Association of candidate genes with flowering time and water-soluble carbohydrate content in Lolium perenne (L.)

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Association of candidate genes with flowering time and water-soluble carbohydrate content in Lolium perenne (L.). / Skøt, Leif; Humphreys, Janet; Humphreys, Mervyn O.; Thorogood, Daniel; Gallagher, Joseph Anthony; Sanderson, Ruth; Armstead, Ian P.; Thomas, Ian D.

Yn: Genetics, Cyfrol 177, Rhif 1, 01.09.2007, t. 535-547.

Allbwn ymchwil: Cyfraniad at gyfnodolynErthygl

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@article{b9a43c0ee39d4ced8f1d04a89323faea,
title = "Association of candidate genes with flowering time and water-soluble carbohydrate content in Lolium perenne (L.)",
abstract = "We describe a candidate gene approach for associating SNPs with variation in flowering time and water-soluble carbohydrate (WSC) content and other quality traits in the temperate forage grass species Lolium perenne. Three analysis methods were used, which took the significant population structure into account. First, a linear mixed model was used enabling a structured association analysis to be incorporated with the nine populations identified in the structure analysis as random variables. Second, a within-population analysis of variance was performed. Third, a tree-scanning method was used, in which haplotype trees were associated with phenotypes on the basis of inferred haplotypes. Analysis of variance within populations identified several associations between WSC, nitrogen (N), and dry matter digestibility with allelic variants within an alkaline invertase candidate gene LpcAI. These associations were only detected in material harvested in one of the two years. By contrast, consistent associations between the L. perenne homolog (LpHD1) of the rice photoperiod control gene HD1 and flowering time were identified. One SNP, in the immediate upstream region of the LpHD1 coding sequence (C-4443-A), was significant in the linear mixed model. Within-population analysis of variance and tree-scanning analysis confirmed and extended this result to the 2118 polymorphisms in some of the populations. The merits of the tree-scanning method are compared to the single SNP analysis. The potential usefulness of the 4443 SNP in marker-assisted selection is currently being evaluated in test crosses of genotypes from this work with turf-grass varieties.",
author = "Leif Sk{\o}t and Janet Humphreys and Humphreys, {Mervyn O.} and Daniel Thorogood and Gallagher, {Joseph Anthony} and Ruth Sanderson and Armstead, {Ian P.} and Thomas, {Ian D.}",
note = "Sk{\o}t, L., Humphreys, J., Humphreys, M. O., Thorogood, D., Gallagher, J. A., Sanderson, R., Armstead, I. P., Thomas, I. D. (2007). Association of candidate genes with flowering time and water-soluble carbohydrate content in Lolium perenne (L.). Genetics, 177 (1), 535-547. Sponsorship: BBSRC RAE2008",
year = "2007",
month = sep,
day = "1",
doi = "10.1534/genetics.107.071522",
language = "English",
volume = "177",
pages = "535--547",
journal = "Genetics",
issn = "0016-6731",
publisher = "Genetics Society of America",
number = "1",

}

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TY - JOUR

T1 - Association of candidate genes with flowering time and water-soluble carbohydrate content in Lolium perenne (L.)

AU - Skøt, Leif

AU - Humphreys, Janet

AU - Humphreys, Mervyn O.

AU - Thorogood, Daniel

AU - Gallagher, Joseph Anthony

AU - Sanderson, Ruth

AU - Armstead, Ian P.

AU - Thomas, Ian D.

N1 - Skøt, L., Humphreys, J., Humphreys, M. O., Thorogood, D., Gallagher, J. A., Sanderson, R., Armstead, I. P., Thomas, I. D. (2007). Association of candidate genes with flowering time and water-soluble carbohydrate content in Lolium perenne (L.). Genetics, 177 (1), 535-547. Sponsorship: BBSRC RAE2008

PY - 2007/9/1

Y1 - 2007/9/1

N2 - We describe a candidate gene approach for associating SNPs with variation in flowering time and water-soluble carbohydrate (WSC) content and other quality traits in the temperate forage grass species Lolium perenne. Three analysis methods were used, which took the significant population structure into account. First, a linear mixed model was used enabling a structured association analysis to be incorporated with the nine populations identified in the structure analysis as random variables. Second, a within-population analysis of variance was performed. Third, a tree-scanning method was used, in which haplotype trees were associated with phenotypes on the basis of inferred haplotypes. Analysis of variance within populations identified several associations between WSC, nitrogen (N), and dry matter digestibility with allelic variants within an alkaline invertase candidate gene LpcAI. These associations were only detected in material harvested in one of the two years. By contrast, consistent associations between the L. perenne homolog (LpHD1) of the rice photoperiod control gene HD1 and flowering time were identified. One SNP, in the immediate upstream region of the LpHD1 coding sequence (C-4443-A), was significant in the linear mixed model. Within-population analysis of variance and tree-scanning analysis confirmed and extended this result to the 2118 polymorphisms in some of the populations. The merits of the tree-scanning method are compared to the single SNP analysis. The potential usefulness of the 4443 SNP in marker-assisted selection is currently being evaluated in test crosses of genotypes from this work with turf-grass varieties.

AB - We describe a candidate gene approach for associating SNPs with variation in flowering time and water-soluble carbohydrate (WSC) content and other quality traits in the temperate forage grass species Lolium perenne. Three analysis methods were used, which took the significant population structure into account. First, a linear mixed model was used enabling a structured association analysis to be incorporated with the nine populations identified in the structure analysis as random variables. Second, a within-population analysis of variance was performed. Third, a tree-scanning method was used, in which haplotype trees were associated with phenotypes on the basis of inferred haplotypes. Analysis of variance within populations identified several associations between WSC, nitrogen (N), and dry matter digestibility with allelic variants within an alkaline invertase candidate gene LpcAI. These associations were only detected in material harvested in one of the two years. By contrast, consistent associations between the L. perenne homolog (LpHD1) of the rice photoperiod control gene HD1 and flowering time were identified. One SNP, in the immediate upstream region of the LpHD1 coding sequence (C-4443-A), was significant in the linear mixed model. Within-population analysis of variance and tree-scanning analysis confirmed and extended this result to the 2118 polymorphisms in some of the populations. The merits of the tree-scanning method are compared to the single SNP analysis. The potential usefulness of the 4443 SNP in marker-assisted selection is currently being evaluated in test crosses of genotypes from this work with turf-grass varieties.

U2 - 10.1534/genetics.107.071522

DO - 10.1534/genetics.107.071522

M3 - Article

C2 - 17660575

VL - 177

SP - 535

EP - 547

JO - Genetics

JF - Genetics

SN - 0016-6731

IS - 1

ER -

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