Introduction
Bread wheat (Triticum
aestivum L.; 2n=6x=42, AABBDD allohexaploid) having three A, B and D
homeologous genomes, has been evolved through a series of natural crossing and
the effect of polyploidy (Gill and Gill 1994). In the evolutionary pathway
of modern wheat, the allopolyploidization was occurred twice. In first step T. urartu
(diploid) hybridized with Aegilops
speltoides (wild grass) that resulted into tetraploid T. turgidum and in the second step, tetraploid AABB, (2n=4x=28)
crossed with diploid goat grass A.
tauschii having the genome DD (2n=2x=14) which produced (hexaploid=AABBDD)
modern wheat (Förster et al. 2012).
According to (Dixon et al. 2009), wheat demand is
increasing faster and it is expected that it will be reach up to 40% in 2030.
So, there is need to increase the wheat production to confirm the food
security. There are many constraints which are responsible for lower wheat
production, including poor quality of seed, using broadcasting method for
sowing, late sowing, poor soil management, unbalanced fertilizer application,
improper weed eradication, diseases and shortage of water, heat and drought
stress due to climatic changes (Ahmed et al. 2017b). Among cereals
crops, wheat crop status is imperative because of nutritional values and more
consumption. Massive growth in population and the liberated life style has
directed to new challenges/problems for wheat breeders to create new wheat
genotypes with prominent yield and improved quality seed (Ahmed et al.
2019).
Use of molecular markers have been demonstrated as a
prominent tool in the assessment of polymorphism and interpretation of genomic
association for intra and inter varieties to obtain desirable genes for the
improvement in yield (Budak et al. 2015). These molecular markers extensively used in
applied plant breeding such as identification of qualitative and quantitative
attributes loci (QTLs) and find out their position on chromosome, gene
pyramiding, gene cloning for desired attributes, genetic diagnostics,
marker-assisted selection (MAS), functional characterization of germplasm,
phylogenetic relationship, genetic diversity
analysis for numerous crop plants (Mwadzingeni et al. 2017). These markers are
detectible gene sequences, specifically situated in the genome and inherited in
the successive generations (Ahmed et al. 2017a).
Molecular markers have been applied enormously in the
evaluation of genetic diversity, mapping of genes and identify the location of
QTLs on chromosomes in plants (Zhang et al. 2011). In the past, molecular
marker techniques also useful to recognize the genomic regions which are linked
to the phenotypic expression of characters and resultantly leads to marker
assisted breeding (MAB) or marker assisted selection (MAS) for the development
of desired variety (Roy et al. 2011). In plants molecular markers as SSR (simple
sequence repeat) and SNPs (single nucleotide polymorphisms) are. Genetic maps
of major field crops have been established by generating the data from these
markers (Lopes et al. 2015). In most of the crop plants, DNA markers are
abundant and easily measurable. Furthermore, these DNA markers are not
influenced due to external factors and can be applied for grouping of
individuals (Mwadzingeni et al. 2017). Profiling of DNA to evaluate whether genetically
and phenotypically similar genotypes is valuable in crop improvement. PCR based
molecular marker techniques are effective techniques in the exposure of
variation at the DNA level and genetic association (Kumar et al. 2016).
Classification of DNA markers divided into three groups
is based on: i) Inheritance pattern. ii) Gene action behavior (dominant or
co-dominant). ii) Hybridization or PCR based molecular markers. Molecular
markers like, SSRs are useful for the determination of genetic diversity
consuming their potential for robotics, co-dominance inheritance is additional
advantage and they disperse in the three genomes on the 21 chromosomes (Ahmed et al.
2017a). Due to the SSR markers’ abundance, chromosome specificity,
co-dominant in nature, highly polymorphic, outstanding reproducibility and evenly genome wide distributed have
been favored over other markers (Kumar et al. 2016). For wheat crop, SSR
markers previously used to demonstrate the genetic diversity in wild and
domesticated species of wheat and their improved germplasm. Presence of maximum
genetic diversity beneficial
for the selection and development of promising wheat varieties (Lopes et al.
2015).
Knowledge about diversity and association between
desired traits is productive in yield enhancement and to obtain the evidence
about the genetic basis of various biological developments (Henkrar et al.
2016). Gene sequencing plans for the kingdom of Plantae is hard
therefore, DNA marker and their relationship with various characters has delivered
a required landmark for explanation of genetic diversity. Cell organelles and
DNA components like mitochondrial, retro-transposons, and chloroplast-based
markers exhibited genetic variation through complex genome coverage (Bassi et al.
2016). Thus, DNA markers like SSR markers seemed to be the best
techniques for accurate assessment of diversity in crop plants and assortment of germplasm (Henkrar et al.
Fig. 1: Genomic
DNA of 105 bread wheat genotypes isolated by CTAB method. Reading from left to right in 1st lane
showing the genotypes from G-1 to G-20, 2nd lane from G-21 to G-40,
3rd lane from G-41 to G-60, 4th lane from G-61 to G-80,
and 5th lane from G-81 to G-100, while 6th lane showing
the last five genotypes from G-101 to G-105
2016). Therefore,
keeping in mind the above information, the current experiment was conducted to
distinguish bread wheat genotypes based on their genetic basis through SSR
markers. The main objective of this study is to estimate the genetic diversity
and genome wide allelic variation of studied germplasm for further selection in
any breeding program.
Materials and Methods
Germplasm collection
The total 105 bread wheat
genotypes were studied in this experiment. According to the maintaining
sources, the germplasm divided into three groups (Supplementary 1
mentioned in Ahmed et al. 2019
published paper). In first group the genotypes G-1 to G-20 developed in
the Department of Plant Breeding and Genetics, University of Agriculture Faisalabad (PBG-UAF), Pakistan, while second
group genotypes G-21 to G-55 were from exotic source and third group genotypes
G-56 to G-105 were from indigenous source.
Plant growing condition and DNA extraction
In
green-house, wheat seeds were sown in small plastic trays for healthy seedlings
at Department of Plant Breeding and Genetics (PBG), University of Agriculture
Faisalabad (U.A.F.), Pakistan. After three weeks, fresh leaves were collected
for DNA isolation using modified Cetyl-Trimethyl Ammonium Bromide (CTAB) method
(Saghai-Maroof et al. 1984) in 96 well-plates. The concentration and
quality of isolated DNA was assessed by Nano-drop (ND1000, Thermo Scientific, U.S.A.).
In Fig. 1 the isolated genomic DNA of 105 bread genotypes was indicated.
SSR markers-based
genotyping
The total
302 genome wide polymorphic SSR markers were selected for study. Among them,
based on the consensus map Ta-SSR-2004, 102, 100 and 100 markers found at the
A, B, and D homeologous genomes, respectively (Somers et al. 2004). According to this
map each genome had 15 polymorphic SSR
markers located on each chromosome (1–7) except 3A,
3B and 3D chromosomes which had 13 polymorphic SSR markers on each chromosome,
while 6B and 6D showed each 12 polymorphic SSR markers and 6A had 14
polymorphic SSR markers.
