Identification of quantitative trait loci with main and epistatic effects for plant architecture traits in Upland cotton (Gossypium hirsutum L.)

Abstract Plant architecture is important for cotton cultivation and breeding. In this study, two mapping generations/populations F 2 and F 2:3 in Upland cotton ( Gossypium hirsutum L.), derived from ‘Baimian1’ and TM‐1, were used to identify quantitative trait loci (QTLs) for 10 plant architecture traits. A total of 55 main‐effect QTLs (M‐QTLs) were detected. Four common M‐QTLs, qTFB ‐10(F 2 /F 2:3 ) for total fruit branches, qFBL ‐26b(F 2 )/ qFBL ‐26(F 2:3 ) for fruit branch length, qFBA ‐5(F 2 /F 2:3 ) for fruit branch angle and qFBN ‐26b(F 2 )/ qFBN ‐26(F 2:3 ) for fruit branch nodes, were found. The synergistic alleles and the negative alleles can be utilized in cotton plant architecture breeding programmes according to specific breeding objectives. Altogether 54 pairs of epistatic QTLs (E‐QTLs) exhibiting the interactions of additive‐by‐additive (AA), additive‐by‐dominant (AD), dominant‐by‐additive (DA) and dominant‐by‐dominant (DD) were detected. The epistasis appeared to be an important contributor to genetic variation in cotton plant architecture traits. Therefore, the identified markers associated with E‐QTLs as well as M‐QTLs will be of importance in future breeding programmes to develop cotton cultivars exhibiting desirable plant architecture.