Unknown

Dataset Information

0

Genome-wide Target Enrichment-aided Chip Design: a 66 K SNP Chip for Cashmere Goat.


ABSTRACT: Compared with the commercially available single nucleotide polymorphism (SNP) chip based on the Bead Chip technology, the solution hybrid selection (SHS)-based target enrichment SNP chip is not only design-flexible, but also cost-effective for genotype sequencing. In this study, we propose to design an animal SNP chip using the SHS-based target enrichment strategy for the first time. As an update to the international collaboration on goat research, a 66 K SNP chip for cashmere goat was created from the whole-genome sequencing data of 73 individuals. Verification of this 66 K SNP chip with the whole-genome sequencing data of 436 cashmere goats showed that the SNP call rates was between 95.3% and 99.8%. The average sequencing depth for target SNPs were 40X. The capture regions were shown to be 200 bp that flank target SNPs. This chip was further tested in a genome-wide association analysis of cashmere fineness (fiber diameter). Several top hit loci were found marginally associated with signaling pathways involved in hair growth. These results demonstrate that the 66 K SNP chip is a useful tool in the genomic analyses of cashmere goats. The successful chip design shows that the SHS-based target enrichment strategy could be applied to SNP chip design in other species.

SUBMITTER: Qiao X 

PROVIDER: S-EPMC5561203 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature

altmetric image

Publications


Compared with the commercially available single nucleotide polymorphism (SNP) chip based on the Bead Chip technology, the solution hybrid selection (SHS)-based target enrichment SNP chip is not only design-flexible, but also cost-effective for genotype sequencing. In this study, we propose to design an animal SNP chip using the SHS-based target enrichment strategy for the first time. As an update to the international collaboration on goat research, a 66 K SNP chip for cashmere goat was created f  ...[more]

Similar Datasets

| S-EPMC4554862 | biostudies-literature
| S-EPMC10218471 | biostudies-literature
| S-EPMC3358123 | biostudies-literature
| S-EPMC11218406 | biostudies-literature
| S-EPMC2194786 | biostudies-literature
| S-EPMC3899236 | biostudies-literature
| S-EPMC3102637 | biostudies-literature
| PRJNA1205530 | ENA
| PRJNA1132486 | ENA
| S-EPMC11047310 | biostudies-literature