Expressed sequence tags (ESTs) are important resource for gene discovery, gene expression and its regulation, molecular marker development, and comparative genomics. We procured 10000 ESTs and analyzed 267 EST-SSRs markers through computational approach. The average density was one SSR/10.45 kb or 6.4% frequency, wherein trinucleotide repeats (66.74%) were the most abundant followed by di- (26.10%), tetra- (4.67%), penta- (1.5%), and hexanucleotide (1.2%) repeats. Functional annotations were done and after-effect newly developed 63 EST-SSRs were used for cross transferability, genetic diversity, and bulk segregation analysis (BSA). Out of 63 EST-SSRs, 42 markers were identified owing to their expansion genetics across 20 different plants which amplified 519 alleles at 180 loci with an average of 2.88 alleles/locus and the polymorphic information content (PIC) ranged from 0.51 to 0.93 with an average of 0.83. The cross transferability ranged from 25% for wheat to 97.22% for
Sugarcane is a bioenergy crop belonging to the genus
A vast array of genomic tools has been developed which has opened new ways to define the genetic architecture of sugarcane and helped to explore its functional system [
Presently, huge amounts of expressed sequence tags have been deposited in public database (NCBI). In silico approaches to retrieve EST sequences from NCBI and functional annotations provide more constructive EST-SSRs or gene-based SSR (genic SSRs) marker development besides own EST libraries development. This method of the EST-SSR markers development provides the easiest way to reduce cost, time, and labours along with more meaningful marker identifications [
Total 10000 EST sequences of the
Assessment of EST sequences having SSR was done through blastn/blastx analysis for homology search and against nonredundant (nr) protein at the NCBI. Furthermore, functional annotation pipeline was also run at online tool for gene ontology (GO) which was intended for different GO functional classes like biological process, cellular component, and molecular function [
PCR reactions were carried out in a total of 10
The cross transferability of
The assessment of EST-SSRs in genetic diversity analysis was done among 20 plants belonging to distinct groups comprising cereals,
Plant materials were used as F2 mapping population comprising 209 genotypes of the sugarcane cultivars which were developed from cross between CoS 91230 (Parent; CoS 775 × Co 1148) with CoS 8436 (Parent; MS 68/47 × Co 1148) from September to March (2010-2011). Grouping of genotypes was done according to their stem diameter (contrasting high and low stem diameter genotypes) into two sets. DNA extractions were carried out from both sets and equal quantities of genomic DNA from 10 extreme high stem diameter and 10 extreme low stem diameter genotypes were pooled into two bulks. PCR amplification was done in both bulks with newly developed EST-SSR primers for informative markers identifications through bulk segregation analysis (BSA) [
Total 10,000 EST sequences related to
The frequency of SSR in EST sequences was 6.4% including all the repeats except mononucleotide repeats. This result is comparatively higher compared to previous studies on sugarcane [
Analysis revealed that trinucleotide repeats (66.74%) were found to be more frequent followed by di- (26.10%), tetra- (4.67%), penta- (1.5%), and hexanucleotide (1.2%) repeats. Our observation of high frequency of trinucleotide repeats is in agreement with previous reports on sugarcane [
Details of 33 different types of nucleotide repeat motifs belonging to di-, tri-, tetra-, penta-, and hexanucleotide repeat motifs with sequence complementarity.
Details of different types of predicted amino acids encoded by trinucleotide repeat motifs.
