Abstract
The key to food security is increasing rice yield. Therefore, we performed a genome-wide association study (GWAS) to analyse and identify the effects of plant height (PH), effective tiller number (ETN), heading date (HD) and grain weight per plant (GWPP) on rice yield using 1,220,522 single-nucleotide polymorphisms (SNPs) from 168 rice accessions. The PH, ETN, HD, and GWPP phenotypes of the 168 rice accessions were analysed in 2019, 2020 and 2021, and an abundance of phenotypic variation was found. One QTL for PH was detected on chromosome 4, one QTL for ETN on chromosome 11, two QTLs for GWPP on chromosome 2, and one QTL for HD on chromosome 5, all of which were detected in 3 years of the study period through a general linear model (GLM) and mixed linear model (MLM). We detected two QTLs related to the traits by using multi-trait GWAS. In addition, we identified four novel genes responsible for rice yield. Haplotype analysis indicated that LOC_Os02g07680 was highly associated with GWPP, LOC_Os11g18570 was highly associated with ETN, LOC_Os04g49210 was highly associated with HD, and LOC_Os05g34600 was highly associated with PH. The results provide important genetic information for PH, ETN, HD and GWPP studies, laying the foundation for increasing rice yield.
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Abbreviations
- GWAS:
-
Genome-wide association study
- LD:
-
Linkage disequilibrium
- PCA:
-
Principal component analysis
- GLM:
-
General linear model
- MLM:
-
Mixed linear model
- CV:
-
Coefficient of variation
- HB 2 :
-
Broad-sense heritability
- PVE:
-
Phenotypic variation explained
- SNP:
-
Single nucleotide polymorphism
- QTL:
-
Quantitative trait locus
- HD:
-
Heading date
- PH:
-
Plant height
- ETN:
-
Effective tiller number
- GWPP:
-
Grain weight per plant
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Acknowledgements
The authors thank Delin Hong, State Key Laboratory of Crop Genetics and Germplasm Innovation, Nanjing Agricultural University, for providing the rice materials used in this study.
Funding
This research was funded by the Natural Science Foundation of Anhui Province, grant number 2108085MC97; National Natural Science Foundation of China, Grant Numbers 32101768 and U21A20214; Natural Science Foundation of Anhui Universities, Grant Number KJ2020A0118; Talent Project of Anhui Agricultural University, Grant Number rc312002; Natural Science Research Project of Colleges and Universities in Anhui Province, Grant Number YJS20210250; and Key Research and Development Program of Anhui Province, Grant Number 202004a06020024.
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XC, YC and EL designed the research, reviewed the writing and drafted the manuscript. YC, XC, JS, MZ, ZL, LL and HS participated in the experiments. MD and MX handled the germplasm. XC revised the manuscript. All the authors read the manuscript carefully and approved it.
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Cheng, X., Chang, Y., Sun, J. et al. Identification of candidate genes and favourable haplotypes for yield traits in rice based on a genome-wide association study. Euphytica 219, 125 (2023). https://doi.org/10.1007/s10681-023-03253-7
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DOI: https://doi.org/10.1007/s10681-023-03253-7