Molecular Plant Breeding 2016, Vol.7, No.11, 1
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16
14
demonstrating the presence of population structure,
identifying distinct genetic populations and assigning
individuals to populations. For inferring, number of
populations (K) was set from 1 to 15 and the program
ran 20 replicates for each K value at 10,000 burning
speed and 50,000 Markov Chain Monte Carlo
(MCMC) cycles. This was used for identifying the
range of the true K value around 3. In addition, the
program was run with setting K value 1 to 6 and a
replicate of 20 for each K at burning in 500,000
repeats and MCMC replication of 750,000. K value
was inferred using the L(K) method which is
determined by identifying the point where the plateau
starts (Rosenberg et al. 2001) and confirmed by an ad
hoc value (
∆
K) calculated using the formula below:
L(K) = an average of 20 values of Ln P(D),
L
’
(K) = L(K)n
–
L(K)n-1,
L
’’
(K) = L
’
(K)n
–
L
’
(K)n-1 and
∆
K = [L
’’
(K)]/Stdv.
Table 8 Primer sequences, amplicon length, SSR motif and annealing temperature of the 28 markers used for the study
S.N. Name
Forward primer
Reverse primer
Amplic
on
length
SSR Motif Ann.T.
o
C
1
AVRDC-PP24 AAAGCATGAAATCACCCTCC
CGGCAAGAAGATGAAAGTCA
126
(AT)18
52
2
AGi096
GGGAAGAGAAATTGTGAAAGCA ATGCCAACAATGGCATCCTA
160
[CAT]7
58
3
AGi101
TGAGGAGACAAACTTCAACTGG GATGAGGACAAAACCAAGGACT 181
[TCA]14
58
4
AGi121
AACACGCCAAGAAAATCATC
TGGAGACCTGAGCCATTG
162
[CA]15
55
5
AVRDC-PP120 CGAATCAGCAAGGAGATCAA
TCAGCAGAAGCCATAATTGG
378
(TAA)12
55
6
AVRDC-PP121 GCGGCCTTTTGATTCATAC
AACACCAGTGCTTGTCGTGT
219
(AT)10
55
7
AVRDC-PP126 GCAGTTGATATCGCCTCCAT
TGCACATTTCGAATCTAGGG
393
(AT)9
55
8
AVRDC-PP128 ATCGATCCAGAGGTGAATCC
TGTACTTCCATCCTCCACAA
233
(TA)12
58
9
AVRDC-PP129 AAGAGCTTCACGGGATCACT
CAGCCATTTCTGCTGTAGGA
374
(TCT)8
55
10 AVRDC-PP133 TCAGTGGTGGTGTTGGAGTT
CAACATGCATCCAGCTTCTT
301
(AT)9
58
11 AVRDC-PP144 TCCTCAGACACAAAATCCCA
CGGGGATTGCTTAGTTGTTT
182
(CA)14
58
12 AVRDC-PP146 AGCAGAATTTTTCCACCCTG
GCATTGATGGTGAAGATTGG
208
(CT)17
55
13 AVRDC-PP147 TTTCGCCAAGACTTGTTCTG
AAACGTGACCAACAACCTCA
261
(CT)11
55
14 AVRDC-PP155 GGAGACAAACTTCAACTGGTCA GCAGATGCAGCAACAGATTT
162,
158
(CAT)9,
(TCA)13
55
15 AVRDC-PP19 GGGTGTCAAGAAATCACACG
AGATACGTATGTGGCCTCTGT
119
(AT)12
55
16 AVRDC-PP37 GCACGAGGAAGACTTGACAG
TGTGCATAGGTGCAGATTGA
150
(AT)11
55
17 AVRDC-PP49 AGGGTTTGACACTGGGAAAG
CGAGCTCGATGAGGATGAAC
140
(AGC)8
55
18 AVRDC-PP5 GCATCAACCAGCAGCATACTA
TTTGTTTCGTGAAGTGCTCC
180
(TA)11
55
19 AVRDC-PP67 TATTCCTTCTTCACCCCTCC
GAAAGAGGCGCTAACTGGAC
197
(AT)13
55
20 AVRDC-PP87 AGCAGCAACTCTAACCACCA
CAGATGAGCCAGTGAGCATT
238
(AAC)10
55
21 AVRDC-PP88 AGTAGCTCCATCGCCAGTTT
TCGAAAGACAACTCCATCGT
114
(CAA)8
55
22 AVRDC-PP95 CGTCTTTCACTTGTCTTTTGTTC AGTGGGTTCACTGACTTGGG
90
(CTT)3(CAT
)9
55
23 CA526211
AAGTGTCAAGGAAGGGGACA
CCTAACCACCCCCAAAAGTT
243
(AGT)14A(G
AA)9
55
