Assessment of Functional EST-SSR Markers (Sugarcane) in Cross-Species Transferability, Genetic Diversity among Poaceae Plants, and Bulk Segregation Analysis
Table 1
Details of selected 63 EST-SSR primer pairs used for cross transferability, genetic diversity, and bulks segregation analysis.
Serial number
Type
Primer sequence
Annealing temperature
SSR motif
PIC value
-value
Putative identities (blastn/blastx)
SYMS28
F
GCGTCAGAGTGTTAAAACAAG
53
(GCT)4
0.81
9.39E − 42
Protein transport protein Sec61 beta
SYMS28
R
GTGTAGAACTGGAGCATTGAG
SYMS29
F
GGGCAAGCAAGAAACCAC
52
(TCC)4
0.91
1.62E − 24
Protein translation factor SUI1
SYMS29
R
GAAGAGGTCAACCAAGAACTC
SYMS30
F
GCGTCAGAGTGTTAAAACAAG
53
(GCT)4
0.86
1.00E − 21
Preprotein translocase Sec
SYMS30
R
GTGTAGAACTGGAGCATTGAG
SYMS31
F
GAAGCTCCCAAGCTGCTA
53
(AGCT)3
0.76
2.00E − 12
Predicted: uncharacterized protein
SYMS31
R
CCTACAGGAAAGATTTTAGGG
SYMS32
F
GTCTCTTCTCCAGTTCTCCTT
55
(TGCG)4
0.84
2.46E − 63
Predicted: actin-depolymerizing factor
SYMS32
R
GCTCAACAAATGTCTCCCTA
SYMS33
F
TGCACTAACATGGTTGATGT
54
(GAAG)3
0.86
2.82E − 90
Hypothetical protein SORBIDRAFT_03g046450
SYMS33
R
GGTGATTGTAAGGGTCATCTT
SYMS34
F
GTTAATGGTGGTTCCGTTC
53
(GGC)6
0.88
4E − 20
Predicted: uncharacterized protein LOC101783547
SYMS34
R
ATTATCAGCGCAGAGACATC
SYMS35
F
GCGTCAGAGTGTTAAAACAAG
52
(GCT)4
0.75
1.00E − 21
Preprotein translocase
SYMS35
R
GTGTAGAACTGGAGCATTGAG
SYMS36
F
GGACTGTACAAGGACGACAG
53
(GCT)4
0.70
1.14E − 41
Protein transport protein Sec61 beta subunit
SYMS36
R
TCTGCTTTCTTGGATATGGTA
SYMS37
F
AAGAAGGATGCAAAGAAGAAG
54
(GAT)4
0.90
3.08E − 81
Hypothetical protein SORBIDRAFT_03g046450
SYMS37
R
AGGCTTAGTAACAGCAGGTTT
SYMS38
F
AAGAAGGATGCAAAGAAGAAG
56
(AGA)4
0.86
9.00E − 37
Hypothetical protein
SYMS38
R
AGGCTTAGTAACAGCAGGTTT
SYMS39
F
GGACTGTACAAGGACGACAG
—
(GCT)4
—
1.14E − 41
Protein transport protein
SYMS39
R
TCTGCTTTCTTGGATATGGTA
SYMS40
F
GGACTGTACAAGGACGACAG
—
(GCT)4
—
1.25E − 40
Preprotein translocase
SYMS40
R
TCTGCTTTCTTGGATATGGTA
SYMS41
F
GGACTGTACAAGGACGACAG
—
(GCT)4
—
9.62E − 42
Protein transport protein Sec61 beta subunit
SYMS41
R
TCTGCTTTCTTGGATATGGTA
SYMS42
F
CCAAAGAGATCTTGCAGACTA
—
(ATG)4
—
1.78E − 53
Jasmonate-induced protein
SYMS42
R
CCCAACACAACAACCAAT
SYMS43
F
CCACACAAGCAAGAAATAAAC
—
(GGT)4
—
8.57E − 74
Dirigent-like protein
SYMS43
R
TCGAACACTATGGTAAAGGTG
SYMS44
F
GGACTGTACAAGGACGACAG
—
(GCT)4
—
1.15E − 41
Homeodomain-like transcription factor
SYMS44
R
TCTGCTTTCTTGGATATGGTA
SYMS45
F
GCGTCAGAGTGTTAAAACAAG
53
(GCT)4
0.69
9.86E − 42
Protein transport protein
SYMS45
R
GACTCTGCTTTCTTGGATATG
SYMS46
F
AGCTATCTTTAGTGGGGACAT
52
(CGT)4
0.90
1.82E − 44
Hypothetical protein SORBIDRAFT_09g006220
SYMS46
R
GAGGTCTCATCGGAGCTTA
SYMS47
F
AGGTCGTTTTAATTCCTTCC
53
(GTTTT)3
0.77
1.00E − 21
Preprotein translocase Sec
SYMS47
R
