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- Title
SNP discovery, validation, haplotype structure and linkage disequilibrium in full-length herbage nutritive quality genes of perennial ryegrass ( Lolium perenne L.).
- Authors
Rebecca Ponting; Michelle Drayton; Noel Cogan; Mark Dobrowolski; Germán Spangenberg; Kevin Smith; John Forster
- Abstract
Abstract  Development of accurate high-throughput molecular marker systems such as SNPs permits evaluation and selection of favourable gene variants to accelerate elite varietal production. SNP discovery in perennial ryegrass has been based on PCR amplification and sequencing of multiple amplicons designed to scan all components of the transcriptional unit. Full-length genes (with complete intronâexon structure and promoter information) corresponding to well-defined biochemical functions such as lignin biosynthesis and oligosaccharide metabolism are ideal for complete SNP haplotype determination. Multiple SNPs at regular intervals across the transcriptional unit were detected within and between the heterozygous parents and validated in the progeny of the F 1(NA6 � AU6) genetic mapping family. Haplotype structures in the parental genotypes were defined and haplotypic abundance, structure and variation were assessed in diverse germplasm sources. Decay of LD to r 2 values of c. 0.2 typically occurs over 500â3,000 bp, comparable with gene length and with little apparent variation between diverse, ecotypic and varietal population sub-groups. Similar patterns were revealed as limited blocks of intragenic LD. The results are compatible with the reproductive biology of perennial ryegrass and the effects of large ancestral population size. This analysis provides crucial information to validate strategies for correlation of haplotypic diversity and phenotypic variation through association mapping.
- Publication
Molecular Genetics & Genomics, 2007, Vol 278, Issue 5, p585
- ISSN
1617-4615
- Publication type
Academic Journal
- DOI
10.1007/s00438-007-0275-4