo J,
Araus JL, Makumbi D, Singh RP, Dreisigacker S, Yan J.
2010. Prediction of genetic values of quantitative traits in
plant breeding using pedigree and molecular markers.
Genetics 186: 713-724
Crossa J, Prez P, de los Campos G, Mahuku G, Dreisigacker
S, Magorokosho C. 2011. Genomic selection and prediction in plant breeding. J. Crop Improv. 25: 239-261
Darvasi A, Weinreb A, Minke V, Weller JI, Soller M. 1993.
Detecting marker-QTL linkage and estimating QTL gene
effect and map location using a saturated genetic map.
Genetics 134: 943-951
Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM,
Blaxter ML. 2011. Genome-wide genetic marker discovery and genotyping using next-generation sequencing.
Nat. Rev. 12: 499-510
Deokar AA, Ramsay L, Sharpe AG, Diapari M, Sindhu A,
Bett K, Warkentin TD, Tar B. 2014. Genome wide SNP
identification in chickpea for use in development of a high
density genetic map and improvement of chickpea reference genome assembly. BMC Genomics 15: 708
Deshmukh R, Sonah H, Patil G, Chen W, Prince S, Mutava
R, Vuong T, Valliyodan B, Nguyen HT. 2014. Integrating
omic approaches for abiotic stress tolerance in soybean.
Front. plant sci. 5: 244
Deschamps S, Rota MI, Ratashak JP, Biddle P, Thuree D,
Farmer A, et al. 2010. Rapid genome-wide single
nucleotide polymorphism discovery in soybean and rice
via deep resequencing of reduced representation libraries
with the illumina genome analyzer. Plant Genome 3: 53-68

JCSB 2015 (December) 18 (5) : 293 ~ 308

Deschamps S, Llaca V, May GD. 2012. Genotyping-bySequencing in plants. Biology 1: 460-483

Ellsworth DL, Rittenhouse KD, Honeycutt RL. 1993.
Artifactual variation in randomly amplified polymorphic
DNA banding patterns. Biotechniques 14: 214-217
Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K,
Buckler ES, Mitchell SE. 2011. A robust, simple genotyping-by sequencing (GBS) approach for high diversity
species. PLoS ONE 6: e19379
Galeano CH, Gomez M, Rodriguez LM, Blair MW. 2009.
CEL I Nuclease digestion for SNP discovery and marker
development in common bean (Phaseolus vulgaris L.) Crop
Sci. 49: 381-394
Ganal MW, Altmann T, Roder MS. 2009. SNP identification
in crop plants. Curr. Opin. Plant Biol. 12: 1-7
Ganal MW, Polley A, Graner E, Plieske J, Wieseke R,
Luerssen H, Durstewitz G. 2012. Large SNP arrays
for genotyping in crop plants. J. Biosci. 37: 821-828
Garg R, Patel RK, Tyagi AK, Jain M. 2011. De novo assembly of chickpea transcriptome using short reads for gene
discovery and marker identification. DNA Res. 18: 53-63
Geleta N, Labuschagne MT, Viljoen CD. 2006. Genetic
diversity analysis in sorghum germplasm as estimated by
AFLP, SSR and morpho-agronomical markers. Biodivers.
Conserv. 15: 3251-3265
Gouy M, Rousselle Y, Bastianelli D, Lecomte P, Bonnal L,
Roques D, Efile JC, Rocher S, Daugrois J, Toubi L. 2013.
Experimental assessment of the accuracy of genomic
selection in sugarcane. Theor. Appl. Genet. 126: 25752586
Grattapaglia D, Resende MD. 2011. Genomic selection in
forest tree breeding. Tree Genet. Genomes 7: 241-255
Grattapaglia D, Vaillancourt RE, Shepherd M, Thumma BR,
Foley W, Klheim C, Potts BM, Myburg AA. 2012.
Progress in Myrtaceae genetics and genomics: Eucalyptus
as the pivotal genus. Tree Genet. Genomes 8: 463-508
Guo S, Liu J, Zheng Y, Huang M, Zhang H, Gong G. et al.
2011. Characterisation of transcriptome dynamics during
watermelon fruit development: sequencing, assembly,
annotation and gene expression profiles. BMC Genomics
12: 454
Gupta PK, Roy JK, Prasad M. 2001. Single nucleotide polymorphisms: a new paradigm for molecular marker technology and DNA polymorphism detection with emphasis
on their use in plants. Curr. Sci. 80:524-535
Gupta PK, Rustgi S, Mir RR. 2013. Array-Based HighThroughput DNA Markers and Genotyping Platforms for
Cereal Genetics and Genomics. inCereal Genomics III,
PKGupta, RKVarshney, eds, Springer, Netherlands, pp 1155
Gupta PK, Varshney RK. 2000. The development and use of
microsatellite markers for genetic analysis and plant
breeding with emphasis on bread wheat. Euphytica 113:
163-185.
Heun M, Helentjaris T.1993. Inheritance of RAPDs in F1
hybrids of corn. Theor. Appl. Genet.85: 961-968

