QTL mapping of agronomic and economic traits for four F2 populations of upland cotton

Abstract

Abstract Background Upland cotton (Gossypium hirsutum) accounts for more than 90% of the annual world cotton output because of its high yield potential. However, yield and fiber quality traits often show negative correlations. We constructed four F2 populations of upland cotton, using two normal lines (4133B and SGK9708) with high yield potential but moderate fiber quality and two introgression lines (Suyuan04–3 and J02–247) with superior fiber quality, and used them to investigate the genetic basis underlying complex traits such as yield and fiber quality in upland cotton. We also phenotyped eight agronomic and economic traits and mapped quantitative trait loci (QTLs). Results Extensive phenotype variations and transgressive segregation were found across the segregation populations. We constructed four genetic maps of 585.97 centiMorgan (cM), 752.45 cM, 752.45 cM, and 1 163.66 cM, one for each of the four F2 populations. Fifty QTLs were identified across the four populations (7 for plant height, 27 for fiber quality and 16 for yield). The same QTLs were identified in different populations, including qBW4 and qBW2, which were linked to a common simple sequence repeat (SSR) marker, NAU1255. A QTL cluster containing eight QTLs for six different traits was characterized on linkage group 9 of the 4133B × Suyuan04–3 population. Conclusions These findings will provide insights into the genetic basis of simultaneous improvement of yield and fiber quality in upland cotton breeding.