Linkage map construction using SSR markers and QTL analyses of stem expansion traits in Brassica juncea

Abstract Tuber mustard ( Brassica juncea (L.) Czern. et Coss. var. tumida Tsen et Lee) is an economically important vegetable crop, valued for its expanded stem. Quantitative trait loci (QTL) analyses of the traits related to stem expansion provide a basis for fine mapping, gene cloning, and marker assisted selective breeding. However, the genetic bases of stem expansion traits remain unclear. In this study, high levels of phenotypic variation were observed for stem expansion traits in an F 2 segregation population derived from the cross between tuber mustard and leaf mustard, which exhibit significantly differing stem traits. A linkage map was constructed containing 116 simple sequence repeat (SSR) markers using 200 randomly selected F 2 individuals. The genetic map consisted of 17 linkage groups (LGs) covering a total of length of 2061.0 cM with an average interval of 17.92 cM. A total of 5 QTLs were identified for the stem expansion traits, stem weight (SW) and stem diameter (SD). Among these, 4 QTLs for SW were detected, SW1 and SW2 were located on LG3 with the remaining located on LG13. And each QTL explained 26.46%–28.18% of the phenotypic variance, and their additive effects were all negative. The QTL SD1 controlling SD explained 6.54% of the phenotypic variance and was located on LG1. Additionally, it possessed a negative additive effect and the shortest distance with flanking markers (BjSSR1811b) displaying 0.99 cM. These data demonstrate the genetic basis of stem expansion and will facilitate the marker-assisted selective breeding of tuber mustard.