Determination of Genetic Structure and Signatures of Selection in Three Strains of Tanzania Shorthorn Zebu, Boran and Friesian Cattle by Genome-Wide SNP Analyses

Abstract

BackgroundMore than 90 percent of cattle in Tanzania belong to the indigenous Tanzania Short Horn Zebu (TSZ) population which has been classified into 12 strains based on historical evidence, morphological characteristics, and geographic distribution. However, specific genetic information of each TSZ population has been lacking and has caused difficulties in designing programs such as selection, crossbreeding, breed improvement or conservation. This study was designed to evaluate the genetic structure, assess genetic relationships, and to identify signatures of selection among cattle of Tanzania with the main goal of understanding genetic relationship, variation and uniqueness among them.Methodology/Principal findingsThe Illumina Bos indicus SNP 80K BeadChip was used to genotype genome wide SNPs in 168 DNA samples obtained from three strains of TSZ cattle namely Maasai, Tarime and Sukuma as well as two comparative breeds; Boran and Friesian. Population structure and signatures of selection were examined using principal component analysis (PCA), admixture analysis, pairwise distances (FST), integrated haplotype score (iHS), identical by state (IBS) and runs of homozygosity (ROH). There was a low level of inbreeding (F~0.01) in the TSZ population compared to the Boran and Friesian breeds. The analyses of FST, IBS and admixture identified no considerable differentiation between TSZ trains. Importantly, common ancestry in Boran and TSZ were revealed based on admixture and IBD, implying gene flow between two populations. In addition, Friesian ancestry was found in Boran. A few common significant iHS were detected, which may reflect influence of recent selection in each breed or strain.ConclusionsPopulation admixture and selection signatures could be applied to develop conservation plan of TSZ cattle as well as future breeding programs in East African cattle.

Weighted likelihood inference of genomic autozygosity patterns in dense genotype data

“…Studies of ROA in the genomes of ancient hominins [29][30][31] and early Europeans [32] have provided unique insights into the mating patterns and effective population sizes of our early forbearers. In non-humans, ROA patterns have provided insights into the differential histories of woolly mammoth [33], great ape [34,35], cat [36], canid [37][38][39][40][41][42], and bird [43] populations, while in livestock breeds they have provided insights into their origins, relationships, and recent management [42,[44][45][46][47][48][49][50][51][52][53][54][55][56][57][58][59][60][61] and the lasting effects of artificial section [58,[61][62][63][64][65][66][67][68][69][70][71][72]…”

Possibilities of Utilizing Biotechnology to Improve Animal and Animal Feeds Productivity in Tanzania – Review of Past Efforts and Available Opportunities

“…3 A larger percent of animals raised in Tanzania belong to the native populations which have been characterized to be low producers of meat, milk and eggs due to poor genetic potential. [4][5][6] For example, Tanzania Shorthorn Zebu (TSZ) animals which form 95% of all cattle and produce over 70% and 90% of milk and meat respectively are characterized by slow growth rates, low mature weight, long calving intervals, as well as low meat and milk yield. 1 Of the 16.7million goats about 98% belongs to the native Small East African (SEA) breed estimated to have low growth rates between 5 and 7g/day, small mature size ranging from 20 to 25kg and low carcass weights about 6 to 13kg.…”

“…Previous examples include characterization of TSZ using random amplified polymorphic DNA (RAPD) and microsatellite markers 4,51 as well as evaluation of genetic diversity in SEA goats using microsatellite DNA markers. 52 Recently Msalya et al 5 reported the genetic structure in three TSZ strains and Tanzanian Boran and Friesian breeds using genome-wide SNPs. 5 In the study, three indigenous strains of TSZ namely Sukuma, Tarime, and Maasai showed low genetic differentiation (F ST ) ranging from 0.011 to 0.013 among them (Table 1).…”

“…52 Recently Msalya et al 5 reported the genetic structure in three TSZ strains and Tanzanian Boran and Friesian breeds using genome-wide SNPs. 5 In the study, three indigenous strains of TSZ namely Sukuma, Tarime, and Maasai showed low genetic differentiation (F ST ) ranging from 0.011 to 0.013 among them (Table 1). Boran and Friesian breeds showed greater values of F ST than the TSZ strains.…”

“…Furthermore, admixtures were observed among the TSZ animals and can be treated as one major cluster. 5 Although TSZ are treated as different strains at present, 6,51 it is currently difficult to define and genetically differentiate one strain of TSZ from another. However, the TSZ were differentiated from Boran and Friesian breeds (Figure 1).…”