Heffner EL, Jannink JL, Sorrells ME. 2011. Genomic

selection accuracy using multifamily prediction models in
a wheat breeding program. Plant Genome 4: 65-75
Hillel J, Schaap T, Haberfeld A, Jeffreys A, Plotzky Y,
Cahaner A, Lavi U. 1990. DNA fingerprints applied to
gene introgression in breeding programs. Genetics 124:
783-789
Hofheinz N, Borchardt D, Weissleder K, Frisch M. 2012.
Genome-based prediction of test cross performance in two
subsequent breeding cycles. Theor. Appl. Genet. 125:
1639-1645
Horner DS, Pavesi G, Castrignano T, De Meo PDO, Liuni S,
Sammeth M, Picardi E, Pesole G. 2009. Bioinformatics
approaches for genomics and post genomics applications
ofnext-generation sequencing. Brief. Bioinform. 11: 181197
Hu Z, Li Y, Song X, Han Y, Cai X, Xu S, Li W. 2011.
Genomic value prediction for quantitative traits under the
epistatic model. BMC Genet. 12: 15
Huang S, Deng L, Guan M, Li J, Lu K, Wang H, Fu D,
Mason AS, Liu S, Hua W. 2013. Identification of genomewide single nucleotide polymorphisms in allopolyploid
crop Brassica napus. BMC Genomics 14: 717
Hyten DL, Cannon SB, Song Q, Weeks N, Fickus EW,
Shoemaker RC, et al. 2010. High-throughput SNP discovery through deep resequencing of a reduced representation
library to anchor and orient scaffolds in the soybean whole
genome sequence. BMC Genomics 11: 38
Elmer I, Sonah H, Belzile F. 2015. Association mapping of
QTLs for sclerotinia stem rot resistance in a collection of
soybean plant introductions using a genotyping by
sequencing (GBS) approach. BMC plant biology 15: 5
Iorizzo M, Senalik DA, Grzebelus D, Bowman M,
Cavagnaro PF, Matvienko M, Ashrafi H, Van Deynze A,
Simon PW. 2011. De novo assembly and characterization
of the carrot transcriptome reveals novel genes, new markers, and genetic diversity. BMC Genomics 12: 389
Isik F, Whetten R, Zapata-Valenzuela J, Ogut F, McKeand S.
2011. Genomic selection in loblolly pine-from lab to field.
In: BMC Proceed. vol Suppl 7. BioMed Central Ltd., p I8
Iwata H, Hayashi T, Terakami S, Takada N, Sawamura Y,
Yamamoto T. 2013. Potential assessment of genome-wide
association study and genomic selection in Japanese pear
Pyrus pyrifolia. Breed. Sci. 63: 125
Jain SM, Brar DS, Ahloowalia BS. 2010. Molecular techniques in crop improvement. In Cereal genomics, PK
Gupta, RK Varshney, eds., Kluwer Academic Publishers,
Dordrecht, The Netherlands, pp 639
Jarqun D, Crossa J, Lacaze X, Du Cheyron P, Daucourt J,
Lorgeou J, Piraux F, Guerreiro L, Prez P, Calus M. 2013.
A reaction norm model for genomic selection using highdimensional genomic and environmental data. Theor.
Appl. Genet. 127: 1-13
Jhanwar S, Priya P, Garg R, Parida SK, Tyagi AK, Jain M.
2012. Transcriptome sequencing of wild chickpea as a

