ISSN 00954527, Cytology and Genetics, 2011, Vol. 45, No. 4, pp. 208213. Allerton Press, Inc., 2011.

Original Ukrainian Text O.V. Galaev, G.Yu. Shevchuk, V.V. Dudchenko, Yu.M. Sivolap, 2011, published in Tsitologiya i Genetika, 2011, Vol. 45, No. 4, pp. 915.

Molecular Genetic Analysis of the Soriz Genome

(Sorghum oryzoidum)
O. V. Galaeva, G. Yu. Shevchuka, V. V. Dudchenkob, and Yu. M. Sivolapa
a
South Plant Biotechnology Center, National Academy of Agrarian Sciences of Ukraine,
ul. Ovidiopolskaya Dor. 3, Odessa, 65036 Ukraine
email: genome2006@mail.ru, anni2901@mail.ru
b
Institute of Rice, National Academy of Agrarian Sciences of Ukraine, Antonovka Village,
Skadovsk District, Kherson Region, 75705 Ukraine
email: rice@askad.net
Received July 30, 2010

AbstractA molecular genetic analysis of soriz genotypes (Sorghum oryzoidum), its parental form Sorghum
bicolor (L.) Moench (grain sorghum), possible parents (Sorghum sudanense (Piper.) Stapf. (Sudan grass) and
Oryza sativa L. (Rice planting), as well as its closest relatives, has been carried out with the use of microsatel
lite loci of sorghum and rice. Based on the obtained data, the genetic distances were calculated and the exam
ined species were clustered. It was shown that soriz did not carry rice DNA fragments, but its genome con
tained DNA fragments, which belonged to Sudan grass. This confirms that the origin of soriz is associated
with representatives of Sorghum sudanense.
DOI: 10.3103/S0095452711040049

INTRODUCTION For the estimation of genetic relationships between

Soriz (Sorghum oryzoidum) is a new variety of
hybrid origin. It was bred in the former Institute of
Selection and Genetics and Moldavian Maize and
Sorghum Science Research Institute (these institu
tions were part of the former Southwestern Selection
Center) in the 1980s. Soriz plants are characterized by
high resistance to drought, high temperatures, and
salinization of soil. They are also characterized by
nonexacting to soil, lodging resistance, and resistance
to smut diseases and are not harmed by cereal plant
lice. Soriz is also characterized by lightyellow grain
and glassy endosperm. Soriz growths look like short
polished rice; this was the reason for naming such sor
ghum varieties as sorghum of a rice grain or soriz [1,
2]. At the present time, the origin of soriz is disputable.
According to the data obtained by Dremlyuk [1], soriz
was bred by complex hybridizations between grain sor
ghum and wild rice varieties, whereas Moraru [2, 3]
suggests that soriz was bred by stepwise hybridizations
between grain sorghum and Sudan grass and wild
smallgrained sorghum (Sorghum virgatum).
The application of molecular markers for the esti
mation of the variability of plant varieties and species
is helpful in both detection of genetic relationships
between them and making a system of plant genera,
which involves the most important agricultural species
(more precise) [4]. DNAtechnologies and markers
that are generated during PCR could serve as an addi
tional tool for the elucidation of the origin of soriz.
species, particular attention is paid to microsatellites
or simple sequenced repeat (SSR). Microsatellite
(MS) sequences (monolocus, polyallelic, codomi
nant, and hypervariable) distributed throughout the
genome of plants are used as genetic markers for the
analysis of the allelic state of loci in related plant spe
cies, such as sorghum [5], rice [6, 7], corn, wheat [4],
etc. It becomes possible to use molecular markers for
the purpose of more precisely determining the origin
of a variety [8].
The goal of the study is to characterize the Sorghum
oryzodium (soriz), Sorghum bicolor (grain sorghum),
Sorghum saccharatum (sugar sorghum), and Sorghum
technicus (besom sorghum) genotypes with the use of
molecular genetic methods and to detect the soriz origin
by comparing its genetic relationships with Sorghum
sudanense (Sudan grass) and Oryza sativa (red rice).
MATERIALS AND METHODS
The following served as study material: grain sor
ghum (Sorghum bicolor (L.) Moench, line K35E5),
sugar sorghum (Sorghum saccharatum (L.) Pers., line
Odeska 1820); besom sorghum (Sorghum technicum
(Koern) Roshev., line 2806 Budjak); Sudan grass (Sor
ghum sudanense (Piper.) Stapf., line Sudanka 1); soriz
(Sorghum oryzoidum, variety Odeska 302 and line
4005 Budjak); four rice varieties from the Institute of
Rice, National Academy of Agrarian Sciences of
Ukraine (Oryza sativa L., Pamyati Gichkina, Pre

