Diversity Of Cattle Breeds Research Articles

Genomic patterns of selection in morphometric traits across diverse Indian cattle breeds.

This study seeks a comprehensive exploration of genome-wide selective processes impacting morphometric traits across diverse cattle breeds, utilizing an array of statistical methods. Morphometric traits, encompassing both qualitative and quantitative variables, play a pivotal role in characterizing and selecting livestock breeds based on their external appearance, size, and physical attributes. While qualitative traits, such as color, horn structure, and coat type, contribute to adaptive features and breed identification, quantitative traits like body weight and conformation measurements bear a closer correlation with production characteristics. This study employs advanced genotyping technologies, including the Illumina BovineSNP50 Bead Chip and next-generation sequencing methods like Reduced Representation sequencing, to identify genomic signatures associated with these traits. We applied four intra-population methods to find evidence of selection, such as Tajima's D, CLR, iHS, and ROH. We found a total of 40 genes under the selection signature, that were associated with morphometric traits in five cattle breeds (Kankrej, Tharparkar, Nelore, Sahiwal, and Gir). Crucial genes such as ADIPDQ, DPP6, INSIG1, SLC35D2 in Kankrej, LPL, ATP6V1B2, CDC14B in Tharparkar, HPSE2, PLAG1 in Nelore, PCSK1, PRKD1 in Sahiwal, and GNAQ, HPCAL1 in Gir were identified in our study. This approach provides valuable insights into the genetic basis of variations in body weight and conformation traits, facilitating informed selection processes and offering a deeper understanding of the evolutionary and domestication processes in diverse cattle breeds.

First characterization of major histocompatibility complex class II DRB3 diversity in cattle breeds raised in Egypt

Genes encoding bovine leukocyte antigen (BoLA) enable the immune system to identify pathogens. Therefore, these genes have been used as genetic markers for infectious and autoimmune diseases as well as for immunological traits in cattle. Although BoLA polymorphisms have been reported in various cattle breeds worldwide, they have not been studied in cattle populations in Egypt. In this study, we characterized BoLA-DRB3 in two local Egyptian populations and one foreign population using polymerase chain reaction-sequence-based typing (PCR-SBT) method. Fifty-four previously reported BoLA-DRB3 alleles and eight new alleles (BoLA-DRB3*005:08, *015:07, *016:03, *017:04, *020:02:02, *021:03, *164:01, and *165:01) were identified. Alignment analysis of the eight new alleles revealed 90.7–98.9 %, and 83.1–97.8 % nucleotide and amino acid identities, respectively, with the BoLA-DRB3 cDNA clone NR-1. Interestingly, BoLA-DRB3 in Egyptian cattle showed a high degree of allelic diversity in native (na = 28, hE > 0.95), mixed (na = 61, hE > 0.96), and Holstein (na = 18, hE > 0.88) populations. BoLA-DRB3*002:01 (14.3 %), BoLA-DRB3*001:01 (8.5 %), and BoLA-DRB3*015:01 (20.2 %) were the most frequent alleles in native, mixed, and Holstein populations, respectively, indicating that the genetic profiles differed in each population. Based on the allele frequencies of BoLA-DRB3, genetic variation among Egyptian, Asian, African, and American breeds was examined using Nei’s distances and principal component analysis. The results suggested that native and mixed cattle populations were most closely associated with African breeds in terms of their gene pool, whereas Holstein cattle were more distinct from the other breeds and were closely related to Holstein cattle populations from other countries.

Genome-Wide Screening for SNPs Associated with Stature in Diverse Cattle Breeds

Cattle breeds used in industrial production tend to be larger than local cattle, as increased dairy and beef productivity is closely related to stature. This study aimed to identify single nucleotide polymorphisms (SNPs) significantly associated with stature in diverse cattle breeds. Thirteen local and transboundary cattle breeds (n = 670) were divided into two groups according to their stature. The high-stature group included the Angus, Ayrshire, Black-and-White, Holstein, Kholmogor, Yaroslavl, Tagil, and Istoben breeds. The low-stature group included Jersey, Kalmyk, Kyrgyz, Mongolian, and Yakut. The average height at withers was 136.3 ± 1.6 and 121.6 ± 2.8 cm in the high- and low-stature groups, respectively. The samples of the 11 breeds were genotyped using high-density DNA arrays. Genotypes of the two remaining breeds were downloaded from the publicly available WIDDE database. Genome-wide association studies revealed seven SNPs strongly associated with stature, including three at 77.3–77.8 cM on BTA4 and four at 24.5–25.2 cM on BTA14. Functional annotation showed the localization within identified regions of genes responsible for growth, exterior characteristics, protein and lipid metabolism, and feed intake. The identified SNPs can be considered useful DNA markers for marker-assisted cattle breeding aimed at increasing stature.

