DE Novo Snp Discovery and Gbs-Based Cotton Genome Map Development
Crop Germplasm Research
2013 Annual Report
1a.Objectives (from AD-416):
Jointly develop and characterize cotton SNP markers, and map these markers in the tetraploid cotton genome through cooperative research.
1b.Approach (from AD-416):
A simplified genotyping-by-sequencing (GBS) approach, developed by cooperator's lab of the Biology Department at Texas A&M University, will be used to genotype recombinant inbred lines (RILs) of an interspecific cross between Gossypium hirsutum x G. barbadense (TM-1 x 3-79), developed by ARS PI's Lab at the USDA-ARS Southern Plains Agricultural Research Center, to discover novel single nucleotide polymorphism (SNP) markers and develop an interspecific linkage map of the tetraploid cotton genome.
This is a new project with the goal of developing and characterizing modern molecular tools known as SNP markers, and mapping these markers in the cotton genome. In FY 2013, the work focused on establishing a simplified and targeted approach (genotyping by sequencing or GBS) with DNA samples from 186 cotton types known as recombinant inbred lines (RILs) derived from a cross between Gossypium hirsutum TM-1 x G. barbadense 3-79. Also, eight cotton populations that exhibited photoperiod independence (derived from different wild cotton germplasm lines) were studied. A key set of photoperiodic regulatory genes, identified in the genetic standard plant, Arabidopsis thaliana, were used to clone and compare with cotton counterparts. Candidate genes identified by project work were aligned to the draft sequence of the D-genome of G. raimondiii, whose progenitor contributes to the D-subgenome of the economically important fiber-producing cotton species, G. hirsutum and G. barbadense. Work by this project, as it progresses, will provide valuable new knowledge that will guide ongoing efforts to map the cotton genome with SNP markers and to clone the genes for photoperiod independence. Exploitation of the knowledge gained through detailed resolution of the cotton genome will greatly facilitate characterization of Gossypium germplasm for exploiting genetic diversity and development of new, more productive and environmentally adapted cotton varieties for use by U.S. cotton farmers.