Breed Ancestry, Divergence, Admixture, and Selection Patterns of the Simbra Crossbreed

Abstract

In this study, we evaluated an admixed South African Simbra crossbred population, as well as the Brahman (Indicine) and Simmental (Taurine) ancestor populations to understand their genetic architecture and detect genomic regions showing signatures of selection. Animals were genotyped using the Illumina BovineLD v2 BeadChip (7K). Genomic structure analysis confirmed that the South African Simbra cattle have an admixed genome, composed of 5/8 Taurine and 3/8 Indicine, ensuring that the Simbra genome maintains favorable traits from both breeds. Genomic regions that have been targeted by selection were detected using the linkage disequilibrium-based methods iHS and Rsb. These analyses identified 10 candidate regions that are potentially under strong positive selection, containing genes implicated in cattle health and production (e.g., TRIM63, KCNA10, NCAM1, SMIM5, MIER3, and SLC24A4). These adaptive alleles likely contribute to the biological and cellular functions determining phenotype in the Simbra hybrid cattle breed. Our data suggested that these alleles were introgressed from the breed's original indicine and taurine ancestors. The Simbra breed thus possesses derived parental alleles that combine the superior traits of the founder Brahman and Simmental breeds. These regions and genes might represent good targets for ad-hoc physiological studies, selection of breeding material and eventually even gene editing, for improved traits in modern cattle breeds. This study represents an important step toward developing and improving strategies for selection and population breeding to ultimately contribute meaningfully to the beef production industry.

Candidate signatures of positive selection for environmental adaptation in indigenous African cattle: A review

“…Studies including African crossbred cattle with exotic breeds (e.g. Cheruiyot et al, 2018; Van der Nest et al, 2021) and/or studies addressing non‐environmental adaptative traits (Nanaei et al, 2020) were excluded. Henceforth, the review was compiled from 22 studies selected using three main criteria: (i) genome‐wide scanning for positive selection; (ii) genome‐wide analysis using genome sequences or SNP‐Chip data; and (iii) inclusion of indigenous African cattle (taurine, zebu, sanga, zenga).…”

Assessing the Genetic Background and Selection Signatures of Huaxi Cattle Using High-Density SNP Array

“…We found that the observed heterozygosity of Huaxi cattle exceeded the expected heterozygosity under the Hardy–Weinberg equilibrium. Hence, crossbreeding is still an important method to expand the genetic variation of modern cattle breeds [ 4 ]. High-intensity artificial selection might promote genetic progress, but it could lead to an increase in the population inbreeding level [ 52 ].…”

“…Hybridization is an important method for improving the desirable performance and overall genetic variation of cattle breeds [ 2 ]. Crossbreeding breeds combine the beneficial traits/genes of their purebred parental breeds, and have more superior production capacity than their parental inbred lines under the effect of heterosis [ 3 , 4 ]. Therefore, the introduction of excellent beef cattle breeds to cultivate specialized beef cattle breeds has become an important way to elevate the individual production efficiency of beef cattle.…”

“…Recently, various statistical methods have been developed to detect footprints of recent selection, including integrated haplotype score (iHS), composite likelihood ratio (CLR), cross-population extended haplotype homozygosity (XPEHH), and relative integrated EHH of a site between populations (Rsb). Application of these methods has greatly promoted the identification of candidate genes related to important economic traits in composite populations, such as Simbra crossbred [ 4 ], Vrindavani cattle [ 26 ], East African Shorthorn Zebu [ 27 ], and Swiss Fleckvieh cattle [ 25 ].…”

Assessing Genomic Diversity and Signatures of Selection in Chinese Red Steppe Cattle Using High-Density SNP Array

“…With the expansion of agricultural society and human activities, extensive blending has occurred between different taurine and indicine populations, so there are more than over 800 live cattle breeds in the world [4]. Hybridization is a common strategy for the formation of modern livestock breeds and improving the undesirable performance of some cattle breeds, which leads to the superiority of a heterozygote over their purebred parental breeds in one or more traits [5]. In China, breeding specialized breeds through crossbreeding with commercial breeds has become an important way to improve the production efficiency of Chinese indigenous breeds.…”