Genome analyses revealed genetic admixture and selection signatures in Bos indicus

The genomic diversity and relationship among seven diverse cattle breeds viz. Sahiwal, Tharparkar, Gir, Vechur, Ongole, Kangayam and Hariana were investigated in 132 random samples based on high density SNP array comprising > 777 K SNPs. A total of 1993 SNPs (0.25% of the total) having greater power (FST ≥ 0.20) to differentiate these cattle populations were identified, and utilized to partition genome of each animal into a predefined number of clusters. The structure of these cattle indicated shared ancestry of dairy breeds viz. Gir, Tharparkar and Sahiwal. Most of the animals (> 76%) of different populations under study except Vechur clustered into their own group of animals called breed. Vechur population retained highest rate of admixture, consistent with its crossing with other breeds. Ongole, Kangayam and Hariana shared comparatively less of their genome (≤ 15%) with other breeds. The study indicated that all seven breeds evolved from their independent ancestry but there was intermixing of these breeds in the recent past. The selection signatures identified between draft (Kangayam) and dairy breeds included several genes like FAM19A2, RAB31P, BEST3, DGKA, AHCY, PIGU and PFKP which are involved in immune response, metabolic pathway, transportation of glucose and sugars, signaling pathways, cellular processes, cell division and glycolysis regulation, respectively. Moreover, these genomic regions also harbour QTLs affecting milk performance traits. The signatures were also identified even between the dairy breeds. In comparison to large-sized cattle, there were significant differences in the number of QTLs affecting production (body weight, growth rate etc.) and morphological traits (height) in short-statured Vechur breed. The presence of HMGA2 gene in the selection signature on chromosome 5 may explain the variations in stature between these cattle.

SNPs in Mammary Gland Epithelial Cells Unraveling Potential Difference in Milk Production Between Jersey and Kashmiri Cattle Using RNA Sequencing

Deep RNA sequencing experiment was employed to detect putative single nucleotide polymorphisms (SNP) in mammary epithelial cells between two diverse cattle breeds (Jersey and Kashmiri) to understand the variations in the coding regions that reflect differences in milk production traits. The low milk-producing Kashmiri cattle are being replaced by crossbreeding practices with Jersey cattle with the aim of improving milk production. However, crossbred animals are prone to infections and various other diseases resulting in unsustainable milk production. In this study, we tend to identify high-impact SNPs from Jersey and Kashmiri cows (utilizing RNA-Seq data) to delineate key pathways mediating milk production traits in both breeds. A total of 607 (442 SNPs and 169 INDELs) and 684 (464 SNPs and 220 INDELs) high-impact variants were found specific to Jersey and Kashmir cattle, respectively. Based on our results, we conclude that in Jersey cattle, genes with high-impact SNPs were enriched in nucleotide excision repair pathway, ABC transporter, and metabolic pathways like glycerolipid metabolism, pyrimidine metabolism, and amino acid synthesis (glycine, serine, and threonine). Whereas, in Kashmiri cattle, the most enriched pathways include endocytosis pathway, innate immunity pathway, antigen processing pathway, insulin resistance pathway, and signaling pathways like TGF beta and AMPK which could be a possible defense mechanism against mammary gland infections. A varied set of SNPs in both breeds, suggests a clear differentiation at the genomic level; further analysis of high-impact SNPs are required to delineate their effect on these pathways.

