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

Qianqian Zhang, Anna Amanda Schönherz, Mogens Sandø Lund and Bernt Guldbrandtsen
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Qianqian Zhang: Institute of Biotechnology Research, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
Anna Amanda Schönherz: Center for Quantitative Genetics and Genomics, Aarhus University, 8000 Aarhus, Denmark
Mogens Sandø Lund: Center for Quantitative Genetics and Genomics, Aarhus University, 8000 Aarhus, Denmark
Bernt Guldbrandtsen: Center for Quantitative Genetics and Genomics, Aarhus University, 8000 Aarhus, Denmark

Agriculture, 2022, vol. 12, issue 6, 1-17

Abstract: 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.

Keywords: positive selection; adaptive introgression; runs of homozygosity; haplotype; cattle (search for similar items in EconPapers)
JEL-codes: Q1 Q10 Q11 Q12 Q13 Q14 Q15 Q16 Q17 Q18 (search for similar items in EconPapers)
Date: 2022
References: View complete reference list from CitEc
Citations: View citations in EconPapers (1)

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