Abstract
Long-term natural and artificial selection leads to change in certain regions of the genome, resulting in selection signatures that can reveal genes associated with selected traits, such as horns (i.e., polled/horned), high-quality wool traits, and high-altitude hypoxia adaptability. These are complex traits determined by multiple genes, regulatory pathways, and environmental factors. A list of genes with considerable effects on horn and adaptability traits has not been found, although multiple quantitative trait loci (QTL) have been identified. Selection signatures could be identified using genetic differentiation (FST), polymorphism levels θπ, and Tajima’s D. This study aimed to identify selection signatures in fine-wool sheep and to investigate the genes annotated in these regions, as well as the biological pathways involved in horn and adaptability traits. For this purpose, the whole-genome sequence of 120 individuals from four breeds, which come from different elevations and habitats in China, was used to analyze selection signatures for horn and adaptability traits. Annotation of the consensus regions of FST and θπ ratios revealed a list of identified genes associated with polled/horned and high-altitude hypoxia adaptability traits, such as RXPF2, EERFC4, MSH6, PP1R12A, THBS1, ATP1B2, RYR2, and PLA2G2E. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified genes related primarily to mismatch repair, metabolism, vascular smooth muscle contraction, and cardiac muscle contraction. This is the first study to demonstrate that selection signatures play an important role in the polled/horned and high-altitude hypoxia adaptability traits of fine-wool sheep breeds that have undergone high-intensity selection and adapted to different ecological environments in China. Changes observed in the genome of fine-wool sheep may have acted on genomic regions that affect performance traits and provide a reference for genome design and breeding.
Highlights
Sheep (Ovis aries) have played an important role in human society as one of the first animals ever domesticated, and have spread almost globally via human migrations
Blood samples were collected from 30 fine-wool sheep of each breed (2-year-old rams from different families) that include four representative breeds [alpine merino sheep (AMS), Chinese merino sheep (CMS), Aohan fine-wool sheep (AHS), and Qinghai fine-wool sheep (QHS)] adapted to various altitudes local environments
We found that θπ>θw in CMS indicates that CMS has higher nucleotide variability and polymorphism than other breeds (Table 3), which means that the genetic diversity is higher than others
Summary
Sheep (Ovis aries) have played an important role in human society as one of the first animals ever domesticated, and have spread almost globally via human migrations. Fine-wool sheep are renowned for their ability to produce high-quality wool, a natural fiber that is an important agricultural commodity used in clothing and textiles. The wool traits of fine-wool sheep have always been the focus of artificial selection in breeding. Their high-altitude adaptability has been subject to natural selection over many years, because of the extreme differences between the ecological environments in which they live. It is important to understand the genetic basis of well-adapted local livestock breeds in extreme environments to develop appropriate breeding programs under scenarios of future climate change (Li et al, 2014). Fine-wool sheep provide an excellent model to gain novel insights into genetic mechanisms underlying the rapid adaptations of livestock to extreme environments within a short period of time
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