Signatures of Selection in Admixed Dairy Cattle in Tanzania

Abstract

Multiple studies have investigated selection signatures in domestic cattle and other species. However, there is a dearth of information about the response to selection in genomes of highly admixed crossbred cattle in relation to production and adaptation to tropical environments. In this study, we evaluated 839 admixed crossbred cows sampled from two major dairy regions in Tanzania namely Rungwe and Lushoto districts, in order to understand their genetic architecture and detect genomic regions showing preferential selection. Animals were genotyped at 150,000 SNP loci using the Geneseek Genomic Profiler (GGP) High Density (HD) SNP array. Population structure analysis showed a large within-population genetic diversity in the study animals with a high degree of variation in admixture ranging between 7 and 100% taurine genes (dairyness) of mostly Holstein and Friesian ancestry. We explored evidence of selection signatures using three statistical methods (iHS, XP-EHH, and pcadapt). Selection signature analysis identified 108 candidate selection regions in the study population. Annotation of these regions yielded interesting genes potentially under strong positive selection including ABCG2, ABCC2, XKR4, LYN, TGS1, TOX, HERC6, KIT, PLAG1, CHCHD7, NCAPG, and LCORL that are involved in multiple biological pathways underlying production and adaptation processes. Several candidate selection regions showed an excess of African taurine ancestral allele dosage. Our results provide further useful insight into potential selective sweeps in the genome of admixed cattle with possible adaptive and productive importance. Further investigations will be necessary to better characterize these candidate regions with respect to their functional significance to tropical adaptations for dairy cattle.

Fifteen Shades of Grey: Combined Analysis of Genome-Wide SNP Data in Steppe and Mediterranean Grey Cattle Sheds New Light on the Molecular Basis of Coat Color

“…Such a large geographic distribution may be consistent with known ancient migration and admixture events during dispersal of cattle out of the domestication center [17,18,20,[55][56][57][58][59][60][61] as well as more recent historical migrations between Asia and Europe and in the Mediterranean [27,62], although admixture phenomena among wild taurine and zebuine progenitors may not be ruled out. Interestingly, we found that several of the candidate genes on BTA14 (XKR4, TMEM68, TGS1, LYN, CHCHD7, SDR16C5, PENK, TOX, RPS20, PLAG1) had been previously reported to harbor signals of selection/association in taurine/zebuine composite populations or zebuine breeds [63][64][65][66][67][68][69][70][71][72][73][74][75][76][77][78]. This evidence possibly supports the speculation that pigment-related gene variants and phenotypes in grey taurine cattle may represent a heritage of zebuine origin, despite the fact that, for PLAG1, an allele with major effects on body size, weight, and reproduction has been shown to be a >1000 year-old-derived allele that increased rapidly in frequency in Northwestern European B. taurus between the 16th and 18th centuries, and that was hence introgressed, towards the 19th and 20th centuries, into non-European B. taurus and Bos indicus breeds likely to increase the stature of modern cattle [79,80].…”

Population Structure, and Selection Signatures Underlying High-Altitude Adaptation Inferred From Genome-Wide Copy Number Variations in Chinese Indigenous Cattle

“…Chinese indigenous cattle inhabit more extensive altitudes than yak, from low-altitude coastal regions to the Tibetan Plateau, and may provide a better model to explore the genetic basis of high-altitude adaptation. The selective signatures of SNPs have been explored extensively in cattle (Pérez O'Brien et al, 2014;Xu et al, 2015;Zhao et al, 2015;Cheruiyot et al, 2018) and other livestock (Wilkinson et al, 2013;Onzima et al, 2018). However, similar analyses of CNVs are still limited.…”

Genetic Signatures of Selection for Cashmere Traits in Chinese Goats

“…Detection of selection signals associated with economic traits has been successfully implemented in several livestock species, such as cattle [ 35 ], pigs [ 36 ], sheep [ 37 ] and horses [ 38 ]. However, many approaches have been proposed to identify selection signals in genomes, such as Fst, XP-EHH and iHS.…”