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.
Highlights
The first-generation animal breeding strategies for important quantitative traits relied heavily on keeping meticulous documentation of animal phenotypes and breeding values over several generations[1]
Another strategy known as genome-wide association (GWA) analysis was proposed, which believed that specific single nucleotide polymorphism (SNP) markers could be in genetic linkage disequilibrium with a causative mutation affecting animal traits[10]
Even though current commercial SNP chips based on the Bead Chip technology for different domestic animals have been successful[22,23,24,25,26,27], we propose to design an animal SNP chip using the solution hybrid selection (SHS)-based target enrichment strategy for the first time
Summary
The first-generation animal breeding strategies for important quantitative traits relied heavily on keeping meticulous documentation of animal phenotypes and breeding values over several generations[1]. The MAS program used a small number of DNA markers to trace limited numbers of QTLs8 This disadvantage lead to the development of genomic selection (GS), which aimed to use simultaneously all available genome-wide dense SNP markers to predict breeding values[9]. Another strategy known as genome-wide association (GWA) analysis was proposed, which believed that specific SNP markers could be in genetic linkage disequilibrium with a causative mutation affecting animal traits[10]. No special SNP chip is designed for cashmere goat till
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