CGTAAATATGAACGAGGTCAG
SYMS48
F
AGGTCGTTTTAATTCCTTCC
53
(TTTA)6
0.90
4.00E − 20
TPA: hypothetical protein
SYMS48
R
CGTAAATATGAACGAGGTCAG
SYMS49
F
GGACTGTACAAGGACGACAG
—
(GCT)4
—
1.15E − 41
Zinc finger A20 and AN1 domains-containing protein
SYMS49
R
TCTGCTTTCTTGGATATGGTA
SYMS50
F
TCCAAGGATTTAGCTATGGAT
—
(TGT)10
—
6.79E − 13
TPA: seed maturation protein
SYMS50
R
TTCAACTACACCCTTCTGTTG
SYMS51
F
GCGTCAGAGTGTTAAAACAAG
—
(GCT)4
—
1.22E − 41
Hypothetical protein
SYMS51
R
ATTGTCACTTGCTATCCATTT
SYMS52
F
CACCTTCTTTCCTTCTCCTC
—
(CGC)4
—
3.32E − 47
V-type proton ATPase 16 kDa proteolipid subunit
SYMS52
R
GTAGATACCGAGCACACCAG
SYMS53
F
TCAGTTCAGGGATGACAATAG
56
(CCGTGG)3
0.87
2.59E − 78
Homeodomain-like transcription factor superfamily protein
SYMS53
R
GGATAGACTGAAATCTGCTCA
SYMS54
F
CAACTCGACTCTTTTCTCTCA
—
(CTC)5
—
4.13E − 08
Protein transport protein SEC31
SYMS54
R
GGAGGTGGAACTTCCTGA
SYMS55
F
GGACTGTACAAGGACGACAG
—
(GCT)4
—
1.12E − 41
Protein transport protein Sec61 subunit beta-like isoform
SYMS55
R
TCTGCTTTCTTGGATATGGTA
SYMS56
F
GGACTGTACAAGGACGACAG
—
(GCT)4
—
8.01E − 42
Protein transport protein Sec61 subunit beta-like isoform
SYMS56
R
TCTGCTTTCTTGGATATGGTA
SYMS57
F
AAACGATCAGATACCGTTGTA
—
(CG)6
—
7.84E − 27
Caltractin
SYMS57
R
ATCAAAGAGATCAAAGGCTTC
SYMS58
F
CATTTCGAAGCTCCTCCT
52
(CCTCCG)6
0.74
5.97E − 66
Zinc finger A20 and AN1 domains-containing protein
SYMS58
R
TAGGCTGCACAACAATAGTCT
SYMS59
F
CTCCCCCATTTCTCTTCC
53
(GCAGCC)6
0.80
4.02E − 65
Predicted: reticulon-like protein B1
SYMS59
R
CAAGTACTCCAGCAGAGATGT
SYMS60
F
CTTTTCCCTCTTCCTCTCTC
—
(CCG)5
—
1.24E − 45
Predicted: uncharacterized tRNA-binding protein
SYMS60
R
TGTCACTAACACGAATCACAA
SYMS61
F
CCCTCTCCCTGCTCTTTC
54
(TCC)5
0.79
4.14E − 57
Actin-depolymerizing factor 3
SYMS61
R
CAGTCACAAAGTCGAAATCAT
SYMS62
F
ACAACTCTTCAGTCTTCACGA
54
(CAAC)3
0.85
4.40E − 66
Truncated alcohol dehydrogenase
SYMS62
R
CCAATCTTGACATCCTTGAC
SYMS63
F
GCACGGTGAAGTTCTAGTTC
54
(TCGAT)4
0.67
3.11E − 31
Hypothetical protein SORBIDRAFT_08g002800
SYMS63
R
CAGCTTCACTCATGAATTTTT
SYMS64
F
GGACTGTACAAGGACGACAG
—
(GCT)4
—
1.08E − 41
Protein transport protein Sec61 subunit beta-like isoform
SYMS64
R
TCTGCTTTCTTGGATATGGTA
SYMS65
F
AACACAAGCAAGAAATAAACG
53
(GGT)4
0.51
3.42E − 74
Dirigent-like protein
SYMS65
R
AACACTATGGTCAAGGTGGTA
SYMS66
F
GCGTCAGAGTGTTAAAACAAG
52
(GCT)4
0.58
1.01E − 41
Protein transport protein Sec61 subunit beta-like isoform
SYMS66
R
GAAATCGCTCTATAAGGTTCC
SYMS67
F
TCTCTCTGAAGATGATGCTTT
52
(AAG)5
0.90
4.25E − 83
Hypothetical protein SORBIDRAFT_03g005100
SYMS67
R
GTTAAGAGGCTTCCAAAGAAC
SYMS68
F
CAGCTCGTCGTCTTCTTTT
—
(GTC)5
2.00E − 55
Putative ubiquitin-conjugating enzyme family
SYMS68
R
GTGGCTTGTTTGGATATTCTT
SYMS69
F
GGACTGTACAAGGACGACAG
54
(GCT)4
0.79
9.28E − 42
Protein transport protein Sec61 subunit beta-like isoform
SYMS69
