QTL mapping using an ultra-high-density SNP map reveals a major locus for grain yield in an elite rice restorer R998

Manshan Zhu,Yilong Liao,Xiaozhi Ma,Dan Li,Jinhua Li,Feng Wang,Chongyun Fu,Huijun Huang,Dilin Liu,Wuge Liu,Fuhong Fu,Xueqin Zeng

doi:10.1038/s41598-017-10666-7

Manshan Zhu, Yilong Liao + Show 10 more

Open Access

https://doi.org/10.1038/s41598-017-10666-7

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Abstract

To dissect the genetic basis of yield formation in restorer line of hybrid rice, we conducted QTL analysis for 6 yield traits including panicles per plant (PPP), grains per panicle (GPP), grain yield per plant (GY), thousand-grain weight (TGW), above-ground biomass (AGB), and harvest index (HI) using SNP markers in a recombinant inbred lines (RILs) population derived from a cross between a tropical japonica inbred Francis and an elite indica restorer Guanghui 998 (R998). A total of 26 QTLs were detected using a high density genetic map consisting of 3016 bin markers. Nineteen out of the 26 QTL alleles from R998 had a beneficial effect on yield traits. Most of the QTLs were co-located with previously reported rice QTLs. qAGB6 and qHI9, controlling AGB and HI respectively, were detected as novel QTLs. Four QTLs for GY were repeatedly detected across two years, with all the beneficial alleles from R998. Notably, qGY8 explained over 20% of the yield variance in both years. Moreover, qGY8 together with qTGW8 and qHI8 formed a QTL cluster. Markers tightly linked with qGY8 were developed. Cloning of qGY8 will facilitate its further exploitation in high-yield breeding.

Highlights

Rice is a staple food crop feeding over half of the population in the world
High density bin map was generated after low-coverage restriction-site associated DNA sequencing (RAD-seq) of each recombinant inbred lines (RILs) line and used for QTL mapping of 6 yield related traits including thousand grain weight (TGW), panicles per plant (PPP), grains per panicle (GPP), above-ground biomass (AGB), grain yield per plant (GYP) and harvest index (HI)
Due to the fact that restorer Guanghui 998 (R998) is an elite restorer line widely used in commercial hybrid rice production, with 16 hybrid combinations released in the market, genetic dissection of yield formation in such an elite line is useful for breeders and may provide insightful guidance in high-yielding molecular breeding

Summary

Introduction

Rice is a staple food crop feeding over half of the population in the world. With the increase of population and decrease of arable land, food production is facing huge challenge over the 20 years. Though a large number of reports on QTL mapping and cloning of yield-related loci have been available[4, 5], information about the QTLs or alleles in many elite parental lines is still lacking, which might prevent efficient use of them in molecular breeding[6]. RAD-seq approach focuses only on short fragments of DNA adjacent to a particular restriction enzyme in the genome and provides significant data complexity reduction and increased throughput, allowing efficient and high density SNP discovery and genotyping. High density bin map was generated after low-coverage RAD-seq of each RIL line and used for QTL mapping of 6 yield related traits including thousand grain weight (TGW), panicles per plant (PPP), grains per panicle (GPP), above-ground biomass (AGB), grain yield per plant (GYP) and harvest index (HI). Due to the fact that R998 is an elite restorer line widely used in commercial hybrid rice production, with 16 hybrid combinations released in the market, genetic dissection of yield formation in such an elite line is useful for breeders and may provide insightful guidance in high-yielding molecular breeding

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