All EST sequences having SSRs were examined by functional annotation (blastn, blastx, and gene ontology). After-effect, sixty-three ESTs having SSRs were successfully identified on the basis of their involvement in the various metabolic processes (Figure
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 |
|
Putative identities (blastn/blastx) |
---|---|---|---|---|---|---|---|
SYMS28 | F | GCGTCAGAGTGTTAAAACAAG | 53 | (GCT)4 | 0.81 | 9.39 |
Protein transport protein Sec61 beta |
SYMS28 | R | GTGTAGAACTGGAGCATTGAG | |||||
SYMS29 | F | GGGCAAGCAAGAAACCAC | 52 | (TCC)4 | 0.91 | 1.62 |
Protein translation factor SUI1 |
SYMS29 | R | GAAGAGGTCAACCAAGAACTC | |||||
SYMS30 | F | GCGTCAGAGTGTTAAAACAAG | 53 | (GCT)4 | 0.86 | 1.00 |
Preprotein translocase Sec |
SYMS30 | R | GTGTAGAACTGGAGCATTGAG | |||||
SYMS31 | F | GAAGCTCCCAAGCTGCTA | 53 | (AGCT)3 | 0.76 | 2.00 |
|
SYMS31 | R | CCTACAGGAAAGATTTTAGGG | |||||
SYMS32 | F | GTCTCTTCTCCAGTTCTCCTT | 55 | (TGCG)4 | 0.84 | 2.46 |
|
SYMS32 | R | GCTCAACAAATGTCTCCCTA | |||||
SYMS33 | F | TGCACTAACATGGTTGATGT | 54 | (GAAG)3 | 0.86 | 2.82 |
Hypothetical protein SORBIDRAFT_03g046450 |
SYMS33 | R | GGTGATTGTAAGGGTCATCTT | |||||
SYMS34 | F | GTTAATGGTGGTTCCGTTC | 53 | (GGC)6 | 0.88 | 4 |
|
SYMS34 | R | ATTATCAGCGCAGAGACATC | |||||
SYMS35 | F | GCGTCAGAGTGTTAAAACAAG | 52 | (GCT)4 | 0.75 | 1.00 |
Preprotein translocase |
SYMS35 | R | GTGTAGAACTGGAGCATTGAG | |||||
SYMS36 | F | GGACTGTACAAGGACGACAG | 53 | (GCT)4 | 0.70 | 1.14 |
Protein transport protein Sec61 beta subunit |
SYMS36 | R | TCTGCTTTCTTGGATATGGTA | |||||
SYMS37 | F | AAGAAGGATGCAAAGAAGAAG | 54 | (GAT)4 | 0.90 | 3.08 |
Hypothetical protein SORBIDRAFT_03g046450 |
SYMS37 | R | AGGCTTAGTAACAGCAGGTTT | |||||
SYMS38 | F | AAGAAGGATGCAAAGAAGAAG | 56 | (AGA)4 | 0.86 | 9.00 |
Hypothetical protein |
SYMS38 | R | AGGCTTAGTAACAGCAGGTTT | |||||
SYMS39 | F | GGACTGTACAAGGACGACAG | — | (GCT)4 | — | 1.14 |
Protein transport protein |
SYMS39 | R | TCTGCTTTCTTGGATATGGTA | |||||
SYMS40 | F | GGACTGTACAAGGACGACAG | — | (GCT)4 | — | 1.25 |
Preprotein translocase |
SYMS40 | R | TCTGCTTTCTTGGATATGGTA | |||||
SYMS41 | F | GGACTGTACAAGGACGACAG | — | (GCT)4 | — | 9.62 |
Protein transport protein Sec61 beta subunit |
SYMS41 | R | TCTGCTTTCTTGGATATGGTA | |||||
SYMS42 | F | CCAAAGAGATCTTGCAGACTA | — | (ATG)4 | — | 1.78 |
Jasmonate-induced protein |
SYMS42 | R | CCCAACACAACAACCAAT | |||||
SYMS43 | F | CCACACAAGCAAGAAATAAAC | — | (GGT)4 | — | 8.57 |
Dirigent-like protein |
SYMS43 | R | TCGAACACTATGGTAAAGGTG | |||||
SYMS44 | F | GGACTGTACAAGGACGACAG | — | (GCT)4 | — | 1.15 |
Homeodomain-like transcription factor |
SYMS44 | R | TCTGCTTTCTTGGATATGGTA | |||||
