Academic Journal
View in EDS
Linked Full Text

Genome-wide association study uncovers the genetic loci for yield-related traits in waxy rice.

Bibliographic Details
Title: Genome-wide association study uncovers the genetic loci for yield-related traits in waxy rice.
Authors: Fei Y; School of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Jurong, 212400, China., Mo Z; Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China. mozhenghai@cnbg.net.
Source: Journal of applied genetics [J Appl Genet] 2026 Sep; Vol. 67 (3), pp. 561-572. Date of Electronic Publication: 2025 Aug 11.
Publication Type: Journal Article
Language: English
Journal Info: Publisher: Springer Country of Publication: England NLM ID: 9514582 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2190-3883 (Electronic) Linking ISSN: 12341983 NLM ISO Abbreviation: J Appl Genet Subsets: MEDLINE
Imprint Name(s): Publication: 2011- : Cheshire, United Kingdom : Springer
Original Publication: Poznań, Poland : Institute of Plant Genetics, Polish Academy of Sciences, 1995-
MeSH Terms: Oryza*/genetics , Oryza*/growth & development , Quantitative Trait Loci* , Genome-Wide Association Study*, Polymorphism, Single Nucleotide ; Phenotype ; Haplotypes ; Chromosome Mapping
Abstract: Improving yield potential is a critical goal for breeders; however, yield-related loci are still less understood in waxy rice, which seriously limited the precise development of high-yield cultivars. Here, we investigated six yield-related traits in a collection of 109 cultivated waxy rice accessions over two seasons and perform genome-wide association study using 1.81 million single nucleotide polymorphisms (SNPs) to elucidate the genetic basis underlying grain yield. Our analysis identified a total of 28 significant quantitative trait loci (QTLs), explaining 0.71-38.46% of phenotype variance. Of these, 17 was previously reported or contained genes known to govern the associated traits, while the remaining 11 appear to be novel alleles. Within the 28 QTLs, 379 residing genes were identified, and candidate yield-related genes in close proximity to the significant SNPs were extracted for haplotype analysis. The results showed that the genetic variations in Os09g0375700, Os09g0396300, and Os03g0609500 were highly associated with variations in thousand grain weight or panicle number. Our results dissected the possible genetic determinants of waxy rice yield and will be conducive to breed new cultivars with high yield in the future.
(© 2025. The Author(s), under exclusive licence to Institute of Plant Genetics Polish Academy of Sciences.)
Competing Interests: Declarations. Ethical approval: Not applicable. Disclaimer: The funder had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results. Competing interests: The authors declare no competing interests.
References: Mol Plant. 2019 Jan 7;12(1):10-12. (PMID: 30543995)
PLoS One. 2015 Mar 18;10(3):e0119873. (PMID: 25785447)
Theor Appl Genet. 2018 Mar;131(3):637-648. (PMID: 29299612)
Gigascience. 2015 Feb 25;4:7. (PMID: 25722852)
Nat Genet. 2010 Nov;42(11):961-7. (PMID: 20972439)
Front Plant Sci. 2022 Oct 24;13:1036177. (PMID: 36352876)
BMC Plant Biol. 2015 Sep 11;15:218. (PMID: 26362270)
J Genet. 2011 Aug;90(2):209-15. (PMID: 21869469)
Bioinformatics. 2009 Aug 15;25(16):2078-9. (PMID: 19505943)
Front Plant Sci. 2020 Jun 19;11:933. (PMID: 32655609)
Bioinformatics. 2009 Jul 15;25(14):1754-60. (PMID: 19451168)
New Phytol. 2023 Nov;240(3):1066-1081. (PMID: 37574840)
BMC Genomics. 2015 Dec 16;16:1067. (PMID: 26673149)
PLoS One. 2015 Dec 29;10(12):e0145577. (PMID: 26714258)
Front Plant Sci. 2020 Mar 02;11:175. (PMID: 32194592)
Innovation (Camb). 2021 Jul 01;2(3):100141. (PMID: 34557778)
J Exp Bot. 2010;61(1):1-5. (PMID: 19959608)
Curr Opin Plant Biol. 2007 Apr;10(2):156-61. (PMID: 17291822)
PLoS One. 2017 Jul 14;12(7):e0180825. (PMID: 28708834)
Sci Rep. 2020 Jun 19;10(1):9958. (PMID: 32561778)
Brief Funct Genomics. 2024 May 15;23(3):193-213. (PMID: 38751352)
Front Plant Sci. 2023 Jan 09;13:1102938. (PMID: 36699845)
Rice (N Y). 2021 Jan 9;14(1):9. (PMID: 33420909)
Bioinformatics. 2018 Sep 1;34(17):i884-i890. (PMID: 30423086)
Sci Rep. 2017 Dec 4;7(1):16885. (PMID: 29203827)
Front Plant Sci. 2023 Feb 02;14:1119218. (PMID: 36818826)
Bioinformatics. 2019 May 15;35(10):1786-1788. (PMID: 30321304)
Plant Biotechnol J. 2018 Nov;16(11):1825-1835. (PMID: 29528555)
Mol Biol Rep. 2022 Jun;49(6):5365-5377. (PMID: 35106687)
Plant Biotechnol J. 2017 May;15(5):568-580. (PMID: 27775871)
Theor Appl Genet. 2013 Sep;126(9):2313-22. (PMID: 23748708)
Am J Hum Genet. 2011 Jan 7;88(1):76-82. (PMID: 21167468)
Trends Plant Sci. 2013 Apr;18(4):218-26. (PMID: 23218902)
Rice (N Y). 2020 Aug 6;13(1):53. (PMID: 32761553)
Nat Biotechnol. 2022 Sep;40(9):1403-1411. (PMID: 35449414)
J Appl Genet. 2019 Feb;60(1):27-31. (PMID: 30353473)
Plants (Basel). 2021 Apr 19;10(4):. (PMID: 33921675)
Rice (N Y). 2013 Feb 06;6(1):4. (PMID: 24280374)
Biochem Biophys Res Commun. 2017 May 6;486(3):720-725. (PMID: 28342864)
BMC Genomics. 2019 Jun 10;20(1):471. (PMID: 31182016)
Annu Rev Plant Biol. 2010;61:421-42. (PMID: 20192739)
Genome Res. 2009 Sep;19(9):1655-64. (PMID: 19648217)
Theor Appl Genet. 2012 Jan;124(1):111-24. (PMID: 21898052)
Genetica. 2016 Dec;144(6):651-664. (PMID: 27722804)
Rice (N Y). 2020 Feb 28;13(1):14. (PMID: 32112146)
Rice (N Y). 2016 Dec;9(1):64. (PMID: 27900723)
Front Plant Sci. 2018 May 22;9:650. (PMID: 29872443)
Grant Information: 2024rc03 high-level talent`s start-up research program; CX(22)3146 Jiangsu Agricultural Science and Technology Innovation Fund
Contributed Indexing: Keywords: Genome-wide association study; Haplotype; Quantitative trait loci; Waxy rice; Yield
Entry Date(s): Date Created: 20250810 Date Completed: 20260901 Latest Revision: 20261008
Update Code: 20261008
DOI: 10.1007/s13353-025-00996-y
PMID: 40784927
Database: MEDLINE
Description
ISSN:2190-3883
DOI:10.1007/s13353-025-00996-y