Abstract
Association analysis was applied to a panel of accessions of Embrapa Rice Core Collection (ERiCC) with 86 SSR and field data from two experiments. A clear subdivision between lowland and upland accessions was apparent, thereby indicating the presence of population structure. Thirty-two accessions with admixed ancestry were identified through structure analysis, these being discarded from association analysis, thus leaving 210 accessions subdivided into two panels. The association of yield and grain-quality traits with SSR was undertaken with a mixed linear model, with markers and subpopulation as fixed factors, and kinship matrix as a random factor. Eight markers from the two appraised panels showed significant association with four different traits, although only one (RM190) maintained the marker-trait association across years and cultivation. The significant association detected between amylose content and RM190 was in agreement with previous QTL analyses in the literature. Herein, the feasibility of undertaking association analysis in conjunction with germplasm characterization was demonstrated, even when considering low marker density. The high linkage disequilibrium expected in rice lines and cultivars facilitates the detection of marker-trait associations for implementing marker assisted selection, and the mining of alleles related to important traits in germplasm.
Highlights
Association analysis, or linkage disequilibrium mapping, is a notable strategy used for identifying genes controlling important traits
Experimental field data were distributed normally, except for traits related to grain quality (AC and milled rice (MR))
Rare alleles were not integrated into analysis, as low frequency alleles inflate variance estimates of linkage disequilibrium (Remington et al, 2001)
Summary
Association analysis, or linkage disequilibrium mapping, is a notable strategy used for identifying genes controlling important traits. In most plant species, the identification of those genomic regions which contribute to important characteristics has been mostly achieved through linkage analysis within segregating populations, the result of crosses between genitors with contrasting phenotypes and genotypes (Buntjer et al, 2005; Skot et al, 2005). The potential use of the genetic diversity available in species is restricted (Peleman and van der Voort, 2003) Another disadvantage as regards the substantiation of a low number of traits per cross, is through the difficulty in identifying parents with contrasting genotypes and phenotypes for all those traits of interest (Buntjer et al, 2005). The high resolution desired for MAS or cloning candidate genes requires developing large segregating populations, possibly difficult in some species (Skot et al, 2005)
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