Development of Three Sets of High-Throughput Genotyped Rice Chromosome Segment Substitution Lines and QTL Mapping for Eleven Traits

Bin Zhang,Hongzhen Jiang,Shenglong Yang,Longbiao Guo,Anpeng Zhang,Kai Hong,Qian Qian,Hai Lin,Jiang Hu,Banpu Ruan,Lianguang Shang,Chaolei Liu,Zhenyu Gao,Dali Zeng

doi:10.1186/s12284-019-0293-y

Abstract

BackgroundDetecting and mapping chromosomal regions that are related to quantitative phenotypic variation in chromosome segment substitution lines (CSSLs) provides an effective means to characterize the genetic basis of complex agronomic trait. CSSLs are also powerful tools for studying the effects of quantitative trait loci (QTLs) pyramiding and interaction on phenotypic variation.ResultsHere, we developed three sets of CSSLs consisting of 81, 55, and 61 lines, which were derived from PA64s × 9311, Nipponbare × 9311 and PA64s × Nipponbare crosses, respectively. All of the 197 CSSLs were subjected to high-throughput genotyping by whole-genome resequencing to obtain accurate physical maps for the 3 sets of CSSLs. The 3 sets of CSSLs were used to analyze variation for 11 major agronomic traits in Hangzhou and Shenzhen and led to the detection of 71 QTLs with phenotypic effect that ranged from 7.6% to 44.8%. Eight QTLs were commonly detected under two environments for the same phenotype, and there were also 8 QTL clusters that were found. Combined with GWAS on grain length and expression profiles on young panicle tissues, qGL1 detected in CSSLs was fine mapped within a 119 kb region on chromosome 1 and LOC_Os01g53140 and LOC_Os01g53250 were the two most likely candidate genes.ConclusionsOur results indicate that developing CSSLs genotyped by whole-genome resequencing are powerful tools for basic genetic research and provide a platform for the rational design of rice breeding. Meanwhile, the conjoint analysis of different CSSLs, natural population and expression profiles can facilitate QTL fine mapping.

Highlights

Detecting and mapping chromosomal regions that are related to quantitative phenotypic variation in chromosome segment substitution lines (CSSLs) provides an effective means to characterize the genetic basis of complex agronomic trait
136 markers denoted as A, AB or AC were used for Marker-assisted selection (MAS) in the population derived from PA64s × 9311 crosses, and 162 markers denoted as B, AB or BC were used for CSSL analysis on the population derived from a cross between 9311 and Nipponbare
The first MAS was performed for BC2F1 generation with 136 polymorphic markers distributed on all 12 chromosomes, and 65 plants were selected from 93 individuals, in which a few of heterozygous substituted segments came from PA64s, while the major genomic regions were homozygous for 9311 alleles

Summary

Introduction

Detecting and mapping chromosomal regions that are related to quantitative phenotypic variation in chromosome segment substitution lines (CSSLs) provides an effective means to characterize the genetic basis of complex agronomic trait. Zhang et al Rice (2019) 12:33 the genetic basis of QTL during early studies (Ahn et al 1993; Li et al 1995; Redona and Mackill 1996) These types of genetic populations can only detect a few major QTLs with large genetic effects due to complex and unstable genetic backgrounds (Yamamoto et al 2000). Chromosome segment substitution lines (CSSLs) can improve the precise detection of QTL regulation of complex traits and make it much easier for QTL fine mapping and cloning (Mei et al 2006; Takai et al 2007). Development of CSSLs is laborious and time-consuming, more and more CSSLs have been developed for their significant advantages (Bessho-Uehara et al 2017; Furuta et al 2014; Hao et al 2006; Kubo et al 2002; Qiao et al 2016; Shim et al 2010; Yoshimura 1997)

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Discussion

Conclusion