208
 MOLECULAR GENETIC ANALYSIS OF THE SORIZ GENOME
mium, Debyut, and Vicont); one representative of
corn (Zea mays L., line GK26); and one representa
tive of wheat (Triticum aestivum L., variety Odeska
semidwarfish).
The DNA isolation was conducted according to the
protocol with the use of Proteinase K [9]. PCR was
carried out in a Tertsik amplificator (DNAtechnol
ogy, Russia). A 20l reactive mixture contained a
buffer (25 mM of KCl; 40 mM of TrisHCl pH 8.4;
15 mM of MgCl2; 0.01% Twin20; 20% saccharose);
0.2 mM of dATP, dCTP, dTTP, and dGTP of each;
0.25 M of primers; 20 ng of DNA; and TaqDNA
Polymerase. Mineral oil (20 l) was stratified above a
reaction solution. The PCR conditions were as fol
lows: initial denaturation at 94C for 2 min; each cycle
included denaturation for 30 sec; annealing at 53, 55,
60, and 63C (depending on the primers) for 30 s;
elongation at 72C for 1 min; 35 cycles; final elonga
tion at 72C for 4 min. The molecular genetic anal
ysis was performed by PCR with the use of 20 pairs of
primers for rice MS loci and 10 pairs for sorghum MS
loci, which were characterized by a high distribution
ability [10, 11]. The conditions of the amplification
product (10 l aliquots of PCR mixture) fractioning
were as follows: 10% PAGE in a 1 TBE buffer, con
stant voltage of 500 V, 60C, 23 h (depending on a
fragment length); for this purpose, we used a vertical
gel electrophoresis apparatus (Hoefer Scientific
Instruments, United States). The visualization of the
electrophoretic distribution was conducted in gel
impregnated with silver nitrate. The images and
lengths of the amplification fragments were received
with the use of an ImageMaster VDS video system
(Amersham Pharmacia Biotech, United States)
according to the user manual. To calibrate the molec
ular mass of the obtained amplicons, we used the pUC
19/MspI standard.
Using the TREES computer program [12] and Nei
and Lis algorithm [13], the genetic distances were
obtained according to the data on the electrophoretic
distribution of amplification products. A cluster anal
ysis of the genetic distances was conducted by the
Unweighted Pair Group Method with Arithmetic
Mean (UPGMA).
RESULTS AND DISCUSSION
There are two suggestions about the origin of soriz:
(1) complex hybridizations between bread (grain) sor
ghum and wild rice forms [1] and (2) stepwise crosses
between grain sorghum and Sudan grass and wild
smallgrained sorghum (Sorghum virgatum) [2, 3]. In
this regard, we carried out a molecular genetic analysis
of soriz genotypes, its possible parents, and the closest
relatives, using PCR with pairs of primers to MS loci
of sorghum and rice.
PCR analysis of sorghum MS loci. After the ampli
fication of ten sorghum MS loci, we obtained the spec
CYTOLOGY AND GENETICS Vol. 45 No. 4 2011
209
tra of DNA soriz specimens (variety Odeska 302,
line 4005 Budjak), four sorghum lines (K35E5,
Odeska 1820, 2806 Budjak, and Sudanka 1), four rice
varieties (Pamyati Gichkina, Premium, Debyut, and
Vicont), and one wheat variety (Odeska semidwarfish).
The PCR analysis of sorghum Sb636 and Sb684 with
two pairs of primers to MS loci revealed amplification
products (amplicons) in four rice varieties; it was
noted that the length of these products coincided with
the length of the products that were amplified in the
sorghum specimens. The amplification products in
the specimen of maize DNA were not obtained when
using a pair of primers to sorghum MS loci, whereas
we revealed an amplicon in the wheat specimen when
using a pair of primers to the MS locus Sb4121. The
number of alleles per locus varied from two to four. In
total, 32 alleles were identified (Table).
Based on the data of the PCR analysis of sorghum
MS loci, we calculated the genetic distances and clus
tering of the examined species. The values of genetic
distances varied from 0 to 0.784. A dendrogram united
specimens that belonged to two generaSorghum L.
and Oryza L. (Fig. 1a). The dendrogram showed that
the specimens were distributed in two clusters; one
cluster contained sorghum and soriz specimens, and
the other one contained rice specimens.
The clustering of the sorghum specimens by sor
ghum species corresponds to the data obtained by the
PCRanalysis with the use of nine pairs of primers to
sorghum MS loci [14] and ten random primers [15].
Based on the PCRanalysis with the use of primers to
sorghum MS loci only, the following conclusion can
be made: soriz does not contain DNAfragments
obtained as a result of distant hybridization.
PCR analysis of rice MS loci. The amplification of
20 rice MS loci revealed the DNA spectra of the exam
ined specimens. The number of alleles per locus varied
from one to three. In total, 40 alleles were identified
(Table). PCR with three pairs of primers to rice MS
loci (RM105, RM125, RM259, RM338, RM452,
RM489, and RM552) revealed amplification products
in two soriz specimens and in some species of the Sor
ghum genus. It is interesting that the specimens of the
lines Sudanka 1 and soriz (variety Odeska 302, line
4005 Budjak) had similar amplification products by
MS loci RM259 and RM338 (the amplification prod
uct lengths were 140 and 174 bp, respectively), which
were absent in the examined rice specimens. This
could confirm that soriz bred as a result of distant
hybridization carries Sorghum sudanense DNAfrag
ments. PCR with five pairs of primers to rice MS loci
produced amplicons in the Zea mays L. specimen, and
PCR with six pairs of primers produced amplicons in
the Triticum aestivum L. specimen.
Based on the data of the PCRanalysis of rice MS
loci, we calculated the genetic distances and clustering of
examined species. The values of genetic distances varied
from 0 to 0.990. The specimens were divided into two
210 GALAEV et al.