R
CGTCAGACGTACTGAAATGTT
SYMS70
F
AACACAAGCAAGAAATAAACG
53
(GGT)4
0.77
1.58E − 73
Putative dirigent protein
SYMS70
R
AACACTATGGTCAAGGTGGTA
SYMS71
F
GGACTGTACAAGGACGACAG
—
(GCT)4
—
9.86E − 42
Protein transport protein Sec61 subunit beta-like isoform
SYMS71
R
TCTGCTTTCTTGGATATGGTA
SYMS72
F
CCCTCTCCCTGCTCTTTC
55
(TCC)4
0.89
4.36E − 57
Actin-depolymerizing factor 3
SYMS72
R
CAGTCACAAAGTCGAAATCAT
SYMS73
F
GGACTGTACAAGGACGACAG
55
(GCT)4
0.83
1.09E − 41
Protein transport protein Sec61 subunit beta-like isoform
SYMS73
R
TCTGCTTTCTTGGATATGGTA
SYMS74
F
GGACTGTACAAGGACGACAG
52
(GCT)4
0.88
9.51E − 42
Preprotein translocase Sec
SYMS74
R
TCTGCTTTCTTGGATATGGTA
SYMS75
F
GCACCCCCAATTCGAACG
52
(ACG)3
0.93
1.78E − 68
TPA: general regulatory factor 1
SYMS75
R
CGGTAGTCCTTGATGAGTGT
SYMS76
F
GGACTGTACAAGGACGACAG
52
(GCT)4
0.78
4.79E − 41
Protein transport protein Sec61 subunit beta-like isoform
SYMS76
R
TCTGCTTTCTTGGATATGGTA
SYMS77
F
CACGCAACGCAAGCACAG
55
(CCAT)3
0.93
8.34E − 70
Hypothetical protein SORBIDRAFT_10g030160
SYMS77
R
AAGTTGATTCACCCTCATTCT
SYMS78
F
CACGCAACGCAAGCACAG
53
(CGATC)3
0.92
1.04E − 41
Translocon-associated protein alpha subunit precursor
SYMS78
R
AAGTTGATTCACCCTCATTCT
SYMS79
F
GGACTGTACAAGGACGACAG
53
(GCT)4
0.91
1.04E − 41
Protein transport protein Sec61 subunit beta-like isoform
SYMS79
R
TCTGCTTTCTTGGATATGGTA
SYMS80
F
CTTGATCCTTGACAAAAGAGA
52
(AG)6
0.87
2.25E − 59
Predicted: ubiquitin-conjugating enzyme E2
SYMS80
R
ATTGCTGTTGATATTTGGATG
SYMS81
F
GCGTCAGAGTGTTAAAACAAG
53
(GCT)4
0.87
8.01E − 42
Protein transport protein Sec61 subunit beta-like isoform
SYMS81
R
GTGTAGAACTGGAGCATTGAG
SYMS82
F
TATCAACAAGCCTTCCATTC
53
(GTG)4
0.90
1.12E − 30
Glycine-rich RNA-binding protein 2
SYMS82
R
GGCTATAGTCACCACGGTAG
SYMS83
F
CGACAGGGAGAAGAGTACAG
55
(GCT)4
0.87
9.39E − 42
Protein transport protein Sec61 subunit beta-like isoform
SYMS83
R
GACTCTGCTTTCTTGGATATG
SYMS84
F
GCGTCAGAGTGTTAAAACAAG
53
(GCT)4
0.75
1.14E − 41
Protein transport protein Sec61 subunit beta-like isoform
SYMS84
R
AATCGCTCTATAAGGTTCCTC
SYMS85
F
CTCTTCTTCACCAATTCCTCT
—
(CCG)6
—
1.14E − 51
Protein transport protein Sec61 subunit beta-like isoform
SYMS85
R
CAAACCTCATAAAGAGTGCAG
SYMS86
F
GGGCAAGCAAGAAACCAC
54
(TCC)4
0.93
1.16E − 28
TPA: translation initiation factor 1
SYMS86
R
CGTACATGAACGTAGTCCTTT
SYMS87
F
GCGTCAGAGTGTTAAAACAAG
—
(GCT)4
—
1.19E − 41
Protein transport protein Sec61 beta subunit
SYMS87
R
AATCGCTCTATAAGGTTCCTC
SYMS88
F
TTATAAGGAAATCCCCCACT
—
(GCC)4
—
7.71E − 55
Hypothetical protein SORBIDRAFT_09g000970
SYMS88
R
CACCAAGTACTCATCCATCAT
SYMS89
F
CATCTCCTGCTAACAATTCAC
55
(TGC)4
0.91
9.64E − 60
Predicted: NAC domain-containing protein
SYMS89
R
ATTTATAGGTTGGCACCAGAG
SYMS90
F
GCGTCAGAGTGTTAAAACAAG
53
(GCT)4
0.85
1.00E − 22
Protein transport protein Sec61 subunit beta-like isoform