SYMS45 | F | GCGTCAGAGTGTTAAAACAAG | 53 | (GCT)4 | 0.69 | 9.86 |
Protein transport protein |
SYMS45 | R | GACTCTGCTTTCTTGGATATG | |||||
SYMS46 | F | AGCTATCTTTAGTGGGGACAT | 52 | (CGT)4 | 0.90 | 1.82 |
Hypothetical protein SORBIDRAFT_09g006220 |
SYMS46 | R | GAGGTCTCATCGGAGCTTA | |||||
SYMS47 | F | AGGTCGTTTTAATTCCTTCC | 53 | (GTTTT)3 | 0.77 | 1.00 |
Preprotein translocase Sec |
SYMS47 | R | CGTAAATATGAACGAGGTCAG | |||||
SYMS48 | F | AGGTCGTTTTAATTCCTTCC | 53 | (TTTA)6 | 0.90 | 4.00 |
TPA: hypothetical protein |
SYMS48 | R | CGTAAATATGAACGAGGTCAG | |||||
SYMS49 | F | GGACTGTACAAGGACGACAG | — | (GCT)4 | — | 1.15 |
Zinc finger A20 and AN1 domains-containing protein |
SYMS49 | R | TCTGCTTTCTTGGATATGGTA | |||||
SYMS50 | F | TCCAAGGATTTAGCTATGGAT | — | (TGT)10 | — | 6.79 |
TPA: seed maturation protein |
SYMS50 | R | TTCAACTACACCCTTCTGTTG | |||||
SYMS51 | F | GCGTCAGAGTGTTAAAACAAG | — | (GCT)4 | — | 1.22 |
Hypothetical protein |
SYMS51 | R | ATTGTCACTTGCTATCCATTT | |||||
SYMS52 | F | CACCTTCTTTCCTTCTCCTC | — | (CGC)4 | — | 3.32 |
V-type proton ATPase 16 kDa proteolipid subunit |
SYMS52 | R | GTAGATACCGAGCACACCAG | |||||
SYMS53 | F | TCAGTTCAGGGATGACAATAG | 56 | (CCGTGG)3 | 0.87 | 2.59 |
Homeodomain-like transcription factor superfamily protein |
SYMS53 | R | GGATAGACTGAAATCTGCTCA | |||||
SYMS54 | F | CAACTCGACTCTTTTCTCTCA | — | (CTC)5 | — | 4.13 |
Protein transport protein SEC31 |
SYMS54 | R | GGAGGTGGAACTTCCTGA | |||||
SYMS55 | F | GGACTGTACAAGGACGACAG | — | (GCT)4 | — | 1.12 |
Protein transport protein Sec61 subunit beta-like isoform |
SYMS55 | R | TCTGCTTTCTTGGATATGGTA | |||||
SYMS56 | F | GGACTGTACAAGGACGACAG | — | (GCT)4 | — | 8.01 |
Protein transport protein Sec61 subunit beta-like isoform |
SYMS56 | R | TCTGCTTTCTTGGATATGGTA | |||||
SYMS57 | F | AAACGATCAGATACCGTTGTA | — | (CG)6 | — | 7.84 |
Caltractin |
SYMS57 | R | ATCAAAGAGATCAAAGGCTTC | |||||
SYMS58 | F | CATTTCGAAGCTCCTCCT | 52 | (CCTCCG)6 | 0.74 | 5.97 |
Zinc finger A20 and AN1 domains-containing protein |
SYMS58 | R | TAGGCTGCACAACAATAGTCT | |||||
SYMS59 | F | CTCCCCCATTTCTCTTCC | 53 | (GCAGCC)6 | 0.80 | 4.02 |
|
SYMS59 | R | CAAGTACTCCAGCAGAGATGT | |||||
SYMS60 | F | CTTTTCCCTCTTCCTCTCTC | — | (CCG)5 | — | 1.24 |
|
SYMS60 | R | TGTCACTAACACGAATCACAA | |||||
SYMS61 | F | CCCTCTCCCTGCTCTTTC | 54 | (TCC)5 | 0.79 | 4.14 |
Actin-depolymerizing factor 3 |
SYMS61 | R | CAGTCACAAAGTCGAAATCAT | |||||
SYMS62 | F | ACAACTCTTCAGTCTTCACGA | 54 | (CAAC)3 | 0.85 | 4.40 |
Truncated alcohol dehydrogenase |
SYMS62 | R | CCAATCTTGACATCCTTGAC | |||||
SYMS63 | F | GCACGGTGAAGTTCTAGTTC | 54 | (TCGAT)4 | 0.67 | 3.11 |
Hypothetical protein SORBIDRAFT_08g002800 |
SYMS63 | R | CAGCTTCACTCATGAATTTTT | |||||
