Resolving Tight Linkages Around Renlon by MAS for High-resolution Recombination in Chromosome-11

Reniform (Rotylenchulus reniformis) nematodes cost US cotton growers over $130M per year.  Extremely strong resistance was found in the wild African diploid species G. longicalyx and introgressed into tetraploid cotton.  Two highly resistant cotton lines were released, LONREN-1 and LONREN-2, but field testing revealed severe stunting of seedlings grown in fields heavily infested with reniform nematodes.  Possible explanations include [1] root damage caused by hypersensitivity to the nematode, and [2] loss of one or more linked (repulsion) G. hirsutum loci that affect susceptibility to soil-borne pathogen(s), e.g. Thielaviopsis, which interact synergistically with the nematode to cause more severe stunting.  Numerous nematode and fungal resistance loci of cotton are known to reside in chromosome 11. To better characterize this chromosomal region and potentially separate the resistance and stunting, we have mounted a map-based approach to recover recombinants that retain the alien resistance gene (Ren^lon) but minimize the flanking alien segments. To exploit this strategy at high resolution, we are saturating this region by developing SNP markers for G. longicalyx, and localizing those in the alien segment region.  Hundreds of Gl-Gh SNPs have been aligned to this region according to D5 genome. And some SNPs have been tested and found to be linked with Ren^lon. The SNPs will then be used on large populations developed from different resistance families by using resistance-linked SSR markers BNL3279, BNL1231, CIR069 to recover recombinants closely flanking the alien resistance gene, as well in nearby regions.  The most closely flanking recombinants will be phenotyped for resistance, stunting and tested for agronomic performance.