Tissue-specific fatty acid composition, cellularity, and gene expression in diverse cattle breeds

The nutritional quality of beef relates to the fatty acid (FA) composition of bovine adipose tissue. Those molecular mechanisms that induce the differing amounts and composition of fat in cattle breeds according to age at maturity and purpose of production remain unclear. Therefore, this study investigated the composition of total FAs, adipocyte size, and expression of some key genes involved in several adipogenesis and lipogenesis pathways measured in distinct adipose tissue depots from bulls of the genetically diverse cattle breeds Aberdeen Angus (n = 9), Gascon (n = 10), Holstein (n = 9), and Fleckvieh (n = 10). The animals were finished under identical housing and feeding conditions until slaughter at a similar age of 17 months. After slaughter, cod adipose tissue (CAT), subcutaneous adipose tissue (SAT), and M. longissimus lumborum (MLL) samples were collected. The saturated FA proportions were higher (P < .01) in CAT than in SAT across all breeds, whereas monounsaturated FA proportions were consistently higher (P < .001) in SAT compared to CAT and MLL. Aberdeen Angus bulls were distinguished from the other breeds in the proportions of mostly de novo synthesized C14:0, C16:0, C14:1n-5, C16:1n-7, and conjugated linoleic acid (P < .05). Adipocyte size decreased in the order CAT > SAT > MLL, and the largest adipocytes were observed in CAT of Holstein bulls (P < .05). Gene expression differences were more pronounced between adipose tissue depots than between breeds. The expression levels of ACACA, FASN, and SCD1 genes were related to tissue-specific, and to a lesser extent also breed-specific, differences in FA composition.

217 Young Scholar Presentation: The use of diverse cattle breeds to understand marbling development and growth

Abstract Wagyu cattle have been genetically selected to have superior marbling deposition compared with many other cattle breeds, including Angus. It was hypothesized that greater marbling deposition by Wagyu influenced cattle may be due to an additional wave of adipogenic gene expression compared with Angus cattle. The present study compared the expression of lipid metabolism genes within the longissimus muscle (LM) of Wagyu and Angus sired cattle at similar harvest endpoints: days on feed and age, or body weight (613 kg). Angus sired steers were sired by an Angus bull selected for marbling (T1), while Wagyu sired steers were sired by either a Wagyu bull selected for growth (T2 &amp; T4) or marbling (T3 &amp; T5), at the respective age or body weight endpoints. Cattle were weaned at 7 months of age, entered the feedlot 54 d later, and consumed the same growing (119 d) and finishing ration. Muscle biopsies were collected from the LM posterior to the 13th rib at approximately 7, 9, 11, 14, and 17 months of age (harvest) for T1, T2, and T3 cattle. Muscle biopsies for T4 and T5 cattle were collected when their body weight was similar to T1 cattle at the time of biopsy, approximately 241, 276, 400, 531, and 613 kg (harvest). The high marbling sired Wagyu steers (T3 &amp;T5) had greater marbling scores and percent LM lipid compared with high growth Wagyu (T2 &amp; T4) and Angus sired steers. Gene expression results from high marbling sired Wagyu steers (T3 &amp;T5) demonstrated additional peaks of PPARδ mRNA expression, greater and earlier PPARγ mRNA expression, and greater or additional peaks of GPAM1, LPIN1, and HSL mRNA expression compared with high growth Wagyu (T2 &amp; T4) and Angus sired steers.

BoLA-DRB3 genetic diversity in Highland Creole cattle from Bolivia.

The genetic diversity of the BoLA-DRB3 gene has been reported in different cattle breeds owing to its central role in the immune response. However, it is still unknown in hundreds of cattle breeds, especially native populations. Here, we studied BoLA-DRB3 genetic diversity in Highland Creole cattle (CrAl) from Western Bolivia, raised at altitudes between 3800 and 4200 m. DNAs from 48 CrAl cattle were genotyped for BoLA-DRB3 exon 2 alleles using polymerase chain reaction-sequence-based typing (PCR-SBT). The results were compared with 1341 previously reported data from Tropical Creole cattle and other breeds raised in the region. Twenty-three BoLA-DRB3 alleles were identified in CrAl, including the BoLA-DRB3*029:02 variant previously detected in other Creole cattle. Observed and expected heterozygosity were 0.87 and 0.93, respectively. Nucleotide diversity and the number of pairwise difference values were 0.078 and 19.46, respectively. The average number of nonsynonymous and synonymous substitutions were 0.037 and 0.097 for the entire BoLA-DRB3 exon 2, and 0.129 and 0.388 for the antigen-binding site, respectively. Venn analysis and the review of the IPD-MHC database and the literature showed that 2 of 64 alleles were only detected in CrAl, including BoLA-DRB3*029:01 previously reported in African cattle and *048:01 detected in Philippine cattle. Two additional alleles, BoLA-DRB3*007:02 and *029:02, were only present in CrAl and Lowland Creole cattle. Principal Component Analysis (PCA) showed that Bolivian Creole cattle breeds were closely located but they were distant from the Colombian Hartón del Valle Creole. FST analysis showed a low degree of genetic differentiation between Highland and Lowland Bolivian Creole cattle (FST = 0.015). The present results contribute to increasing our knowledge of BoLA-DRB3 genetic diversity in cattle breeds.

