Identification of Major Genomic Regions for Soybean Seed Weight by Genome-wide Association Study

Overview

Journal Mol Breed

Specialties Biotechnology
Molecular Biology

Date 2023 Jun 14

PMID 37313505

Authors

Yongce Cao

Shihao Jia

Liuxing Chen

Shunan Zeng

Tuanjie Zhao

Benjamin Karikari

Affiliations

Soon will be listed here.

Abstract

Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-022-01310-y.

Citing Articles

GWAS analysis revealed genomic loci and candidate genes associated with the 100-seed weight in high-latitude-adapted soybean germplasm.

Bhat J, Yu H, Weng L, Yuan Y, Zhang P, Leng J Theor Appl Genet. 2025; 138(1):29.

PMID: 39799549 DOI: 10.1007/s00122-024-04815-6.

Identification of superior haplotypes and candidate gene for seed size-related traits in soybean ( L.).

Zhang Y, Yang X, Bhat J, Zhang Y, Bu M, Zhao B Mol Breed. 2024; 45(1):3.

PMID: 39717350 PMC: 11663835. DOI: 10.1007/s11032-024-01525-1.

Candidate genes for alkali tolerance identified by genome-wide association study at the seedling stage in rice (Oryza sativa L.).

Sheng W, Zhang G, Zhai L, Xu J Sci Rep. 2024; 14(1):30063.

PMID: 39627306 PMC: 11614934. DOI: 10.1038/s41598-024-79273-7.

Genome-Wide Association Analysis of Yield-Related Traits and Candidate Genes in Vegetable Soybean.

Gao H, Wu G, Wu F, Zhou X, Zhou Y, Xu K Plants (Basel). 2024; 13(11).

PMID: 38891251 PMC: 11174663. DOI: 10.3390/plants13111442.

Identification of Single Nucleotide Polymorphic Loci and Candidate Genes for Seed Germination Percentage in Okra under Salt and No-Salt Stresses by Genome-Wide Association Study.

Xu G, Cheng Y, Wang X, Dai Z, Kang Z, Ye Z Plants (Basel). 2024; 13(5).

PMID: 38475435 PMC: 10934433. DOI: 10.3390/plants13050588.

References

Sun Y, Pan J, Shi X, Du X, Wu Q, Qi Z . Multi-environment mapping and meta-analysis of 100-seed weight in soybean. Mol Biol Rep. 2012; 39(10):9435-43. DOI: 10.1007/s11033-012-1808-4. View

Ren D, Wang X, Yang M, Yang L, He G, Deng X . A new regulator of seed size control in Arabidopsis identified by a genome-wide association study. New Phytol. 2018; 222(2):895-906. DOI: 10.1111/nph.15642. View

Meyer K, Stecca K, Ewell-Hicks K, Allen S, Everard J . Oil and protein accumulation in developing seeds is influenced by the expression of a cytosolic pyrophosphatase in Arabidopsis. Plant Physiol. 2012; 159(3):1221-34. PMC: 3387706. DOI: 10.1104/pp.112.198309. View

Beche E, Gillman J, Song Q, Nelson R, Beissinger T, Decker J . Nested association mapping of important agronomic traits in three interspecific soybean populations. Theor Appl Genet. 2020; 133(3):1039-1054. DOI: 10.1007/s00122-019-03529-4. View

Zhang Y, Jia Z, Dunwell J . Editorial: The Applications of New Multi-Locus GWAS Methodologies in the Genetic Dissection of Complex Traits. Front Plant Sci. 2019; 10:100. PMC: 6378272. DOI: 10.3389/fpls.2019.00100. View

Qi Z, Song J, Zhang K, Liu S, Tian X, Wang Y . Identification of QTNs Controlling 100-Seed Weight in Soybean Using Multilocus Genome-Wide Association Studies. Front Genet. 2020; 11:689. PMC: 7378803. DOI: 10.3389/fgene.2020.00689. View

Barrett J, Fry B, Maller J, Daly M . Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics. 2004; 21(2):263-5. DOI: 10.1093/bioinformatics/bth457. View

Daviere J, Achard P . Gibberellin signaling in plants. Development. 2013; 140(6):1147-51. DOI: 10.1242/dev.087650. View

Chen L, Lin I, Qu X, Sosso D, McFarlane H, Londono A . A cascade of sequentially expressed sucrose transporters in the seed coat and endosperm provides nutrition for the Arabidopsis embryo. Plant Cell. 2015; 27(3):607-19. PMC: 4558658. DOI: 10.1105/tpc.114.134585. View

10.

