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.

Single nucleotide polymorphisms within exon four of the prolactin gene and their effect on milk traits in cattle populations of Ethiopia.

Bovine prolactin (PRL) gene is essential for the initiation and maintenance of lactation and exerts multiple effects on mammary alveoli to promote the synthesis and secretion of major components of milk. The objectives of this study were to identify mutations in PRL gene and to evaluate the mutations as potential markers of milk performance traits in cattle populations of Ethiopia. For this purpose, genomic DNA from whole blood was extracted through salting out procedure from 87 animals of five cattle populations of Ethiopia. Accordingly, three single nucleotide polymorphisms (SNPs) were identified of which one SNP g.8323T > A showed missense mutation while the other two SNPs revealed silent mutations. FST values showed statistically significant genetic differentiation among the studied populations. Intermediate polymorphic information content was noted for most SNPs, which indicates the presence of sufficient genetic variation at this locus. Two SNPs showed heterozygote deficiency as a result of positive FIS values. Only g.8398A > G SNP have statistically significant (p < 0.05) effect on average daily milk yield, fat and solid not fat percentage in all studied cattle populations. Therefore, g.8398A > G SNP identified in this study influences cattle milk production and may be used as possible candidate SNP for marker-assisted selection programs in cattle populations of Ethiopia.

Multivariate characterization of phenotypic traits of five native cattle populations from Tigray, Northern Ethiopia.

Abergelle, Arado, Begait, Irob, and Raya are important native cattle populations that are well adapted to the harsh natural conditions in Tigray, Ethiopia. However, little is known about their phenotypic characteristics and inter-population variability. Understanding the phenotypic characteristics is the crucial step in an effort of maintaining genetic diversity and conserving important traits for adaptation. A total of 1650 native matured cattle from the five populations were used to investigate the phenotypic characteristics and variability based on 21 qualitative traits and 21 body measurements using uni- and multivariate, and discriminant analysis. All the qualitative traits and body measurements showed highly significant breed difference except the tail base thickness. Values for most of the body measurements were higher in Begait cattle compared to the other cattle populations. The stepwise discriminant analysis extracted eighteen variables for characterizing the female populations and thirteen variables for the male populations. The pair-wise Mahalanobis distance showed the highest morphological distance between Begait and Irob, and the closest distance between Abergelle and Irob cattle populations. High correct assignment to source population was obtained for both sexes of all breeds except Abergelle and Irob. The discriminant function graph discerned each population with no clear distinction between Abergelle and Irob. These results indicate that the five cattle populations under investigation are clustered into four distinct breeds. However, the present phenotypic characterization should be confirmed with molecular genetic diversity investigation to use as a base in their conservation, breeding, and selection strategies.

Precipitation extremes in recent decades impact cattle populations at the global and national scales.

Cattle populations are one of the most important global ecological drivers. The global cattle population tripled during the past century, leading to large impacts on nutrient cycling, greenhouse gas emissions and biodiversity loss. Nonetheless, their populations have not increased uniformly through the last seven decades (1961-2018), with large unexplained variation between years. We hypothesized a main driver for such fluctuation was climate variability and thus examined global and national level relationships between cattle population growth and precipitation anomalies for the period 1961-2017. We showed that the variation in the global cattle population growth rate was related to precipitation anomalies following a distinctive parabolic relationship, where extreme wetness or dryness decreased population growth. When the analysis was downscaled to the national level, we found the strength of such relationship to be determined by the background climate and management intensity. Countries in drier climates and with less intensive cattle management showed the largest susceptibility to extreme annual precipitation. We propose a general model to explain the relationship between precipitation extremes and cattle populations at multiple scales, based on ecological processes applicable to grazing systems.

Genome-wide detection of signatures of selection in three Valdostana cattle populations.

The Valdostana is a local dual purpose cattle breed developed in Italy. Three populations are recognized within this breed, based on coat colour, production level, morphology and temperament: Valdostana Red Pied (VPR), Valdostana Black Pied (VPN) and Valdostana Chestnut (VCA). Here, we investigated putative genomic regions under selection among these three populations using the Bovine 50K SNP array by combining three different statistical methods based either on allele frequencies (FST ) or extended haplotype homozygosity (iHS and Rsb). In total, 8, 5 and 8 chromosomes harbouring 13, 13 and 16 genomic regions potentially under selection were identified by at least two approaches in VPR, VPN and VCA, respectively. Most of these candidate regions were population-specific but we found one common genomic region spanning 2.38 Mb on BTA06 which either overlaps or is located close to runs of homozygosity islands detected in the three populations. This region included inter alia two well-known genes: KDR, a well-established coat colour gene, and CLOCK, which plays a central role in positive regulation of inflammatory response and in the regulation of the mammalian circadian rhythm. The other candidate regions identified harboured genes associated mainly with milk and meat traits as well as genes involved in immune response/inflammation or associated with behavioural traits. This last category of genes was mainly identified in VCA, which is selected for fighting ability. Overall, our results provide, for the first time, a glimpse into regions of the genome targeted by selection in Valdostana cattle. Finally, this study illustrates the relevance of using multiple complementary approaches to identify genomic regions putatively under selection in livestock.

