Population structure, genetic diversity and prolificacy in pishan red sheep under an extreme desert environment

Abstract

Extreme environmental conditions are a major challenge for livestock production. Changes in climate conditions, especially those that lead to extreme weather, can reduce livestock production. The screening of genes and molecular markers is of great significance to explore the genetic mechanism of sheep prolificacy traits in Taklimakan Desert environment. We selected healthy adult Pishan Red Sheep (PRS) and Qira Black Sheep (QR) which live in Taklimakan Desert environment, collected blood from jugular vein, extracted DNA, and prepared Illumina Ovine SNP50 chip. For PRS, linkage disequilibrium (LD) was calculated using the ovine SNP50 Beadchip and the effective population size (Ne) was estimated using SMC++. The genetic characteristics of PRS were analyzed by integrated haplotype score (iHS) and fixation index (FST). The result showed that r2 of PRS was 0.233 ± 0.280 in the range of 0–10 Kb and decreased with increasing distances. SMC++ tested that the Ne of PRS remained at 236.99 in recent generations. 184 genes were screened out under iHS 1% threshold, and 1148 genes were screened out with FST under the 5% threshold, and 29 genes were obtained from the intersection of the two gene sets. In this study, the genetic characteristics of PRS and QR were compared by ovine genome chip, and the related excellent genes were searched, providing reference for the protection of sheep germplasm resources and molecular breeding in a desert environment.

VCF2PCACluster: a simple, fast and memory-efficient tool for principal component analysis of tens of millions of SNPs

“…Next, we will further improve VCF2PCACluster by adopting additional input formats, such as PLINK2, and implementing more clustering algorithm for users to choose from. Since its initial release one year ago, four studies have used VCF2PCACluster (previously known as MingPCACluster) [ 19 , 20 ] to conduct their analyses and visualize the results.…”