Detection of Novel QTLs Regulating Grain Size in Extra-Large Grain Rice (Oryza sativa L.) Lines.

Shuhei Segami,Tomonori Noda,Tatsuya Yamamoto,Harumi Sasaki,Satomi Mori,Hiroyuki Kanamori,Yukimoto Iwasaki,Kotaro Miura,Motoyuki Ashikari,Katsuyuki Oki,Hidemi Kitano,Yuichi Katayose

doi:10.1186/s12284-016-0109-2

Abstract

BackgroundGrain size is an important trait that affects rice yield. Although many genes that contribute to grain size have been cloned from mutants or by quantitative trait locus (QTL) analysis based on bi-parental mapping, the molecular mechanisms underlying grain-size determination remain poorly understood. In this study, we identified the lines with the largest grain size and detected novel QTLs affecting the grain size.ResultsWe screened the National Institute for Agrobiological Sciences Genebank database and identified two rice lines, BG23 with the widest grain and LG10 with the longest grain. Using these two lines, we performed QTL analysis for grain size. Eight QTLs were detected during the QTL analyses using F2 populations derived from crosses between the large-grain lines BG23 or LG10 and the middle-size grain cultivars Nipponbare and Kasalath. Both BG23 and LG10 possessed large-grain alleles of four major QTLs: GW2, GS3, qSW5/GW5, and GW8. Other three minor QTLs were derived from BG23. However, these QTLs did not explain the differences in grain size between these two lines. Additionally, four QTLs for grain length or width were detected in an F2 population derived from a cross between BG23 and LG10; this population lacked the strong effects of the four major QTLs shared by both parent plants. Of these newly detected QTLs, the effects of two QTLs, GL3b and GL6, were confirmed by progeny testing. Comparison of the length of inner epidermal cells in plants homozygous for BG23 and LG10 alleles indicated that GL3b and GL6 genes regulate cell elongation and cell division, respectively.ConclusionsIn this study, we detected 12 loci including 14 QTLs regulating grain size from two lines with largest grains available in Japanese stock. Of these loci, we confirmed the effect of two gene loci and mapped their candidate region. Identification of novel genes regulating grain size will contribute to our understanding of the molecular mechanisms controlling grain size.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-016-0109-2) contains supplementary material, which is available to authorized users.

Highlights

Grain size is an important trait that affects rice yield
We succeeded in classifying srs3, Srs5, d1, and d61 into cell elongation- or division-type mutants by comparing the cell length and cell number of the inner-epidermal cells of lemma (Izawa et al 2010; Kitagawa et al 2010; Segami et al 2012)
GS3 controls grain length and weight (Fan et al 2006; Mao et al 2010; Takano-Kai et al 2009); GW2 and qSW5/GW5 control grain width and weight (Shomura et al 2008; Song et al 2007; Weng et al 2008); GS5 controls grain width, filling, and weight (Li et al 2011); GW8 controls grain width (Wang et al 2012); GL3.1 controls grain length (Qi et al 2012; Zhang et al 2012); TGW6 and GW6a control grain weight (Ishimaru et al 2013; Song et al 2015); and GL7/GW7 controls grain length and width (Wang et al 2015a, b). Among these genes cloned by quantitative trait locus (QTL) analysis, only GL7/GW7 was involved in cell elongation, whereas the others were involved in cell division

Summary

Introduction

Grain size is an important trait that affects rice yield. many genes that contribute to grain size have been cloned from mutants or by quantitative trait locus (QTL) analysis based on bi-parental mapping, the molecular mechanisms underlying grain-size determination remain poorly understood. D1 and TUD1 encode the α-subunit of a heterotrimeric G-protein and U-box ubiquitin ligase, respectively, and d1 is epistatic to the tud mutation (Ashikari et al 1999; Fujisawa et al 1999; Hu et al 2013) Of these mutants, we succeeded in classifying srs, Srs, d1, and d61 into cell elongation- or division-type mutants by comparing the cell length and cell number of the inner-epidermal cells of lemma (Izawa et al 2010; Kitagawa et al 2010; Segami et al 2012).

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