Genome-Wide Association Study of Rice Grain Shape and Weight in Different Environments

Overview

Journal Plants (Basel)

Date 2023 Jul 14

PMID 37447110

Authors

Nansheng Wang

Wanyang Zhang

Xinchen Wang

Zhenzhen Zheng

Di Bai

Keyang Li

Xueyu Zhao

Jun Xiang

Zhaojie Liang

Yingzhi Qian

Wensheng Wang

Yingyao Shi

Affiliations

Soon will be listed here.

Abstract

Drought is one of the key environmental factors affecting the growth and yield potential of rice. Grain shape, on the other hand, is an important factor determining the appearance, quality, and yield of rice grains. Here, we re-sequenced 275 accessions and then conducted a genome-wide association study (GWAS) on six agronomic traits with the 404,411 single nucleotide polymorphisms (SNPs) derived by the best linear unbiased prediction (BLUP) for each trait. Under two years of drought stress (DS) and normal water (NW) treatments, a total of 16 QTLs associated with rice grain shape and grain weight were detected on chromosomes 1, 2, 3, 4, 5, 7, 8, 11, and 12. In addition, these QTLs were analyzed by haplotype analysis and functional annotation, and one clone () and five new candidate genes were identified in the candidate interval. The findings provide important genetic information for the molecular improvement of grain shape and weight in rice.

References

Hu J, Wang Y, Fang Y, Zeng L, Xu J, Yu H . A Rare Allele of GS2 Enhances Grain Size and Grain Yield in Rice. Mol Plant. 2015; 8(10):1455-65. DOI: 10.1016/j.molp.2015.07.002. View

Li H, Zhang Y, Wu C, Bi J, Chen Y, Jiang C . Fine-tuning OsCPK18/OsCPK4 activity via genome editing of phosphorylation motif improves rice yield and immunity. Plant Biotechnol J. 2022; 20(12):2258-2271. PMC: 9674324. DOI: 10.1111/pbi.13905. View

Guo Z, Yang W, Chang Y, Ma X, Tu H, Xiong F . Genome-Wide Association Studies of Image Traits Reveal Genetic Architecture of Drought Resistance in Rice. Mol Plant. 2018; 11(6):789-805. DOI: 10.1016/j.molp.2018.03.018. View

Song X, Huang W, Shi M, Zhu M, Lin H . A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet. 2007; 39(5):623-30. DOI: 10.1038/ng2014. View

Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y . Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet. 2010; 42(11):961-7. DOI: 10.1038/ng.695. View

Kitagawa K, Kurinami S, Oki K, Abe Y, Ando T, Kono I . A novel kinesin 13 protein regulating rice seed length. Plant Cell Physiol. 2010; 51(8):1315-29. DOI: 10.1093/pcp/pcq092. View

Habier D, Fernando R, Garrick D . Genomic BLUP decoded: a look into the black box of genomic prediction. Genetics. 2013; 194(3):597-607. PMC: 3697966. DOI: 10.1534/genetics.113.152207. View

Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira M, Bender D . PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007; 81(3):559-75. PMC: 1950838. DOI: 10.1086/519795. View

Price A, Patterson N, Plenge R, Weinblatt M, Shadick N, Reich D . Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet. 2006; 38(8):904-9. DOI: 10.1038/ng1847. View

10.

Li N, Xu R, Li Y . Molecular Networks of Seed Size Control in Plants. Annu Rev Plant Biol. 2019; 70:435-463. DOI: 10.1146/annurev-arplant-050718-095851. View

11.

Qin F, Shinozaki K, Yamaguchi-Shinozaki K . Achievements and challenges in understanding plant abiotic stress responses and tolerance. Plant Cell Physiol. 2011; 52(9):1569-82. DOI: 10.1093/pcp/pcr106. View

12.

Wang N, Chen H, Qian Y, Liang Z, Zheng G, Xiang J . Genome-Wide Association Study of Rice Grain Shape and Chalkiness in a Worldwide Collection of Xian Accessions. Plants (Basel). 2023; 12(3). PMC: 9919668. DOI: 10.3390/plants12030419. View

13.

Ying J, Ma M, Bai C, Huang X, Liu J, Fan Y . TGW3, a Major QTL that Negatively Modulates Grain Length and Weight in Rice. Mol Plant. 2018; 11(5):750-753. DOI: 10.1016/j.molp.2018.03.007. View

14.

Tang W, Wu T, Ye J, Sun J, Jiang Y, Yu J . SNP-based analysis of genetic diversity reveals important alleles associated with seed size in rice. BMC Plant Biol. 2016; 16:93. PMC: 4837510. DOI: 10.1186/s12870-016-0779-3. View

15.

Tan Y, Li J, Yu S, Xing Y, Xu C, Zhang Q . The three important traits for cooking and eating quality of rice grains are controlled by a single locus in an elite rice hybrid, Shanyou 63. Theor Appl Genet. 2012; 99(3-4):642-8. DOI: 10.1007/s001220051279. View

16.

Zhang J, Singh A, Mueller D, Singh A . Genome-wide association and epistasis studies unravel the genetic architecture of sudden death syndrome resistance in soybean. Plant J. 2015; 84(6):1124-36. DOI: 10.1111/tpj.13069. View

17.

Guo T, Chen K, Dong N, Shi C, Ye W, Gao J . Negatively Regulates the OsMKKK10-OsMKK4-OsMPK6 Cascade to Coordinate the Trade-off between Grain Number per Panicle and Grain Size in Rice. Plant Cell. 2018; 30(4):871-888. PMC: 5973843. DOI: 10.1105/tpc.17.00959. View

18.

Khush G . What it will take to feed 5.0 billion rice consumers in 2030. Plant Mol Biol. 2005; 59(1):1-6. DOI: 10.1007/s11103-005-2159-5. View

19.

Bradbury P, Zhang Z, Kroon D, Casstevens T, Ramdoss Y, Buckler E . TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics. 2007; 23(19):2633-5. DOI: 10.1093/bioinformatics/btm308. View

20.

Liu Q, Han R, Wu K, Zhang J, Ye Y, Wang S . G-protein βγ subunits determine grain size through interaction with MADS-domain transcription factors in rice. Nat Commun. 2018; 9(1):852. PMC: 5829230. DOI: 10.1038/s41467-018-03047-9. View