63K SNP chip based linkage mapping and QTL analysis for fibre quality and yield component traits in Gossypium barbadense L. cotton

The Gossypium barbadense L. cotton is known for its superior quality fibre. A study on the identification of quantitative trait loci (QTL) responsible for fibre quality and other economic traits in this species will ultimately hasten the process of cotton improvement. In the present study, using 63K Illumina Infinium SNP bead chip, 525 homozygous polymorphic markers were detected between the parents, Suvin and BCS 23-18-7 (G. barbadense) and were used in genotyping of 185 F2 plants. About 11.4% (60 markers) recorded segregation distortion from the expected Mendelian F2 ratio (1:2:1). The linkage map covering 1219.4 cM was constructed with 460 SNP loci distributed on 21 chromosomes with an average marker interval of 2.7 cM. Through composite interval mapping, 29 QTLs were identified on 13 chromosomes, with LOD values ranging from 2.51 to 11.56 and explaining 0.4 to 28.0% of the phenotypic variation. Of these, 29 QTLs, 13 and 16 QTLs were identified for yield components and fibre quality traits, respectively. Major QTLs responsible for fibre quality traits were, Uhml-1, Uhml-2, Str-2 and El-3 which were detected on the chromosomes 5, 6 and 23 of G. barbadense. These major fibre QTLs, after validation can be used in introgression breeding to improve fibre quality of G. hirsutum.