Day-neutral flowering candidate genes identified by selection mapping in an upland cotton (Gossypium hirsutum L.) RIL population.

Variants of flowering time genes identified from selective sweep selection of cotton breeding lines. Day-neutrality is essential for modern upland cotton (Gossypium hirsutum L.) cultivation at temperate latitudes, yet the molecular basis of the transition from photoperiod sensitive to day-neutral achieved by selective breeding remains incompletely understood. We conducted whole-genome resequencing of the day-neutral cultivar DP61, the reniform nematode-resistant line MT2468 Ren1, and 40 recombinant inbred lines (RILs) derived from their cross, all selected for day-neutral flowering. Since MT2468 was derived from a population that included photoperiod sensitive T2468 as a parent, there may be residual variation in the genes that affect photoperiodism. Using a selection mapping approach, we identified 23,961 SNPs fixed for the DP61 allele across all RILs from an initial set of 1,092,427 parental polymorphisms. A major peak resulting from the selection was detected on chromosome D07:1.20-2.45 Mb (433 SNPs). Variant effect annotation identified 17 missense variants across 16 candidate genes within this region. Two candidate genes for involvement in photoperiodism with non-synonymous variants and nearby indels, Gohir.D07G014500, orthologous to ELF8/VIP6 (AT2G06210) and Gohir.D07G013300, orthologous to VIP3/SKI8 (AT4G29830), both encode components of the PAF1 transcriptional elongation complex required for expression of the floral repressor FLOWERING LOCUS C in Arabidopsis. Loss of function mutations in either gene confers early, photoperiod-insensitive flowering in Arabidopsis. A 16.5 kb deletion on Chr. D07 in the MT2468 Ren1 parent may disrupt cis-regulatory elements upstream of these candidate genes. These results identify the PAF1 complex as a priority candidate for the control of day-neutral flowering in upland cotton and warrant further investigation as a potential source of markers for marker-assisted introgression of reduced photoperiod sensitivity.