Outlier analyses and genome-wide association study identify glgC and ERD6-like 4 as candidate genes for foliar water-soluble carbohydrate accumulation in Trifolium repens.

Pearson SM; Griffiths AG; Maclean P; Larking AC; Hong SW; Jauregui R; Miller P; McKenzie CM; Lockhart PJ; Tate JA; Ford JL; Faville MJ

Outlier analyses and genome-wide association study identify glgC and ERD6-like 4 as candidate genes for foliar water-soluble carbohydrate accumulation in Trifolium repens.

dc.citation.volume	13
dc.contributor.author	Pearson SM
dc.contributor.author	Griffiths AG
dc.contributor.author	Maclean P
dc.contributor.author	Larking AC
dc.contributor.author	Hong SW
dc.contributor.author	Jauregui R
dc.contributor.author	Miller P
dc.contributor.author	McKenzie CM
dc.contributor.author	Lockhart PJ
dc.contributor.author	Tate JA
dc.contributor.author	Ford JL
dc.contributor.author	Faville MJ
dc.contributor.editor	Xie W
dc.contributor.editor	Rodriguez VM
dc.coverage.spatial	Switzerland
dc.date.accessioned	2024-08-22T21:35:07Z
dc.date.available	2024-08-22T21:35:07Z
dc.date.issued	2022-01-09
dc.description.abstract	Increasing water-soluble carbohydrate (WSC) content in white clover is important for improving nutritional quality and reducing environmental impacts from pastoral agriculture. Elucidation of genes responsible for foliar WSC variation would enhance genetic improvement by enabling molecular breeding approaches. The aim of the present study was to identify single nucleotide polymorphisms (SNPs) associated with variation in foliar WSC in white clover. A set of 935 white clover individuals, randomly sampled from five breeding pools selectively bred for divergent (low or high) WSC content, were assessed with 14,743 genotyping-by-sequencing SNPs, using three outlier detection methods: PCAdapt, BayeScan and KGD-FST. These analyses identified 33 SNPs as discriminating between high and low WSC populations and putatively under selection. One SNP was located in the intron of ERD6-like 4, a gene coding for a sugar transporter located on the vacuole membrane. A genome-wide association study using a subset of 605 white clover individuals and 5,757 SNPs, identified a further 12 SNPs, one of which was associated with a starch biosynthesis gene, glucose-1-phosphate adenylyltransferase, glgC. Our results provide insight into genomic regions underlying WSC accumulation in white clover, identify candidate genomic regions for further functional validation studies, and reveal valuable information for marker-assisted or genomic selection in white clover.
dc.description.confidential	false
dc.edition.edition	2023
dc.format.pagination	1095359-
dc.identifier.author-url	https://www.ncbi.nlm.nih.gov/pubmed/36699852
dc.identifier.citation	Pearson SM, Griffiths AG, Maclean P, Larking AC, Hong SW, Jauregui R, Miller P, McKenzie CM, Lockhart PJ, Tate JA, Ford JL, Faville MJ. (2022). Outlier analyses and genome-wide association study identify glgC and ERD6-like 4 as candidate genes for foliar water-soluble carbohydrate accumulation in Trifolium repens.. Front Plant Sci. 13. (pp. 1095359-).
dc.identifier.doi	10.3389/fpls.2022.1095359
dc.identifier.eissn	1664-462X
dc.identifier.elements-type	journal-article
dc.identifier.issn	1664-462X
dc.identifier.number	1095359
dc.identifier.uri	https://mro.massey.ac.nz/handle/10179/71369
dc.language	eng
dc.publisher	Frontiers Media S.A.
dc.publisher.uri	https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2022.1095359/full
dc.relation.isPartOf	Front Plant Sci
dc.rights	(c) 2023 The Author/s
dc.rights	CC BY 4.0
dc.rights.uri	https://creativecommons.org/licenses/by/4.0/
dc.subject	genome-wide association study
dc.subject	genotyping-by-sequencing
dc.subject	outlier detection
dc.subject	water-soluble carbohydrate
dc.subject	white clover
dc.title	Outlier analyses and genome-wide association study identify glgC and ERD6-like 4 as candidate genes for foliar water-soluble carbohydrate accumulation in Trifolium repens.
dc.type	Journal article
pubs.elements-id	459541
pubs.organisational-group	Other