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

Hui Wang,Hongtao Cheng,Wenhui Huang,Qiong Hu,Wenxiang Wang,Mengyu Hao,Jia Liu,Desheng Mei,Li Fu,Bingli Ding,Qamar U Zaman

doi:10.3389/fpls.2019.01579

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 qSL_ZR_A09 and qSL_RR_A09b on A09 were identified from ZR and RR populations, respectively. Both QTL could be stably detected in four environments. QTL qSL_RR_A09b and qSL_ZR_A09 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 qSL_ZR_A09 and gene annotation in Arabidopsis, 26 genes were identified with SNP/Indel variation between parents and two genes (BnaA09g41180D and BnaA09g41380D) were selected as the candidate genes. Expression analysis further revealed BnaA09g41180D, encoding homologs of Arabidopsis fasciclin-like arabinogalactan proteins (FLA3), as the most promising candidate gene for qSL_ZR_A09. The QTL identification and candidate gene analysis will provide new insight into the genomic regions controlling SL in Brassica napus as well as candidate genes underlying the QTL.

Highlights

Introductionquantitative trait loci (QTL) for Silique Length (Wu et al, 2019)
The genetic control of domesticated traits has been studied in various crop plants (Nasyrov, 2003; Aitken et al, 2008), including rapeseed, by quantitative trait loci (QTL) mapping using different pairs of crosses between distinct varieties, for specific traits especially to enhance yield (Udall et al, 2006; Bouchet et al, 2014), oil content (Jin et al, 2007; Rout et al, 2018), and disease resistanceQTL for Silique Length (Wu et al, 2019)
The 280 Zhongshuang11 × R11 (ZR) double haploid (DH), 95 R1 × R2 (RR) DH lines, and their corresponding parents were grown in winter–spring seasons

Summary

Introduction

QTL for Silique Length (Wu et al, 2019). Comparative genomic studies showed that the A genome of B. rapa and B. napus exhibited collinearity with fewer genomic changes and translocations (Wang et al, 2011). Silique length (SL) is one of the most effective components for yield selection in rapeseed, by which seed yield can be increased and the total oil yield (Samizadeh et al, 2007; Bennet et al, 2011). The understanding of silique development in B. napus is limited and only few functional genes for SL have been explored due to high ploidy level

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Results

Conclusion