Comparative quantitative trait loci for silique length and seed weight in Brassica napus.

Ying Fu,Yixin Cui,Jiaqin Mei,Xiaorong Li,Jiana Li,Huafang Wan,Wolfgang Friedt,Yajun He,Dayong Wei,Wei Qian,Rod Snowdon,Hongli Dong

doi:10.1038/srep14407

Abstract

Silique length (SL) and seed weight (SW) are important yield-associated traits in rapeseed (Brassica napus). Although many quantitative trait loci (QTL) for SL and SW have been identified in B. napus, comparative analysis for those QTL is seldom performed. In the present study, 20 and 21 QTL for SL and SW were identified in doubled haploid (DH) and DH-derived reconstructed F2 populations in rapeseed, explaining 55.1–74.3% and 24.4–62.9% of the phenotypic variation across three years, respectively. Of which, 17 QTL with partially or completely overlapped confidence interval on chromosome A09, were homologous with two overlapped QTL on chromosome C08 by aligning QTL confidence intervals with the reference genomes of Brassica crops. By high density selective genotyping of DH lines with extreme phenotypes, using a Brassica single-nucleotide polymorphism (SNP) array, the QTL on chromosome A09 was narrowed, and aligned into 1.14-Mb region from 30.84 to 31.98 Mb on chromosome R09 of B. rapa and 1.05-Mb region from 27.21 to 28.26 Mb on chromosome A09 of B. napus. The alignment of QTL with Brassica reference genomes revealed homologous QTL on A09 and C08 for SL. The narrowed QTL region provides clues for gene cloning and breeding cultivars by marker-assisted selection.

Highlights

Silique length (SL) and seed weight (SW) are important yield-associated traits in rapeseed (Brassica napus)
Wide variation was detected in both the doubled haploid (DH) and reconstructed F2 (RC-F2) populations for silique length (SL) and SW across the years analyzed (Fig. 1)
The normal distribution for SL and SW in both populations suggested that SL and SW were controlled by multiple genes (Fig. 1)

Summary

Introduction

Silique length (SL) and seed weight (SW) are important yield-associated traits in rapeseed (Brassica napus). By high density selective genotyping of DH lines with extreme phenotypes, using a Brassica single-nucleotide polymorphism (SNP) array, the QTL on chromosome A09 was narrowed, and aligned into 1.14-Mb region from 30.84 to 31.98 Mb on chromosome R09 of B. rapa and 1.05-Mb region from 27.21 to 28.26 Mb on chromosome A09 of B. napus. In comparison with the traditional QTL mapping, the NGS-aided strategy provides a simple and effective alternative to rapidly identify QTL of interest by genotyping small number of samples from two sets of individuals with distinct or opposite extreme phenotypes[23,24]. By using the NGS-aided strategy, a few QTL of the interested traits have been successfully identified in yeast[23,25,26,27], rice[24,28,29], Arabidopsis thaliana[30], sunflower[31], cucumber[32], wheat[33], tomato[34] and chickpea[35]

Methods

Results

Discussion

Conclusion