Li X, Zhang Y, Hou M, Sun F, Shen Y, Xiu Z . Small kernel 1 encodes a pentatricopeptide repeat protein required for mitochondrial nad7 transcript editing and seed development in maize (Zea mays) and rice (Oryza sativa). Plant J. 2014; 79(5):797-809. DOI: 10.1111/tpj.12584. View

11.

Kumawat G, Xu D . A Major and Stable Quantitative Trait Locus for Seed Size and Shape Traits in a Soybean RIL Population. Front Genet. 2021; 12:646102. PMC: 8085556. DOI: 10.3389/fgene.2021.646102. View

12.

Hina A, Cao Y, Song S, Li S, Sharmin R, Elattar M . High-Resolution Mapping in Two RIL Populations Refines Major "QTL Hotspot" Regions for Seed Size and Shape in Soybean ( L.). Int J Mol Sci. 2020; 21(3). PMC: 7038151. DOI: 10.3390/ijms21031040. View

13.

Karikari B, Chen S, Xiao Y, Chang F, Zhou Y, Kong J . Utilization of Interspecific High-Density Genetic Map of RIL Population for the QTL Detection and Candidate Gene Mining for 100-Seed Weight in Soybean. Front Plant Sci. 2019; 10:1001. PMC: 6737081. DOI: 10.3389/fpls.2019.01001. View

14.

Zhang W, Xu W, Zhang H, Liu X, Cui X, Li S . Comparative selective signature analysis and high-resolution GWAS reveal a new candidate gene controlling seed weight in soybean. Theor Appl Genet. 2021; 134(5):1329-1341. DOI: 10.1007/s00122-021-03774-6. View

15.

Severin A, Woody J, Bolon Y, Joseph B, Diers B, Farmer A . RNA-Seq Atlas of Glycine max: a guide to the soybean transcriptome. BMC Plant Biol. 2010; 10:160. PMC: 3017786. DOI: 10.1186/1471-2229-10-160. View

16.

Lu X, Li Q, Xiong Q, Li W, Bi Y, Lai Y . The transcriptomic signature of developing soybean seeds reveals the genetic basis of seed trait adaptation during domestication. Plant J. 2016; 86(6):530-44. DOI: 10.1111/tpj.13181. View

17.

Li M, Chen L, Zeng J, Razzaq M, Xu X, Xu Y . Identification of Additive-Epistatic QTLs Conferring Seed Traits in Soybean Using Recombinant Inbred Lines. Front Plant Sci. 2020; 11:566056. PMC: 7758492. DOI: 10.3389/fpls.2020.566056. View

18.

Zhang J, Song Q, Cregan P, Jiang G . Genome-wide association study, genomic prediction and marker-assisted selection for seed weight in soybean (Glycine max). Theor Appl Genet. 2015; 129(1):117-30. PMC: 4703630. DOI: 10.1007/s00122-015-2614-x. View

19.

Karikari B, Wang Z, Zhou Y, Yan W, Feng J, Zhao T . Identification of quantitative trait nucleotides and candidate genes for soybean seed weight by multiple models of genome-wide association study. BMC Plant Biol. 2020; 20(1):404. PMC: 7466808. DOI: 10.1186/s12870-020-02604-z. View

20.

Rafalski J . Association genetics in crop improvement. Curr Opin Plant Biol. 2010; 13(2):174-80. DOI: 10.1016/j.pbi.2009.12.004. View