SYMS64 | F | GGACTGTACAAGGACGACAG | — | (GCT)4 | — | 1.08 |
Protein transport protein Sec61 subunit beta-like isoform |
SYMS64 | R | TCTGCTTTCTTGGATATGGTA | |||||
SYMS65 | F | AACACAAGCAAGAAATAAACG | 53 | (GGT)4 | 0.51 | 3.42 |
Dirigent-like protein |
SYMS65 | R | AACACTATGGTCAAGGTGGTA | |||||
SYMS66 | F | GCGTCAGAGTGTTAAAACAAG | 52 | (GCT)4 | 0.58 | 1.01 |
Protein transport protein Sec61 subunit beta-like isoform |
SYMS66 | R | GAAATCGCTCTATAAGGTTCC | |||||
SYMS67 | F | TCTCTCTGAAGATGATGCTTT | 52 | (AAG)5 | 0.90 | 4.25 |
Hypothetical protein SORBIDRAFT_03g005100 |
SYMS67 | R | GTTAAGAGGCTTCCAAAGAAC | |||||
SYMS68 | F | CAGCTCGTCGTCTTCTTTT | — | (GTC)5 | 2.00 |
Putative ubiquitin-conjugating enzyme family | |
SYMS68 | R | GTGGCTTGTTTGGATATTCTT | |||||
SYMS69 | F | GGACTGTACAAGGACGACAG | 54 | (GCT)4 | 0.79 | 9.28 |
Protein transport protein Sec61 subunit beta-like isoform |
SYMS69 | R | CGTCAGACGTACTGAAATGTT | |||||
SYMS70 | F | AACACAAGCAAGAAATAAACG | 53 | (GGT)4 | 0.77 | 1.58 |
Putative dirigent protein |
SYMS70 | R | AACACTATGGTCAAGGTGGTA | |||||
SYMS71 | F | GGACTGTACAAGGACGACAG | — | (GCT)4 | — | 9.86 |
Protein transport protein Sec61 subunit beta-like isoform |
SYMS71 | R | TCTGCTTTCTTGGATATGGTA | |||||
SYMS72 | F | CCCTCTCCCTGCTCTTTC | 55 | (TCC)4 | 0.89 | 4.36 |
Actin-depolymerizing factor 3 |
SYMS72 | R | CAGTCACAAAGTCGAAATCAT | |||||
SYMS73 | F | GGACTGTACAAGGACGACAG | 55 | (GCT)4 | 0.83 | 1.09 |
Protein transport protein Sec61 subunit beta-like isoform |
SYMS73 | R | TCTGCTTTCTTGGATATGGTA | |||||
SYMS74 | F | GGACTGTACAAGGACGACAG | 52 | (GCT)4 | 0.88 | 9.51 |
Preprotein translocase Sec |
SYMS74 | R | TCTGCTTTCTTGGATATGGTA | |||||
SYMS75 | F | GCACCCCCAATTCGAACG | 52 | (ACG)3 | 0.93 | 1.78 |
TPA: general regulatory factor 1 |
SYMS75 | R | CGGTAGTCCTTGATGAGTGT | |||||
SYMS76 | F | GGACTGTACAAGGACGACAG | 52 | (GCT)4 | 0.78 | 4.79 |
Protein transport protein Sec61 subunit beta-like isoform |
SYMS76 | R | TCTGCTTTCTTGGATATGGTA | |||||
SYMS77 | F | CACGCAACGCAAGCACAG | 55 | (CCAT)3 | 0.93 | 8.34 |
Hypothetical protein SORBIDRAFT_10g030160 |
SYMS77 | R | AAGTTGATTCACCCTCATTCT | |||||
SYMS78 | F | CACGCAACGCAAGCACAG | 53 | (CGATC)3 | 0.92 | 1.04 |
Translocon-associated protein alpha subunit precursor |
SYMS78 | R | AAGTTGATTCACCCTCATTCT | |||||
SYMS79 | F | GGACTGTACAAGGACGACAG | 53 | (GCT)4 | 0.91 | 1.04 |
Protein transport protein Sec61 subunit beta-like isoform |
SYMS79 | R | TCTGCTTTCTTGGATATGGTA | |||||
SYMS80 | F | CTTGATCCTTGACAAAAGAGA | 52 | (AG)6 | 0.87 | 2.25 |
|
SYMS80 | R | ATTGCTGTTGATATTTGGATG | |||||
SYMS81 | F | GCGTCAGAGTGTTAAAACAAG | 53 | (GCT)4 | 0.87 | 8.01 |
Protein transport protein Sec61 subunit beta-like isoform |
