Validation of a QTL for Grain Size and Weight Using an Introgression Line from a Cross between Oryza sativa and Oryza minuta

Yue Feng,Hanyong Yu,Qun Xu,Yaolong Yang,Xinghua Wei,Mengchen Zhang,Shan Wang,Xiaoping Yuan,Xiaojun Niu,Yiping Wang

doi:10.1186/s12284-021-00472-1

Abstract

BackgroundGrain size and weight are important target traits determining grain yield and quality in rice. Wild rice species possess substantial elite genes that can be served as an important resource for genetic improvement of rice. In this study, we identify and validate a novel QTL on chromosome 7 affecting the grain size and weight using introgression lines from cross of Oryza sativa and Oryza minuta.ResultsAn introgression line ‘IL188’ has been achieved from a wild species Oryza minuta (2n = 48, BBCC, W303) into O. sativa japonica Nipponbare. The F2 and F2:3 populations derived from a cross between IL188 and Nipponbare were used to map QTLs for five grain size traits, including grain length (GL), grain width (GW), grain length to width ratio (LWR), grain thickness (GT) and thousand grain weight (TGW). A total of 12 QTLs for the five grain traits were identified on chromosomes 1, 2, 3, 6, 7, and 8. The QTL-qGL7 controlling GL on chromosome 7 was detected stably in the F2 and F2:3 populations, and explained 15.09–16.30% of the phenotypic variance. To validate the effect of qGL7, eight residual heterozygous line (RHL) populations were developed through selfing four F2:3 and four F2:4 plants with different heterozygous segments for the target region. By further developing SSR and Indel markers in the target interval, qGL7 was delimited to a ~ 261 kb region between Indel marker Y7–12 and SSR marker Y7–38, which also showed significant effects on grain width and thousand grain weight. Comparing with the reference genome of Nipponbare, stop or frameshift mutations in the exon of the three putative genes LOC_Os07g36830, LOC_Os07g36900 and LOC_Os07g36910 encoding F-box domain-containing proteins may be the candidate genes for qGL7. Scanning electron microscopy analysis of the glume’s epidermal cells showed that the cell length and width of NIL-qGL7IL188 was higher than NIL-qGL7Nip, indicating that qGL7 increases grain size and weight by regulating cell expansion.ConclusionsIn this study, we detected 12 QTLs regulating grain size and weight using an introgression line from a cross between Oryza sativa and Oryza minuta. Of these loci, we confirmed and delimited the qGL7 to a ~ 261 kb region. Three putative genes, LOC_Os07g36830, LOC_Os07g36900 and LOC_Os07g36910 encoding F-box domain-containing proteins may be the candidate genes for qGL7. These results provide a basis for map-based cloning of the qGL7 gene and useful information for marker assisted selection in rice grain quality improvement.

Highlights

Grain size and weight are important target traits determining grain yield and quality in rice
Genetic Background of IL188 A total of 512 Simple sequence repeat (SSR) markers were screened for polymorphism between W303 and Nipponbare
These 30 markers were further used to genotype the F2 and F2:3 populations derived from a cross between Nipponbare and IL188

Summary

Introduction

Grain size and weight are important target traits determining grain yield and quality in rice. Grain size and weight are important components determining rice grain yield, and they are controlled by multiple quantitative trait loci (QTLs) (Zhang et al 2012a; Yu et al 2018). Only a few major QTLs including GS3, qSW5, GW2, qGL3/GL3.1, GW8, GL7/ GW7, TGW6 and GS9 have been isolated by map-based cloning methods (Mao et al 2010; Shomura et al 2008; Song et al 2007; Qi et al 2012; Zhang et al 2012b; Wang et al 2012; Wang et al 2015a; Wang et al 2015b; Ishimaru et al 2013; Zhao et al 2018) The isolation of these genes has enhanced our knowledge of the molecular regulatory mechanisms responsible for grain size and weight (Song and Ashikari 2008)

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