An ultra-high-density genetic map provides insights into genome synteny, recombination landscape and taproot skin colour in radish (Raphanus sativus L.).

Xiaobo Luo,Liwang Liu,Lianxue Fan,Junhui Dong,Yinglong Chen,Liang Xu,Yuelin Zhu,Yan Wang,Mingjia Tang

doi:10.1111/pbi.13195

Abstract

SummaryHigh‐density genetic map is a valuable tool for exploring novel genomic information, quantitative trait locus (QTL) mapping and gene discovery of economically agronomic traits in plant species. However, high‐resolution genetic map applied to tag QTLs associated with important traits and to investigate genomic features underlying recombination landscape in radish (Raphanus sativus) remains largely unexplored. In this study, an ultra‐high‐density genetic map with 378 738 SNPs covering 1306.8 cM in nine radish linkage groups (LGs) was developed by a whole‐genome sequencing‐based approach. A total of 18 QTLs for 11 horticulture traits were detected. The map‐based cloning data indicated that the R2R3‐MYB transcription factor RsMYB90 was a crucial candidate gene determining the taproot skin colour. Comparative genomics analysis among radish, Brassica rapa and B. oleracea genome revealed several genomic rearrangements existed in the radish genome. The highly uneven distribution of recombination was observed across the nine radish chromosomes. Totally, 504 recombination hot regions (RHRs) were enriched near gene promoters and terminators. The recombination rate in RHRs was positively correlated with the density of SNPs and gene, and GC content, respectively. Functional annotation indicated that genes within RHRs were mainly involved in metabolic process and binding. Three QTLs for three traits were found in the RHRs. The results provide novel insights into the radish genome evolution and recombination landscape, and facilitate the development of effective strategies for molecular breeding by targeting and dissecting important traits in radish.

Highlights

High-density genetic maps are crucial for genetic and genomic studies, such as mapping quantitative trait loci (QTLs) associated with important agronomic traits in crops
To construct a high-resolution genetic linkage map in radish, the whole-genome resequencing of 137 F2 individuals together with the parental lines was performed on Illumina HiSeqTM 2500 platform
A total of homozygous 821 217 single nucleotide polymorphisms (SNPs) were detected between the two parental lines

Summary

Introduction

High-density genetic maps are crucial for genetic and genomic studies, such as mapping quantitative trait loci (QTLs) associated with important agronomic traits in crops. QTL mapping resolution is dependent on marker density and genetic population size (Xu et al, 2013). It has been widely applied to construct the recombinant bin map based on the SNP markers and identify important QTLs or genes in various important crops including rice (Gao et al, 2013), Brassica rapa (Yu et al, 2013) and soybean (Lu et al, 2017). A bin map was constructed by genotyping a recombinant inbred line (RIL) population and identified the candidate genes involved in yield-associated trait in rice (Gao et al, 2013). The high-density maps generated from WGRS were effectively applied in mapping a QTL harbouring candidate genes PP2C for seed weight (Lu et al, 2017). Using high-density map based on sequencing-based genotyping method, these findings provide solid basis for QTL mapping associates with important traits

Results

Discussion

Conclusion