Interpretation of SNP Haplotype Complexity in White Clover (Trifolium repens L.), an Outbreeding Allotetraploid Species
Single nucleotide polymorphisms (SNPs) within genic sequences provide the basis for functionally-associated genetic marker development. Gene-associated SNP discovery in white clover has been based on cloning and sequencing of PCR amplicons from parents and progeny of two-way pseudo-testcross mapping families. Target genes were selected from functional categories including phytohormone metabolism, nodulation, cell wall biosynthesis, metal binding, flavonoid biosynthesis and organic acid biosynthesis. Sequence alignments revealed haplotypic complexity that may be attributable to both paralogous gene structure and homoeologous sequence variation between sub-genomes. A high proportion of predicted allelic SNPs failed to verify in a Mendelian transmission test, confirming the prevalence of non-homologous variation. Incidence and frequency of haplotypes within and between genotypes was determined and interpreted in terms of models of sequence evolution and isolation. Methods for enhanced recovery of genome- and gene-specific sequences from white clover based on computational analysis, exploitation of large-insert DNA libraries and comparison with progenitor sequences are proposed and discussed.
KeywordsBacterial Artificial Chromosome Association Mapping White Clover Perennial Ryegrass Haplotype Complexity
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