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Phenomics: A Challenge for Crop Improvement
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Research Report

Open Access

Phenomics: A Challenge for Crop Improvement in Genomic Era

Bhat J.A.1, Salgotra R.K.2, Dar M.Y3

1.Division of Plant Breeding & Genetics, Sher-e-Kashmir University of Agricultural Sciences & Technology of Jammu, Chatha, Jammu (J & K), India
2.School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences & Technology of Jammu, Chatha, Jammu (J & K), India
3.Division of Veterinary Anatomy, Sher-e-Kashmir University of Agricultural Sciences & Technology of Jammu, R.S.Pora, Jammu (J & K), India
Corresponding authors email: dr@aau.in, javid.akhter69@gmail.com
Molecular Plant Breeding, 2015, Vol.6, No.20 doi: 10.5376/mpb.2015.06.0020
Received: 22 Jun., 2015
Accepted: 11 Aug., 2015
Published: 10 Sep., 2015
Koohdar 2015 Bhat et al., This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted
use, distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:
Bhat J.A., Salgotra R.K., and Dar M.Y., 2015, Phenomics: A Challenge for Crop Improvement in Genomic Era., Interaction, Molecular Plant Breeding, 6(20):
1-8 (doi: 10.5376/mpb.2015.06.0020)

Abstract The last two decades have observed tremendous progress in the genomics for plant breeding research, especially the
availability of a large number of high-throughput cost-effective molecular markers and genotyping platforms, advances in sequencing
technologies leading the reduction in sequencing costs and making available genome sequences of major crop genomes, etc. But the
advance in phenomics is lagging far behind our present day capacity to generate high-throughput molecular genotyping data, thus
creating phenotypic bottleneck. The accurate and precise phenotypic data is an essential component in the discovery of genes/QTLs
of important agronomic traits using modern genomic approaches; otherwise it leads to false positives and false negatives. Therefore,
it necessitates the development of high-throughput phenotyping facilities. Although, several phenotyping facilities have been
developed around the world that can scan and record precise and accurate data for thousands of plants quickly by making use of
non-invasive imaging, spectroscopy, image analysis, robotics and high-performance computing facilities, but more efforts and funds
are required to be allocated in this field to achieve fruitful results from genomics/molecular breeding approaches like QTL interval
mapping, association mapping, genome-wide association studies (GWAS), QTL cloning, QTL validation, marker-assisted selection
(MAS), marker-assisted recurrent selection (MARS), TILLING (Targeting Induced Local Lesions in Genomes) and genomic
selection (GS) or genome-wide selection (GWS).
Keywords Phenomics; complex traits; gene discovery; phenotypic bottleneck; crop improvement

Introduction

2014). The population of the world is also expected to

rise by 50% till 2050 (Tester and Langridge, 2010),
therefore, to feed these increasing mouths the crop
production must increase by 70% (Furbank and Tester,
2011). Hence, to fight against the climate change as
well as increasing population growth and to maintain
sustainable agriculture we need new crop varieties of
increased productivity and could withstand better
under abiotic and biotic pressures. Gene for such traits
are often available in crop gene pool including wild
species and landraces and have thus to be exploited
fully to achieve desired objectives. To meet these
challenges scientist are looking for new and more
efficient strategies, that combine genomics and
high-throughput phenomics, so as to utilize the
genetic variation effectively for crop improvement
(Jackson et al., 2011; Furbank and Tester, 2011).
Genomics in integration with other other omics
approaches viz., phenomics, epigenomics, transcriptomics,
metabolomics and proteomics etc, are considered the
emerging options to solve the problems associated

