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

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.

Gnp4/LAX2, a RAWUL protein, interferes with the OsIAA3–OsARF25 interaction to regulate grain length via the auxin signaling pathway in rice

“…In previous studies, several quantitative trait loci located near Gnp4 conferring grain length have been isolated in different rice cultivars, such as GWT4a , qLWR4 , and qGL4b ( Lin et al , 1996 ; Ying et al , 2012 ; Segami et al , 2016 ). To investigate the natural variation of Gnp4 in different germplasm types, we further analysed the sequences of Gnp4 in 259 cultivated and nine wild rice types and found 17 haplotypes (Hap) based on 46 SNPs.…”

Fine mapping qGL2H, a major locus controlling grain length in barley (Hordeum vulgare L.)

“…This is due to the fact that grain length is to a large extent controlled at the cellular level by cell elongation and proliferation in the longitudinal direction in developing endosperm and husk tissues (Rabiei et al 2004;Yu et al 2017). In contrast, grain width and thickness correlate primarily with endosperm cell proliferation in the transverse direction (Segami et al 2016;Wang et al 2015). In the present study, qGL2H did not coincide with other grain size-related characteristics; however, it did represent a major locus for grain yield explaining 10.2% of the phenotypic variation for this trait using MET-BLUP data but not individual trial BLUPs.…”

Identification of a novel QTL for the number of spikelets per panicle using a cross between indica‐ and japonica‐type high‐yielding rice cultivars in Japan

“…The QTL for grain length was narrowed down to the 1.4‐Mb region between RM6987‐1 and RM7389. The region partly overlapped with that of GL3b , a QTL for grain length recently mapped within a 1.2‐Mb region on the long arm of chromosome 3 (Segami et al., ). Further study is also required to confirm whether our QTL is identical to GL3b .…”