Whole-genome resequencing of the native sheep provides insights into the microevolution and identifies genes associated with reproduction traits

Abstract

Background Sheep genomes undergo numerous genes losses, gains and mutation that generates genome variability among breeds of the same species after long time natural and artificial selection. However, the microevolution of native sheep in northwest China remains elusive. Our aim was to compare the genomes and relevant reproductive traits of four sheep breeds from different climatic environments, to unveil the selection challenges that this species cope with, and the microevolutionary differences in sheep genomes. Here, we resequenced the genomes of 4 representative sheep breeds in northwest China, including Kazakh sheep and Duolang sheep of native breeds, and Hu sheep and Suffolk sheep of exotic breeds with different reproductive characteristics. Results We found that these four breeds had a similar expansion experience from ~ 10,000 to 1,000,000 years ago. In the past 10,000 years, the selection intensity of the four breeds was inconsistent, resulting in differences in reproductive traits. We explored the sheep variome and selection signatures by FST and θπ. The genomic regions containing genes associated with different reproductive traits that may be potential targets for breeding and selection were detected. Furthermore, non-synonymous mutations in a set of plausible candidate genes and significant differences in their allele frequency distributions across breeds with different reproductive characteristics were found. We identified PAK1, CYP19A1 and PER1 as a likely causal gene for seasonal reproduction in native sheep through qPCR, Western blot and ELISA analyses. Also, the haplotype frequencies of 3 tested gene regions related to reproduction were significantly different among four sheep breeds. Conclusions Our results provide insights into the microevolution of native sheep and valuable genomic information for identifying genes associated with important reproductive traits in sheep.

Polymorphisms of the BMPR1B, BMP15 and GDF9 fecundity genes in four Chinese sheep breeds

“…In sheep, the BMPR1B, BMP15 and GDF9 genes were found to be closely associated with a genetic basis for prolificacy The numbers of haplotypes are in the parentheses. (Lv et al, 2022;Ji et al, 2023;Zhu et al, 2023). Abdoli et al (2013) detected polymorphisms of GDF9 exon 1 and BMPR1B exon 8 in Mehraban ewes.…”

Genomic regions associated with resistance to gastrointestinal parasites in Australian Merino sheep

“…Five candidate genes were identified on OAR 8: FAM120B, SMOC2, TBP, THBS2, WDR27, and WDR27. The THBS2 gene is related to growth and development traits [58] and high prolificacy in sheep [59], while the WDR27 gene has been associated with the cow milk fat trait [60].…”

Comparative whole-genome resequencing to uncover selection signatures linked to litter size in Hu Sheep and five other breeds

“…Hu sheep, a prolific native breed in China, serve as valuable animal models for understanding the genetic underpinnings of prolific sheep breeds [ 23 ]. Furthermore, analyzing the genome data in Hu sheep could provide new insight into differences in reproduction performance, potentially enabling the replication of the multiple birth characteristics of Hu sheep in other sheep breeds [ 24 ].…”