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

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dc.citation.issue1
dc.citation.volume24
dc.contributor.authorZhu M
dc.contributor.authorYang Y
dc.contributor.authorYang H
dc.contributor.authorZhao Z
dc.contributor.authorZhang H
dc.contributor.authorBlair HT
dc.contributor.authorZheng W
dc.contributor.authorWang M
dc.contributor.authorFang C
dc.contributor.authorYu Q
dc.contributor.authorZhou H
dc.contributor.authorQi H
dc.coverage.spatialEngland
dc.date.accessioned2024-10-02T19:34:48Z
dc.date.available2024-10-02T19:34:48Z
dc.date.issued2023-07-11
dc.description.abstractBACKGROUND: 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.
dc.description.confidentialfalse
dc.format.pagination392-
dc.identifier.author-urlhttps://www.ncbi.nlm.nih.gov/pubmed/37434152
dc.identifier.citationZhu M, Yang Y, Yang H, Zhao Z, Zhang H, Blair HT, Zheng W, Wang M, Fang C, Yu Q, Zhou H, Qi H. (2023). Whole-genome resequencing of the native sheep provides insights into the microevolution and identifies genes associated with reproduction traits.. BMC Genomics. 24. 1. (pp. 392-).
dc.identifier.doi10.1186/s12864-023-09479-y
dc.identifier.eissn1471-2164
dc.identifier.elements-typejournal-article
dc.identifier.issn1471-2164
dc.identifier.number392
dc.identifier.pii10.1186/s12864-023-09479-y
dc.identifier.urihttps://mro.massey.ac.nz/handle/10179/71570
dc.languageeng
dc.publisherBioMed Central Ltd
dc.publisher.urihttps://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-023-09479-y#citeas
dc.relation.isPartOfBMC Genomics
dc.rights(c) 2023 The Author/s
dc.rightsCC BY 4.0
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectGWAS
dc.subjectMicroevolution
dc.subjectReproductive trait
dc.subjectSelection signature
dc.subjectSheep
dc.subjectWhole-genome resequencing
dc.subjectAnimals
dc.subjectSheep
dc.subjectSequence Analysis, DNA
dc.subjectGenomics
dc.subjectChina
dc.subjectCytochrome P-450 CYP1A1
dc.subjectReproduction
dc.titleWhole-genome resequencing of the native sheep provides insights into the microevolution and identifies genes associated with reproduction traits
dc.typeJournal article
pubs.elements-id477984
pubs.organisational-groupOther
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