Discovery of single nucleotide polymorphism in Gossypium hirsutum and G. barbadense through next generation sequencing approach


169 / 68

Authors

  • Reddy S. Sudakara University of Agricultural Sciences, Agricultural Research Station, Dharwad Farm, Dharwad 07
  • I. S. Katageri University of Agricultural Sciences, Agricultural Research Station, Dharwad Farm, Dharwad 07
  • N. V. Mohan Kumar University of Agricultural Sciences, Agricultural Research Station, Dharwad Farm, Dharwad 07
  • M. P. Jadhav University of Agricultural Sciences, Agricultural Research Station, Dharwad Farm, Dharwad 07
  • Sateesh Adiger University of Agricultural Sciences, Agricultural Research Station, Dharwad Farm, Dharwad 07
  • Navajeet Chakravartty University of Agricultural Sciences, Agricultural Research Station, Dharwad Farm, Dharwad 07
  • H. M. Vamadevaiah University of Agricultural Sciences, Agricultural Research Station, Dharwad Farm, Dharwad 07
  • V. B. Reddy University of Agricultural Sciences, Agricultural Research Station, Dharwad Farm, Dharwad 07

Abstract

Single nucleotide polymorphism was identified using
ddRAD and pooled amplicon sequencing between the
allotetraploid cotton genotypes of G. hirsutum var. DS-28
(POOL-H) and G. barbadense var. SBYF-425 (POOL-B). The
471270 (470161 SNP and 1109 INDELs), 2723 (2621 SNP and
102 INDELs) and 780 (759 SNP and 21 INDELs) variant calling
were predicted at read depth of 10 in the genotypes by
using G. raimondii (D5), G. arboreum (A2) and G. hirsutum
(AD) as reference genomes, respectively. Further, filtered
out false positive homoeologous SNPs between parents
(DS-28 and SBYF-425) at read depth of 10, identified 245
and 45 homozygous polymorphic SNPs between parents
based on pooled amplicon sequencing and ddRAD
sequencing by using G. raimondii, G. arboreum and G.
hirsutum as a reference genomes. Based on gene function,
5 SNPs were converted into KASPar markers and genotyped
in 21 RILs for fibre quality traits. Identified polymorphic
SNPs and INDELs can be used for genotyping and QTL
mapping after converting into functional markers.

Downloads

Submitted

2017-02-27

Published

2017-02-27

Issue

Vol. 77 No. 1 (2017): The Indian Journal of Genetics and Plant Breeding

Section

Articles

How to Cite

Sudakara, R. S., Katageri, I. S., Kumar, N. V. M., Jadhav, M. P., Adiger, S., Chakravartty, N., Vamadevaiah, H. M., & Reddy, V. B. (2017). Discovery of single nucleotide polymorphism in Gossypium hirsutum and G. barbadense through next generation sequencing approach. The Indian Journal of Genetics and Plant Breeding, 77(1). https://epubs.icar.org.in/index.php/IJGPB/article/view/68242