Allelic characteristic of the examined sorghum and rice microsatellite loci

Sorghum Soriz Rice

(Odeska 1820)

(2806 Budjak)
Marker

(Sudanka 1)
Sudan grass

semidwarf)
(location on

(K35E5)

Gichkina

Premium

(Odeska
(GK26)
Pamyati
of alleles
Number

Odeska

Debyut
a chromo

Budjak
Besom

Vicont

Wheat
Maize
Grain

Sugar
some)

4005
302
Allele length, bp.

OSR13 (3) 1 null null null null null null 100 100 100 100 null null
RM1 (1) 3 null null null null null null 97 91 97 94 97 97
RM19 (12) 2 null null null null null null 213 213 213 213 217 213
RM20 (11) 3 null null null null null null 204 204 201 201 null 165
RM21 (11) 2 null null null null null null 143 130 143 130 null null
RM105 (9) 2 106 106 106 106 106 106 111 111 111 111 null null
RM125 (7) 2 null null 105 105 105 105 114 114 114 114 105 105
RM161 (5) 2 null null null null null null 172 172 170 172 null null
RM222 (10) 1 null null null null null null 184 184 184 null null null
RM259 (1) 3 null null null 140 140 140 159 159 164 159 null null
RM283 (1) 2 null null null null null null 155 157 155 155 null null
RM307 (4) 2 null null null null null null 133 130 133 130 null null
RM338 (3) 2 null null null 174 174 174 164 164 164 164 null null
RM408 (8) 1 null null null null null null 128 128 128 128 null null
RM452 (2) 1 212 null null 212 212 212 212 212 212 212 212 212
RM455 (7) 2 null null null null null null 132 132 132 132 130 null
RM489 (3) 1 null null null 269 269 269 269 269 269 269 null null
RM495 (1) 1 null null null null null null 160 160 160 160 null null
RM510 (6) 2 null null null null null null 119 121 121 121 null null
RM552(11) 3 null null null 215 215 215 215 215 222 208 null 215
Sb415 (7) 2 158 158 161 161 161 161 null null null null null null
Sb636 (3) 2 169 169 169 163 169 169 163 169 169 169 null null
Sb6342(6) 3 271 268 265 271 271 271 null null null null null null
Sb432(7) 4 195 201 207 201 195 204 null null null null null null
Sb657(3) 4 293 302 299 293 290 290 null null null null null null
Sb684 (9) 3 180 177 189 189 177 177 180 180 180 180 null null
Xtxpl8 (8) 4 128 140 134 137 128 134 null null null null null null
Xtxp250 (8) 3 409 415 415 421 409 409 null null null null null null
Xtxp400 (8) 3 338 450 450 450 459 450 null null null null null null
SM121 (4) 4 203 197 185 185 185 185 null null null null null 220
Note: Nullno amplification product.

