Genome mapping and molecular markers identification for yield, yield component and fibre quality traits in tetraploid cotton

The identification of quantitative trait loci (QTL) across different environments is a prerequisite for marker-assisted selection (MAS) in crop improvement programmes. CottonSNP63k Illumina infinium array was used for genotyping 178 inter-specific recombinant inbred lines and the parents, and identified 1,667 homozygous polymorphic markers between the parents. Of these, 1,430 markers were used for the construction of linkage map after removing 237 redundant markers. The genetic map spans a total genetic length of 3,149.8 cM with an average marker interval size of 2.2 cM. The phenotypic data from five environments were analysed separately using inclusive composite interval mapping which identified a total of 56 QTL explaining phenotypic variances (PVE) in the range of 8.18%-28.91%. There were 11 and 24 major QTL found for fibre quality and yield components, respectively. A total of 64 QTL were identified through Multi-Environment Trials analysis, of which 34 recorded QTL x Environment interactions.