Identification of Non-Pleiotropic Loci in Flowering and Maturity Control in Soybean

Sedivy, Eric J.; Akpertey, Abraham; Vela, Angela; Abadir, Sandra; Khan, Awais; Hanzawa, Yoshie

doi:10.3390/agronomy10081204

Cited by 5 publications

(2 citation statements)

References 36 publications

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“…Furthermore, brassinosteroid‐deficient mutants cause a strong delay in days to flowering (Li et al, 2018). Lastly, another QTL was found on Vu03 near Vigun03g104200 , an ortholog of the soybean E6 gene, which affects both flowering and maturity (Li et al, 2017; Sedivy et al, 2020). E6 plays an important role in the long‐juvenile trait (delayed flowering) in soybean (Bonato & Vello, 1999).…”

Section: Discussionmentioning

confidence: 99%

The UCR Minicore: a resource for cowpea research and breeding

Muñoz‐Amatriaín

Herniter

et al. 2021

Legume Science

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Incorporation of new sources of genetic diversity into plant breeding programs is crucial for continuing to improve yield and quality, as well as tolerance to abiotic and biotic stresses. A minicore (the “University of California, Riverside (UCR) Minicore”) composed of 368 worldwide accessions of cultivated cowpea has been assembled, having been derived from the UCR cowpea collection. High‐density genotyping with 51,128 SNPs followed by principal component and genetic assignment analyses identified six subpopulations in the UCR Minicore, mainly differentiated by cultivar group and geographic origin. All six subpopulations were present to some extent in West African material, suggesting that West Africa is a center of diversity for cultivated cowpea. Additionally, population structure analyses supported two routes of introduction of cowpea into the U.S.: (1) from Spain to the southwest U.S. through Northern Mexico and (2) from Africa to the southeast U.S. via the Caribbean. Genome‐wide association studies (GWAS) narrowed several traits to regions containing strong candidate genes. For example, orthologs of the Arabidopsis FLOWERING LOCUS T lie within a major QTL for flowering time. In summary, this diverse, yet compact cowpea collection constitutes a suitable resource to identify loci controlling complex traits, consequently providing markers to assist with breeding to improve this crop of high relevance to global food and nutritional security.

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Section: Discussionmentioning

confidence: 99%

The UCR Minicore: a resource for cowpea research and breeding

Muñoz‐Amatriaín

Herniter

et al. 2021

Legume Science

View full text Add to dashboard Cite

show abstract

“…Furthermore, brassinosteroid-deficient mutants cause a strong delay in days to flowering [64]. Lastly, another QTL was found on Vu03 near Vigun03g104200, an ortholog of the soybean E6 gene, which affects both flowering and maturity [65,66]. E6 plays an important role in the long-juvenile trait (delayed flowering) in soybean [67].…”

Section: Flowering Timementioning

confidence: 99%

The UCR Minicore: a valuable resource for cowpea research and breeding

Muñoz‐Amatriaín

Herniter

et al. 2021

Preprint

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Incorporation of new sources of genetic diversity into plant breeding programs is crucial for continuing to improve yield and quality, as well as tolerance to abiotic and biotic stresses. A minicore (the 'UCR Minicore') composed of 368 worldwide accessions of cultivated cowpea has been assembled, having been derived from the University of California, Riverside cowpea collection. High-density genotyping with 51,128 SNPs followed by principal component and genetic assignment analyses identified six subpopulations in the UCR Minicore, mainly differentiated by cultivar group and geographic origin. All six subpopulations were present to some extent in West African material, suggesting that West Africa is a center of diversity for cultivated cowpea. Additionally, population structure analyses supported two routes of introduction of cowpea into the U.S.: (1) from Spain to the southwest U.S. through Northern Mexico, and (2) from Africa to the southeast U.S. via the Caribbean. Genome-wide association studies (GWAS) of important agronomic traits including flowering time, resulted in the identification of significant SNPs for all traits and environments. The mapping resolution achieved by high-density genotyping of this diverse minicore collection allowed the identification of strong candidate genes, including orthologs of the Arabidopsis FLOWERING LOCUS T. In summary, this diverse, yet compact cowpea collection constitutes a suitable resource to identify loci controlling complex traits, consequently providing markers to assist with breeding to improve this crop of high relevance to global food and nutritional security.

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Epistasis and pleiotropy‐induced variation for plant breeding

Dwivedi,

Heslop‐Harrison,

Amas

et al. 2024

Plant Biotechnology Journal

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SummaryEpistasis refers to nonallelic interaction between genes that cause bias in estimates of genetic parameters for a phenotype with interactions of two or more genes affecting the same trait. Partitioning of epistatic effects allows true estimation of the genetic parameters affecting phenotypes. Multigenic variation plays a central role in the evolution of complex characteristics, among which pleiotropy, where a single gene affects several phenotypic characters, has a large influence. While pleiotropic interactions provide functional specificity, they increase the challenge of gene discovery and functional analysis. Overcoming pleiotropy‐based phenotypic trade‐offs offers potential for assisting breeding for complex traits. Modelling higher order nonallelic epistatic interaction, pleiotropy and non‐pleiotropy‐induced variation, and genotype × environment interaction in genomic selection may provide new paths to increase the productivity and stress tolerance for next generation of crop cultivars. Advances in statistical models, software and algorithm developments, and genomic research have facilitated dissecting the nature and extent of pleiotropy and epistasis. We overview emerging approaches to exploit positive (and avoid negative) epistatic and pleiotropic interactions in a plant breeding context, including developing avenues of artificial intelligence, novel exploitation of large‐scale genomics and phenomics data, and involvement of genes with minor effects to analyse epistatic interactions and pleiotropic quantitative trait loci, including missing heritability.

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Identification of Non-Pleiotropic Loci in Flowering and Maturity Control in Soybean

Cited by 5 publications

References 36 publications

The UCR Minicore: a resource for cowpea research and breeding

The UCR Minicore: a resource for cowpea research and breeding

The UCR Minicore: a valuable resource for cowpea research and breeding

Epistasis and pleiotropy‐induced variation for plant breeding

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