303

304

Advances in Molecular Marker Techniques

rich resource for marker development. Plant Biotechnol. J.

10: 690-702
Jia Y, Jannink JL. 2012. Multiple-trait genomic selection
methods increase genetic value prediction accuracy.
Genetics 192: 1513-1522
Jones N, Ougham H, Thomas H, Pasakinskiene I. 2009.
Markers and mapping revisited: finding your gene. New
Phytol. 183: 935-966.
Kale SM, Pardeshi VC, Kadoo NY, Ghorpade PB, Jana MM,
Gupta VS. 2012. Development of genomic simple
sequence repeat markers for linseed using next generation
sequencing technology. Mol. Breed. 30: 597-606
Kiialainen A, Karlberg O, Ahlford A, Sigurdsson S,
Lindblad-Toh K, Syvnen AC. 2011. Performance of
microarray and liquid based capture methods for target
enrichment for massively parallel sequencing and SNP
discovery. PLoS ONE 6: e16486
Kim MY, Leeb S, Vana K, Kim TH, Jeong SC, Choi IY, et
al. 2010. Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. And
Zucc.) genome. PNAS 107: 22032-22037
King J, Thomas A, James C, King I, Armstead I. 2013. DArT
marker genetic map of perennial ryegrass (Loliumperenne
L.) integrated with detailed comparative mapping information; comparison with existing DArT marker genetic
maps of Loliumperenne, L. multiflorum and Festucapratensis. BMC Genomics 14: 437
Koebner RMD. 2005. Marker-assisted selection in the cereals: the dream and the reality. in Cereal genomics, PK
Gupta, RKVarshney, eds, Springer, Netherlands, pp 317329
Kondetti P, Jawali N, Apte SK, Shitole MG. 2012.
Comparative study of genetic diversity in Indian soybean
(Glycine max L. Merr.) by AP-PCR and AFLP. Ann. Biol.
Res. 3: 3825-3837
Korzun V. 2002. Use of molecular markers in cereal breeding. Cell. Mol. Biol. Lett. 7: 811-820
Kumar S, You FM, Cloutier S. 2012. Genome wide SNP discovery in flax through next generation sequencing of
reduced representation libraries. BMC Genomics 13: 684
Kwok P. 2001. Methods for genotyping single nucleotide
polymorphisms. Annu. Rev. Genom.Hum. Genet. 2: 235258
Leonforte A, Sudheesh S, Cogan NO, Salisbury PA, Nicolas
ME, Materne M, Forster JW, Kaur S. 2013. SNP marker
discovery, linkage map construction and identification of
QTLs for enhanced salinity tolerance in field pea (Pisum
sativum L.). BMC Plant Biol. 13: 161
LiD, Deng Z, Qin B, Liu X, Men Z. 2012. De novo assembly
and characterization of bark transcriptome using Illumina
sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.). BMC Genomics
13: 192
Li H, Homer N. 2010. A survey of sequence alignment algorithms for next-generation sequencing. Brief. Bioinform.
11: 473-483

Liu S, Yeh CT, Tang HM, Nettleton D, Schnable PS. 2012.

