Genome-wide comparative analyses reveal selection signatures underlying adaptation and production in Tibetan and Poll Dorset sheep

Abstract

The identification of genome-wide selection signatures can provide insights on the mechanisms of natural and/or artificial selection and uncover genes related to biological functions and/or phenotypes. Tibetan sheep are an important livestock in Tibet, providing meat and wool for Tibetans who are renown for breeding livestock that adapt well to high altitudes. Using whole-genome sequences with an effective sequencing depth of 5×, we investigated the genomic diversity and structure and, identified selection signatures of White Tibetan, Oula and Poll Dorset sheep. We obtained 30,163,679 Single Nucleotide Polymorphisms (SNPs) and 5,388,372 indels benchmarked against the ovine Oar_v4.0 genome assembly. Next, using FST, ZHp and XP-EHH approaches, we identified selection signatures spanning a set of candidate genes, including HIF1A, CAPN3, PRKAA1, RXFP2, TRHR and HOXA10 that are associated with pathways and GO categories putatively related to hypoxia responses, meat traits and disease resistance. Candidate genes and GO terms associated with coat color were also identified. Finally, quantification of blood physiological parameters, revealed higher levels of mean corpuscular hemoglobin measurement and mean corpuscular hemoglobin concentration in Tibetan sheep compared with Poll Dorset, suggesting a greater oxygen-carrying capacity in the Tibetan sheep and thus better adaptation to high-altitude hypoxia. In conclusion, this study provides a greater understanding of genome diversity and variations associated with adaptive and production traits in sheep.

Position of Hungarian Merino among other Merinos, within-breed genetic similarity network and markers associated with daily weight gain

“…Since nowadays the most important parameter of the Hungarian sheep-breeding industry is the weight-gain of lambs, we decided to deliver markers suitable to improving the daily weight-gain of Hungarian Merino lambs. Our investigation overlaps other activities like investigating growth and meat production traits in several other sheep breeds [16,17,18,19] and highlights regions in the sheep genome that are usable not only for Hungarian Merino but for other breeds as well.…”

Selection Signature Analyses Revealed Genes Associated With Adaptation, Production, and Reproduction in Selected Goat Breeds in Kenya

“…However, linkage disequilibrium-based methods are more powerful than population differentiated-based methods ( Jacobs et al, 2016 ). These methods have been used in cattle ( Cheruiyot et al, 2018 ; Tijjani et al, 2019 ), goats ( Henkel et al, 2019 ; Islam et al, 2019 ), and sheep ( Saravanan et al, 2021 ; Zhang et al, 2021 ). To enhance the accuracy of selection sweep detection and also to exclude unknown biasness, it is essential to combine various statistical approaches ( Qanbari and Simianer, 2014 ).…”

The Quest for Genes Involved in Adaptation to Climate Change in Ruminant Livestock

“…iHS methods have been used to detect signatures of adaptation to environments in French Charolais cattle, sheep and goats [161][162][163][164][165]. Cross-population EHH-based tests have been used to detect hot climate adaptation in cattle [166][167][168] and sheep [169][170][171], and hypoxia adaptation in new world camelids [172]. Detecting runs of homozygosity (ROHs) to find regions containing genes associated with adaptation has been demonstrated in several domestic species [157,162,163,173,174].…”