Natural Variation in OsMKK3 Contributes to Grain Size and Chalkiness in Rice.

Yinghua Pan,Gaoxing Dai,Yuntao Liang,Jingcheng Li,Guofu Deng,Weiyong Zhou,Haifeng Guo,Yan Zhao,Muhammad Abdul Rehman Rashid,Dongjing Qing,Hao Wu,Lei Chen,Xingka Yang,Chunju Lu,Danting Li,Lijun Gao

doi:10.3389/fpls.2021.784037

Abstract

Rice (Oryza sativa L.) is an important staple food crop for more than half of the world’s population. Enhancing the grain quality and yield of rice to meet growing demand remains a major challenge. Here, we show that OsMKK3 encode a MAP kinase kinase that controls grain size and chalkiness by affecting cell proliferation in spikelet hulls. We showed that OsSPL16, GS5, and GIF1 have a substantial effect on the OsMKK3-regulated grain size pathway. OsMKK3 has experienced strong directional selection in indica and japonica. Wild rice accessions contained four OsMKK3 haplotypes, suggesting that the OsMKK3 haplotypes present in cultivated rice likely originated from different wild rice accessions during rice domestication. OsMKK3-Hap1, gs3, and gw8 were polymerized to enhance the grain length. Polymerization of beneficial alleles, such as OsMKK3-Hap1, gs3, gw8, fgr, alk, chalk5, and wx, also improved the quality of hybrid rice. Overall, the results indicated that beneficial OsMKK3 alleles could be used for genomic-assisted breeding for rice cultivar improvement and be polymerized with other beneficial alleles.

Highlights

Rice (Oryza sativa L.) is an important staple food crop for over half of the world’s population
To characterize the genetic interaction between OsMKK3 and GS3 in controlling grain length, we examined the haplotypes of OsMKK3 and GS3 in the rice 3K project, 342 Guangxi common wild rice core germplasm accessions, 419 Guangxi core germplasm landrace accessions, and 94 improved varieties
Grain length increased with OsMKK3-Hap1/gs3/gw8 (Figure 6B). These results indicated that the grain length in indica rice is improved by the presence of beneficial alleles of OsMKK3-Hap1, gs3, and gw8. gs3 is a beneficial allele that was only present in 0.31% of wild rice accessions, 15.71% of landrace accessions, and 72.04% of improved varieties. gw8 was a beneficial allele that appeared in a few wild rice accessions, landrace accessions, and improved varieties

Summary

Introduction

Rice (Oryza sativa L.) is an important staple food crop for over half of the world’s population. Grain size is an important breeding target that affects both yield and appearance quality and is determined by the length, width, and thickness of the grain. Many quantitative trait loci (QTLs) of grain length have been mapped, and some of these QTLs, such as GS3, OSLG3, qGL3, SMG1, and OsSPL13, have been cloned as well. GS3 is an evolutionarily important gene controlling grain size in rice by a C to A mutation in the second exon of GS3 (A allele) (Takano-Kai et al, 2009). OSLG3 was found to encode an AP2 domain class transcription factor that positively regulates grain length and improves rice yield without affecting grain quality. OsSPL13 encodes a plant-specific transcription factor that regulates the cell size of the grain hull and enhances rice grain length and yield (Si et al, 2016). There is a need to study the genetic and molecular bases of grain size (Mao et al, 2010)

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