Understanding population structure and detection of QTLs for curding-related traits in Indian cauliflower by genotyping by sequencing analysis

Curd initiation and development are complex traits and highly responsive for different temperature ranges in cauliflower. The present study was aimed to identify QTLs for eight traits associated with curding behaviour in diverse germplasm of Indian cauliflower. For this, 92 genotypes of cauliflower and 2 each of tropical broccoli and cabbage were genotyped through genotyping by sequencing (GBS). It generated ≈302 million reads (9.1226E + 10 bp) and identified 35,381 SNPs, maximum from chromosome 3 (4735) with a mean value of 3981.1 SNPs. Ts/Tv ratio was 1.74, suggesting transition bias. STRUCTURE analysis revealed delta value of K = 4 and four subpopulations and prominence of population admixture. In total, 121 significant SNPs were detected for eight traits, 38 for Delhi (North Indian plain) and 83 for Barapani (North-East India). Twelve QTLs were detected for traits associated with regulation of curd formation and development, five of which were for marketable curd length, curd width, days to 50% curd harvest and marketable curd weight from Delhi region and seven for curd length, curd width, days to 50% curd harvest, gross plant weight, leaf length, marketable/net curd weight and number of leaves per plant for Barapani area of North East India. The SNPs identified will be useful for development of markers for curding-related traits and their use in breeding varieties with wider curding plasticity.