The plant genetics and breeding is an important source

for the development of improved varieties of crop
species and is the responsible field for green
revolution occurred in the 1960 s. However, these
disciplines of crop improvement need to become
empowered in view of ever increasing threats and
vagaries of global climate challenges (Jackson et al.,
2011). The role of climate change in relation to crop
production and global food security is being currently
discussed globally (Reynolds, 2010). IPCC (2007) has
shown that the average global surface temperature has
increased by 0.74 oC since the late 19th Century and is
expected to increase by 1.4 oC-5.8 oC by 2100 AD
with significant regional variations. The climate
change includes higher temperatures, changes in
precipitation (droughts and floods), and higher
atmospheric Co2 concentrations which may negatively
affect the yield (both quality and quantity), growth
rates, photosynthesis and transpiration rates, and also
disease and pest epidemics become frequent (Mahato,
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with improvement of the complex traits that are key to
release global hunger (Houle et al., 2010). There is a
close link between plant genomics involved in the
identification of genes and sustainable crop
improvement/production. It has already played a
direct role in the field of global climate change
including control of photosynthesis, adaptation to
water deficit, cold tolerance and reproductive
development (White et al., 2004).

(GWS) (Cobb et al., 2013). In this review, we try to

make it understand how phenomics can help to
harness the true benefits of the genomic era for crop
improvement.

Why genomics
Conventional pre-genomics scientific breeding
methodologies have made a significant contribution in
crop improvement and have led to the development of
modern cultivars of most major crops since the middle
of the 20th century. But these methods were slow in
targeting complex traits (yield, quality traits and stress
resistance etc) because the selection was largely based
on phenotypic evaluation which produce an
environmental noise. These classical methods were
also time-consuming, laborious, require large land and
population size, and are less precise and reliable. The
study of minor genes was impossible through these
methods which are as important as the major genes for
crop improvement and are considered key to release
global hunger.

However, tremendous progress has been made in plant

genomics especially the rapid developments in next
generation sequencing (NGS) technologies over the
last decade that have opened the scope to better
understand the relationship between genotype and
phenotype with greater precision and resolution than
ever before (Varshney et al., 2014). The genomic
technologies have made possible gene discovery for
complex traits, therefore, helps to better understand
the genetics of these traits. Thus, genomics tools have
enhanced the precision in conventional breeding
programs and in several cases led to the development
of superior cultivars with enhanced resistance/tolerance to
biotic and abiotic stresses through genomics-assisted
breeding (GAB) (Varshney et al., 2012). But, there is a
considerable gap between the genomic information
available on model crop species and its integration
into practical crop improvement. One of the most
important reasons is the lack of availability of precise
and high-throughput phenotyping tools leading to
poor results of gene/QTL discovery for GAB
applications.

Genomic-based approaches have made it possible to

discover genes for the complex traits and their precise
transfer into the elite background (Varshney and
Tuberosa, 2007). Genomics-assisted crop improvement
(GACI) provides an unusual opportunity to identify
major loci influencing the target traits and to select for
plants with the desirable combination of alleles via
MAS, MABC or MARS (Varshney and Tuberosa,
2007). The QTL mapping techniques have been used
for the discovery and identification of QTLs/genes for
the number of agriculturally important traits including
yield, quality traits, biotic and abiotic stress resistance
in almost all the major growing crops species (Toure
et al., 2007).

The era of phenomics is believed to give plant

scientists the tools that are necessary to unlock the
information coded in plant genomes (Finkel, 2009),
thus phenomics will help plant geneticists to tackle the
ever increasing threats of climate change. Some
progress has been made in the area of phenomics in
the world (Table 2) but more efforts (in terms
phenomic research) and funds are required to be
allocated in this field to achieve fruitful results from
genomics/molecular breeding approaches like QTL
interval mapping, association mapping, genome-wide
association studies (GWAS), QTL cloning, QTL
validation, marker-assisted selection (MAS), markerassisted recurrent selection (MARS), TILLING
(Targeting Induced Local Lesions in Genomes) and
genomic selection (GS) or genome-wide selection

