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Positive Selection and Adaptive Introgression of Haplotypes from Bos indicus Improve the Modern Bos taurus Cattle

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Complex evolutionary processes, such as positive selection and introgression can be characterized by in-depth assessment of sequence variation on a whole-genome scale. Here, we demonstrate the combined effects of positive selection and adaptive introgression on genomes, resulting in observed hotspots of runs of homozygosity (ROH) haplotypes on the modern bovine (Bos taurus) genome. We first confirm that these observed ROH hotspot haplotypes are results of positive selection. The haplotypes under selection, including genes of biological interest, such as PLAG1, KIT, CYP19A1 and TSHB, were known to be associated with productive traits in modern Bos taurus cattle breeds. Among the haplotypes under selection, we demonstrate that the CYP19A1 haplotype under selection was associated with milk yield, a trait under strong recent selection, demonstrating a likely cause of the selective sweep. We further deduce that selection on haplotypes containing KIT variants affecting coat color occurred approximately 250 generations ago. The study on the genealogies and phylogenies of these haplotypes identifies that the introgression events of the RERE and REG3G haplotypes happened from Bos indicus to Bos taurus. With the aid of sequencing data and evolutionary analyses, we here report introgression events in the formation of the current bovine genome.

TidsskriftAgriculture (Switzerland)
StatusUdgivet - jun. 2022

Bibliografisk note

Funding Information:
We are grateful to the Nordic Cattle Genetic Evaluation (NAV, Aarhus, Denmark) for providing the phenotypic data used in this study and 1000 Bull Genome Project for providing sequence data. Qianqian Zhang benefited from a joint grant from the European Commission within the framework of the Erasmus-Mundus joint doctorate “EGS-ABG”. This research was supported by the Center for Genomic Selection in Animals and Plants (GenSAP) funded by Innovation Fund Denmark (grant 0603-00519B) and Beijing New Science Star Program from Beijing Academy of Science and Technology, China (grant Z20110000682091).

Publisher Copyright:
© 2022 by the authors. Licensee MDPI, Basel, Switzerland.

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