Gene mapping via Bulked Segregant RNA-Seq (BSRSeq). PLoS ONE 7: e36406
Lorenzana RE, Bernardo R. 2009. Accuracy of genotypic
value predictions for marker-based selection in biparental
plant populations. Theor. Applied Genet 120: 151-161
Mace ES, Xia L, Jordan DR, Halloran K, Parh DK, Huttner
E, Wenzl P, Kilian A. 2008. DArT markers: diversity
analyses and mapping in Sorghum bicolor. BMC
Genomics 9: 26
Maughan PJ, Yourstone SM, Jellen EN, Udall JA. 2009. SNP
discovery via genomic reduction, barcoding, and 454pyrosequencing in amaranth. Plant Genome 2: 260-270
Meng L, Li H, Zhang L, Wang J. 2015. QTL IciMapping:
Integrated software for genetic linkage map construction
and quantitative trait locus mapping in biparental populations. Crop J. 3: 269-283
Metzker ML. 2010. Sequencing technologies-the next generation. Nat. Rev. Genet. 1: 31-46
Mudalkar S, Golla R, Ghatty S, Reddy AR. 2014. De novo
transcriptome analysis of an imminent biofuel crop,
Camelina sativa L. using Illumina GAIIX sequencing
platform and identification of SSR markers. Plant Mol.
Biol. 84: 159-171
Murtaza N. 2006. Cotton genetic diversity study by AFLP
markers. Electron. J. Biotechnol. 9: 1-5
Nicolai M, Pisani C, Bouchet JP, Vuylsteke M, Palloix A.
2013. Discovery of a large set of SNP and SSR genetic
markers by high-throughput sequencing of pepper
(Capsicum annuum). Genet. Mol. Res. 11: 2295-2300
Nielsen R, Paul JS, Albrechtsen A, Song YS. 2011.
Genotype and SNP calling from next-generation sequencing data. Nature Reviews Genetics 12: 443-451.
Pegadaraju V, Nipper R, Hulke B, Qi L, Schultz Q. 2013. De
novo sequencing of sunflower genome for SNP discovery
using RAD (Restriction site Associated DNA) approach.
BMC Genomics 14: 556
Prez-Rodrguez P, Gianola D, Gonzlez-Camacho JM,
Crossa J, Mans Y, Dreisigacker S. 2012. Comparison
between linear and non-parametric regression models for
genome-enabled prediction in wheat. G3: Genes Genomes
Genet. 2: 1595-1605
Peterson TW, Nam SJ, Darby A. 2010. Next-gen sequencing
survey, in North America Equity Research, New York: JP
Morgan Chase & Co.
Rabbi I, Hamblin M, Gedil M, Kulakow P, Ferguson M,
Ikpan AS, Ly D, Jannink J. 2014. Genetic mapping using
genotyping-by-sequencing in the clonally-propagated cassava. Crop Sci. 54: 1384-1396
Rafalski A 2002. Applications of single nucleotide polymorphisms in crop genetics. Curr. Opin. Plant Biol. 5: 94-100
Raman H, Raman R, Schondelmaier J. 2012. Diversity Array
Technology Markers: Genetic diversity analyses and linkage map construction in Rapeseed (Brassica napus L.).
DNA Res.18: 51-65
Resende M, Del Valle PM, Acosta J, Resende M,

