
An ultra‐high‐density genetic map provides insights into genome synteny, recombination landscape and taproot skin colour in radish ( Raphanus sativus L.)
Author(s) -
Luo Xiaobo,
Xu Liang,
Wang Yan,
Dong Junhui,
Chen Yinglong,
Tang Mingjia,
Fan Lianxue,
Zhu Yuelin,
Liu Liwang
Publication year - 2020
Publication title -
plant biotechnology journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.525
H-Index - 115
eISSN - 1467-7652
pISSN - 1467-7644
DOI - 10.1111/pbi.13195
Subject(s) - raphanus , biology , quantitative trait locus , brassica rapa , synteny , genetics , genome , gene , locus (genetics) , brassica oleracea , candidate gene , genomics , botany
Summary High‐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 SNP s covering 1306.8 cM in nine radish linkage groups ( LG s) was developed by a whole‐genome sequencing‐based approach. A total of 18 QTL s for 11 horticulture traits were detected. The map‐based cloning data indicated that the R2R3‐ MYB transcription factor Rs MYB 90 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 SNP s and gene, and GC content, respectively. Functional annotation indicated that genes within RHRs were mainly involved in metabolic process and binding. Three QTL s 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.