Exploring Genetic Architecture for Pod-related Traits in Soybean Using Image-based Phenotyping

Overview

Journal Mol Breed

Specialties Biotechnology
Molecular Biology

Date 2023 Jun 13

PMID 37309355

Authors

Fangguo Chang

Wenhuan Lv

Peiyun Lv

Yuntao Xiao

Wenliang Yan

Shu Chen

Lingyi Zheng

Ping Xie

Ling Wang

Benjamin Karikari

Salah Fatouh Abou-Elwafa

Haiyan Jiang

Tuanjie Zhao

Affiliations

Soon will be listed here.

Abstract

Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-021-01223-2.

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References

He J, Meng S, Zhao T, Xing G, Yang S, Li Y . An innovative procedure of genome-wide association analysis fits studies on germplasm population and plant breeding. Theor Appl Genet. 2017; 130(11):2327-2343. DOI: 10.1007/s00122-017-2962-9. View

Tian D, Wang P, Tang B, Teng X, Li C, Liu X . GWAS Atlas: a curated resource of genome-wide variant-trait associations in plants and animals. Nucleic Acids Res. 2019; 48(D1):D927-D932. PMC: 6943065. DOI: 10.1093/nar/gkz828. View

Hu D, Kan G, Hu W, Li Y, Hao D, Li X . Identification of Loci and Candidate Genes Responsible for Pod Dehiscence in Soybean via Genome-Wide Association Analysis Across Multiple Environments. Front Plant Sci. 2019; 10:811. PMC: 6598122. DOI: 10.3389/fpls.2019.00811. View

Duan P, Xu J, Zeng D, Zhang B, Geng M, Zhang G . Natural Variation in the Promoter of GSE5 Contributes to Grain Size Diversity in Rice. Mol Plant. 2017; 10(5):685-694. DOI: 10.1016/j.molp.2017.03.009. 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

Wurschum T . Mapping QTL for agronomic traits in breeding populations. Theor Appl Genet. 2012; 125(2):201-10. DOI: 10.1007/s00122-012-1887-6. View

Xiao H, Jiang N, Schaffner E, Stockinger E, Knaap E . A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit. Science. 2008; 319(5869):1527-30. DOI: 10.1126/science.1153040. View

Liu J, Chen J, Zheng X, Wu F, Lin Q, Heng Y . GW5 acts in the brassinosteroid signalling pathway to regulate grain width and weight in rice. Nat Plants. 2017; 3:17043. DOI: 10.1038/nplants.2017.43. View

Wu S, Zhang B, Keyhaninejad N, Rodriguez G, Kim H, Chakrabarti M . A common genetic mechanism underlies morphological diversity in fruits and other plant organs. Nat Commun. 2018; 9(1):4734. PMC: 6226536. DOI: 10.1038/s41467-018-07216-8. View

10.

Wang S, Chang Y, Guo J, Chen J . Arabidopsis Ovate Family Protein 1 is a transcriptional repressor that suppresses cell elongation. Plant J. 2007; 50(5):858-72. DOI: 10.1111/j.1365-313X.2007.03096.x. View

11.

Tang Y, Liu X, Wang J, Li M, Wang Q, Tian F . GAPIT Version 2: An Enhanced Integrated Tool for Genomic Association and Prediction. Plant Genome. 2016; 9(2). DOI: 10.3835/plantgenome2015.11.0120. View

12.

Pascual L, Albert E, Sauvage C, Duangjit J, Bouchet J, Bitton F . Dissecting quantitative trait variation in the resequencing era: complementarity of bi-parental, multi-parental and association panels. Plant Sci. 2015; 242:120-130. DOI: 10.1016/j.plantsci.2015.06.017. View

13.

Gomez C, Conejero G, Torregrosa L, Cheynier V, Terrier N, Ageorges A . In vivo grapevine anthocyanin transport involves vesicle-mediated trafficking and the contribution of anthoMATE transporters and GST. Plant J. 2011; 67(6):960-70. DOI: 10.1111/j.1365-313X.2011.04648.x. View

14.

Yang Z, Xin D, Liu C, Jiang H, Han X, Sun Y . Identification of QTLs for seed and pod traits in soybean and analysis for additive effects and epistatic effects of QTLs among multiple environments. Mol Genet Genomics. 2013; 288(12):651-67. DOI: 10.1007/s00438-013-0779-z. View

15.

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

16.

Zhou Y, Srinivasan S, Mirnezami S, Kusmec A, Fu Q, Attigala L . Semiautomated Feature Extraction from RGB Images for Sorghum Panicle Architecture GWAS. Plant Physiol. 2018; 179(1):24-37. PMC: 6324233. DOI: 10.1104/pp.18.00974. View

17.

Albert N, Davies K, Lewis D, Zhang H, Montefiori M, Brendolise C . A conserved network of transcriptional activators and repressors regulates anthocyanin pigmentation in eudicots. Plant Cell. 2014; 26(3):962-80. PMC: 4001404. DOI: 10.1105/tpc.113.122069. View

18.

Diaz-Garcia L, Covarrubias-Pazaran G, Schlautman B, Grygleski E, Zalapa J . Image-based phenotyping for identification of QTL determining fruit shape and size in American cranberry ( L.). PeerJ. 2018; 6:e5461. PMC: 6098679. DOI: 10.7717/peerj.5461. View

19.

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

20.

Gomez C, Terrier N, Torregrosa L, Vialet S, Fournier-Level A, Verries C . Grapevine MATE-type proteins act as vacuolar H+-dependent acylated anthocyanin transporters. Plant Physiol. 2009; 150(1):402-15. PMC: 2675721. DOI: 10.1104/pp.109.135624. View