Sustainable Intensification of Beef Production in the Tropics: The Role of Genetically Improving Sexual Precocity of Heifers

Increasing productivity through continued animal genetic improvement is a crucial part of implementing sustainable livestock intensification programs. In Zebu cattle, the lack of sexual precocity is one of the main obstacles to improving beef production efficiency. Puberty-related traits are complex, but large-scale data sets from different “omics” have provided information on specific genes and biological processes with major effects on the expression of such traits, which can greatly increase animal genetic evaluation. In addition, genetic parameter estimates and genomic predictions involving sexual precocity indicator traits and productive, reproductive, and feed-efficiency related traits highlighted the feasibility and importance of direct selection for anticipating heifer reproductive life. Indeed, the case study of selection for sexual precocity in Nellore breeding programs presented here show that, in 12 years of selection for female early precocity and improved management practices, the phenotypic means of age at first calving showed a strong decreasing trend, changing from nearly 34 to less than 28 months, with a genetic trend of almost −2 days/year. In this period, the percentage of early pregnancy in the herds changed from around 10% to more than 60%, showing that the genetic improvement of heifer’s sexual precocity allows optimizing the productive cycle by reducing the number of unproductive animals in the herd. It has a direct impact on sustainability by better use of resources. Genomic selection breeding programs accounting for genotype by environment interaction represent promising tools for accelerating genetic progress for sexual precocity in tropical beef cattle.

Validation of somatic cell score-associated SNPs from Holstein cattle in Sudanese Butana and Butana × Holstein crossbred cattle

The Bos indicus zebu cattle Butana is the most commonly used indigenous dairy cattle breed in Sudan. In the last years, high-yielding Holstein dairy cattle were introgressed into Butana cattle to improve their milk yield and simultaneously keep their good adaption to extreme environmental conditions. With the focus on the improvement of milk production, other problems arose such as an increased susceptibility to mastitis. Thus, genetic selection for mastitis resistance should be considered to maintain healthy and productive cows. In this study, we tested 10 single nucleotide polymorphisms (SNPs) which had been associated with somatic cell score (SCS) in Holstein cattle for association with SCS in 37 purebred Butana and 203 Butana × Holstein crossbred cattle from Sudan. Animals were genotyped by competitive allele-specific PCR assays and association analysis was performed using a linear mixed model. All 10 SNPs were segregating in the crossbred Butana × Holstein populations, but only 8 SNPs in Sudanese purebred Butana cattle. The SNP on chromosome 13 was suggestively associated with SCS in the Butana × Holstein crossbred population (rs109441194, 13:79,365,467, PBF = 0.054) and the SNP on chromosome 19 was significantly associated with SCS in both populations (rs41257403, 19:50,027,458, Butana: PBF = 0.003, Butana × Holstein: PBF = 6.2 × 10−16). The minor allele of both SNPs showed an increase in SCS. Therefore, selection against the disadvantageous minor allele could be used for genetic improvement of mastitis resistance in the studied populations. However, investigations in a bigger population and across the whole genome are needed to identify additional genomic loci.

Phenotypic characteristics and Gene Frequency of the Banyo Gudali zebu (Bos indicus) variety in the high Guinean Savannah zone of Cameroon

This study is aimed at evaluating the phenptypic and genetic diversity of local cattle breeds in Cameroon. To this end, biometric data were collected randomly in six (6) localities of the Mayo-Banyo Division, on a sample of 321 adult Banyo Gudali zebu cattle (234 cows and 87 bulls) aged between 6 and 16 years and having a body condition score varying from 2 to 4. Results reveal a variability of the coat color i.e., 19,00% white coat and its derivatives (speckled, stoat, grey, truiture); 9.99% black coat and its derivatives (black list and black piebald); 18.06% piebald (4.67% black piebald and 13.39 red piebald); 52.94% red and its derivatives (red piebald and red list). The single-colored coats are less represented (38.94%)compared to double-colored coats (61.06%). The frequency of alleles S+, D, ED, Aa, E+, s, A+, e and P are respectively 0.315; 0.201; 0.140; 0.267; 0.859; 0.685; 0.733; 0.386 and 1.000. There is a predominance of white-black horns (50.2%) over grey horns (42.4%). This population is characterized by long hairs, straight-edged ears oriented laterally and with humps occupying a cervico-thoracic position. The facial and back profiles are straight. The neck has a horizontal curved profile, the rump with a low set tail. Crescent shaped horns predominate (73,5%) followed by the horns in low lyre (15,9%) with the other shapes (stump, lateral pointed tip, crown and asymmetrical deformed right or left) being the least represented. The raised horns (92.5%) are predominant. Erect and moderate humps (86.6%) are dominant over drooping ones (13.4%).

A Survey of Tick Infestation and Tick-Borne Piroplasm Infection of Cattle in Oudalan and Séno Provinces, Northern Burkina Faso