JCSB 2015 (December) 18 (5) : 293 ~ 308

Grattapaglia D, Kirst M. 2011. Stability of genomic selection prediction models across ages and environments. In:
BMC Proceed., vol. Suppl 7. BioMed Central Ltd, p O14
Resende MF, Munoz P, Acosta J, Peter G, Davis J,
Grattapaglia D, Resende M, Kirst M. 2012a. Accelerating
the domestication of trees using genomic selection: accuracy of prediction models across ages and environments.
New Phytol. 193: 617-624
Resende MF, Muoz P, Resende MD, Garrick DJ, Fernando
RL, Davis JM, Jokela EJ, Martin TA, Peter GF, Kirst M.
2012b. Accuracy of genomic selection methods in a standard data set of loblolly pine (Pinus taeda L.). Genetics
190: 1503-1510
Riedelsheimer C, Technow F, Melchinger AE. 2012.
Comparison of whole-genome prediction models for traits
with contrasting genetic architecture in a diversity panel of
maize inbred lines. BMC Genomics 13: 452
Sansaloni CP, Petroli CD, Carling J, Hudson CJ, Steane DA,
Myburg AA, Grattapaglia D, Vaillancourt RE, Kilian A.
2010. A high-density Diversity Arrays Technology
(DArT) microarray for genome-wide genotyping in
Eucalyptus. Plant Methods 6: 16
Schneeberger K, Ossowski S, Lanz C, Juul T, Petersen AH,
Nielsen KL, Jrgensen J, Weigel D, Andersen SU. 2009.
SHORE map: simultaneous mapping and mutation identification by deep sequencing. Nat. Meth. 6: 550-551
Schulz-Streeck T, Ogutu JO, Piepho HP. 2013. Comparisons
of single-stage and two-stage approaches to genomic
selection. Theor. Appl. Genet. 126: 69-82
Sexton TR, Shapter FM. 2012. Amplicon sequencing for
marker discovery in Molecular Markers in Plants, RJ
Henry, eds, Blackwell Publishing Ltd., Oxford, UK, pp
35-56
Shu Y, Yu D, Wang D, Bai X, Zhu Y, Guo C. 2012.
Genomic selection of seed weight based on low-density
SCAR markers in soybean. Genetics Mol. Res. GMR 12:
2178-2188
Singh H, Deshmukh RK, Singh A, Singh AK, Gaikwad K,
Sharma TR. et al. 2010. Highly variable SSR markers suitable for rice genotyping using agarose gels. Mol. Breed.
25, 359-364
Snowdon RJ, Luy FLI. 2012. Potential to improve oilseed
rape and canola breeding in the genomics era. Plant Breed.
131: 351-360
Sonah H, Bastien M, Iquira E, Tardivel A, Lgar G, Boyle
B, Normandeau , Laroche J, Larose S, Jean M. 2013. An
improved genotyping by sequencing (GBS) approach
offering increased versatility and efficiency of SNP discovery and genotyping. PloS ONE 8: e54603
Sonah H, Deshmukh RK, Sharma A, Singh VP, Gupta DK,
Gacche RN. et al. 2011. Genome-wide distribution and
organization of microsatellites in plants: an insight into
marker development in Brachypodium. PLoS ONE 6:
e21298
Sonah H, ODonoughue L, Cober E, Rajcan I, Belzile F.
2014. Identification of loci governing eight agronomic