Recent advances in genomics includes the availability

of large repertoire of molecular markers, genotyping
platforms, advances in genetic mapping procedures, a
study of marker-traits associations leading the
discovery of genes/QTLs, sequencing technologies
leading the reduction in sequencing costs and
available genome sequences of major crop genomes,
etc. The availability of molecular markers has enabled
us to prepare the dense molecular maps in most of the
major crops and mapping of QTLs/genes. Recently a
new molecular approach for molecular-assisted
selection of yield and other complex traits has been
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made possible by genome-wide selection (GWS;
Bernardo et al., 2008). The main advantage of GWS is
that it does not require any prior information or
knowledge about the loci influencing the target traits
but instead, GWS considers the effects of a marker set
sufficiently large to capture most of the additive
variation underlying complex quantitative traits. This
approach was mainly adopted by animal breeders
during the past decade; it is only recently that GWS is
being used to improve crop performance. Encouraging
results and simulation studies clearly indicate GWS at
the best option for increasing the selection gain for
yield and other complex quantitative traits (Bernardo,
2010). Cheap and high-throughput DArT and SNP
markers make GWS increasingly affordable and
applicable on a broader scale. The low sequencing
costs which are made possible by next-generation
sequencing platforms has provided new opportunities
for gene discovery and allele mining (Varshney et al.,
2009), thus expanding the germplasm pool available
for improving crop performance. By the incorporation
of molecular and genomics tools in crop improvement,
it is possible to design the model plant practically for
the crop species, having all desirable traits. Thus
makes the concept called breeding by design possible
that aims to control all allelic variation for all genes of
agronomic importance. This concept can be achieved
through a combination of precise genetic mapping,
high-resolution chromosome haplotyping and extensive
phenotyping (Peleman and Voort, 2003).

developments in so-called next-generation DNA

sequencing (NGS) technologies that offer exciting
opportunities for crop genetics and breeding (Edwards
et al., 2012). The advancements that occur in
sequencing technologies made the sequencing of plant
and crop genomes a routine (Jackson et al., 2011). The
identification of allelic variation through resequencing of crop genomes is also expected to
become routine in near future (Furbank and Tester,
2011).The cost for genotyping the plant genomes will
also get continuously decreased due to evolution and
emergence of high-throughput markers and genotypic
platforms. Therefore, to take the advantage of this
wealth of genomic information for crop improvement
and harness the full benefits, one needs to link and
integrate this information with the phenotype in a real
world environment (Furbank and Tester, 2011).
However, our capacity to collect reliable phenotypic
data is still lagging behind to our present day capacity
to generate high-throughput molecular genotypic data.
Thus creates a phenotypic bottleneck in capitalizing
on this huge amount of data that genomics produces
daily and is considered a new and major hindrance for
plant breeders in making progress in breeding
(Edwards et al., 2012; Stamp and Visser, 2012). The
important issues related to plant phenomics included
phenotyping large mapping populations for QTL/gene
discovery and cloning of major QTLs, phenotyping in
replicated trials in several environments over number
of years, phenotyping using destructive tools at fixed
times/growth stage, slow and costly phenotyping and
less precise estimates of phenotypic data for testing
allelic variations of a candidate gene in a germplasm
set (Furbank and Tester, 2011). This creates a gap
between genotype and phenotype (GP-Gap). Hence,
there is an immediate need of phenomics revolution in
order to harness the full advantage of genomic data
especially in changing climate and increasing world
population. Efforts are being made throughout the
world to alleviate the phenotyping bottleneck by
developing plant phenomics facilities that can scan
and record data for thousands of plants in a day in
sophisticated manner (Table 1 and 2). These
high-throughput phenomics facilities make use of
sophisticated non-invasive imaging, spectroscopy, image
analysis, robotics and high-performance computing
facilities. Thus save time, labor and cost and brings us
to the age of phenomics.

The rapid development of the functional genomics and

gene technologies that occur over the past decade as
discussed led to the functional analysis of the major
crop species genome to enter into the high-throughput
stage. The dozens of key genes of many major crop
species (rice, wheat, maize etc) have been cloned and
characterized for their functions in controlling
important agronomic traits (Yang et al., 2013). But the
available genomic/genetic information has not been
adequately exploited due to manual and laborious
phenotyping tools. It became apparent that the high
throughput phenotyping is an important component in
crop breeding and plant biology as will be discussed
in the following section.