Using autoclaved Double Distilled Water 6.1 µL,
Buffer (10C) 1 L, MgCl2 (25 mM) 0.2 µL,
dNTPs (2.5 mM) 0.3 µL, M13 fluorophores (10 µM) 0.08 µL,
Taq DNA Polymerase (5 Units µL-1) 0.2 µL, FORWARD
Primer (10 µM) 0.02 µL and
REVERSE Primer (10 µM) 8.0 µL
with the Total Volume 8.0 µL for 1X (1 PCR reaction) and multiplied with
96 if used 96-well plate and further multiplied with 4 for 384-well plate. Here
four types of M13 fluorophores were used, (1) FAM for Blue color (2) HEX Green color (3) NED for Yellow color and (4) PET for Red color peaks in capillary electrophoresis (John et al. 2012). After this, sealed the plate using the
sealing mat (BIOEXPRESS T-3109-3). Centrifuged and put the plate in
thermo-cycler using the following PCR steps. (1) Denature at 94°C for 5 min,
(2) Denature at 94°C for 30 s and (3) Anneal at 60°C for 45 s (4) extension at
72°C for 60 s. In step 2 to 4 total 37 cycles were programmed. Finally extend
at 72°C for 10 min.
After PCR, prepared the ABI plate, used one 384
well-plate to made DILUTION PLATE (GENEMATE T-6061-1) and another 384 well
plate (single notch GENEMATE plate; GENEMATE T-3157-1) to made ABI plate along
with four PCR amplified plates and one formamide plate (mixture of formamide
dye with specific molecular weight marker or size standard) mix them into one
plate. Finally, plates were ready for capillary electrophoresis in ABI (ABI Prism 3100 Genetic Analyzer, Applied Biosystems) (Daware et al.
2016). After running ABI, the data recorded and converted on Gene
Mapper software which peaks (indicating the SSR base pair position just like on
Gel electrophoresis) converted into numeric format like, 1 for presence and 0
for absence (Kujur et al. 2015).
Molecular data analysis
Polymorphic alleles were
estimated in numeric by using Gene Marker on the basis of peaks which showed
different allelic pattern of SSR markers. Four types of peaks were separated on
the basis of different M13 fluorophores and then further aligned for genetic
diversity and the genome wide allelic variation study. Total numbers of allele
per markers and allelic frequency were measured through the statistical
software GenAlEx version 6.5 (Smouse and Peakall
2012) and UPGMA (Un-weighted pair group method with arithmetic mean, or
un-weighted neighbor joining tree) branching tree were created by statistical
software DARWIN version 6 (Perrier et al. 2003) for the grouping of
studied germplasm. POWER MARKER software version 3.23 (Liu and Muse 2005) applied for estimation of polymorphic
information contents (
Results
Genome wide allelic variation
The total 302 genome wide polymorphic SSR markers
selected for study, out of them 102, 100 and 100 found at the A, B, and D
homeologous genomes, respectively. From each genome 15 polymorphic SSR markers
located on each chromosomes except 3A, 3B and 3D chromosomes had each 13
polymorphic SSR markers, while 6B and 6D showed each 12 polymorphic SSR markers
and 6A had 14 polymorphic SSR markers as displayed in Table 1. The total number
of alleles in all genome was 2308 for 302 polymorphic SSR markers. Out of these,
the total 685, 869 and 754 alleles were recorded for 102, 100 and 100
polymorphic SSR loci in A, B and D genome respectively. The mean value of polymorphic information content was
0.72, and the gene diversity (GD) value was 0.76 among the genome wide 302
polymorphic SSR markers. The total number of
alleles (TNA) per marker ranged from 2 to
Table 1:
List of polymorphic 302 SSR markers used to evaluate 105 bread wheat genotypes
S. No |
MN |
CL |
TNA |
PSM |
SRBP |
GD |
PIC |
S. No |
MN |
CL |
TNA |
PSM |
SRBP |
GD |
PIC |
1 |
Xgdm33 |
1A |
15 |
92.38 |
120-280 |
0.90 |
0.88 |
152 |
Xbarc68 |
4B |
5 |
94.29 |
220-260 |
0.76 |
0.72 |
2 |
Xgwm136 |
1A |
9 |
100.00 |
210-290 |
0.80 |
0.76 |
153 |
Xgwm495 |
4B |
5 |
94.29 |
220-260 |
0.72 |
0.67 |
3 |
Xgwm11 |
1A |
5 |
94.29 |
220-260 |
0.76 |
0.72 |
154 |
Xgwm113 |
4B |
15 |
100.00 |
100-320 |
0.90 |
0.89 |
4 |
Xcfa2226 |
1A |
5 |
94.29 |
220-260 |
0.72 |
0.67 |
155 |
Xbarc25 |
4B |
8 |
100.00 |
80-150 |
0.79 |
0.76 |
5 |
Xwmc33 |
1A |
11 |
100.00 |
100-200 |
