Population Genetics Of Cashmere Goats Based On High-throughput Sequencing

Inner Mongolia Cashmere goat and Liaoning Cashmere goat are the specific animal genetic resources in China. After long-term natural selection and intensive selection in the past decades, has formed two varieties of resources, which are famous for its quality and quantity respectively. The application of traditional systematic breeding, cross-breeding, directional artificial selection and artificial insemination technology also leads to a fewer sires in their offspring, which to some extent resulted in the reduction of genetic diversity and the loss of local genetic resources. Studying their genetic structure and genetic polymorphism at the population level is beneficial to the discovery of a great numbers of molecular markers and the protection of local genetic resources. With Illumina Hiseq 2000 sequencing platform and bioinformatic analysis method, a total of 80 individuals of Inner Mongolia Cashmere goats （Erlangshan and Arbas and Alxa type） and Liaoning cashmere goats was used for further analysis in this study. In addition, to detect the signature of selection in cashmere goat breeds and compared to non-cashmere goat under the long-term history, whole genome sequencing data from 12 non-cashmere goat breeds was aslo downloaded. The main results are as follows:（1）A total of 6,737,432 SNPs and 194,273 InDels were obtained by genetic variant detection and stringent criterion through the high quality reads comparison to the reference genome CHR₂.0; the distribution of genetic variation in the genome region was annotated, found that only 0.77%（3720） of the SNP mutations were distributed in the exon region,and the gene region accounted for 24.5% and intron region accounted for 68.79%. The distribution of InDels is decreased with the increase of lengths.（2）With the application of linkage disequilibrium, NJ-tree, population structure, population heterozygosity, inbreeding coefficient and other methods to analyze population genetic structure, the genetic relationship between different population and the existence of gene introgression among population were found; There are a great genetic difference and genetic diversity among three types of Inner Mongolia Cashmere goats with LD analysis.（3）Through the analysis of differences between Inner Mongolia Cashmere goats （Alashan, Arbas） and Liaoning Cashmere goats while scanning whole genome,206 candidate genes（5%） was annotated. GO functional annotation indicated that candidate genes mainly enriched in cells, cells part, catalysis functions and other biological processes. KEGG pathway analysis showed that these genes were involved in Hippo signaling pathway, melanin production, Wnt signaling pathway, thyroid hormone synthesis, cAMP signaling pathway, carbohydrate digestion and absorption with 16 metabolic pathways were significantly enriched.（4）The principal component analysis about genetic relationship between cashmere goats and non cashmere goats found that Saanen dairy goats and West African dwarf goats have a close genetic relationship with cashmere goats and have a far genetic relationship with other breeds. Non-cashmere goats have a far genetic relationship except Saanen dairy goats and West African dwarf goats.（5） Through the comparison between cashmere goats and 12 non-cashmere goat breeds,211 candidate genes （5%） was annotated after scanning whole genome. GO functional annotation showed that the signature of selection were mainly enriched in cells, cells part; then binding and catalytic function participated in molecular function; biological processes are mainly involved in cellular processes and metabolic process. KEGG metabolic pathway analysis found candidate genes were mainly involved in amino sugars and sugar nucleotides metabolism, melanoma, oxidative phosphorylation pathway and in other 8 metabolic pathways were significantly enriched.