Genome-Wide Identification of Discriminative Genetic Variations in Beef and Dairy Cattle via an Information-Theoretic Approach

Analyzing the associations between genotypic changes and phenotypic traits on a genome-wide scale can contribute to understanding the functional roles of distinct genetic variations during breed development. We performed a whole-genome analysis of Angus and Jersey cattle breeds using conditional mutual information, which is an information-theoretic method estimating the conditional independency among multiple factor variables. The proposed conditional mutual information-based approach allows breed-discriminative genetic variations to be explicitly identified from tens of millions of SNP (single nucleotide polymorphism) positions on a genome-wide scale while minimizing the usage of prior knowledge. Using this data-driven approach, we identified biologically relevant functional genes, including breed-specific variants for cattle traits such as beef and dairy production. The identified lipid-related genes were shown to be significantly associated with lipid and triglyceride metabolism, fat cell differentiation, and muscle development. In addition, we confirmed that milk-related genes are involved in mammary gland development, lactation, and mastitis-associated processes. Our results provide the distinct properties of Angus and Jersey cattle at a genome-wide level. Moreover, this study offers important insights into discovering unrevealed genetic variants for breed-specific traits and the identification of genetic signatures of diverse cattle breeds with respect to target breed-specific properties.

DNA Sequence Variants and Protein Haplotypes of Casein Genes in German Black Pied Cattle (DSN).

Casein proteins were repeatedly examined for protein polymorphisms and frequencies in diverse cattle breeds. The occurrence of casein variants in Holstein Friesian, the leading dairy breed worldwide, is well known. The frequencies of different casein variants in Holstein are likely affected by selection for high milk yield. Compared to Holstein, only little is known about casein variants and their frequencies in German Black Pied cattle (“Deutsches Schwarzbuntes Niederungsrind,” DSN). The DSN population was a main genetic contributor to the current high-yielding Holstein population. The goal of this study was to investigate casein (protein) variants and casein haplotypes in DSN based on the DNA sequence level and to compare these with data from Holstein and other breeds. In the investigated DSN population, we found no variation in the alpha-casein genes CSN1S1 and CSN1S2 and detected only the CSN1S1*B and CSN1S2*A protein variants. For CSN2 and CSN3 genes, non-synonymous single nucleotide polymorphisms leading to three different β and κ protein variants were found, respectively. For β-casein protein variants A 1, A 2, and I were detected, with CSN2*A 1 (82.7%) showing the highest frequency. For κ-casein protein variants A, B, and E were detected in DSN, with the highest frequency of CSN3*A (83.3%). Accordingly, the casein protein haplotype CSN1S1*B-CSN2*A 1-CSN1S2*A-CSN3*A (order of genes on BTA6) is the most frequent haplotype in DSN cattle.

Evaluation of genetic diversity and relationships among eight Russian and Ukrainian cattle breeds based on microsatellite markers