Genetic variability of Tropical Milking Criollo cattle of Mexico estimated from genealogy information / Variabilidad genética de la raza bovina criolla Lechero Tropical de México estimada a partir de información genealógica / Variabilidade genética da raça bovina crioula Leiteiro Tropical do México estimada a partir de informação genealógica

Abstract Background: Genetic variability of populations is essential for their genetic conservation and improvement, and genealogy analysis is a useful tool to estimate it. Objective: To determine genetic variability and inbreeding levels in Tropical Milking Criollo (LT). Methods: This study analyzed the genealogy of LT using the ENDOG software. Registration certificates of 3,427 LT animals born between 1945 and 2013, and from 608 born between 1950 and 2013 were used. Two populations were defined: the first one with all registered animals (PLT), and the second with nucleus animals (PCP). Results: Estimates for PLT and PCP were: founders 890, 114; ancestors 855, 102; effective founders 111, 43; effective ancestors 72, 26, and effective population size 68.1 and 64.6, respectively. Inbreeding coefficients were 4.32 and 3.48% for the highest genetic integrity index; and the average relatedness (AR) coefficients were 1.19 and 5.55 for PLT and PCP, respectively. Genealogy depth was shallow in both populations, with full equivalent generations of 2.00 and 3.53. Global generation intervals were about seven years. Conclusions: The LT population is not endangered and its genetic improvement program should continue.

Resumen Antecedentes: la variabilidad genética de las poblaciones es esencial para su conservación y mejora genética, y el análisis de genealogía es útil para estimarla. Objetivo: determinar la variabilidad genética y los niveles de consanguinidad en la raza criolla Lechero Tropical (LT). Métodos: el estudio analizó la genealogía de la raza criolla LT con el programa ENDOG v4.8. Se utilizaron 3.427 registros de animales LT nacidos entre 1945 y 2013, y de 608 nacidos entre 1950 y 2013. Se definieron dos poblaciones, una que incluye todos los animales registrados (PLT) y otra solamente con los animales provenientes del núcleo genético (PCP). Resultados: en la PLT y PCP se estimaron animales fundadores 890, 114; ancestros 855, 102; número efectivo de fundadores 111, 43; número efectivo de ancestros 72, 26, y tamaño efectivo de población 68,1, 64,6, respectivamente. Para la categoría más alta de índice de integridad genética, los coeficientes de consanguinidad fueron 4,32 y 3,48%; y el coeficiente medio de relación global (AR) fue 1,19 y 5,55 para PLT y PCP, respectivamente. La profundidad de la genealogía en ambas poblaciones fue superficial con generaciones completas equivalentes de 2,00 y 3,53. Los intervalos generacionales globales fueron cercanos a siete años. Conclusiones: la población LT no se encuentra en riesgo de extinción y puede continuar con su programa de mejora genética.

Resumo Antecedentes: a variabilidade genética das populações é essencial para sua conservação e melhora genética e a análise da genealogia é útil para estimá-la. Objetivo: determinar a variabilidade genética e os níveis de consanguinidade na raça crioula Leiteiro Tropical (LT). Métodos: o estudo analisou a genealogia da raça crioula LT com o programa ENDOG v4.8. Foram utilizaram 3.427 registros de animais LT nascidos de 1945 a 2013, e de 608 nascidos entre 1950 e 2013. Foram definidas duas populações, uma que inclui todos os animais registrados (PLT) e outra somente com os animais provenientes do núcleo genético (PCP). Resultados: na PLT e PCP foram estimados animais fundadores 890, 114; ascendentes 855, 102; número efetivo de fundadores 111, 43; número efetivo de ascendentes 72, 26 e tamanho efetivo da população 68,1, 64.6, respectivamente. Para a categoria mais alta de índice de integridade genética os coeficientes de consanguinidade foram 4,32 e 3,48%; o coeficiente médio da relação global (AR) foi 1,19 e 5,55 para PLT e PCP, respectivamente. A profundidade da genealogia em ambas populações foi superficial com gerações completas equivalentes de 2,00 e 3,53. Os intervalos geracionais globais foram próximos a sete anos. Conclusões: a população LT não se encontra em risco de extinção e pode continuar com seu programa de melhoria genética.

Population genetic structure of Theileria parva field isolates from indigenous cattle populations of Uganda.

