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

TY - JOUR

T1 - Positive Selection and Adaptive Introgression of Haplotypes from Bos indicus Improve the Modern Bos taurus Cattle

AU - Zhang, Qianqian

AU - Schönherz, Anna Amanda

AU - Lund, Mogens Sandø

AU - Guldbrandtsen, Bernt

N1 - Publisher Copyright: © 2022 by the authors. Licensee MDPI, Basel, Switzerland.

PY - 2022/6

Y1 - 2022/6

N2 - 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.

AB - 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.

KW - adaptive introgression

KW - cattle

KW - haplotype

KW - positive selection

KW - runs of homozygosity

UR - http://www.scopus.com/inward/record.url?scp=85132159814&partnerID=8YFLogxK

U2 - 10.3390/agriculture12060844

DO - 10.3390/agriculture12060844

M3 - Journal article

AN - SCOPUS:85132159814

SN - 2077-0472

VL - 12

JO - Agriculture (Switzerland)

JF - Agriculture (Switzerland)

IS - 6

M1 - 844

ER -