Substitution of Gossypium tomentosum Chromosome Segments Into Upland Cotton (G. hirsutum) & Development of Segment-Targeted SNP Assays

Abstract

Genetic diversity is essential to the genetic improvement of every crop. Goals of this project have been [1] to genetically diversify upland cotton (Gossypium hirsutum L.) by creating numerous chromosome segment substitution lines (CSSLs), each containing a small amount of G. tomentosum (Nuttall ex Seemann) germplasm, and [2] to empower wide-cross cotton breeding by improving the genome coverage provided by simplex SNP assays. Putative BC5Sn CSSLs were selected using existing simplex SNP assays. Subsequent whole-genome analysis using the CottonSNP63K array identified the locations, sizes and zygosity of all donor segment(s). BC5Sn CSSLs collectively included 43% of the donor genome in homozygous form, and 15% in heterozygous form. Other BC3F1 plants contained another 36% coverage of the donor genome in heterozygous form, i.e., develop BC5Sn CSSLs that expand coverage. Targeted development of 85 PACE assays reduced gaps between SNP assays, thereby improving genome coverage and amenability to marker-assisted selection (MAS).