In recent years, special attention has been paid both to the preservation of the genetic diversity of cattle breeds in the Russian Federation and Ukraine, and to the evaluation of the breeds’ ‘purity’, especially in relation to undesirable recessive lethal mutations. The main goal of our work was to assess the genetic diversity of the main cattle breeds bred in the Russian Federation and Ukraine using microsatellite DNA loci, as well as to evaluate the phylogenetic relationships between them. An analysis of molecular genetic diversity was carried out in different cattle breeds represented both in the Russian Federation and Ukraine. A total of 752 individuals, which belonged to eight breeds of the dairy and meat productivity directions were studied. Ten microsatellite loci recommended by ISAG-FAO and arranged in one multiplex panel (ETH3, INRA023, TGLA227, BM1818, TGLA122, SPS115, TGLA53, BM2113, BM1824 and ETH10) were used as DNA markers. Some alleles were found with a very high frequency in most of the studied cattle breeds and, thus, they can be considered as species-specific for the species Bos taurus as a whole. These were alleles 262 and 266 bp (for BM1818), 180 and 188 bp (for BM1824), 125-127 and 133-135 bp (for BM2113), 217-219 bp (for ETH10), 248 and 252 bp (for SPS115). All breeds included in the analysis are characterized by a very high genetic uniqueness based on microsatellite loci; the accuracy of assigning the studied individuals to their own population varied within the range of 95–100%. In general, all breeds studied are grouped into two clusters. Cluster No. 1 contains genetic groups originating from Holstein, and cluster No. 2 contains the remaining breeds. Three breeds (Ayrshire, Simmental and Russian Red Pied) are characterized by very low estimates of the effective population size (less than 50 animals), which may lead to the loss of their genetic uniqueness in the future. In the study of eight dairy and meat cattle breeds that are bred in the Russian Federation and Ukraine, we found that the breeds differ significantly in the genetic polymorphism indicators over ten MS-DNA loci used. Moreover, the level of allelic diversity for the studied breeds was determined, primarily, by the presence and number of rare (and/or “private”) alleles. This may be due to the manifestation of different mechanisms of the formation and maintenance of genetic polymorphism in breeds, based on productivity direction.

Conservation status and historical relatedness of Italian cattle breeds

BackgroundIn the last 50 years, the diversity of cattle breeds has experienced a severe contraction. However, in spite of the growing diffusion of cosmopolite specialized breeds, several local cattle breeds are still farmed in Italy. Genetic characterization of breeds represents an essential step to guide decisions in the management of farm animal genetic resources. The aim of this work was to provide a high-resolution representation of the genome-wide diversity and population structure of Italian local cattle breeds using a medium-density single nucleotide polymorphism (SNP) array.ResultsAfter quality control filtering, the dataset included 31,013 SNPs for 800 samples from 32 breeds. Our results on the genetic diversity of these breeds agree largely with their recorded history. We observed a low level of genetic diversity, which together with the small size of the effective populations, confirmed that several breeds are threatened with extinction. According to the analysis of runs of homozygosity, evidence of recent inbreeding was strong in some local breeds, such as Garfagnina, Mucca Pisana and Pontremolese. Patterns of genetic differentiation, shared ancestry, admixture events, and the phylogenetic tree, all suggest the presence of gene flow, in particular among breeds that originate from the same geographical area, such as the Sicilian breeds. In spite of the complex admixture events that most Italian cattle breeds have experienced, they have preserved distinctive characteristics and can be clearly discriminated, which is probably due to differences in genetic origin, environment, genetic isolation and inbreeding.ConclusionsThis study is the first exhaustive genome-wide analysis of the diversity of Italian cattle breeds. The results are of significant importance because they will help design and implement conservation strategies. Indeed, efforts to maintain genetic diversity in these breeds are needed. Improvement of systems to record and monitor inbreeding in these breeds may contribute to their in situ conservation and, in view of this, the availability of genomic data is a fundamental resource.

The analysis of factors affecting the calving difficulty in Slovak Spotted cattle

