Natural Variation in the Promoter of GSE5 Contributes to Grain Size Diversity in Rice

Abstract

The utilization of natural genetic variation greatly contributes to improvement of important agronomic traits in crops. Understanding the genetic basis for natural variation of grain size can help breeders develop high-yield rice varieties. In this study, we identify a previously unrecognized gene, named GSE5, in the qSW5/GW5 locus controlling rice grain size by combining the genome-wide association study with functional analyses. GSE5 encodes a plasma membrane-associated protein with IQ domains, which interacts with the rice calmodulin protein, OsCaM1-1. We found that loss of GSE5 function caused wide and heavy grains, while overexpression of GSE5 resulted in narrow grains. We showed that GSE5 regulates grain size predominantly by influencing cell proliferation in spikelet hulls. Three major haplotypes of GSE5 (GSE5, GSE5, and GSE5) in cultivated rice were identified based on the deletion/insertion type in its promoter region. We demonstrated that a 950-bp deletion (DEL1) in indica varieties carrying the GSE5 haplotype and a 1212-bp deletion (DEL2) in japonica varieties carrying the GSE5 haplotype associated with decreased expression of GSE5, resulting in wide grains. Further analyses indicate that wild rice accessions contain all three haplotypes of GSE5, suggesting that the GSE5 haplotypes present in cultivated rice are likely to have originated from different wild rice accessions during rice domestication. Taken together, our results indicate that the previously unrecognized GSE5 gene in the qSW5/GW5 locus, which is widely utilized by rice breeders, controls grain size, and reveal that natural variation in the promoter region of GSE5 contributes to grain size diversity in rice.

Rice microtubule‐associated protein IQ67‐DOMAIN14 regulates grain shape by modulating microtubule cytoskeleton dynamics

“…A range of grain size and/or shape regulators have been identified through studying natural variation or mutagenesis (Li and Li, ; Zheng et al , ). Identification of causal genes has revealed a clear role for transcription factors such as OsSPL16 (Wang et al , ), OsSPL13 (Si et al , ), OsGRF4 (Hu et al , ), a TRM‐containing protein GW7 (Wang et al , ), an auxin‐metabolism protein TGW6 (Ishimaru et al , ), and a plasma membrane‐localized IQD protein GW5 (Duan et al , ; Liu et al , ), among others.…”

“…Recently, the plant‐specific IQ67‐DOMAIN (IQD) family emerged as regulators of fruit shape and grain size in several plant species including tomato (Xiao et al , ), watermelon (Duo et al, ), cucumber (Pan et al , ) and rice (Duan et al , ; Liu et al , ). For example, the tomato SUN gene encodes a member of IQD family and is involved in regulating fruit shape.…”

Genome-wide association study of cold tolerance of Chinese indica rice varieties at the bud burst stage

“…Two of the three genes involved in microtubule-based process, and another one associated with glycolytic pathway and expressed in response to abiotic stress. Recently, many novel genes have been cloned as a result of GWAS (Duan et al 2017, Si et al 2016Yano et al 2016). However, in our study, because the genotype was from the 5K SNPs array, the SNPs density was insufficient to cover every gene.…”

Alternative splicing of OsLG3b controls grain length and yield in japonica rice

“…The QTL for grain width 5 (GW5/qSW5/GSE5) was a key gene involved in japonica rice domestication and natural variation in its promoter region contributed to diversity of grain size. Both the DEL1 (the 950-bp deletion) and the DEL2 (the 1212-bp deletion) were thought to be selected during the propagation of cultivation areas for indica and japonica, respectively (Duan et al, 2017;Liu et al, 2017;Shomura et al, 2008;Weng et al, 2008). Another gene, GRAIN NUMBER, GRAIN LENGTH AND AWN DEVELOP-MENT 1 (GAD1), encodes a small secretary signal peptide that belongs to the EPIDERMAL PATTERNING FACTOR-LIKE family (Jin et al, 2016).…”