Cumulative and different genetic effects contributed to yield heterosis using maternal and paternal backcross populations in Upland cotton

Heterosis has been utilized in commercial production, but the heterosis mechanism has remained vague. Hybrid cotton is suitable to dissect the heterosis mechanism. In order to explore the genetic basis of heterosis in Upland cotton, we generated paternal and maternal backcross (BC/P and BC/M) populations. Data for yield and yield-component traits were collected over 2 years in three replicated BC/P field trials and four replicated BC/M field trials. At single-locus level, 26 and 27 QTLs were identified in BC/P and BC/M populations, respectively. Six QTLs shared in both BC populations. A total of 27 heterotic loci were detected. Partial dominant and over-dominant QTLs mainly determined yield heterosis in the BC/P and BC/M populations. QTLs for different traits displayed varied genetic effects in two BC populations. Eleven heterotic loci overlapped with QTLs but no common heterotic locus was detected in both BC populations. We resolved the 333 kb (48 genes) and 516 kb (25 genes) physical intervals based on 16 QTL clusters and 35 common QTLs, respectively, in more than one environment or population. We also identified 189 epistatic QTLs and a number of QTL × environment interactions in two BC populations and the corresponding MPH datasets. The results indicated that cumulative effects contributed to yield heterosis in Upland cotton, including epistasis, QTL × environment interaction, additive, partial dominance and over-dominance.