0.86 |
0.84 |
156 |
Xbarc20 |
4B |
13 |
100.00 |
170-290 |
0.86 |
0.84 |
6 |
Xwmc336 |
1A |
11 |
97.14 |
100-200 |
0.77 |
0.73 |
157 |
Xbarc163 |
4B |
7 |
100.00 |
50-120 |
0.76 |
0.72 |
7 |
Xwmc95 |
1A |
15 |
100.00 |
100-320 |
0.90 |
0.89 |
158 |
Xwmc692 |
4B |
7 |
85.71 |
160-220 |
0.83 |
0.81 |
8 |
Xwmc24 |
1A |
7 |
93.33 |
120-190 |
0.78 |
0.74 |
159 |
Xbarc109 |
4B |
8 |
100.00 |
110-190 |
0.84 |
0.82 |
9 |
Xbarc83 |
1A |
4 |
93.33 |
120-150 |
0.64 |
0.56 |
160 |
Xwmc617 |
4B |
8 |
100.00 |
80-150 |
0.79 |
0.76 |
10 |
Xgwm164 |
1A |
5 |
94.29 |
140-180 |
0.73 |
0.68 |
161 |
Xcfd5 |
5B |
13 |
100.00 |
170-290 |
0.86 |
0.84 |
11 |
Xbarc28 |
1A |
5 |
94.29 |
140-180 |
0.69 |
0.63 |
162 |
Xwmc773 |
5B |
14 |
100.00 |
100-280 |
0.88 |
0.87 |
12 |
Xgwm135 |
1A |
14 |
100.00 |
100-280 |
0.88 |
0.87 |
163 |
Xwmc630 |
5B |
8 |
98.10 |
120-190 |
0.81 |
0.79 |
13 |
Xbarc17 |
1A |
8 |
98.10 |
120-190 |
0.81 |
0.79 |
164 |
Xwmc47 |
5B |
3 |
96.19 |
240-260 |
0.51 |
0.45 |
14 |
Xbarc145 |
1A |
3 |
96.19 |
240-260 |
0.51 |
0.45 |
165 |
Xgwm443 |
5B |
8 |
100.00 |
80-150 |
0.79 |
0.76 |
15 |
Xwmc59 |
1A |
4 |
96.19 |
230-260 |
0.64 |
0.59 |
166 |
Xcfa2121 |
5B |
13 |
100.00 |
170-290 |
0.86 |
0.84 |
16 |
Xbarc212 |
2A |
6 |
97.14 |
120-170 |
0.77 |
0.73 |
167 |
Xwmc740 |
5B |
8 |
100.00 |
80-150 |
0.79 |
0.76 |
17 |
Xwmc382 |
2A |
8 |
100.00 |
120-190 |
0.86 |
0.84 |
168 |
Xgwm66 |
5B |
13 |
100.00 |
170-290 |
0.86 |
0.84 |
18 |
Xcfd36 |
2A |
8 |
100.00 |
100-170 |
0.79 |
0.76 |
169 |
Xgwm68 |
5B |
7 |
100.00 |
50-120 |
0.76 |
0.72 |
19 |
Xgwm359 |
2A |
5 |
95.24 |
200-240 |
0.74 |
0.69 |
170 |
Xbarc89 |
5B |
7 |
85.71 |
160-220 |
0.83 |
0.81 |
20 |
Xwmc149 |
2A |
7 |
90.48 |
110-170 |
0.78 |
0.75 |
171 |
Xgwm371 |
5B |
8 |
100.00 |
110-190 |
0.84 |
0.82 |
21 |
Xwmc453 |
2A |
6 |
100.00 |
270-320 |
0.70 |
0.64 |
172 |
Xgwm499 |
5B |
8 |
83.81 |
140-230 |
0.81 |
0.78 |
22 |
Xgwm339 |
2A |
8 |
98.10 |
120-190 |
0.73 |
0.70 |
173 |
Xwmc537 |
5B |
5 |
100.00 |
260-300 |
0.69 |
0.63 |
23 |
Xgwm448 |
2A |
2 |
100.00 |
200-210 |
0.50 |
0.37 |
174 |
Xcfd7 |
5B |
7 |
98.10 |
120-190 |
0.77 |
0.73 |
24 |
Xgwm95 |
2A |
10 |
100.00 |
90-190 |
0.77 |
0.73 |
175 |
Xwmc289 |
5B |
5 |
100.00 |
190-230 |
0.78 |
0.74 |
25 |
Xwmc702 |
2A |
7 |
100.00 |
80-140 |
0.75 |
0.71 |
176 |
Xgwm613 |
6B |
3 |
98.10 |
210-230 |
0.46 |
0.38 |
26 |
Xgwm328 |
2A |
5 |
94.29 |
150-190 |
0.74 |
0.69 |
177 |
Xwmc486 |
6B |
3 |
98.10 |
170-190 |
0.60 |
0.53 |
27 |
Xwmc819 |
2A |
8 |
100.00 |
80-150 |
0.79 |
0.76 |
178 |
Xgwm132 |
6B |
15 |
100.00 |
100-320 |
0.90 |
0.89 |
28 |
Xgwm47 |
2A |
13 |
100.00 |
170-290 |
0.86 |
0.84 |
179 |
Xwmc79 |
6B |
14 |
100.00 |
100-280 |
0.88 |
0.87 |
29 |
Xcfd168 |
2A |
7 |
100.00 |
50-120 |
0.76 |
0.72 |
180 |
Xgdm113 |
6B |
8 |
98.10 |
120-190 |
0.81 |
0.79 |
30 |
Xwmc181 |
2A |
7 |
85.71 |
160-220 |
0.83 |
0.81 |
181 |
Xwmc494 |
6B |
3 |
96.19 |
240-260 |
0.51 |
0.45 |
31 |
Xgwm369 |
3A |
8 |
100.00 |
110-190 |
0.84 |
0.82 |
182 |
Xgwm361 |
6B |
15 |
92.38 |
120-280 |
0.90 |
0.88 |
32 |
Xwmc532 |
3A |
2 |
100.00 |
160-170 |
0.50 |
0.37 |
183 |
Xbarc146 |
6B |
9 |
100.00 |
210-290 |
0.80 |
0.76 |
33 |
Xwmc11 |
3A |
4 |
100.00 |
240-270 |
0.54 |
0.49 |
184 |
Xbarc198 |
6B |
5 |
94.29 |
220-260 |
0.76 |
0.72 |
34 |
Xwmc215 |
3A |
4 |
100.00 |
160-190 |
0.55 |
0.44 |
185 |
Xbarc127 |
6B |
5 |
94.29 |
220-260 |
0.72 |
0.67 |
35 |
Xgwm155 |
3A |
8 |
100.00 |
200-270 |
0.76 |
0.73 |
186 |
Xgwm133 |
6B |
15 |
100.00 |
100-320 |
0.90 |
0.89 |
36 |
Xgwm2 |
3A |
6 |
100.00 |
100-150 |
0.76 |
0.72 |
187 |
Xbarc24 |
6B |
14 |
100.00 |
100-280 |
0.88 |
0.87 |
37 |
Xgwm32 |
3A |
7 |
100.00 |
80-150 |
0.82 |
0.79 |
188 |
Xgwm569 |
7B |
8 |
98.10 |
120-190 |
0.81 |
0.79 |
38 |
Xwmc651 |
3A |
3 |
100.00 |
270-290 |
0.62 |
0.54 |
189 |
Xwmc606 |
7B |
3 |
96.19 |
240-260 |
0.51 |
0.45 |
39 |
Xwmc627 |
3A |
2 |
100.00 |
250-260 |
0.49 |
0.37 |
190 |
Xgwm537 |
7B |
8 |
100.00 |
80-150 |
0.79 |
0.76 |
40 |
Xwmc527 |
3A |
7 |
99.05 |
170-230 |
0.81 |
0.77 |
191 |
Xgwm68 |
7B |
13 |
100.00 |
170-290 |
0.86 |
0.84 |
41 |
Xgwm391 |
3A |
7 |
99.05 |
130-190 |
0.82 |
0.79 |
