Dissecting a heterotic gene through GradedPool-Seq mapping informs a rice-improvement strategy

Changsheng Wang,Ziqun Wang,Yingying Shangguan,Wuqi Wang,Jicheng Gong ,Yiqi Lu,Chuanrang Zhu,Qilin Zhan,Qingqing Hou,Jingjie Zhu,Xuehui Huang,Chenglong Zhang ,Shican Tang,Qi Feng,Danfeng Lyu,Huaan Xie,Congcong Zhou,Yongchun Wang,Yan Zhao,Qiang Zhao,Yan Li,Lingling Cui,Shan Yang ,Jiashun Miao,Bin Han

doi:10.1038/s41467-019-11017-y

Abstract

Hybrid rice breeding for exploiting hybrid vigor, heterosis, has greatly increased grain yield. However, the heterosis-related genes associated with rice grain production remain largely unknown, partly because comprehensive mapping of heterosis-related traits is still labor-intensive and time-consuming. Here, we present a quantitative trait locus (QTL) mapping method, GradedPool-Seq, for rapidly mapping QTLs by whole-genome sequencing of graded-pool samples from F2 progeny via bulked-segregant analysis. We implement this method and map-based cloning to dissect the heterotic QTL GW3p6 from the female line. We then generate the near isogenic line NIL-FH676::GW3p6 by introgressing the GW3p6 allele from the female line Guangzhan63-4S into the male inbred line Fuhui676. The NIL-FH676::GW3p6 exhibits grain yield highly increased compared to Fuhui676. This study demonstrates that it may be possible to achieve a high level of grain production in inbred rice lines without the need to construct hybrids.

Highlights

Hybrid rice breeding for exploiting hybrid vigor, heterosis, has greatly increased grain yield
To accelerate the genetic mapping processes, we develop a quantitative trait locus (QTL) mapping approach, GradedPool-Seq (GPS), that combines high-throughput sequencing with bulked-segregant analysis (BSA)
Compared to previous methods using BSA coupled with wholegenome sequencing, such as MutMap[26], SHOREmap[27], nextgeneration mapping[28] and QTL-seq[29,30], the GPS approach has the advantage of performing genetic mapping to simultaneously detect several QTLs at high resolution (~400-kb) by only requiring F2 population

Summary

Introduction

Hybrid rice breeding for exploiting hybrid vigor, heterosis, has greatly increased grain yield. To accelerate the genetic mapping processes, we develop a quantitative trait locus (QTL) mapping approach, GradedPool-Seq (GPS), that combines high-throughput sequencing with bulked-segregant analysis (BSA). This method is to score and assign F2 generations derived from a distant cross of parental lines exhibiting contrasting phenotypes into three or more graded groups based on their measured phenotypic values. Benefitting from the robust GPS method coupled with follow-up experiments, we identified and validated a heterotic gene, GW3p6 (OsMADS1), from the female line (male-sterile line), that contributed greatly to 1000-grain weight and grain yield per plant in an elite hybrid rice variety Guang-Liang-You-676 (GLY-676). Rice hybrid breeding is currently hindered by bottlenecks of inefficiency and directionlessness[31], and the results of this study inform that it can open the door to achieving a high level of grain production using inbred lines instead of generating hybrids

Methods

Results

Conclusion