Theileria parva causes East Coast Fever (ECF) a protozoan infection which manifests as a non-symptomatic syndrome among endemically stable indigenous cattle populations. Knowledge of the current genetic diversity and population structure of T. parva is critical for predicting pathogen evolutionary trends to inform development of effective control strategies. In this study the population genetic structure of 78 field isolates of T. parva from indigenous cattle (Ankole, n=41 and East African shorthorn Zebu (EASZ), n=37) sampled from the different agro ecological zones (AEZs) of Uganda was investigated. A total of eight mini- and micro-satellite markers encompassing the four chromosomes of T. parva were used to genotype the study field isolates. The genetic diversity of the surveyed T. parva populations was observed to range from 0.643±0.55 to 0.663±0.41 among the Central and Western AEZs respectively. The overall Wright's F index showed significant genetic variation between the surveyed T. parva populations based on the different AEZs and indigenous cattle breeds (FST=0.133, p<0.01) and (FST=0.101, p<0.01) respectively. Significant pairwise population genetic differentiations (p<0.05) were observed with FST values ranging from 0.048 to 0.173 between the eastern and northern, eastern and western populations respectively. The principal component analysis (PCA) showed a high level of genetic and geographic sub-structuring among populations. Linkage disequilibrium was observed when populations from all the study AEZs were treated as a single population and when analysed separately. On the overall, the significant genetic diversity and geographic sub-structuring exhibited among the study T. parva isolates has critical implications for ECF control.

Spatial distribution of Brucella antibodies with reference to indigenous cattle populations among contrasting agro-ecological zones of Uganda.

Indigenous cattle populations exhibit various degrees of agro-ecological fitness and provide desirable opportunities for investments to improve sustainable production for better rural small-scale farmers' incomes globally. However, they could be a source of infection to their attendants and other susceptible livestock if their brucellosis status remains unknown. This study investigated the spatial distribution of Brucella antibodies among indigenous cattle populations in Uganda. Sera from a total of 925 indigenous cattle (410 Ankole Bos taurus indicus, 50 Nganda and 465 East African Shorthorn Zebu (EASZ) - B. indicus) obtained randomly from 209 herds spread throughout Uganda were sequentially analysed for Brucella antibodies using the indirect (I) and competitive (C) enzyme linked Immuno-sorbent assays (ELISA). Recent incidences of abortion within the previous 12 months and routine hygienic practices during parturition were explored for public health risks. Brucella antibodies occurred in approximately 8.64% (80/925) and 28.70% (95% CI: 22.52, 34.89) of the sampled individual cattle and herds, respectively. Findings have shown that Ankole and EASZ cattle had similar seroprevalences. Indigenous cattle from the different study agro-ecological zones (AEZs) exhibited varying seroprevalences ranging from approximately 1.78% (95% CI: 0, 5.29) to 19.67% (95% CI: 8.99, 30.35) in the Lake Victoria Crescent (LVC) and North Eastern Drylands (NED) respectively. Significantly higher odds for Brucella antibodies occurred in the NED (OR: 3.40, 95% CI: 1.34, 8.57, p=0.01) inhabited by EASZ cattle compared to the KP (reference category) AEZ. Recent incidences of abortions within the previous 12 months were significantly (p<0.001) associated with seropositive herds. These findings add critical evidence to existing information on the widespread occurrence of brucellosis among indigenous cattle populations in Uganda and could guide allocation of meagre resources for awareness creation. And deployment of control strategies including culling of older cattle and those which have aborted during advanced gestation, enforcement of hygiene practices and mass vaccination.

Linkage disequilibrium and genomic scan to detect selective loci in cattle populations adapted to different ecological conditions in Ethiopia.

Despite the wide range of observed phenotypic diversities and adaptation to different ecological conditions, little has been studied regarding the genetics of adaptation in the genome of indigenous cattle breeds of developing countries. Here, we investigated the linkage disequilibrium (LD) and identified the subset of outlier loci that are highly differentiated among cattle populations adapted to different ecological conditions in Ethiopia. Specifically, we genotyped 47 unrelated animals sampled from high- versus low-altitude environments using a Bovine 50K SNP BeadChip. Linkage disequilibrium was assessed using both D' and r(2) between adjacent SNPs. We calculated FST and heterozygosity at different significance levels as measures of genetic differentiation for each locus between high- and low-altitude populations following the hierarchical island model approach. We identified 816 loci (p < 0.01) showing selection signals and are associated with genes that might have roles in local adaptation. Some of them are associated with candidate genes that are involved in metabolism (ATP2A3, CA2, MYO18B, SIK3, INPP4A, and IREB2), hypoxia response (BDNF, TFRC, and PML) and heat stress (PRKDC, CDK1, and TFDC). Average r(2) and D' values were 0.14 ± 0.21 and 0.57 ± 0.34, respectively, for a minor allele frequency (MAF) ≥ 0.05 and were found to increase with increasing MAF value. The outlier loci identified in the studied Ethiopian cattle populations indicate the presence of genetic variation produced/shaped by adaptation to different environmental conditions and provide a basis for further validation and functional analysis using a reasonable sample size and high-density markers.