192 |
Xbarc85 |
7B |
7 |
100.00 |
50-120 |
0.76 |
0.72 |
42 |
Xwmc264 |
3A |
4 |
100.00 |
200-230 |
0.68 |
0.61 |
193 |
Xwmc426 |
7B |
7 |
85.71 |
160-220 |
0.83 |
0.81 |
43 |
Xgwm162 |
3A |
5 |
100.00 |
90-130 |
0.62 |
0.58 |
194 |
Xgwm46 |
7B |
8 |
100.00 |
110-190 |
0.84 |
0.82 |
44 |
Xwmc516 |
4A |
6 |
98.10 |
200-250 |
0.65 |
0.58 |
195 |
Xwmc475 |
7B |
8 |
100.00 |
80-150 |
0.79 |
0.76 |
45 |
Xbarc206 |
4A |
7 |
100.00 |
130-190 |
0.81 |
0.78 |
196 |
Xbarc267 |
7B |
13 |
100.00 |
170-290 |
0.86 |
0.84 |
46 |
Xwmc15 |
4A |
6 |
99.05 |
290-340 |
0.62 |
0.54 |
197 |
Xbarc95 |
7B |
15 |
100.00 |
100-320 |
0.90 |
0.89 |
47 |
Xwmc491 |
4A |
11 |
100.00 |
230-350 |
0.82 |
0.80 |
198 |
Xwmc396 |
7B |
14 |
100.00 |
100-280 |
0.88 |
0.87 |
48 |
Xgwm601 |
4A |
7 |
91.43 |
240-300 |
0.84 |
0.81 |
199 |
Xwmc653 |
7B |
8 |
98.10 |
120-190 |
0.81 |
0.79 |
49 |
Xwmc617 |
4A |
9 |
99.05 |
180-280 |
0.71 |
0.66 |
200 |
Xgwm274 |
7B |
3 |
96.19 |
240-260 |
0.51 |
0.45 |
50 |
Xgwm397 |
4A |
9 |
99.05 |
140-220 |
0.86 |
0.84 |
201 |
Xgwm302 |
7B |
8 |
100.00 |
80-150 |
0.79 |
0.76 |
51 |
Xbarc170 |
4A |
13 |
98.10 |
240-420 |
0.77 |
0.74 |
202 |
Xwmc723 |
7B |
13 |
100.00 |
170-290 |
0.86 |
0.84 |
52 |
Xwmc468 |
4A |
7 |
100.00 |
150-220 |
0.78 |
0.75 |
203 |
Xgwm147 |
1D |
7 |
100.00 |
50-120 |
0.76 |
0.72 |
53 |
Xgwm565 |
4A |
11 |
100.00 |
70-180 |
0.82 |
0.80 |
204 |
Xbarc149 |
1D |
7 |
85.71 |
160-220 |
0.83 |
0.81 |
54 |
Xcfd257 |
4A |
4 |
87.62 |
240-270 |
0.73 |
0.67 |
205 |
Xgwm33 |
1D |
8 |
100.00 |
110-190 |
0.84 |
0.82 |
55 |
Xwmc283 |
4A |
12 |
99.05 |
100-260 |
0.82 |
0.79 |
206 |
Xcfd21 |
1D |
15 |
92.38 |
120-280 |
0.90 |
0.87 |
56 |
Xwmc232 |
4A |
5 |
95.24 |
140-190 |
0.61 |
0.53 |
207 |
Xgwm106 |
1D |
9 |
100.00 |
210-290 |
0.80 |
0.76 |
57 |
Xbarc78 |
4A |
6 |
97.14 |
140-190 |
0.73 |
0.68 |
208 |
Xbarc119 |
1D |
5 |
94.29 |
220-260 |
0.76 |
0.72 |
58 |
Xwmc722 |
4A |
5 |
100.00 |
150-190 |
0.68 |
0.62 |
209 |
Xbarc99 |
1D |
5 |
94.29 |
220-260 |
0.72 |
0.67 |
59 |
Xbarc69 |
5A |
7 |
100.00 |
100-190 |
0.64 |
0.57 |
210 |
Xbarc169 |
1D |
8 |
100.00 |
80-150 |
0.79 |
0.76 |
60 |
Xwmc173 |
5A |
3 |
97.14 |
210-230 |
0.50 |
0.44 |
211 |
Xbarc66 |
1D |
13 |
100.00 |
170-290 |
0.86 |
0.84 |
61 |
Xcfa2076 |
5A |
5 |
99.05 |
130-170 |
0.71 |
0.65 |
212 |
Xgwm642 |
1D |
14 |
100.00 |
100-280 |
0.88 |
0.87 |
62 |
Xbarc10 |
5A |
5 |
99.05 |
150-190 |
0.77 |
0.72 |
213 |
Xcfd63 |
1D |
8 |
98.10 |
120-190 |
0.81 |
0.79 |
63 |
Xgwm443 |
5A |
8 |
83.81 |
140-230 |
0.81 |
0.78 |
214 |
Xgdm126 |
1D |
3 |
96.19 |
240-260 |
0.51 |
0.45 |
64 |
Xwmc713 |
5A |
5 |
100.00 |
260-300 |
0.69 |
0.63 |
215 |
Xgdm11 |
1D |
8 |
100.00 |
80-150 |
0.79 |
0.76 |
65 |
Xgwm154 |
5A |
7 |
98.10 |
120-190 |
0.77 |
0.73 |
216 |
Xwmc405 |
1D |
13 |
100.00 |
170-290 |
0.86 |
0.84 |
66 |
Xcfa2190 |
5A |
5 |
100.00 |
190-230 |
0.78 |
0.74 |
217 |
Xbarc62 |
1D |
7 |
100.00 |
50-120 |
0.76 |
0.72 |
67 |
Xgwm129 |
5A |
3 |
98.10 |
210-230 |
0.46 |
0.37 |
218 |
Xgwm210 |
2D |
7 |
85.71 |
160-220 |
0.83 |
0.81 |
Table
1:
Continued
68 |
Xbarc117 |
5A |
3 |
98.10 |
170-190 |
0.60 |
0.53 |
219 |
Xcfd36 |
2D |
8 |
100.00 |
110-190 |
0.84 |
0.82 |
69 |
Xbarc180 |
5A |
12 |
99.05 |
60-190 |
0.88 |
0.86 |
220 |
Xwmc818 |
2D |
8 |
83.81 |
140-230 |
0.81 |
0.78 |
70 |
Xbarc56 |
5A |
8 |
97.14 |
90-190 |
0.77 |
0.75 |
221 |
Xgwm455 |
2D |
5 |
100.00 |
260-300 |
0.69 |
0.63 |
71 |
Xbarc186 |
5A |
3 |
100.00 |
170-190 |
0.49 |
0.39 |
222 |
Xwmc503 |
2D |
7 |
98.10 |
120-190 |
0.77 |
0.73 |
72 |
Xgwm156 |
5A |
8 |
95.24 |
100-180 |
0.84 |
0.81 |
223 |
Xgwm261 |
2D |
5 |
100.00 |
190-230 |
0.78 |
0.74 |
73 |
Xwmc795 |
5A |
16 |
100.00 |
240-400 |
0.88 |
0.86 |
224 |
Xwmc470 |
2D |
3 |
98.10 |
210-230 |
0.45 |
0.37 |
74 |
Xgwm334 |
6A |
4 |
100.00 |
160-190 |
0.74 |
0.69 |
225 |
Xbarc59 |
2D |
3 |
98.10 |
170-190 |
0.60 |
0.53 |
75 |
Xbarc206 |
6A |
2 |
98.10 |
120-130 |
0.45 |
0.33 |
226 |
Xwmc453 |
2D |
14 |
100.00 |
100-280 |
0.88 |
0.87 |
76 |
Xbarc23 |
6A |
4 |
99.05 |
240-270 |
0.65 |
0.58 |
227 |
Xwmc81 |
2D |
8 |
98.10 |
120-190 |
0.81 |
0.79 |
77 |
Xbarc3 |
6A |
4 |
99.05 |
160-190 |
0.73 |
