QTL and Candidate Gene Identification for Silique Length Based on High-Dense Genetic Map in Brassica napus L.

Abstract

Silique length (SL) is an important yield trait and positively correlates with seeds per silique and seed weight. In the present study, two double haploid (DH) populations, established from crosses Zhongshuang11 × R11 (ZR) and R1 × R2 (RR), containing 280 and 95 DH lines, respectively, were used to map quantitative trait loci (QTL) for SL. A high-dense genetic map from ZR population was constructed comprising 14,658 bins on 19 linkage groups, with map length of 2,198.85 cM and an average marker distance of 0.15 cM. Genetic linkage map from RR population was constructed by using 2,046 mapped markers anchored to 19 chromosomes with 2,217-cM map length and an average marker distance of 1.08 cM. Major QTL <i>qSL_ZR_A09</i> and <i>qSL_RR_A09b</i> on A09 were identified from ZR and RR populations, respectively. Both QTL could be stably detected in four environments. QTL <i>qSL_RR_A09b</i> and <i>qSL_ZR_A09</i> were located on 68.5-70.8 cM and 91.33-91.94 cM interval with R² values of 14.99-39.07% and 15.00-20.36% in RR and ZR populations, respectively. Based on the physical positions of single nucleotide polymorphism (SNP) markers flanking <i>qSL_ZR_A09</i> and gene annotation in <i>Arabidopsis</i>, 26 genes were identified with SNP/Indel variation between parents and two genes (<i>BnaA09g41180D</i> and <i>BnaA09g41380D</i>) were selected as the candidate genes. Expression analysis further revealed <i>BnaA09g41180D</i>, encoding homologs of <i>Arabidopsis</i> fasciclin-like arabinogalactan proteins (FLA3), as the most promising candidate gene for <i>qSL_ZR_A09</i>. The QTL identification and candidate gene analysis will provide new insight into the genomic regions controlling SL in <i>Brassica</i> napus as well as candidate genes underlying the QTL.