Genome-Wide Identification of QTL for Seed Yield and Yield-Related Traits and Construction of a High-Density Consensus Map for QTL Comparison in Brassica napus.

Weiguo Zhao,Hongbo Chao,Baojun Li,Xiaodong Wang,Wusheng Liang,Jun Xiang,Hao Wang,Jianping Gan,Jianhua Tian,Li Chen,Maoteng Li,Yan Long

doi:10.3389/fpls.2016.00017

Abstract

Seed yield (SY) is the most important trait in rapeseed, is determined by multiple seed yield-related traits (SYRTs) and is also easily subject to environmental influence. Many quantitative trait loci (QTLs) for SY and SYRTs have been reported in Brassica napus; however, no studies have focused on seven agronomic traits simultaneously affecting SY. Genome-wide QTL analysis for SY and seven SYRTs in eight environments was conducted in a doubled haploid population containing 348 lines. Totally, 18 and 208 QTLs for SY and SYRTs were observed, respectively, and then these QTLs were integrated into 144 consensus QTLs using a meta-analysis. Three major QTLs for SY were observed, including cqSY-C6-2 and cqSY-C6-3 that were expressed stably in winter cultivation area for 3 years and cqSY-A2-2 only expressed in spring rapeseed area. Trait-by-trait meta-analysis revealed that the 144 consensus QTLs were integrated into 72 pleiotropic unique QTLs. Among them, all the unique QTLs affected SY, except for uq.A6-1, including uq.A2-3, uq.C1-2, uq.C1-3, uq.C6-1, uq.C6-5, and uq.C6-6 could also affect more than two SYRTs. According to the constructed high-density consensus map and QTL comparison from literatures, 36 QTLs from five populations were co-localized with QTLs identified in this study. In addition, 13 orthologous genes were observed, including five each gene for SY and thousand seed weight, and one gene each for biomass yield, branch height, and plant height. The genomic information of these QTLs will be valuable in hybrid cultivar breeding and in analyzing QTL expression in different environments.

Highlights

Brassica napus (AACC, 2n = 38) originated from hybridization between Brassica rapa (AA, 2n = 20) and Brassica oleracea (CC, 2n = 18; UN, 1935), and is the second most important oilseed crop after soybean (Basunanda et al, 2010)
The results indicated that seed yield (SY) was highly and positively correlated with seed yield related traits (SYRTs) except for first effective branch number (FBN), and especially for biomass yield (BY) with a correlation coefficient of 0.83
length of main inflorescence (LMI) was significantly positively correlated with SY and SYRTs except for FBN

Summary

Introduction

SY is indirectly influenced by other seed yield related traits (SYRTs), such as biomass yield (BY), plant height (PH), first effective branch height (BH), first effective branch number (FBN), length of main inflorescence (LMI), and pod number of main inflorescence (PMI) in B. napus (Qiu et al, 2006; Li et al, 2007; Shi et al, 2009). Shi et al (2009) and Ding et al (2011) obtained the candidate genes controlling flower time and seed phosphorus concentration, respectively, by comparative mapping with the Arabidopsis genome. Comparative mapping among B. napus, Arabidopsis, B. rapa, and B. oleracea genomes is necessary to obtain candidate genes in the confidence intervals (CIs) of QTLs for SY and SYRTs

Methods

Results

Discussion

Conclusion