0.68 |
228 |
Xgwm102 |
2D |
3 |
96.19 |
240-260 |
0.51 |
0.45 |
78 |
Xbarc195 |
6A |
2 |
98.10 |
110-120 |
0.50 |
0.37 |
229 |
Xgwm515 |
2D |
8 |
100.00 |
80-150 |
0.79 |
0.76 |
79 |
Xbarc48 |
6A |
5 |
100.00 |
230-270 |
0.72 |
0.66 |
230 |
Xbarc145 |
2D |
13 |
100.00 |
170-290 |
0.86 |
0.84 |
80 |
Xbarc146 |
6A |
9 |
97.14 |
240-370 |
0.80 |
0.77 |
231 |
Xcfd2 |
2D |
7 |
100.00 |
50-120 |
0.76 |
0.72 |
81 |
Xbarc165 |
6A |
4 |
98.10 |
160-190 |
0.47 |
0.40 |
232 |
Xcfd10 |
2D |
7 |
85.71 |
160-220 |
0.83 |
0.81 |
82 |
Xwmc672 |
6A |
3 |
93.33 |
160-180 |
0.50 |
0.42 |
233 |
Xgwm114 |
3D |
8 |
100.00 |
110-190 |
0.84 |
0.82 |
83 |
Xwmc201 |
6A |
10 |
97.14 |
240-330 |
0.81 |
0.78 |
234 |
Xbarc68 |
3D |
8 |
83.81 |
140-230 |
0.81 |
0.78 |
84 |
Xgwm570 |
6A |
7 |
98.10 |
60-120 |
0.79 |
0.76 |
235 |
Xcfd141 |
3D |
5 |
100.00 |
260-300 |
0.69 |
0.63 |
85 |
Xgwm617 |
6A |
4 |
98.10 |
160-190 |
0.70 |
0.64 |
236 |
Xgwm183 |
3D |
7 |
98.10 |
120-190 |
0.77 |
0.73 |
86 |
Xgwm169 |
6A |
8 |
96.19 |
150-220 |
0.78 |
0.75 |
237 |
Xbarc128 |
3D |
5 |
100.00 |
190-230 |
0.78 |
0.74 |
87 |
Xwmc417 |
6A |
3 |
97.14 |
130-150 |
0.67 |
0.59 |
238 |
Xwmc43 |
3D |
3 |
98.10 |
210-230 |
0.45 |
0.37 |
88 |
Xgwm666 |
7A |
5 |
93.33 |
180-220 |
0.78 |
0.74 |
239 |
Xcfd34 |
3D |
3 |
98.10 |
170-190 |
0.60 |
0.53 |
89 |
Xgwm233 |
7A |
3 |
100.00 |
120-140 |
0.60 |
0.53 |
240 |
Xwmc529 |
3D |
8 |
83.81 |
140-230 |
0.81 |
0.78 |
90 |
Xgwm350 |
7A |
5 |
94.29 |
140-180 |
0.76 |
0.71 |
241 |
Xgwm456 |
3D |
5 |
100.00 |
260-300 |
0.69 |
0.63 |
91 |
Xgwm471 |
7A |
3 |
96.19 |
160-180 |
0.55 |
0.46 |
242 |
Xwmc492 |
3D |
7 |
98.10 |
120-190 |
0.77 |
0.73 |
92 |
Xgwm60 |
7A |
6 |
100.00 |
220-270 |
0.78 |
0.74 |
243 |
Xcfd201 |
3D |
5 |
100.00 |
190-230 |
0.78 |
0.74 |
93 |
Xwmc283 |
7A |
9 |
100.00 |
240-320 |
0.84 |
0.81 |
244 |
Xwmc630 |
3D |
3 |
98.10 |
210-230 |
0.45 |
0.37 |
94 |
Xbarc154 |
7A |
6 |
100.00 |
100-160 |
0.73 |
0.68 |
245 |
Xcfd127 |
3D |
3 |
98.10 |
170-190 |
0.60 |
0.53 |
95 |
Xwmc826 |
7A |
8 |
98.10 |
50-140 |
0.84 |
0.81 |
246 |
Xwmc285 |
4D |
14 |
100.00 |
100-280 |
0.88 |
0.87 |
96 |
Xbarc174 |
7A |
14 |
100.00 |
100-280 |
0.88 |
0.87 |
247 |
Xwmc818 |
4D |
8 |
98.10 |
120-190 |
0.81 |
0.79 |
97 |
Xbarc23 |
7A |
8 |
98.10 |
120-190 |
0.81 |
0.79 |
248 |
Xwmc52 |
4D |
3 |
96.19 |
240-260 |
0.51 |
0.45 |
98 |
Xwmc17 |
7A |
3 |
96.19 |
240-260 |
0.51 |
0.45 |
249 |
Xwmc457 |
4D |
8 |
100.00 |
80-150 |
0.79 |
0.76 |
99 |
Xwmc65 |
7A |
8 |
100.00 |
80-150 |
0.79 |
0.76 |
250 |
Xgwm165 |
4D |
13 |
100.00 |
170-290 |
0.86 |
0.84 |
100 |
Xbarc121 |
7A |
13 |
100.00 |
170-290 |
0.86 |
0.84 |
251 |
Xwmc206 |
4D |
7 |
100.00 |
50-120 |
0.76 |
0.72 |
101 |
Xcfd20 |
7A |
7 |
100.00 |
50-120 |
0.76 |
0.72 |
252 |
Xwmc331 |
4D |
7 |
85.71 |
160-220 |
0.83 |
0.81 |
102 |
Xcfa2019 |
7A |
7 |
85.71 |
160-220 |
0.83 |
0.81 |
253 |
Xcfd84 |
4D |
8 |
100.00 |
110-190 |
0.84 |
0.82 |
103 |
Xgwm608 |
1B |
8 |
100.00 |
110-190 |
0.84 |
0.82 |
254 |
Xgwm194 |
4D |
8 |
83.81 |
140-230 |
0.81 |
0.78 |
104 |
Xgwm550 |
1B |
15 |
92.38 |
120-280 |
0.90 |
0.88 |
255 |
Xwmc825 |
4D |
5 |
100.00 |
260-300 |
0.69 |
0.63 |
105 |
Xwmc798 |
1B |
9 |
100.00 |
210-290 |
0.80 |
0.76 |
256 |
Xgwm609 |
4D |
7 |
98.10 |
120-190 |
0.77 |
0.73 |
106 |
Xwmc406 |
1B |
5 |
94.29 |
220-260 |
0.76 |
0.72 |
257 |
Xwmc720 |
4D |
5 |
100.00 |
190-230 |
0.78 |
0.74 |
107 |
Xgwm33 |
1B |
5 |
94.29 |
220-230 |
0.72 |
0.67 |
258 |
Xwmc48 |
4D |
3 |
98.10 |
210-230 |
0.45 |
0.37 |
108 |
Xgwm18 |
1B |
15 |
100.00 |
100-320 |
0.90 |
0.89 |
259 |
Xwmc489 |
4D |
3 |
98.10 |
170-190 |
0.60 |
0.53 |
109 |
Xwmc813 |
1B |
8 |
100.00 |
80-150 |
0.79 |
0.76 |
260 |
Xwmc399 |
4D |
15 |
100.00 |
120-280 |
0.90 |
0.89 |
110 |
Xbarc181 |
1B |
13 |
100.00 |
170-290 |
0.86 |
0.84 |
261 |
Xbarc130 |
5D |
8 |
100.00 |
80-150 |
0.79 |
0.76 |
111 |
Xgwm374 |
1B |
7 |
100.00 |
50-120 |
0.76 |
0.72 |
262 |
Xgwm190 |
5D |
13 |
100.00 |
170-290 |
0.86 |
0.84 |
112 |
Xwmc416 |
1B |
7 |
85.71 |
160-220 |
0.83 |
0.81 |
263 |
Xcfd189 |
5D |
7 |
100.00 |
50-120 |
0.76 |
0.72 |
113 |
Xwmc134 |
1B |
8 |
100.00 |
110-190 |
0.84 |
0.82 |