Phenomics: A bottleneck for crop improvement

To understand and unravel crop genomes have
become easy with the advent and unprecedented
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High-throughput precise and accurate

phenotyping

levels of biological organization while reducing costs

and minimizing labor through automation, remote
sensing, data integration and experimental design
(Cobb et el., 2013). The accuracy and precision
are the two different terms but are often used
interchangeably, the accuracy involves the degree of
closeness of a measured or calculated quantity to its
actual (true) value, whereas precision also known as
reproducibility or repeatability, means the degree to
which further measurement or calculations show the
same or similar results.

The recent advances in the area of computational

biology, bioinformatics and genomics as already
stated have helped us to meet the demands set by the
genomic revolution to some extent. The valid and
applicable results reported with non-conventional
approaches so far have not yield expected results, in
spite of huge molecular genotypic data generated
during the last few years (Edmeades et al., 2004;
Araus et al., 2008; Collins et al., 2008; Xu and Crouch,
2008; Passioura, 2010). One of the important reasons
is the slow progress that has been made in the area of
phenomics involving the number of approaches for
recording precise and high-throughput phenotyping
data. The phenotypic data is the primary data required
for the genetic dissection of quantitative traits, and to
obtain the clean set of reproducible and precise
phenotypic data of complex traits like salinity
tolerance from larger germplasm collection remain an
open challenge even in the era of phenomics-driven
technology (Yang et al., 2013). The phenotypic data
should be taken with care because these characters are
highly influenced by environmental variations and are
thus more subjected to experimental errors. The
GP-gap is reduced through proper, accurate and
precise phenotyping of quantitative traits (Tuberosa,
2012). The precision with which the relevant QTLs or
chromosomal regions are identified and their effects
are estimated depends on how precisely the
phenotyping data is recorded used to establish the
phenotype-genotype association (Tuberosa, 2012; Fig.
1). Simultaneous treatment of phenotypic data from
multiple environments provides a significant increase
in statistical power of QTL detection and accuracy of
the estimates of QTL position and effect (Jansen et al.,
1995). Thus, molecular approaches for crop
improvement depends upon how well and how
accurately the target trait has been assessed
phenotypically in mapping population or diversity
panel, because if the phenotypic data is not taken
accurately there will be false positives and false
negatives .The genomic approach called genome-wide
selection that disregards QTL identification, and relies
on the molecular profiling and accurate phenotyping
of each progeny (Bernardo, 2008; Bernardo and Yu,
2007; Heffner et al., 2009).The good phenotyping
increases accuracy, precision and throughput at all

