阿拉善型绒山羊基因组参考面板构建及绒性状基因组选择OA

This study aimed to construct a high-density filled reference panel for Alxa cashmere goats and conduct genomic selection research on their down fineness and down yield.A total of 579 healthy Alxa cashmere goats aged 1-6 years were subjected to whole-genome resequencing.Among them,50 goats(30 ewes and 20 rams)were randomly selected for high-depth resequencing(sequencing depth of 10×),and the remaining 529 goats were subjected to low-depth resequencing(sequencing depth of 1×).Fifty high-depth resequencing data were combined with 57 cashmere goat download data(sequencing depth of 10×)for quality control.Then,Beagle 5.2 software was used for phase determination,and GLIMPSE2 software was used for genotype filling to construct a high-quality Alxa cashmere goat reference panel.Low-depth sequencing data were imputed to high-depth using this reference panel.Genomic selection analyses for cashmere fiber fineness and cashmere yield were then performed using ABLUP,GBLUP,and ssGBLUP methods within a single-trait repeatability model framework.After evaluation,the average accuracy rate of panel filling reached 0.979.This panel analyzed the regulatory effects of gender,measurement year,sample age,and group on down fineness and down yield,which were extremely significant(P＜0.01),while the age of the mother had no significant effect on down fineness and down yield(P＞0.05).The genetic parameters were estimated by ABLUP,GBLUP and ssGBLUP methods.The prediction accuracy of the ssGBLUP method was determined by 5-fold cross-validation(down fineness:0.375±0.089,down yield:0.347±0.082)was significantly superior to the traditional method and was the optimal method for calculating the estimated breeding value.The estimated heritabilities were 0.42 for down fineness and 0.43 for down yield.The breeding of Alxa cashmere goats will rely on the species-specific reference panel and adopt a comprehensive strategy of"phenotypic preliminary selection+genomic verification"to achieve the sustainable development of the high-quality cashmere industry.At the same time,it also provides a reference for the construction of reference panels for other local breeds.