Article Details: Received: 2018-09-10 | Accepted: 2018-10-25 | Available online: 2018-09-31 https://doi.org/10.15414/afz.2018.21.03.119-124 The aim of this study was to analyse several genetic and non-genetic factors that can affect the calving difficulty of Slovak Spotted cattle and to find out their statistical significance. A total of 417030 calving difficulty records from 174795 dams were collected during the calving parity from 2001 to 2017. The impact of factors affecting the calving difficulty was analysed by using procGLM implemented in SAS 9.3 on the basis of multifactor analysis of variance. The effects of the herd, a year of calving, the sex of a calf, a breed type, a month of calving, the parity and the sire were tested. The sex of born calf was the most statistically significant factor (R2 =25,5 %). The calving difficulty was significantly affected also by the herd, a year of calving, a month of calving, the parity and sire. Each of these effects showed high level of significance (P<0.001). The lowest level of statistical significance was found for effect of breed type. Based on obtained results we recommend continuing to use the recording of calving difficulty for the purposes of evaluation of effect of sire on inheritance. Keywords: cattle, calving difficulty, non-genetic factors, reproduction References BOGDANYI I. et al. (1996) Breeding target and breed standard of Slovak spotted cattle. Trebisov: Slovak Simmental Breeders Association. CORTES-LACRUZ, X. et al. (2017) Genetic evaluation of calving ease in Parda de Montana beef breed based on linear and threshold models. Web of Science, vol. 113, no. 2, pp. 158– 175. doi: https://doi.org/10.12706/itea.2017.010 EAGLEN, S. A. E. and BIJMA, P. (2009) Genetic parameters of direct and maternal effects for calving ease in Dutch HolsteinFriesian cattle. Journal of Dairy Science, vol. 92, no. 5, pp. 2229– 2237. doi: https://doi.org/10.3168/jds.2008-1654 GAAFAR, H. M. A. et al. (2011) Dystocia in Friesian cows and its effects on postpartum reproductive performance and milk production. Tropical animal health and production, vol. 43, no. 1, pp. 229–234. doi: https://dx.doi.org/10.1007/ s11250-010-9682-3 GRAESBŒLL, K. et al. (2015) Danish Holsteins favor bull offspring: biased milk production as a function of fetal sex, and calving difficulty. Plos One. doi: https://doi.org/10.1371/journal. pone.0124051 HINRICHS, D. and THALLER, G. (2011) Pedigree analysis and inbreeding effects on calving traits in large dairy herds in Germany. Journal of Animal Science, vol. 94, no. 9, pp. 4726– 4733. doi: https://doi.org/10.3168/jds.2010-4100 INOUE, K. et al. (2017) Inferring causal structures and comparing the causal effects among calving difficulty, gestation length and calf size in Japanese Black cattle. Animal, vol. 11, no. 12, pp. 2120–2128. doi: https://doi.org/10.1017/ S1751731117000957 JOHANSON, J. M. and BERGER, P. J. (2003) Birth weight as a predictor of calving ease and perinatal mortality in Holstein cattle. Journal of Dairy Science, vol. 86, no. 11, pp. 3745–3755. doi: https://doi.org/10.3168/jds.S0022-0302(03)73981-2 JUOZAITIENE, V. et al. (2017) Relationship between dystocia and the lactation number, stillbirth and mastitis prevalence in dairy cows. Acta Veterinaria Brno, vol. 86, no. 4, pp. 345–352. doi: https://doi.org/10.2754/avb20178604034 KADLECIK, O. et al. (2013) Diversity of cattle breeds in Slovakia. Slovak Journal of Animal Science, vol. 46, no. 4, pp. 145–150. KOTASEK, M. S. (2012) Evaluation calving difficulty of heifers and cows in the Slovak Republic: Ph.D. Thesis. Nitra: SUA (in Slovak). OLSON, K.M. et al. (2009) Dystocia, stillbirth, gestation length, and birth weight in Holstein, Jersey, and reciprocal crosses from a planned experiment. Journal of Dairy Science, vol. 92, no. 12, pp. 6167–6175. doi: https://doi.org/10.3168/ jds.2009-2260 RYBA, S. (2010) Evaluation calving difficulty cows of individual breeds in the Slovak Republic: Ph.D. Thesis. Nitra: Slovak university of agriculture (in Slovak). SAS Institute Inc. (2011) SAS 9.3 Statements: Reference. Cary, NC: SAS Institute Inc. SCHAEFFER, L. R. (2003) Application of random regression models in animal breeding. Livestock production Science, vol. 86, no. 1–3, pp. 35–45. doi: https://doi.org/10.1016/ S0301-6226(03)00151-9 SHAVHUZHEV, A. and BELIK N. (2017) Milk productivity of Simmental cows Austrian selection. In: 16th International Scientific Conference Engineering for Rural Development: Proceedings, 24–26. 5. 2017 Jelgava, Latvia, pp. 1354–1358. doi: http://dx.doi.org/10.22616/ERDev2017.16.N304 SILVESTRE, A. Et al. (2018) Genetic parameters of calving ease in dairy cattle using threshold and linear models. 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Whole Genome Resequencing of Heugu (Korean Black Cattle) for the Genome-Wide SNP Discovery