High-throughput phenotyping: Present status

and future possibilities
In the era of phenomics, high-throughput phenotyping
helps us to collect high quality accurate phenotyping
data. The high quality phenotypic data is very
important and useful for meaningful genetic dissection
and genomics-assisted breeding applications,
including: (i) QTL interval mapping, (ii) candidate
-gene based association mapping (iii) genome-wide
association studies (GWAS), (iv) QTL cloning, (v)
QTL meta-analysis, (vi) marker-assisted selection
(MAS), (vii) marker-assisted recurrent selection
(MARS), (viii) TILLING (Targeting Induced Local
Lesions in Genomes) and (ix) genomic selection (GS)
or genome-wide selection (GWS) (Welcker, 2011;
Tuberosa et al., 2012; Cobb et al., 2013; Fig. 1). This
importance can be realized by the fact that an
International Plant Phenomics Initiative was
launched recently to address crop productivity
(http://www .plantphenomics.org/). The earlier use of
invasive or destructive methods of plant phenotyping
is now giving way to high-throughput precise
non-destructive imaging techniques. Several ph
-enomics platforms are opening around the world with
good facilities allowing scientists new windows into
the inner workings of living plants. These facilities
include: (i) infrared cameras to scan temperature
profiles/transpiration; (ii) fluorescent microscopy/
spectroscopy to assess photosynthesis/ photosynthetic
rates, (iii) three-dimensional camera to record minute
changes in growth responses after wheat plants
transplanted into salty soil went into osmotic shock;
(iv) lidars (light detection and ranging) to measure
growth rates, and (v) magnetic resonance imaging
(MRI) to examine root/leaf physiology (Finkel, 2009;
Gupta et al., 2012). Digital imaging, considered
cornerstone for measuring quantitative phenotypes has
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allowed to monitor, measure and track many aspects
of plant development, function, and health which was
unimaginable using conventional measurement
techniques. A number of software programs have
been developed for extracting data from the digital
images from roots, shoots, leaves, seeds, grains etc. A
list of software programs and phenotyping platforms
for high-throughput precise phenotyping is available
elsewhere (Cobb et al., 2013). These high-throughput
phenotyping platforms and software are being used in
several laboratories across the world. These
phenomics facilities make sure to scan thousands of
plants in a day, so that this phenotyping technology
will become similar to high-throughput DNA
sequencing in the field of genomics (Finkel, 2009;
Table 1). In some countries, these phenomics
platforms are already being used for a variety of
phenotypic screens and developing root imaging
(Table 1). For instance, the name of the few
phenotyping platforms developed around the world
include Australian Plant Phenomics Facility in South
Australia, Plant Accelerator in Adelaide Australia,
Jlich Phenomics Centre by Institute for Phytosphere
Research (IPR) in Jlich Germany and Leibniz
Institute of Plant Genetics and Crop Plant Research in
Gatersleben Germany etc. (Table 2).

global hunger, but these traits have low heritability,

environmental sensitive and high experimental noise.
There improvement requires multi-location and
multi-seasonal data collected over a number of years
and locations, that too for large population size.
Targeting these traits through conventional breeding
were not found much effective as is evident from the
stagnation of yield from the past few decades, possible
reason may be the phenotyping. Gene mapping of
complex traits through both approaches i.e., linkage
mapping and association mapping require accurate
and precise phenotyping data taken for large sized
population. The population size and precision in gene
discovery are highly related with each other (Beavis,
1994 and 1998). Beavis (1994, 1998) conducted
simulation studies and observed that small population
size often leads to detection of only major QTLs and
overestimation of their effects. The statistical power of
detecting a minor QTL with a small population size of
100 could be as low as 3%, and the estimated effects
could be inflated as much as 10-fold (Beavis effect).
The power of QTL detection, defined as the probability of
detecting a QTL at a given level of statistical
significance (Manly and Olson, 1999), depends upon
the number of progeny in the population (sample size),
heritability of the trait, genetic dissimilarity among
progenies, the effect of the QTLs, and the
environment used for phenotypic evaluation. The
multi-parent mapping population (MAGIC, NAM etc)
emerging an effective approaches for unlocking the
genetic architecture of complex traits involves large
size of population (Buckler et al., 2009; McMullen et
al., 2009, Rakshit et al., 2012, Bandillo et al., 2013,
Mackay et al., 2014), hence demands the high-throughput
precise phenotyping. Genomic selection (GS) or
genome-wide selection (GWS) an approach for
molecular-assisted selection of yield and other
complex traits integrates marker and phenotypic data
from a training population to generate prediction
model. The model is used to estimate genomic
estimated breeding values (GEBV), for all genotyped
individuals of the reference set (Meuwissen et al.,
2001). The prediction model depends upon the
precision and accuracy the phenotypic data is taken on
training population. GS allows the selection of better
parents for crossing and generation advancement
based on genotypic value, independent of environment
influence, thereby accelerates the selection process
and genetic improvement of complex traits which are

