Development of an Alfalfa SNP Array and Its Use to Evaluate Patterns of Population Structure and Linkage Disequilibrium

<div><p>A large set of genome-wide markers and a high-throughput genotyping platform can facilitate the genetic dissection of complex traits and accelerate molecular breeding applications. Previously, we identified about 0.9 million SNP markers by sequencing transcriptomes of 27 diverse alfalfa genotypes. From this SNP set, we developed an Illumina Infinium array containing 9,277 SNPs. Using this array, we genotyped 280 diverse alfalfa genotypes and several genotypes from related species. About 81% (7,476) of the SNPs met the criteria for quality control and showed polymorphisms. The alfalfa SNP array also showed a high level of transferability for several closely related <i>Medicago</i> species. Principal component analysis and model-based clustering showed clear population structure corresponding to subspecies and ploidy levels. Within cultivated tetraploid alfalfa, genotypes from dormant and nondormant cultivars were largely assigned to different clusters; genotypes from semidormant cultivars were split between the groups. The extent of linkage disequilibrium (LD) across all genotypes rapidly decayed to 26 Kbp at r² = 0.2, but the rate varied across ploidy levels and subspecies. A high level of consistency in LD was found between and within the two subpopulations of cultivated dormant and nondormant alfalfa suggesting that genome-wide association studies (GWAS) and genomic selection (GS) could be conducted using alfalfa genotypes from throughout the fall dormancy spectrum. However, the relatively low LD levels would require a large number of markers to fully saturate the genome.</p></div

Plots of the first three principal components derived from a principal component analysis (PCA) of 263 alfalfa genotypes using SNP markers generated on an Infinium array, with (a) PC1 vs. PC2 and (b) PC2 vs. PC3.

<p>(C1: diploid subsp. <i>falcata</i>, C2: diploid subsp. <i>caerulea</i>, C3: miscellaneous tetraploid alfalfa, C4: dormant and semi-dormant tetraploid subsp. <i>sativa</i>, and C5: semi-dormant and non-dormant tetraploid subsp. <i>sativa</i>)</p

The number of individual plants evaluated for each of five breeding populations developed from non-dormant germplasm and the number of each population that were assigned to a particular cluster.

<p>The number of individual plants evaluated for each of five breeding populations developed from non-dormant germplasm and the number of each population that were assigned to a particular cluster.</p

The number of individual plants evaluated of the standard fall dormancy and winter hardiness check cultivars and the number that were assigned to either cluster 4 (C4) or cluster 5 (C5).

<p>The number of individual plants evaluated of the standard fall dormancy and winter hardiness check cultivars and the number that were assigned to either cluster 4 (C4) or cluster 5 (C5).</p

The number of polymorphic SNPs within and between four clusters developed based on a model-based clustering analysis.

<p>Cluster 3, which included only six genotypes, was omitted from the analysis.</p

Mapping of chickpea TACs onto <i>Medicago</i> genome.

<p>Mapping of chickpea TACs onto <i>Medicago</i> genome.</p

Correspondences of chickpea genic molecular markers to <i>Medicago</i>.

<p>Correspondences of chickpea genic molecular markers to <i>Medicago</i>.</p

Pairwise genetic distances among five clusters of alfalfa genotypes based on SNP markers generated by the Infinium array.

<p>Pairwise genetic distances among five clusters of alfalfa genotypes based on SNP markers generated by the Infinium array.</p

Influência dos parâmetros do processo de obtenção nas propriedades de argilas organofílicas brasileira e cubana

As argilas são um dos principais tipos de adsorventes usados para o tratamento de óleos minerais, vegetais e animais, de diversos tipos de correntes químicas e petroquímicas e de diversos tipos de bebidas. As argilas também vem desempenhando um papel importante no tratamento de efluentes e de sítios contaminados

Distribution of ISRs on chickpea linkage groups.

<p>Distribution of ISRs on chickpea linkage groups.</p