CYTOLOGY AND GENETICS Vol. 45 No. 4 2011

 MOLECULAR GENETIC ANALYSIS OF THE SORIZ GENOME 211

(a)
S. bicolor (K35E5)
S. saccharatum (Odeska 1820)
S. technicus (2806 Budjak)
I
S. oryzoidum (Odeska 302)
S. oryzoidum (4005 Budjak)
S. sudanense (Sudanka 1)
O. sativa (Pamyati Gichkina)
O. sativa (Premium)
II
O. sativa (Debyut)
O. sativa (Vicontt)

0.812 0.696 0.580 0.464 0.348 0.232 0.116 0

(b)
S. bicolor (K35E5)
S. saccharatum (Odeska 1820)
S. technicus (2806 Budjak)
S. sudanense (Sudanka 1) I
S. oryzoidum (Odeska 302)
S. oryzoidum (4005 Budjak)
O. sativa (Pamyati Gichkina)
O. sativa (Premium)
II
O. sativa (Vicontt)
O. sativa (Debyut)

0.890 0.763 0.636 0.508 0.381 0.254 0.127 0

(c)
S. bicolor (K35E5)
S. saccharatum (Odeska 1820)
S. technicus (2806 Budjak)
I
S. sudanense (Sudanka 1)
S. oryzoidum (Odeska 302)
S. oryzoidum (4005 Budjak)
O. sativa (Pamyati Gichkina)
O. sativa (Debyut)
II
O. sativa (Premium)
O. sativa (Vicontt)

0.890 0.763 0.636 0.508 0.381 0.254 0.127 0

Fig. 1. Dendrograms with the results of a UPGMA analysis based on the data of a SSRPCR analysis of microsatellite loci: (a)
sorghum; (b) genetic distances among rice varieties; and (c) sorghum and rice.

clusters on the dendrogram (Fig. b). One cluster con paid to the absence of differentiation between the speci
tained sorghum and soriz specimens, the other one con mens of Sorghum sudanense (line Sudanka 1) and Sor
tained representatives of the Oryza genus. Attention is ghum oryzoidum (variety Odeska 302, line 4005 Budjak).