With the availability of high-throughput phenotyping

tools and obtaining a lot of images and data, but to run
the data storage, handling and analysis will be another
challenge in plant phenomics. The volume of data
mainly depends on the resolution of the image
detectors and the number of acquired images from
each inspection. The data analysis methods, such as
principle component analysis (PCA) (Yang et al.,
2009), support vector machine (SVM) (Romer et al.,
2011) and artificial neural network (ANN) (Karkee et
al., 2009), are often used for data dimension reduction
and efficient parameters extraction. In the future for
promoting the application of high-throughput plant
phenotyping the less expensive, less laborious and
well sophisticated data analysis infrastructure such as
HTPheno (Hartmann et al., 2011) and IAP (Klukas et
al., 2012) in-corporating the open-source software
image J, needs to be developed and popularized.

Phenomics: Importance for complex traits

Complex quantitative traits represent most important
agronomically and economically, and are key for
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Table 1 Genetic dissection of complex traits using high-throughput phenotyping technique/platform
S.No

Crop

Trait

No. of
QTL

High-throughput phenotyping
Technique/platform

Reference/website

Rice

Root system architecture

traits

89

3D root imaging and analysis

platform

Toppa et al. (2013)

Rice

Seed shape

13

SmartGrain

Tanabata et al. (2012)

Rice

Traditional agronomic
traits and newly defined
traits

141

High-throughput rice phenotyping

facility (HRPF)

Yang et al. (2014)

Rice

Salanity tolerance

Image-based Phenomics

Campbell et al. (2015)

Wheat

Osmatic tolerance

The Plant Accelerator, University of

Adelaide Waite Campus

http://www.plantphenomic
s.org.au/

Wheat

Seedling root traits

29

Root imaging (Nikon D600 DSLR

camera)

Atkinson et al. (2015)

Wheat

Grain morphology

197

Digital imaging based phenomics

Rasheed et al. (2014)

Barley

Boron/germanium
tolerance

The Plant Accelerator, University of

Adelaide Waite Campus

http://www.plantphenomic
s.org.au/

Barley

Drought tolerance

44

The Plant Accelerator, University of

Adelaide Waite Campus

Honsdorf et al. (2014)

10

Brassica
napus

Root architectural and

biomass traits

38

Agar-based high-throughput
phenotyping system

Shi et al. (2012)

11

Arabidop
sis
thaliana

Water deficit-related traits

Phenopsis

Granier et al. (2006)

12

Soybean

Total carotenoids

14

High-throughput canopy spectral

reflectance

Dhanapal et al. (2015)

root

Phenome-wide association studies

highly influenced by environment. The GS are

reported to be best option for increasing the selection
gain for yield and other complex traits based on
results obtained and simulation studies (Bernardo,
2010). For elucidating the genetic architecture of
complex traits and, identifying the genes and specific
alleles underlying trait variation using above
approaches, the improvement of phenotyping in terms
of accuracy, precision, size of population, labor and
cost are the challenges to break yield barrier and
release global food hunger. Hence, the need for
high-throughput phenotyping is felt as is described in
Fig.1. The high throughput phenotyping have been
already used for the genetic dissection of number of
complex traits in different crops as is depicted in Table 1.

Phenome-wide association study (PheWAS) an

approach that is complementary to genome-wide
association studies (GWAS) that test the association
between hundreds of thousands, to over a million,
genotyped single nucleotide polymorphisms (SNPs)
and single phenotypic or limited phenotypic traits.
Thus, the main limitation of GWAS is focusing on
only a few phenotypic traits. An alternative approach
has emerged to overcome the above limitation called
Phenome-wide association study (PheWAS), which
utilizes all the available phenotypic information and
all genetic variants in the estimation of association
between genotype and phenotype (Pendergrass et al.,
2013). Therefore by investigating the association
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Table 2 List of worldwide facilities undertaking global assessments of plant phenotypes.
S.
No.
1

Phenotyping
platform
LEPSE(Laborat
ory of Plant
Ecophysiologic
al responses to
Environmental
Stresses)

