Imputation of low-density marker chip data in plant breeding: Evaluation of methods based on sugar beet.

Low-density genotyping followed by imputation reduces genotyping costs while still providing high-density marker information. An increased marker density has the potential to improve the outcome of all applications that are based on genomic data. This study investigates techniques for 1k to 20k genomic marker imputation for plant breeding programs with sugar beet (Beta vulgaris L.

Genome Scan for Selection in Structured Layer Chicken Populations Exploiting Linkage Disequilibrium Information.

An increasing interest is being placed in the detection of genes, or genomic regions, that have been targeted by selection because identifying signatures of selection can lead to a better understanding of genotype-phenotype relationships. A common strategy for the detection of selection signatures is to compare samples from distinct populations and to search for genomic regions with outstanding genetic differentiation. The aim of this study was to detect selective signatures in layer chicken populations using a recently proposed approach, hapFLK, which exploits linkage disequilibrium information while accounting appropriately for the hierarchical structure of populations.

Population genomic analyses based on 1 million SNPs in commercial egg layers.

Identifying signatures of selection can provide valuable insight about the genes or genomic regions that are or have been under selective pressure, which can lead to a better understanding of genotype-phenotype relationships. A common strategy for selection signature detection is to compare samples from several populations and search for genomic regions with outstanding genetic differentiation. Wright's fixation index, FST, is a useful index for evaluation of genetic differentiation between populations.

Development of a high density 600K SNP genotyping array for chicken.

Background: High density (HD) SNP genotyping arrays are an important tool for genetic analyses of animals and plants. Although the chicken is one of the most important farm animals, no HD array is yet available for high resolution genetic analysis of this species.

Results: We report here the development of a 600 K Affymetrix® Axiom® HD genotyping array designed using SNPs segregating in a wide variety of chicken populations.

A tailed PCR procedure for cost-effective, two-order multiplex sequencing of candidate genes in polyploid plants.

Complex polyploid crop genomes can be recalcitrant towards conventional DNA sequencing approaches for allele mining in candidate genes for valuable traits. In the past, this has greatly complicated the transfer of knowledge on promising candidate genes from model plants to even closely related polyploid crops. Next-generation sequencing offers diverse solutions to overcome such difficulties.