SYMS81 | R | GTGTAGAACTGGAGCATTGAG | |||||
SYMS82 | F | TATCAACAAGCCTTCCATTC | 53 | (GTG)4 | 0.90 | 1.12 |
Glycine-rich RNA-binding protein 2 |
SYMS82 | R | GGCTATAGTCACCACGGTAG | |||||
SYMS83 | F | CGACAGGGAGAAGAGTACAG | 55 | (GCT)4 | 0.87 | 9.39 |
Protein transport protein Sec61 subunit beta-like isoform |
SYMS83 | R | GACTCTGCTTTCTTGGATATG | |||||
SYMS84 | F | GCGTCAGAGTGTTAAAACAAG | 53 | (GCT)4 | 0.75 | 1.14 |
Protein transport protein Sec61 subunit beta-like isoform |
SYMS84 | R | AATCGCTCTATAAGGTTCCTC | |||||
SYMS85 | F | CTCTTCTTCACCAATTCCTCT | — | (CCG)6 | — | 1.14 |
Protein transport protein Sec61 subunit beta-like isoform |
SYMS85 | R | CAAACCTCATAAAGAGTGCAG | |||||
SYMS86 | F | GGGCAAGCAAGAAACCAC | 54 | (TCC)4 | 0.93 | 1.16 |
TPA: translation initiation factor 1 |
SYMS86 | R | CGTACATGAACGTAGTCCTTT | |||||
SYMS87 | F | GCGTCAGAGTGTTAAAACAAG | — | (GCT)4 | — | 1.19 |
Protein transport protein Sec61 beta subunit |
SYMS87 | R | AATCGCTCTATAAGGTTCCTC | |||||
SYMS88 | F | TTATAAGGAAATCCCCCACT | — | (GCC)4 | — | 7.71 |
Hypothetical protein SORBIDRAFT_09g000970 |
SYMS88 | R | CACCAAGTACTCATCCATCAT | |||||
SYMS89 | F | CATCTCCTGCTAACAATTCAC | 55 | (TGC)4 | 0.91 | 9.64 |
|
SYMS89 | R | ATTTATAGGTTGGCACCAGAG | |||||
SYMS90 | F | GCGTCAGAGTGTTAAAACAAG | 53 | (GCT)4 | 0.85 | 1.00 |
Protein transport protein Sec61 subunit beta-like isoform |
SYMS90 | R | GTGTAGAACTGGAGCATTGAG |
Most promising results of gene ontology (GO) as horizontal bar graphs. These graphs represent the distribution of GO terms categorized as a biological process (a), cellular component (b), and molecular function (c).
A set of 63 EST-SSR primers were evaluated for PCR optimization, polymorphism, and cross amplification in twenty genotypes belonging to cereals plants and
The gel represents PCR amplification profile with SYMS37 primer among twenty different plant species. Lanes: 1
The potentials of EST-SSR primers were examined for cross transferability among 20 plant species belonging to cereals and
Details of cross transferability of 42 EST-SSR markers in twenty genotypes belonging to cereals and
S. number/lane | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | Primer |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
SY 28 | 4 | 5 | 6 | 1 | 2 | 3 | 0 | 2 | 5 | 5 | 3 | 2 | 3 | 2 | 3 | 3 | 1 | 3 | 2 | 3 | 95 |
SY 29 | 6 | 3 | 5 | 9 | 3 | 12 | 3 | 5 | 12 | 6 | 7 | 7 | 8 | 7 | 7 | 6 | 7 | 6 | 6 | 8 | 100 |
SY 30 | 1 | 0 | 4 | 0 | 0 | 7 | 0 | 5 | 6 | 6 | 3 | 3 | 4 | 3 | 2 | 3 | 2 | 3 | 2 | 3 | 80 |
SY 31 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 3 | 2 | 1 | 1 | 2 | 2 | 2 | 0 | 2 | 2 | 0 | 0 | 50 |
SY 32 | 1 | 0 | 0 | 1 | 0 | 2 | 0 | 2 | 4 | 3 | 1 | 3 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 55 |
