Single Nucleotide Polymorphisms (SNPs)


NBRI has utilized the high throughput 454 pyrosequencing technology to discover large number of single nucleotide polymorphism (SNP) markers from the genic-enriched G. hirsutum libraries. Six diverse G. hirsutum genotypes were used for genic-enriched sequencing using methylation sensitive digestion. SNPs were mined from the different combination of these genotypes using autoSNP 2.0 program. Clusters with minimum of 6 reads were considered for the SNP calling. Clusters with minimum of 6 reads were considered for the SNP predictions. A custom script was made to remove orthologus polymorphism and contigs with less than 3 reads (depth within genotype) at polymorphic position for the analysis. The SNPs were distributed among genic or non-genic SNPs. The genic SNPs were further classified into exonic, intronic as well as from UTR regions. Novelty of SNPs were determined by their comparison with NCBI dbSNP data.

All the SNPs have been submitted to NCBI dbSNP under accession numberss: ss538789672- ss538865759.

  Distribution of SNPs identified across 15 combinations of G. hirsutum genotypes  
Genotype combinations SNPs
JKC 703 X JKC 725 4180
JKC 703 X JKC 737 5317
JKC 703 X JKC 770 4981
JKC 703 X LRA 5166 5834
JKC 703 X MCU 5 3492
JKC 725 X JKC 737 5665
JKC 725 X JKC 770 4461
JKC 725 X LRA 5166 4475
JKC 725 X MCU 5 3722
JKC 737 X JKC 770 4620
JKC 737 X LRA 5166 5312
JKC 737 X MCU 5 3816
JKC 770 X LRA 5166 3520
JKC 770 X MCU 5 2955
LRA 5166 X MCU 5 4094
Total SNPs 66444
  Detail statistics of SNPs identification and their distribution  
Details of identified SNPs Number
Total identified SNPs 422617
True SNPs called 75714
Total non-redundant SNPs 66444
Total contigs having SNPs 34032
Non-genic SNPs 41832
Genic SNPs  24612
SNPs in UTRs  4424
Intronic SNPs 4518
Exonic SNPs 15648
Synonymous SNPs 2608
Non-synonymous SNPs 6521