Heugu (Korea Black Cattle) is one of the indigenous cattle breeds in Korea; however there has been severe lack of genomic studies on the breed. In this study, we report the first whole genome resequencing of Heugu at higher sequence coverage using Illumina HiSeq 2000 platform. More than 153.6 Giga base pairs sequence was obtained, of which 97% of the reads were mapped to the bovine reference sequence assembly (UMD 3.1). The number of non-redundantly mapped sequence reads corresponds to approximately 28.9-fold coverage across the genome. From these data, we identified a total of over six million single nucleotide polymorphisms (SNPs), of which 29.4% were found to be novel using the single nucleotide polymorphism database build 137. Extensive annotation was performed on all the detected SNPs, showing that most of SNPs were located in intergenic regions (70.7%), which is well corresponded with previous studies. Of the total SNPs, we identified substantial numbers of non-synonymous SNPs (13,979) in 5,999 genes, which could potentially affect meat quality traits in cattle. These results provide genome-wide SNPs that can serve as useful genetic tools and as candidates in searches for phenotype-altering DNA difference implicated with meat quality traits in cattle. The importance of this study can be further pronounced with the first whole genome sequencing of the valuable local genetic resource to be used in further genomic comparison studies with diverse cattle breeds.

Detection of selective sweeps in cattle using genome-wide SNP data

BackgroundThe domestication and subsequent selection by humans to create breeds and biological types of cattle undoubtedly altered the patterning of variation within their genomes. Strong selection to fix advantageous large-effect mutations underlying domesticability, breed characteristics or productivity created selective sweeps in which variation was lost in the chromosomal region flanking the selected allele. Selective sweeps have now been identified in the genomes of many animal species including humans, dogs, horses, and chickens. Here, we attempt to identify and characterise regions of the bovine genome that have been subjected to selective sweeps.ResultsTwo datasets were used for the discovery and validation of selective sweeps via the fixation of alleles at a series of contiguous SNP loci. BovineSNP50 data were used to identify 28 putative sweep regions among 14 diverse cattle breeds. Affymetrix BOS 1 prescreening assay data for five breeds were used to identify 85 regions and validate 5 regions identified using the BovineSNP50 data. Many genes are located within these regions and the lack of sequence data for the analysed breeds precludes the nomination of selected genes or variants and limits the prediction of the selected phenotypes. However, phenotypes that we predict to have historically been under strong selection include horned-polled, coat colour, stature, ear morphology, and behaviour.ConclusionsThe bias towards common SNPs in the design of the BovineSNP50 assay led to the identification of recent selective sweeps associated with breed formation and common to only a small number of breeds rather than ancient events associated with domestication which could potentially be common to all European taurines. The limited SNP density, or marker resolution, of the BovineSNP50 assay significantly impacted the rate of false discovery of selective sweeps, however, we found sweeps in common between breeds which were confirmed using an ultra-high-density assay scored in a small number of animals from a subset of the breeds. No sweep regions were shared between indicine and taurine breeds reflecting their divergent selection histories and the very different environmental habitats to which these sub-species have adapted.

Genomic diversity in cattle breeds assessed using polymorphism of intermicrosatellite markers

Genomic diversity in cattle breeds assessed using polymorphism of intermicrosatellite markers

Evaluation of genetic diversity and population structure of west-central Indian cattle breeds

Evaluations of genetic diversity in domestic livestock populations are necessary to implement region-specific conservation measures. We determined the genetic diversity and evolutionary relationships among eight geographically and phenotypically diverse cattle breeds indigenous to west-central India by genotyping these animals for 22 microsatellite loci. A total of 326 alleles were detected, and the expected heterozygosity ranged from 0.614 (Kenkatha) to 0.701 (Dangi). The mean number of alleles among the cattle breeds ranged from 7.182 (Khillar) to 9.409 (Gaolao). There were abundant genetic variations displayed within breeds, and the genetic differentiation was also high between the Indian cattle breeds, which displayed 15.9% of the total genetic differentiation among the different breeds. The genetic differentiation (pairwise FST ) among the eight Indian breeds varied from 0.0126 for the Kankrej-Malvi pair to 0.2667 for Khillar-Kenkatha pair. The phylogeny, principal components analysis, and structure analysis further supported close grouping of Kankrej, Malvi, Nimari and Gir; Gaolao and Kenkatha, whereas Dangi and Khillar remained at distance from other breeds.