SY 33 | 0 | 0 | 2 | 2 | 3 | 5 | 3 | 7 | 6 | 4 | 6 | 5 | 5 | 5 | 2 | 3 | 0 | 2 | 3 | 3 | 85 |
SY 34 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 2 | 5 | 4 | 5 | 5 | 5 | 9 | 9 | 85 |
SY 35 | 0 | 0 | 0 | 1 | 0 | 4 | 0 | 5 | 2 | 1 | 0 | 0 | 1 | 1 | 1 | 2 | 2 | 1 | 2 | 1 | 65 |
SY 36 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 0 | 5 | 2 | 2 | 2 | 0 | 2 | 0 | 0 | 2 | 35 |
SY 37 | 9 | 7 | 5 | 6 | 6 | 5 | 5 | 9 | 12 | 10 | 11 | 8 | 8 | 8 | 8 | 6 | 7 | 6 | 5 | 6 | 100 |
SY 38 | 0 | 0 | 0 | 3 | 0 | 2 | 0 | 7 | 8 | 1 | 0 | 0 | 2 | 2 | 1 | 2 | 0 | 0 | 3 | 0 | 50 |
SY 45 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 5 | 1 | 0 | 1 | 2 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 35 |
SY 46 | 0 | 1 | 4 | 4 | 1 | 0 | 0 | 4 | 4 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 35 |
SY 47 | 0 | 1 | 3 | 3 | 2 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 25 |
SY 48 | 0 | 0 | 0 | 0 | 5 | 3 | 0 | 8 | 12 | 0 | 5 | 3 | 3 | 2 | 1 | 3 | 2 | 2 | 0 | 0 | 60 |
SY 53 | 0 | 0 | 0 | 1 | 1 | 3 | 3 | 12 | 9 | 2 | 1 | 1 | 2 | 2 | 1 | 3 | 2 | 1 | 3 | 1 | 85 |
SY 58 | 0 | 0 | 0 | 1 | 1 | 0 | 3 | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 25 |
SY 59 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 4 | 0 | 3 | 3 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 20 |
SY 61 | 0 | 3 | 7 | 5 | 4 | 0 | 3 | 4 | 5 | 6 | 3 | 4 | 1 | 5 | 3 | 5 | 5 | 5 | 5 | 5 | 90 |
SY 62 | 0 | 0 | 0 | 1 | 0 | 2 | 0 | 4 | 5 | 3 | 2 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 35 |
SY 63 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 4 | 1 | 6 | 1 | 1 | 1 | 0 | 1 | 0 | 2 | 1 | 55 |
SY 65 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 1 | 0 | 1 | 2 | 3 | 2 | 2 | 2 | 1 | 50 |
SY 66 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 3 | 1 | 2 | 0 | 0 | 3 | 2 | 2 | 1 | 40 |
SY 67 | 1 | 2 | 5 | 6 | 3 | 3 | 0 | 2 | 5 | 6 | 3 | 2 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 60 |
SY 69 | 1 | 5 | 2 | 0 | 1 | 0 | 0 | 3 | 1 | 2 | 1 | 1 | 1 | 1 | 1 | 2 | 1 | 0 | 3 | 2 | 80 |
SY 70 | 1 | 0 | 0 | 1 | 0 | 1 | 0 | 5 | 2 | 0 | 0 | 1 | 0 | 0 | 2 | 0 | 3 | 3 | 0 | 0 | 45 |
SY 72 | 1 | 0 | 2 | 0 | 0 | 0 | 0 | 1 | 4 | 5 | 0 | 8 | 5 | 8 | 1 | 3 | 6 | 4 | 6 | 8 | 70 |
SY 73 | 0 | 0 | 2 | 0 | 1 | 2 | 0 | 2 | 2 | 0 | 1 | 3 | 1 | 4 | 1 | 0 | 3 | 0 | 0 | 3 | 60 |
SY 74 | 2 | 1 | 1 | 0 | 1 | 1 | 3 | 1 | 3 | 2 | 1 | 4 | 1 | 5 | 1 | 0 | 3 | 0 | 0 | 2 | 80 |
SY 75 | 1 | 0 | 2 | 3 | 3 | 0 | 0 | 0 | 6 | 3 | 9 | 7 | 6 | 7 | 6 | 0 | 4 | 6 | 0 | 0 | 65 |
SY 76 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 1 | 2 | 1 | 4 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 30 |