264 |
Xwmc150 |
5D |
7 |
85.71 |
160-220 |
0.83 |
0.81 |
114 |
Xwmc631 |
1B |
15 |
100.00 |
100-320 |
0.90 |
0.89 |
265 |
Xwmc608 |
5D |
8 |
100.00 |
110-190 |
0.84 |
0.82 |
115 |
Xwmc673 |
1B |
14 |
100.00 |
100-280 |
0.88 |
0.87 |
266 |
Xgwm358 |
5D |
15 |
92.38 |
120-280 |
0.90 |
0.88 |
116 |
Xcfa2147 |
1B |
8 |
98.10 |
120-190 |
0.81 |
0.79 |
267 |
Xcfd266 |
5D |
9 |
100.00 |
170-290 |
0.80 |
0.76 |
117 |
Xwmc44 |
1B |
3 |
96.19 |
240-260 |
0.51 |
0.45 |
268 |
Xcfd17 |
5D |
5 |
94.29 |
220-260 |
0.76 |
0.72 |
118 |
Xwmc661 |
2B |
8 |
83.81 |
140-230 |
0.81 |
0.78 |
269 |
Xgdm136 |
5D |
5 |
94.29 |
220-260 |
0.72 |
0.67 |
119 |
Xwmc35 |
2B |
5 |
100.00 |
260-300 |
0.69 |
0.63 |
270 |
Xgwm174 |
5D |
13 |
100.00 |
170-290 |
0.86 |
0.84 |
120 |
Xwmc25 |
2B |
7 |
98.10 |
120-190 |
0.77 |
0.73 |
271 |
Xcfd7 |
5D |
7 |
100.00 |
50-120 |
0.76 |
0.72 |
121 |
Xwmc213 |
2B |
5 |
100.00 |
190-230 |
0.78 |
0.74 |
272 |
Xcfd12 |
5D |
7 |
85.71 |
160-220 |
0.83 |
0.81 |
122 |
Xgwm257 |
2B |
3 |
98.10 |
210-230 |
0.45 |
0.37 |
273 |
Xwmc95 |
5D |
8 |
100.00 |
110-190 |
0.84 |
0.82 |
123 |
Xgwm429 |
2B |
3 |
98.10 |
170-190 |
0.60 |
0.53 |
274 |
Xwmc97 |
5D |
8 |
100.00 |
80-150 |
0.79 |
0.76 |
124 |
Xgwm148 |
2B |
15 |
100.00 |
100-320 |
0.90 |
0.89 |
275 |
Xwmc357 |
5D |
13 |
100.00 |
170-290 |
0.86 |
0.84 |
125 |
Xgwm374 |
2B |
8 |
100.00 |
80-150 |
0.79 |
0.76 |
276 |
Xcfd49 |
6D |
8 |
100.00 |
110-190 |
0.84 |
0.82 |
126 |
Xbarc167 |
2B |
13 |
100.00 |
170-290 |
0.86 |
0.84 |
277 |
Xcfd135 |
6D |
14 |
100.00 |
100-280 |
0.88 |
0.87 |
127 |
Xwmc498 |
2B |
7 |
100.00 |
50-120 |
0.76 |
0.72 |
278 |
Xcfd75 |
6D |
8 |
98.10 |
120-190 |
0.81 |
0.79 |
128 |
Xgwm388 |
2B |
7 |
85.71 |
160-220 |
0.83 |
0.81 |
279 |
Xgwm469 |
6D |
3 |
96.19 |
240-260 |
0.51 |
0.45 |
129 |
Xgwm120 |
2B |
8 |
100.00 |
110-190 |
0.84 |
0.82 |
280 |
Xcfd9 |
6D |
8 |
100.00 |
80-150 |
0.79 |
0.76 |
130 |
Xgwm47 |
2B |
15 |
92.38 |
120-280 |
0.90 |
0.88 |
281 |
Xcfd132 |
6D |
13 |
100.00 |
170-290 |
0.86 |
0.84 |
131 |
Xwmc332 |
2B |
9 |
100.00 |
210-290 |
0.80 |
0.76 |
282 |
Xcfd19 |
6D |
7 |
100.00 |
50-120 |
0.76 |
0.72 |
132 |
Xwmc434 |
2B |
5 |
94.29 |
220-260 |
0.76 |
0.72 |
283 |
Xgwm325 |
6D |
7 |
85.71 |
160-220 |
0.83 |
0.81 |
133 |
Xwmc430 |
3B |
5 |
94.29 |
220-260 |
0.72 |
0.67 |
284 |
Xcfd37 |
6D |
8 |
100.00 |
110-190 |
0.84 |
0.82 |
134 |
Xbarc92 |
3B |
8 |
98.10 |
120-190 |
0.81 |
0.79 |
285 |
Xcfd287 |
6D |
8 |
100.00 |
110-190 |
0.84 |
0.82 |
135 |
Xwmc597 |
3B |
3 |
96.19 |
240-260 |
0.51 |
0.45 |
286 |
Xbarc175 |
6D |
14 |
100.00 |
100-280 |
0.88 |
0.87 |
136 |
Xwmc808 |
3B |
15 |
92.38 |
120-280 |
0.90 |
0.88 |
287 |
Xbarc96 |
6D |
8 |
98.10 |
120-190 |
0.81 |
0.79 |
Table
1:
Continued
137 |
Xwmc51 |
3B |
9 |
100.00 |
210-290 |
0.80 |
0.76 |
288 |
Xwmc646 |
7D |
3 |
96.19 |
240-260 |
0.51 |
0.45 |
138 |
Xbarc173 |
3B |
5 |
94.29 |
220-260 |
0.76 |
0.72 |
289 |
Xwmc506 |
7D |
8 |
100.00 |
80-150 |
0.79 |
0.76 |
139 |
Xwmc615 |
3B |
5 |
94.29 |
220-260 |
0.72 |
0.67 |
290 |
Xbarc184 |
7D |
13 |
100.00 |
170-290 |
0.86 |
0.84 |
140 |
Xwmc653 |
3B |
8 |
100.00 |
80-150 |
0.79 |
0.76 |
291 |
Xwmc450 |
7D |
7 |
100.00 |
50-120 |
0.76 |
0.72 |
141 |
Xwmc418 |
3B |
13 |
100.00 |
170-290 |
0.86 |
0.84 |
292 |
Xgwm635 |
7D |
7 |
85.71 |
160-220 |
0.83 |
0.81 |
142 |
Xgwm131 |
3B |
7 |
100.00 |
50-120 |
0.76 |
0.72 |
293 |
Xbarc70 |
7D |
8 |
100.00 |
110-190 |
0.84 |
0.82 |
143 |
Xcfd283 |
3B |
7 |
85.71 |
160-220 |
0.83 |
0.81 |
294 |
Xcfd41 |
7D |
8 |
83.81 |
140-230 |
0.81 |
0.78 |
144 |
Xbarc229 |
3B |
8 |
100.00 |
110-190 |
0.84 |
0.82 |
295 |
Xcfd26 |
7D |
5 |
100.00 |
260-300 |
0.69 |
0.63 |
145 |
Xgwm108 |
3B |
8 |
100.00 |
80-150 |
0.79 |
0.76 |
296 |
Xcfd31 |
7D |
7 |
98.10 |
120-190 |
0.77 |
0.73 |
146 |
Xwmc632 |
4B |
13 |
100.00 |
170-290 |
0.86 |
0.84 |
297 |
Xcfd21 |
7D |
5 |
100.00 |
190-230 |
0.78 |
0.74 |
147 |
Xgwm547 |
4B |
14 |
100.00 |
100-280 |
0.88 |
0.87 |
298 |
Xwmc438 |
7D |
3 |
98.10 |
210-230 |
0.45 |
0.37 |
148 |
Xwmc125 |
4B |
8 |
98.10 |
120-190 |
0.81 |
0.79 |
299 |
Xcfd14 |
7D |
3 |
98.10 |
170-190 |
0.60 |
0.53 |
149 |
Xbarc10 |
4B |