traits using a GBS-GWAS approach and validation by

QTL mapping in soya bean. Plant Biotechnol. J. 13: 211221
Steemers FJ, Chang W, Lee G, Barker DL, Shen R,
Gunderson KL. 2006 Whole-genome genotyping with the
single-base extension assay. Nat. Meth. 3: 31-33
Studer B, Jensen LB, Fiil A, Asp T. 2009. Blind mapping of
genic DNA sequence polymorphisms in Lolium perenne
L. by high resolution melting curve analysis. Mol. Breed.
24: 191-199
Syvanen AC. 2005. Toward genome-wide SNP genotyping.
Nat. Genet. 37: 5-10
Tardivel A, Sonah H, Belzile F, ODonoughue LS.
2014.Rapid identification of alleles at the soybean maturity gene E3 using genotyping by sequencing and a haplotype-based approach. Plant Genome 7: 1-9
Tewhey R, Warner JB, Nakano M, Libby B, Medkova M,
David PH. et al. 2009. Microdroplet-based PCR enrichment for large-scale targeted sequencing. Nat. Biotechnol.
27: 1025-1031
Thomson MJ, Zhao K, Wright M, McNally KL, Rey J, Tung
CW, et al. 2011. High-throughput single nucleotide polymorphism for breeding applications in rice using the
BeadXpress platform. Mol. Breed. 29: 875-886
Thudi M, Li Y, Jackson SA, May GD, Varshney RK. 2012.
Current state-of-the-art sequencing technologies for plant
genomics research. Brief. Funct. Genomics 11: 3-11
Trick M, Long Y, Meng J, Bancroft I. 2009. Single
nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexatranscriptome sequencing. Plant Biotechnol. J. 7: 334-346
Uitdewilligen JGAML, A-MA W, Dhoop BB, BormTJA,
Visser RGF, van Eck HJ. 2013. A next-generation
sequencing method for genotyping-by-sequencing of highly heterozygous autotetraploid potato. PLoS ONE 8:
e62355
Varshney RK, Graner A, Sorrells ME. 2005. Genomicsassisted breeding for crop improvement. Trends Plant Sci.
10: 621-630.
Varshney RK, Nayak SN, May GD, Jackson SA. 2009. Nextgeneration sequencing technologies and their implications
for crop genetics and breeding. Trends Biotechnol. 27:
522-530
Vos P, Hogers R, Bleeker M, Reijans M, Van de Lee T,
Hornes M, et al. 1995. AFLP: a new technique for DNA
fingerprinting. Nucleic Acids Research 3: 4407-4414
Wang DG, Fan JB, Siao CJ. 1998. Large-scale identification,
mapping, and genotyping of single nucleotide polymorphisms in the human genome. Science 280: 1077-1082
Wang J, Chuang K, Ahluwalia M, Patel S, Umblas N, Mirel
D, Higuchi D, Germer S. 2005. High-throughput SNP
genotyping by single-tube PCR with Tm-shift primers.
BioTechniques 39: 885-893
Wetterstrand KA. 2014. DNA sequencing costs: data from the
NHGRI large-scale genome sequencing program. 2011
Wetterstrand KA. DNA Sequencing Costs: Data from the

305

306

Advances in Molecular Marker Techniques

NHGRI Genome Sequencing Program (GSP) Available at:

www.genome.gov/sequencingcosts. Accessed [12 March
2015].
Williams JGK, Kubelic AR, Livak KJ, Rafalski JA, Tingey
SV. 1990. DNA polymorphism amplified by arbitrary
primers are useful as genetic markers. Nucleic Acids Res.
18: 6532-6535
Wu X, Ren C, Joshi T, Vuong T, Xu D, Nguyen HT. 2010.
SNP discovery by high-throughput sequencing in soybean.
BMC Genomics 11: 469
Wrschum T, Abel S, Zhao Y. 2013. Potential of genomic
selection in rapeseed (Brassica napus L.) breeding. Plant
Breed. 133: 45-51
Xu DH, Ban T. 2004. Conversion of AFLP markers associated with FHB resistance in wheat into STS markers with
an extension-AFLP method. Genome 47: 660-665
Xu X, Zeng L, Tao Y, Vuong T, Wan J, Boerma R, Noe J, Li
Z, Finnerty S, Pathan SM. 2013. Pinpointing genes underlying the quantitative trait loci for root-knot nematode
resistance in palaeopolyploid soybean by whole genome
resequencing. PNAS 110: 13469-13474
Yamamoto T, Nagasaki H, Yonemaru J, Ebana K, Nakajima
M, Shibaya T, Yano M. 2010. Fine definition of the pedigree haplotypes of closely related rice cultivars by means
of genome-wide discovery of single-nucleotide polymorphisms. BMC Genomics 11: 267
Yan JB, Yang XH, Shah T, Snchez-Villeda H, Li J,
Warburton M, Zhou Y, Crouch JH, Xu Y. 2010. Highthroughput SNP genotyping with the Golden Gate assay in
maize. Mol. Breed. 25: 441-451
Yang H, Tao Y, Zheng Z, Li C, Sweetingham MW,
Howieson JG. 2012. Application of next-generation
sequencing for rapid marker development in molecular
plant breeding: a case study on anthracnose disease resistance in Lupinus angustifolius L. BMC Genomics 13: 318
Yu X, Wang H, Zhong W, Bai J, Liu P, He Y. 2013. QTL
Mapping of leafy heads by genome resequencing in the
RIL population of Brassica rapa. PLoS ONE 8: e76059
Zhang W, Chen J, Yang Y, Tang Y, Shang J, Shen B. 2011.
A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies.
PLoS ONE 6: e17915
Zhang Y, Wang L, Xin H, Li D, Ma C, Ding X, Hong W,
Zhang X. 2013. Construction of a high-density genetic
map for sesame based on large scale marker development
by specific length amplified fragment (SLAF) sequencing.
BMC Plant Biol. 13: 141
Zhao K, Tung CW, Eizenga GC, Wright MH, Ali ML, Price
AH, et al. 2011. Genome-wide association mapping
reveals a rich genetic architecture of complex traits in
Oryza sativa. Nature Communications 2: 467
Zhao Q, Huang X, Lin Z, Han B. 2010. SEG-Map: A novel
software for genotype calling and genetic map construction from next-generation sequencing. Rice 3: 98-102
Zhou L, Holliday JA. 2012. Targeted enrichment of the black
cottonwood (Populus trichocarpa) gene space using