SY 77 | 2 | 5 | 6 | 6 | 8 | 4 | 3 | 9 | 6 | 9 | 3 | 0 | 4 | 4 | 3 | 4 | 3 | 0 | 2 | 0 | 85 |
SY 78 | 2 | 2 | 5 | 6 | 4 | 6 | 4 | 5 | 7 | 6 | 4 | 10 | 9 | 10 | 3 | 2 | 8 | 7 | 5 | 9 | 100 |
SY 79 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 3 | 5 | 2 | 0 | 5 | 1 | 7 | 7 | 2 | 1 | 0 | 0 | 6 | 55 |
SY 80 | 1 | 1 | 0 | 4 | 0 | 1 | 0 | 4 | 5 | 6 | 2 | 5 | 4 | 5 | 5 | 3 | 5 | 4 | 5 | 5 | 85 |
SY 81 | 0 | 0 | 0 | 1 | 2 | 6 | 0 | 6 | 6 | 8 | 7 | 3 | 3 | 4 | 3 | 3 | 3 | 3 | 3 | 2 | 80 |
SY 82 | 0 | 0 | 10 | 3 | 1 | 4 | 3 | 9 | 1 | 1 | 6 | 5 | 4 | 3 | 5 | 3 | 4 | 4 | 3 | 2 | 90 |
SY 83 | 1 | 2 | 0 | 6 | 2 | 3 | 4 | 2 | 7 | 2 | 1 | 3 | 2 | 3 | 1 | 3 | 3 | 2 | 3 | 3 | 95 |
SY 84 | 0 | 0 | 0 | 1 | 2 | 3 | 0 | 0 | 2 | 0 | 0 | 3 | 3 | 1 | 0 | 3 | 3 | 3 | 3 | 3 | 60 |
SY 86 | 1 | 5 | 6 | 3 | 2 | 5 | 4 | 5 | 8 | 11 | 6 | 5 | 3 | 11 | 5 | 12 | 7 | 6 | 7 | 10 | 100 |
SY 89 | 9 | 6 | 5 | 4 | 1 | 7 | 3 | 7 | 4 | 3 | 10 | 4 | 4 | 5 | 7 | 3 | 4 | 7 | 3 | 5 | 100 |
SY 90 | 5 | 0 | 3 | 2 | 5 | 2 | 3 | 4 | 3 | 4 | 0 | 4 | 3 | 6 | 4 | 4 | 2 | 3 | 6 | 4 | 90 |
Average of transferability | 27.22 | 27.22 | 47.22 | 46.67 | 36.11 | 55.56 | 26.11 | 88.33 | 98.89 | 71.11 | 60.0 | 73.33 | 55.56 | 75.56 | 55.0 | 50.56 | 58.89 | 51.11 | 52.78 | 60.0 |
In order to evaluate the potential of EST-SSRs, the genetic analysis was done among 20 genotypes belonging to 7 cereals (wheat, maize, barley, rice, pearl millet, oat, and
Dendrogram is constructed based on allelic data produced from 42 EST-SSR markers using FreeTree and TreeView software.
All the 42 EST-SSR markers were evaluated in pooled DNA bulks of contrasting trait of sugarcane cultivars (CoS 91230 (CoS 775 × Co 1148) cross with CoS 8436 (MS 68/47 × Co 1148)) for the identification of reporter EST-SSR markers based on their allelic differences between them. Interestingly, 10 markers showed polymorphic nature and apparently discriminating potential between bulks through bulk segregation analysis (Figure
The gel represents polymorphism and discrimination between bulks of pooled DNA with contrasting high and low plant diameter through bulk segregation analysis.
The present study was intended for identification and characterization of SSR in
The authors declare that there is no conflict of interests regarding the publication of this paper.
Authors are highly grateful to the Division of Biotechnology, UP Council of Sugarcane Research, for providing an opportunity and facilities for research works. Authors are also grateful to Director, UP Council of Sugarcane Research, Shahjahanpur, UP, India for their moral support. Authors also acknowledge University of Rajasthan for providing DBT-IPLS and DBT-BIF facilities.