Country

Reference/web link

France

http://www1.montpellier.inra.fr/ibip/lepse/english/

The Jlich Plant

Phenotyping
Centre (JPPC)

Germany

http://www.fz-juelich.de/ibg/ibg-2/EN/Research/Phenotyping/Phenotyping_article.h
tml?nn=548814

Biotron
Experimental
Climate Change
Research
Facility

Canada

http://www.thebiotron.ca/

Green Crop
Network (GCN)

Canada

http://www.greencropnetwork.com/

IBERS,
Aberystwyth
University

U.K

http://www.aber.ac.uk/en/ibers/facilities/new_builds_at_ibers/
Howarth et al., 2011

International
Plant
Phenomics
Network (IPPN)

Several Countries
includingAustrali
a,
France,Germany,
Canada

http://www.plantphenomics.com/

Mutant
genotype and
phenotype
dataset

U.S.A.

http://www.plantphysiol.org/content/early/2012/01/13/pp.111.192393.short?rss=1

New European
Ecotron
of
Montpellier

France

http://www.ecotron.cnrs.fr/

PhenoPhyte

U.S.A.

https://vphenodbs.rnet.missouri.edu/PhenoPhyte/index.php

10

SciNetS

Japan

https://database.riken.jp/

11

The Australian
Plant
Phenomics
Facility

Australia

http://www.plantphenomics.org.au/

12

High-throughpu
t rice
phenotyping
facility (HRPF)

China

Yang et al. (2014)

13

PHENOME

France

(https://urgi.versailles.inra.fr/Projects/PHENOME/)

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between SNPs and a diverse range of phenotypes, a
broader picture of the relationship between genetic
variation and network of phenotypes is possible. The
phenome-wide association study has also potential to
expose pleiotropy. Till date, the phenome-wide
association studies (PheWAS) have been used only in
human beings, but in the future it will definitely find
its applicability in plants as well and allow a much
broader view of testing the relationship between
genetic polymorphism and phenotypic network.
However, the PheWAS too faces challenges like
availability of large studies with genotypic data that
are also linked to a wide array of high quality
phenotypic measurements and traits for study. The
most important advantage of PheWAS is that it
provides us information about the complexity of
relationship between genetic polymorphism and
interrelated as well as independent phenotypes. Thus,
this new approach of PheWAS will change the
paradigm of phenotypes and allow for exploratory
research in both genomics and phenomics.

assess thousands and millions of plant phenotypes.

The improvement of complex traits whether through
conventional or genomic approach had an extreme
requirement of precise HTP (Fig. 1). These new HTP
platform can expand the germplasm evaluation in crop
improvement programs and thus directly benefit
attempts to address the challenge of increasing global
hunger in the face of growing population, decreasing
arable land area and global climate change. Thus,
phonemics is considered an important single factor to
release global hunger in the genomic era, and has
tremendous impact on crop breeding and variety
development.

Need to have phenotypic database

There exist the publicly accessible and curated
repositories built for the deposition of DNA and
protein sequence data, but unlikely there exist no
equivalent public repository for the deposition of raw
data generated from the hundreds of plant phenotypic
studies conducted each year. In other words, we can
say that data which sometimes need large amount of
money to generate is lost forever. This lose of
phenotypic data especially of the crop productivity
traits which occur due to lack of phenotyping warehousing
is to stopped in order to meet the challenges of
increasing food production by 70-100% to feed 9
billion people estimated to populate the earth by 2050
(Godfray et al., 2010). It was proposed that the more
phenotypic data we share, the faster we will achieve
crop yield improvement (Zamir, 2013). By making the
historic data available publicly, it would allow the
plant researchers to share results, to compare their
phenotypes, and to analyze that have been deposited
in the past in order to identify new and sometimes rare,
alleles that improve productivity. A scientist encounters a
situation in which he finds resistance to a certain
pathogen in a few of the accession of some crop and
wants to incorporate the trait into a breeding program.
His first priority remains to introduce the resistance
from the most agriculturally adapted accessions. But
without the availability of data on yield phenotypes,
such a decision cannot be made, thus delaying
progress. Thus, there is a need of publicly accessible
bioinformatics resource that would allow plant
breeders to explore a multitude of experiment in
which traits that are of importance to future
agriculture developments, such as yield stability, are