sequence capture. BMC Genomics 13: 703

Zou Z, Ishida M, Li F, Kakizaki T, Suzuki S, Kitashiba H,
Nishio T. 2013. QTL analysis using SNP markers developed by next-generation sequencing for identification of
candidate genes controlling 4-methylthio-3-butenyl glucosinolate contents in roots of radish, Raphanus sativus L.
PLoS ONE 8: e53541

JCSB 2015 (December) 18 (5) : 293 ~ 308

Table S1. Genomic selection efforts performed for trait improvement in different crops using different statistical models and marker genotyping platforms
Population type

Population size

Total markers

Accuracy of
GEBVs

Models used for

GEBV

Reference

Arabidopsis Flowering time, dry matter,

free amino acid
thaliana

RILs

415

69 SSR

0.90-0.93

BLUP

(Lorenzana and
Bernardo 2009)

Barley

Plant height, grain yield, 3

chemical components

DHLs

150

223RFLP

0.64-0.83

BLUP

(Lorenzana and
Bernardo 2009)

Barley

Plant height, two chemical

components

DHLs

140

107 RFLP and AFLP

0.66-0.85

BLUP

(Lorenzana and
Bernardo 2009)

Species

Traits

Eucalyptus

Height, diameter at breast

height, wood density, pulp 75 full-sib family 55
yield, lignin content,
elite parents
Puccinia rust resistance

920

3564 DArTs

0.54-0.62

BLUP

(Grattapaglia and
Resende 2011)

Eucalyptus

Height, diameter at breast

height, wood density, pulp 43 full-sib family 11
interspecinc hybrid
yield, lignin content,
Puccinia rust resistance

783

3120 DArTs

0.53-0.69

BLUP

(Grattapaglia et al.
2012)

Loblolly pine

Diameter at breast height,

total height

61 full-sib families

790 - 840

3938 SNPs

0.64-0.77

BLUP

(Resende et al.
2011)

Loblolly pine

Growth and quality traits

Full-sib offspring

149

3406 SNPs

0.3-0.83

Pedigree model

(Isik et al. 2011)

Loblolly pine

17 traits

70 full-sib families

951

4853 SNPs

0.37-0.77

RR-BLUP, Bayes A,
Bayes C, Bayesian
LASSO

(Resende et al.
2012b)

50 haploids

769

4755 SNP

0.33-0.94

GBLUP, BayesA,
and BayesCp

(Jia and Jannink

2012)

resistance Rust and

Loblolly pine disease
Rust gall volume
Loblolly pine

diameter and height

61 full-sib families

800

4825 SNP

0.63-0.75

BLUP

(Resende et al.
2012a)

