Selection Analysis Of Candidate Genes Associated With Cashmere Traits And Its Low Density Chips Design

The cashmere of Inner Mongolia Cashmere goat has been a high elasticity, a small fine, feel high, luster and reputation. However, Chinese’s cashmere market in the process of circulation in the transaction, regardless of class and quality, resulting in the cashmere yield and quality declined. At the same time, whole-genome selection techniques can effectively shorten the generation interval, thereby increasing genetic progress, it has become a hot research breeder. But the gene chips for goat value in itself, it is rather expensive, this study takes advantage of genomic selection and genetic infiltration methods, combined with goat genome-wide high density microarray data, also makes use of transcriptome data cashmere goat secondary follicle, Located cashmere growth and quality of candidate genes or marker signal. On the one hand can provide some theoretical basis for the function of the gene; the other hand, these signals through low-density chip design, to reduce the cost of genomic selection in breeding, but also to achieve the early breeding cashmere goat economic traits, aim to improve the quality of cashmere. The main findings are as follows:1. Integrated the goat whole genome SNP Chip, Illumina GoatSNP60 Bead Chip (60K), and RR-BLUP model, our lab has exploited a set of method which can used to select the candidate loci associated with economic traits, and these selected SNP loci have highly estimated accuracy in the experimental population.2. In this study, we obtained 323 key SNPs associated with cashmere yield trait from 120 cashmere goats using genome-wide association study. These SNPs can be used to design the low density chips related to the cashmere yield trait.3. We obtained 293 key SNPs associated with cashmere fiber diameter trait from 120 cashmere goats using genome-wide association study. The EBV of these 293 SNPs is more accurate compared with others, thus these SNPs can be used to design the low density chips related to the cashmere fiber diameter trait.4. To gain further insight into three goat populations (Cashmere goat, Cashmere-Ibex Hybrid, Ibex), we analyzed the genotype data and RNA-seq data from cashmere second follicles. Totally,166 candidate genes and 10 significant KEGG pathways (p<0.05) were obtained which play an important role in hair growth.