Cattle in the West African savanna: evidence from 1st millennium CE Kirikongo, Burkina Faso

The West African sahel and savanna are today home to diverse cattle breeds derived from complex social, political and environmental processes over at least the past four thousand years. Current evidence from the sahel and its floodplains indicates multiple sizes of cattle over time that may correspond to modern breeds. However, little is known about the cattle further south in the savanna, such as the West African Shorthorn. These humpless cattle are well adapted to the environmental conditions of more humid zones, including their significant resistance to trypanosomiasis, or sleeping sickness. In this paper I present new archaeozoological data from the Iron Age village of Kirikongo, Burkina Faso (100–1700 CE) that indicate the presence of small cattle in the 1st millennium CE similar in size to West African Shorthorn. These results are contextualized through comparisons with other archaeological sites and environmental data in Central West Africa, suggesting that small cattle are generally associated with the savanna environment over time, and their distributions may have oscillated with climatic changes. Lastly, interregional processes are assessed given Kirikongo’s evidence for small savanna cattle in western Burkina Faso and their subsequent adoption in the Inland Niger Delta of Mali.

Telomere Length Diversity in Cattle Breeds

Telomeres are specialized nucleoprotein structures that have two important functions: (i) protection of the chromosomal ends from deleterious events such as chromosome fusion and degradation; (ii) counteraction of the “end replication problem” by allowing telomerase-dependent or, more rarely, telomerase-independent telomere elongation. The DNA sequences underlying these activities are short simple tandem repeats, which in vertebrate consist of a variable number of TTAGGG. Telomeres dysfunction may be caused either by the absence of telomerase activity or by mutations in telomeric proteins involved in telomere length and structure regulation. Additionally, increasing experimental evidence suggests that telomeres take part in the complex network regulating cell proliferation. Accordingly, telomeres are involved in biological process such as aging and tumor progression. In this study we determined the telomere length in two bovine Italian cattle breeds, Chianina and Maremmana, which are characterized by high longevity and range breeding. In order to account for possible variation among different tissues, we have determined telomere length in different organs such as spleen, lung and liver. Overall, the median telomere length was significant lower in Chianina (11 ± 0.69 kb) than in Maremmana (12.05 ± 1.57 kb). Moreover, telomere length variation among individuals was very low in Chianina but rather high in Maremmana. These data suggest that telomere length is influenced by the breeds. This hypothesis is confirmed by the different history of these Italian breeds. Indeed, Chianina has a long history and its size was maintained by the Breeders Association without necessity to crossbreed with other breeds, whereas the population of Maremmana underwent a dramatic shrinkage in the recent past. Therefore, breeders have crossed Maremmana with other breeds, like Charolais, and have relaxed the rules for the inclusion in the herd book.

Analysis of copy number variations among diverse cattle breeds

Genomic structural variation is an important and abundant source of genetic and phenotypic variation. Here, we describe the first systematic and genome-wide analysis of copy number variations (CNVs) in modern domesticated cattle using array comparative genomic hybridization (array CGH), quantitative PCR (qPCR), and fluorescent in situ hybridization (FISH). The array CGH panel included 90 animals from 11 Bos taurus, three Bos indicus, and three composite breeds for beef, dairy, or dual purpose. We identified over 200 candidate CNV regions (CNVRs) in total and 177 within known chromosomes, which harbor or are adjacent to gains or losses. These 177 high-confidence CNVRs cover 28.1 megabases or approximately 1.07% of the genome. Over 50% of the CNVRs (89/177) were found in multiple animals or breeds and analysis revealed breed-specific frequency differences and reflected aspects of the known ancestry of these cattle breeds. Selected CNVs were further validated by independent methods using qPCR and FISH. Approximately 67% of the CNVRs (119/177) completely or partially span cattle genes and 61% of the CNVRs (108/177) directly overlap with segmental duplications. The CNVRs span about 400 annotated cattle genes that are significantly enriched for specific biological functions, such as immunity, lactation, reproduction, and rumination. Multiple gene families, including ULBP, have gone through ruminant lineage-specific gene amplification. We detected and confirmed marked differences in their CNV frequencies across diverse breeds, indicating that some cattle CNVs are likely to arise independently in breeds and contribute to breed differences. Our results provide a valuable resource beyond microsatellites and single nucleotide polymorphisms to explore the full dimension of genetic variability for future cattle genomic research.