3 |
96.19 |
240-260 |
0.51 |
0.45 |
300 |
Xcfd193 |
7D |
8 |
83.81 |
140-230 |
0.81 |
0.78 |
150 |
Xgwm6 |
4B |
15 |
92.38 |
120-280 |
0.90 |
0.88 |
301 |
Xwmc150 |
7D |
5 |
100.00 |
260-300 |
0.69 |
0.63 |
151 |
Xbarc60 |
4B |
9 |
100.00 |
210-290 |
0.80 |
0.76 |
302 |
Xcfd25 |
7D |
5 |
100.00 |
190-230 |
0.78 |
0.74 |
MN= marker name, CL=Chromosome Location,
TNA=total number of alleles, PSM= Polymorphism, SRB=Size range in base pairs,
GD= Gene diversity and PIC= Polymorphic Information Content
Table 2: Mean Allelic variations across
302 polymorphic SSRs in studied wheat germplasm
Population |
Mean |
Standard Error |
No. of Average Alleles (Na) |
7.642 |
0.204 |
No. of Alleles with a Frequency >=5% (Na Freq.>=
5%) |
5.212 |
0.098 |
No. of Effective Alleles (Ne) = 1 / (Sum pi^2) |
4.905 |
0.116 |
Shannon's Information Index (I) = -1* Sum (pi * Ln
(pi)) |
1.650 |
0.026 |
No. of private Alleles = Unique to a Single Population |
0.000 |
0.000 |
Heterozygosity (He) = 1 - Sum pi^2 |
0.754 |
0.007 |
Unbiased Expected Heterozygosity (uHe )= (2N / (2N-1))
* He |
0.758 |
0.007 |
Polymorphic
information contents (
Among 102 polymorphic SSR markers in A genome 44 markers
showed 100% polymorphism in 105 studied wheat genotypes, while 11 markers
showed 99% followed by 14 markers showed 98%, 8 markers had 97% and the
remaining markers showed 96 to 84% polymorphism (Table 1). In A-genome the
maximum
In B-genome, among 100 polymorphic SSR markers the 57
markers showed 100% polymorphism in 105 studied wheat genotypes followed by 13
markers showed 98% and the remaining markers showed 96 to 84% polymorphisms as
displayed in Table 1. The highest
The total 100 polymorphic SSR markers in D-genome, out
of them 55 markers showed 100% polymorphism in 105 studied wheat genotypes,
followed by 20 markers showed 98% and the remaining markers showed 96 to
Fig. 2: This result achieved of 105 bread wheat genotypes using 302 polymorphic SSR markers
from Structure Harvester analysis. It's based on the second order derivation on the variance of
the maximum likelihood estimation of your model given a specific K. Delta K
shows only the uppermost clustering level and number of subpopulations in main
population
88% polymorphisms were mentioned in Table 1. The D
genome was conceded at Xwmc399, Xgwm358
and Xcfd21 marker found on 4D, 5D and
1D chromosomes having maximum
Genetic diversity
Bayesian
technique implemented in statistical software STRUCTURE to access the genetic
structure of studied germplasm and the outcomes showed that highest (peak)
number of K=4 demonstrating the germplasm distributed into 4 sub-population
(Fig. 2). Different types colored in Fig. 2 exhibits the distinct group and
overall germplasm allocated into four sub-groups. Molecular UPGMA cluster
DARWIN tree analyses and STRUCTURE Bayesian results exhibited that genotypes
from department of PBG-UAF containing genetic diversity and were not present in
the similar cluster which undoubtedly show that these genotypes derived from
diverse forefathers. Additionally, evaluation of each group exposed that
genotypes G-1 to G-10 and G-27 to G-28 located in the similar cluster, while the
G-11 to G-26 and G-29 to G-30 genotypes were entirely seemed in the second
cluster. The third cluster composed of a combination of the diverse genotypes
had G-34 to G-70. The fourth cluster contained the G-73 to G-105. Similar
results obtained from the STRUCTURE Bayesian and DARWIN tree analyses using 302
polymorphic SSR markers in 105 bread wheat genotypes (Fig. 3 and 4).
Discussion
Fig. 3: UPGAMA DARWIN tree displaying the distribution of the 105
bread wheat genotypes in four groups, and presenting the genetic similarities
and dissimilarities within and between the groups
Fig. 4: Population structure of 105 bread wheat genotypes based
on Bayesian method analyzed with 302 polymorphic SSRs detecting 4 groups. The
dissimilar colors in this figure demonstrating the different group
Molecular
markers like simple sequence repeats (SSRs) have been extensively used to
detect variability in wheat genotypes and to evaluate their genetic diversity.
