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 watersoluble 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.

Applied Genetics and Genomics in Alfalfa Breeding

“…Association analysis of lignin biosynthesis genes in wild diploid alfalfa germplasm found two SNP associated with yield and stem characteristics [92]. Sequencing of the LpHD1 gene in diverse perennial ryegrass genotypes identified one SNP associated with flowering time [98]. The limitation of the candidate gene approach, of course, is that genes other than the selected candidate genes may be the cause of phenotypic variation, and they will be missed.…”

Comparative Genomics and Functional Characterisation of the GIGANTEA Gene from the Temperate Forage Perennial Ryegrass Lolium perenne

“…Flowering time in the cereals has a strong influence on grain production and yield. In ryegrass, the major impacts of plant phenology, especially flowering time and duration, are on production, forage quality and persistence of this important grassland crop (Skøt et al 2007;Wilkins and Humphreys 2003).…”

Population structure and linkage disequilibrium in elite barley breeding germplasm from the United States

“…The developments of numerous molecular markers for various plant species, high throughput sequencing techniques (Metzker, 2009), and modern analytical tools (Yu et al, 2005;Kang et al, 2008;Kang and Sul, 2010;Zhang et al, 2010) have led to new initiatives for utilizing AM to identify causal variants for diverse traits (Zhu et al, 2008) such as flowering time, kernel composition, and kernel color in maize Palaisa et al, 2004;Wilson et al, 2004); developmental and floweringrelated traits in Arabidopsis (Atwell et al, 2010); multiple agronomic traits in sugar beet (Würschum et al, 2011); quality traits in potato (D′Hoop et al, 2008); disease resistance in sugarcane (Wei et al, 2006); wood property traits in Pinus taeda (González-Martínez et al, 2007); disease resistance in barley (Massman et al, 2011); and flowering time in ryegrass (Skøt et al, 2007).…”