Maize

Grain yield, female flowering, male flowering, anthesis-silking interval

CIMMYT lines

300

1148 SNPs

0.42-0.79

M-BL

(Crossa et al. 2011)

Maize

3 morphological traits,
grain moisture

F2

349

160 SSR

0.59-0.72

BLUP

(Lorenzana and
Bernardo 2009)

Maize

3 morphological traits,
grain moisture

Testcrosses of DHLs

371

125SNPs

0.31-0.55

BLUP

(Lorenzana and
Bernardo 2009)

Maize

8 morphological traits, 3
chemical components,
grain moisture

RILs

223

1339SSR and RFLP

0.48-0.73

BLUP

(Lorenzana and
Bernardo 2009)

Maize

5 morphological traits,
grain moisture

RILs

119

1339SSR and RFLP

0.40-0.50

BLUP

(Lorenzana and
Bernardo 2009)

Maize

3 agronomic traits and 3

metabolites

Inbred lines

289

56,110 SNPs

0.45-0.82

RR-BLUP, LASSO

(Riedelsheimer et al.
2012)

Maize

grain yield

DHLs

177

768 SNP

0.476 to 0.710

RR-BLUP

(Schulz-Streeck et
al. 2013)

Maize

Drought

F2:3

300

286 SNPs

(Beyene et al. 2015)

Pear

9 Traits

cultivars

76

155SSRs,
4 RAPD-STS

0.2-0.75

Bayesian regression

(Iwata et al. 2013)

Rapeseed

6 Traits

DHLs

391

253 SNP

0.41-0.84

RR-BLUP

(Wurschum et al.
2013)

Soybean

HSW

Accessions
(Guadeloupe)

288

79 SCAR

0.69-0.904

RR-BLUP, BLR

(Shu et al. 2012)

307

308

Sowing time on buckwheat yield

Species

Traits

Population type

Population size

Total markers

Accuracy of
GEBVs

Models used for

GEBV

Reference

Soybean

Primary embryogenesis
capacity

RILs

126

80SSRs

0.12- 0.78

Empirical Bayesian
method

(Hu et al. 2011)

Sugar beet

6 Traits

Elite inbred lines

924

677 SNP

0.48-0.80

RR-BLUP

(Wurschum et al.
2013)

Sugar beet

sugar content and loss to

molasses

inbred lines derived

from 34 crosses

310

384 SNP

0.4-0.86

RR-BLUP

(Hofheinz et al.
2012)

Sugarcane

10 Traits

Accessions (Reunion
Island)

167

1499 DArT

0.29 - 0.62

LASSO

(Gouy et al. 2013)

Sugarcane

10 Traits

Accessions
(Guadeloupe)

167

1499 DArT

0.11 - 0.5

LASSO

(Gouy et al. 2013)

Wheat

Grain yield

CIMMYT lines

599

1279 DArTs

0.48-0.61

PM-RKHS

(Crossa et al. 2010)

Wheat

8 grain quality

DHLs

209

399 SSRs, DArTs,

AFLPs, TRAPs, STS

0.32-0.84

RR-BLUP

(Heffner et al. 2011)

Wheat

8 grain quality

DHLs

174

574 DArTs

0.41?0.73

RR-BLUP

(Heffner et al. 2011)

Wheat

grain yield

Commercial lines

139

2395 SNPs

0.175-0.514

G-BLUP

(Jarquin et al. 2013)

Wheat

Days to heading and grain

yield

Elite lines

306

1717 DArT

0.20-0.75

Bayesian LASSO,
BRR,

(Perez-Rodriguez et
al. 2012)

Fig. S1. Sequencing cost reduction over the last fourteen years. Data
was obtained from NHGRI Genome Sequencing Program
(www.genome.gov/sequencingcosts/).

Fig. S2. Increasing number of studies involving genomic selection over

last decade. Data was obtained by search performed at Google Scholar.
(http://scholar.google.ca/) using genomic selection OR genomic prediction key word only in title.