The PIC values of SSR markers could be used to access the amount of genetic
variability in plant sciences. When the PIC value is greater than 0.5 the
marker is suggested to be of maximum diversity, if the PIC values is less than
0.25 the marker is suggested to be of minimum diversity (Ramadugu et al. 2015) and (Sönmezoğlu
and Terzi 2018). In this experiment most of the markers having PIC
values greater than 0.5 which indicate the presence of high allelic diversity
in studied germplasm. SSR markers have also been widely applied to perceive
gene variability in wheat germplasm and to estimate their genetic diversity (Raza et al.
2019). The mean values and SE values presented in Table 2 proposing that
there is great genetic diversity at SSR loci among studied germplasm. In
current study no presence of rare alleles (number of alleles unique to a single
population) similar study was conducted
by (Sajjad
et al. 2018). The maximum mean
values of gene diversity were identified in B-genome (0.78) followed by
D-genome (0.77) and A-genome (0.71) which suggesting that the B-genome showed
more variation and the existence of genetic diversity in studied germplasm (Kumar et al.
2016). In bread wheat, genome wide 65 SSRs specifically 1–4 markers for
each chromosome were applied previously by wheat breeders (Wang et al.
2013; Ahmed et al. 2017a) to
determine the genetic diversity. Those markers perceiving the minimum total
number of alleles displayed minimum gene diversity as compared to those which
have high total number of alleles depicted the maximum gene diversity (Salehi et al.
2018; Sönmezoğlu and Terzi 2018). In current experiment, based on
the mean values of total number of alleles per markers in B-genome exhibited
the maximum genetic diversity as compared to the D-genome followed by A-genome
which showed the minimum genetic diversity. Similar findings were described by
wheat scientists (Ahmed et al. 2017a) where they described that the total number of
alleles per markers ranged from 2–15. Our results are not similar with the
findings of Tascioglu et al. (2016), they reported the lower values as compared
to current experiment. They observed the average value of total numbers of
allele 5 in A-genome and D-genome while 6 in B-genome. Dvojković (2010) described the higher total number of alleles
as 8.86, 8.893 and 9.65 for A, B and D-genome respectively as compared to this
study.
The total numbers of allele per locus ranged from 3 to 22
with the mean value of 7.8 was previously reported by plant scientists is
similar to this experiment (Jain et al. 2004). In current study
PIC values revealed a significant positive association with the gene diversity
(GD) and total numbers of allele for SSR markers. All the results (GD, TNA and
The UPGMA cluster DARWIN tree and STRUCTURE analysis
concentrating to the distribution of 105 bread wheat genotypes into 4 subgroups
or clusters (Fig. 3 and 4). These techniques have been applied in wheat
breeding scheme by many scientists and were obtained the explanatory outcomes (Ahmed et al.
2017a; Salehi et al. 2018). In
current experiment, distances among cluster or group clearly show the
variations between 105 bread wheat genotypes and all subgroups showed
genetically diverse to one another. The presence of maximum genetic distance
between clusters indicates that they were genetically dissimilar from each
other. Fundamentally, this is the indication of genetic divergence between the
clusters or groups and resultantly the presence of more genetic diversity in
studied germplasm. There is a minor genetic distance among the genotypes within
each cluster or group which shows the genetic similarity among 105 genotypes,
closer genotypes showed more genetic similarity as mentioned in the Figure 3.
Several wheat breeders evaluated the genetic diversity (Tascioglu et al. 2016; Ahmed et al. 2017a) using the similar
techniques which were applied in current study and they got the similar
results. Using 296 SSRs in 90 bread wheat genotypes by (Chen et al. 2012) and
they observed the 3 clusters which convening the geographical origin and
genetic diversity among germplasm. Development of novel bread wheat genotypes
should be attaining the significance level of genetic diversity. Presence of
more variation in 105 bread wheat genotypes which indicate the maximum genetic
diversity, fearlessly, that the studied germplasm introduced from different
sources or assumable mechanical mixing.
According to the provided pedigree record there are
three groups of 105 bread wheat genotypes as shown in Supplementary Table 1. In
first group, genotypes G-1 to G-20 which was developed in PBG-UAF, while in
second group the genotypes G21 to G-55 were from exotic source, and in third
group, genotypes G-56 to G-105 was from indigenous sources. But according to
molecular analysis these genotypes divided into four clusters or groups. Wheat
genotypes developed in PBG-UAF comprised the cluster 1, genotypes G-27 and G-28
are also included in this cluster which exhibited the genetic similarity with
each other. Total 18 genotypes constituted in cluster 2, among them, some
genotypes related to the PBG-UAF sources and some genotypes were from exotic
sources. It exhibited that these genotypes originated from the ancestors of
similar genetic makeup. Total 67 wheat genotypes were appeared in cluster 3 and
4. Out of them, 35 genotypes included in cluster 3 and 32 genotypes included in
cluster 4. These genotypes produced by a mixture of the diverse genetic
constitutions which suggesting the diverse pedigrees of these genotypes.
Genotypes G-31, G-32 and G-33 contained the combination of genetic makeup from
the cluster 2 and cluster 3 covering genotypes. The genotypes G-71 and G-72
contained the genetic constitution from cluster 3 and cluster 4 which showed
that their origin from these clusters and assuming the similar descendants.
Particularly, results were useable conferring to the previously known pedigree
record and origin of wheat genotypes. Genetic diversity evaluation could be
helpful to identify the different genotypes for the advancement and improve the
future wheat breeding scheme (Yadav and Chand 2018; Ahmed et al. 2019; Lazzaro et al. 2019). The genotypes with
different genetic makeup can be selected for desirable combinations to develop
complex and significant attributes to obtaining maximum yield. Discrimination
of wheat genotypes based on their genetic basis would be useful for effective
and early selection of desired genotypes in wheat breeding scheme for
developing promising wheat genotypes.
Conclusion
A natural
population of 105 bread wheat genotypes was genotyped with 302 polymorphic SSR
loci, and a total 2308 alleles with average density of 7.64 alleles per marker
were observed to determine the genetic diversity and genome wide allelic
variation. The maximum (0.89) polymorphic information contents (PIC) value was
observed for markers Xwmc95, Xbarc95
and Xwmc399. These markers with
maximum alleles (15) possessed the 100–320, 100–280 and 120–280 base pair
genomic range at chromosomes 1A, 7B and 4D, respectively. These three and other
similar SSR markers can use to evaluate the diversity and to classify any of
the natural population of wheat. The polymorphic information contents (PIC) and
Gene diversity (GD) values indicated the maximum genetic variation in B-genome
followed by D- and A-genomes. It can be concluded that any of the agronomic
traits linked to the B-genome can get the advantage of maximum genetic
variation in a selection process. The UPGMA cluster DARWIN tree and STRUCTURE
analysis classified the 105 bread wheat genotypes into four clusters. The
clusters information can help to reduce the redundancy among genetically
similar accession and to select the genotypes of diverse genetic back ground in
any wheat breeding program.
Acknowledgment
This work was funded by the China Agriculture Research System
(CARS-05-01A-04).
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