High-throughput phenotyping: Implications

in Crop improvement
The greatest challenge of plant science and crop
improvement in the 21st century is predicting how a
plant appearance (phenotype) is dictated by its genetic
makeup (genotype). The spectacular advances made in
the area of crop genomics especially the emergence of
next generation sequencing (NGS) technologies have
made the availability of high-density markers and
made GS affordable and possible in both model and
non-model crop species (Varshney et al., 2014). In
contrast, the methods for rapid characterization of
plant traits (i.e. phenotype) has evolved little over the
30 years and accurate measurement of phenotypic data
of large population for multiple traits in multiple
environment field trials remain costly and laborious,
especially for dynamic traits that are repeatedly
measured during the life cycle of a plant. The
measurement of phenotypic data on complex traits
which are considered hunger traits has generally
remained problematic. The most challenging and least
tractable of such traits are those related to heat and
drought stress tolerance (Bita and Gerats, 2013). To
make the 21st century biology truly in the genomic and
information age, high-throughput phenotyping platform
must be developed with the capacity to quantitatively
8

Molecular Plant Breeding 2015, Vol.6, No.20, 1-11

http://mpb.biopublisher.ca

Figure 1 Showing importance of high- throughput phenotyping (HTP) in genomics-assisted breeding for crop improvement. HTP
occupies critical position in a genomics-assisted breeding pipeline; it helps to increase the precision and accuracy in trait mapping to
identify genes and QTLs that are targets of MAS as well as it increase the precision of genomic selection (GS) to calculate GEBVs
that predict the breeding value of individuals in a breeding population.

available for a variety of crops from different

environments and climates (Zamir, 2013). Such a
publically accessible database is already been created
for the tomato called the Phenome Network database
(http://phnserver.phenome-network.com/), in which
historical data can be analyzed.

important reasons behind this, a) lack of the effective

high-throughput phenotyping facilities, as the
phenotyping data is an integral component of these
genomic approaches, and b) lack of integration
of phenomics with other omics approaches viz.,
epigenomics, transcriptomics, metabolomics and
proteomics etc, that are important to reduce the
genotype-phenotype gap. Hence, to achieve fruitful
results from genomics/molecular approaches like QTL
interval mapping, association mapping, genome-wide
association studies (GWAS), QTL cloning, QTL
validation, marker-assisted selection (MAS), marker
-assisted recurrent selection (MARS), TILLING
(Targeting Induced Local Lesions in Genomes) and
genomic selection (GS) or genome-wide selection
(GWS), much more efforts and funds are required to
be allocated in above fields. Therefore to fight against
the climate change and to keep pace with increasing
world human population as well as to maintain
sustainability in agriculture high-throughput
phenotyping and its integration with other omics
approaches is the ultimate option.

Conclusion
The improvement of complex quantitative tra its
through conventional breeding has not yielded the
better results because these traits have low heritability
and were highly influenced by environmental
conditions. The plant genomics and biotechnology
provides the new tools and techniques to the plant
breeders/researchers to solve the problems associated
with these complex traits that combine the genomic
and phenomic data to identify the genes governing
these traits, and were subsequently introgressed to the
adapted/elite crop varieties to improve the particular
trait of interest. In this way the crop varieties having
increased yield, quality as well as resistance to various
biotic and abiotic stresses have been developed in a
number of crop species including rice, wheat, maize,
soybean and chickpea etc. However, valid and
applicable results reported with these non
-conventional approaches so far have not yielded
expected results, in spite of huge molecular genotypic
data generated during the last few years. The most

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