CYTOLOGY AND GENETICS Vol. 45 No. 4 2011

212 GALAEV et al.
Based on a PCRanalysis with a pair of primers to
rice MS loci, a conclusion can be made that the soriz
genome contains DNAfragments, which belong to
Sudan grass. This confirms that the origin of soriz is
associated with representatives of Sorghum sudanense.
Clustering of the examined species based on the
total data of PCRanalysis. Based on the total data of
PCR analysis of sorghum and rice MS loci, we per
formed a calculation of the genetic distances and clus
tering of the examined species. The values of the
genetic distances varied from 0.226 to 0.994. The spec
imens are presented in the dendrogram by two clusters
(Fig. c). The first cluster contains representatives of
the Sorghum genus; the S. sudanense (line Sudanka 1)
specimen occupies the closest position to the repre
sentatives of the Sorghum genus. The second cluster is
formed of rice representatives.
Based on a molecular genetic analysis with the use
of two pairs of primers to sorghum and rice MS loci, it
was shown that soriz did not carry rice DNAfrag
ments, but its genome contained DNAfragments that
belonged to Sorghum sudanense and Sorghum bicolor.
Thus, it is possible to make a conclusion about the
association between the origin of soriz and representa
tives of Sudan grass (S. sudanense) and grain sorghum
(S. bicolor).
Comparative molecular genetic analysis of the Sor
ghum and Oryza genomes. The sorghum and rice
genomes possess a high degree of macrocollinearity;
however, the genome of S. bicolor (818 Mbp), which is
twofold bigger compared to the O. sativa genome
(389 Mbp), is distributed in ten chromosomes; the
O. sativa genome is distributed in 12 chromosomes
[16]. The difference in the number of sorghum and
rice chromosomes is explained by chromosome
fusion, which had occurred before the differentiation
in sorghum, corn, and Pennisetum [1719]. Although,
the difference in the sizes of S. bicolor and O. sativa is
connected to the differential accumulation of repeated
sequences in sorghum. By comparing the size, archi
tecture, and density of the genes in sorghum and rice
chromosomes, the study identified eight homologous
pairs of sorghum and rice chromosomes (S. bicolor
(SBI) chromosome 03 is homologous to O. sativa (Os)
chromosome 01, SBI04 to Os02, SBI05 to Os11,
SBI06 to Os04, SBI07 to Os08, SBI08 to Os12,
SBI09 to Os05, and SBI10 to Os06). It was also
found that sorghum chromosomes 1 and 2 were a
result of fusion of rice chromosomes 3 and 10, 7 and 9,
respectively [17, 18]. The content and order of genes
remain unchanged in cereals [20], which are one
genetic system [21]. Taking into consideration that
the analysis of SSR sequences of several cereal species
showed a high degree of homology in different flank
ing regions [22], pairs of primers to MS loci designed
for one species can be used for SSR amplification in
related cereal species [2325]. Thus, Ramu et al. [26]
used 2000 ESTs (expressed sequence tags, which con
tain SSR motifs) in the sorghum genome for the search
for analogous sequences in the genome database; they
revealed that 600 sorghum ESTSSR were homolo
gous to sequences in the rice genome. The pairs of
primers flanking SSR sequences of these 600 EST were
designed for the detection of the synteny of regions in
the rice and sorghum genomes.
In our study, the use of ten primers to sorghum MS
loci revealed amplification products in four rice variet
ies by the Sb636 and Sb684 loci, which are located
on chromosome 3 of S. bicolor (homologous to chro
mosome 1 of O. sativa (Os)) and on chromosome 9 of
S. bicolor (homologous to Os05). The lengths of these
amplification products coincided with those of the
amplicons in the sorghum specimens. PCRanalysis
with 20 pairs of primers to rice MS loci demonstrated
that 7 of them were helpful in obtaining amplification
products in the sorghum specimens: RM259 was
located on rice chromosome 1 (homologous to chro
mosome 3 of S. bicolor (SBI)), RM452 was located on
rice chromosome 2 (homeologic to SBI04), RM338
and RM489 were located on rice chromosome 3
(homologous to SBI01), RM 125 and RM105 were
located on rice chromosomes 7 and 9, respectively
(homologous to SBI02), and RM552 was located on
rice chromosome 11 (homologous to SBI05). It was
shown that 20% of the sorghum MS loci were helpful
in obtaining amplification products in O. sativa,
whereas 35% of the rice MS loci were amplified in
S. sudanense; 10% of the loci were amplified in S. tech
nicum and S. bicolor; and 5% were amplified in S. sac
charatum. This may confirm the conservative charac
ter of the flanking regions of rice amplification frag
ments, which contain microsatellite motifs. This fact
is confirmed due to the amplification of 30% of the
O. sativa MS loci in T. aestivum, amplification of 25%
of them in Z. mays, whereas using pairs of primers to
sorghum MS loci only discovered their 10% amplifica
tion in T. aestivum and failed to discover any amplifi
cation products in Z. mays.
CONCLUSIONS
PCRanalysis with the use of pairs of primers to
MS loci of sorghum and rice has shown that soriz
(Sorghum oryzoidum) does not carry rice DNAfrag
ments; however, its genome contains DNAfragments that
belong to Sorghum sudanense and Sorghum bicolor. This
indicates that the origin of soriz is associated with Sudan
grass (S. sudanense) and grain sorghum (S. bicolor).
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