In this study, cattle farms located in Oudalan and Séno, two provinces in the Sahel region, northern Burkina Faso, were surveyed. Cattle owners were interviewed, cattle were examined for tick infestation, and ticks as well as blood samples were collected during the dry season (October). Blood DNA samples were tested for Babesia and Theileria infections using nested PCRs and sequencing. A total of 22 herds, 174 Zebu cattle were investigated at 6 different sites. Overall, 76 cattle (43.7 %) from 18 farms (81.8%) were found infested with ticks. Cattle in Séno, adult cattle (>5 years) and those owned by the Fulani ethnic group were significantly (p < 0.05) more likely to be tick-infested. A total of 144 adult ticks belonging to five species namely: Hyalomma impeltatum, Hyalomma impressum, Hyalomma rufipes, Rhipicephalus evertsi evertsi, and Rhipicephalus guilhoni were collected from the animals. Piroplasms were detected in the blood DNA of 23 (13.2%) cattle. The cattle in Séno and adult cattle were significantly more likely to be piroplasm-positive. Five pathogens diversely distributed were identified. Theileria mutans (12/174), Babesia bigemina (5/174), Theileria annulata (3/174), and Theileria velifera (3/174) were detected for the first time in northern Burkina Faso, whereas Babesia occultans (1/174) was found for the first time in cattle in West Africa. The analysis of the sequences, including B. bigemina RAP-1a, T. annulata Tams1 genes, and the 18S rRNA genes of all the five protozoa, revealed identities ranging from 98.4 to 100% with previously published sequences. Phylogenetic analysis based on the 18S rRNA gene sequences located north Burkina Faso piroplasms in the same clade as isolates from Africa and other regions of the world. Notably, T. mutans sequences were distributed in two clades: the T. mutans Intona strain clade and the Theileria sp. (strain MSD)/ Theileria sp. B15a clade, suggesting the presence of at least two strains in the area. These findings indicate that the control of ticks and tick-borne diseases should be taken into account in strategies to improve animal health in the Sahel region.

Genomic signatures of desert adaptation at gene-rich regions in zebu cattle from the African drylands

Sudan, the largest country in Africa, acts as a corridor between North and sub-Saharan Africa along the river Niles. It comprises warm arid and semi-arid grazing lands, and it is home to the second-largest African population of indigenous livestock. Indigenous Sudanese cattle are mainly indicine/zebu (humped) type. They thrive in the harshest dryland environments characterised by high temperatures, long seasonal dry periods, nutritional shortages, and vector diseases challenges. We investigated genome diversity in six indigenous African zebu breeds sampled in Sudan (Aryashai, Baggara, Butana, Fulani, Gash, and Kenana). We adopted three genomic scan approaches to identify candidate selective sweeps regions (ZHp, FST, XP-EHH). We identified a set of gene-rich selective sweep regions shared across African and Asian zebu or unique to Sudanese zebu. In particular, African and Asian zebu candidate gene-rich regions are detected on chromosomes 2, 5 and 7. They include genes involved in immune response, body size and conformation, and stress response to heat. In addition, a 250 kb selective sweep on chromosome 16 was detected exclusively in five Sudanese zebu populations. This region spans seven genes, including PLCH2, PEX10, PRKCZ and SKI, which are involved in alternative adaptive metabolic strategies of insulin signalling, glucose homeostasis, and fat metabolism. Together, these genes may contribute to the zebu cattle resilience to heat, nutritional and water shortages. Our results highlight the putative importance of selection at gene-rich genome regions, which might be under a common regulatory genetic control, as an evolutionary mechanism for rapid adaptation to the complexity of environmental challenges.

Backfat Thickness Does Affect the Restoration of Ovarian Activity Postpartum in Different Breeding Programs in Zebu Cattle

The backfat thickness (BFT) was used to forecast the onset of ovarian activity and predict the calf growth. Eighty Brahman cows with their calves were allocated in two groups of 40 distributed in 4 months according to the month of calving, starting in March and finishing in June. One was synchronized and inseminated at fixed time following by natural mating (TAI+NM); whilst the other only by natural mating (NM). The programs started at 60 ± 5 days postpartum and ended 60 days later. From day 30 postpartum, serial ultrasound examinations and progesterone samples were used to monitor the onset of ovarian activity. The BFT in the rump area was measured by ultrasound from 30 days postpartum and every 15 days thereafter. The weight of the calves was recorded at birth and at weaning on 160 days. The adjusted effect of BFT on ovarian activity and the calves' development was assessed by binomial logistic regression at 30, 60, 75, and 120 days postpartum. The cycling cows averaged higher BFT irrespective of breeding program (P &lt; 0.001). Also, slower changes in BFT were recorded during the follow-up at each time for all cows. However, the former had the higher BFT values from calving to the end of the study (P &lt; 0.001). At 60, 75, and 120 days, the BFT measured, at the preceding time, was the only factor predicting the commencement of cyclicity (P &lt; 0.001). The accumulative pregnancy through time was higher in TAI+NM (P = 0.003). Daily weight gain and weaning weight of the calves born in March was significantly heavier (P &lt; 0.001) than peers born in April, May, or June. The most critical element to forecast the onset of ovarian activity is the monitoring of BFT around calving regardless of the breeding program. BFT to estimate the development of the calves until weaning was unpredictable.

Prevalence of Trypanosome Species in Cattle Near Ruma National Park, Lambwe Valley, Kenya: An Update From the Historical Focus for African Trypanosomosis

The effective control of diseases in areas shared with wildlife depends on the validity of the epidemiologic parameters that guide interventions. Epidemiologic data on animal trypanosomosis in Lambwe valley are decades old, and the recent suspected outbreaks of the disease in the valley necessitate the urgent bridging of this data gap. This cross-sectional study estimated the prevalence of bovine trypanosomosis, identified risk factors, and investigated the occurrence of species with zoonotic potential in Lambwe valley. The area is ~324 km2, of which 120 km2 is the Ruma National Park. Blood was sampled from the jugular and marginal ear veins of 952 zebu cattle between December 2018 and February 2019 and tested for trypanosomes using the Buffy Coat Technique (BCT) and PCR-High-Resolution Melting (HRM) analysis of the 18S RNA locus. Risk factors for the disease were determined using logistic regression. The overall trypanosome prevalence was 11.0% by BCT [95% confidence interval (CI): 9.0–13.0] and 27.9% by PCR-HRM (95% CI: 25.1–30.8). With PCR-HRM as a reference, four species of trypanosomes were detected at prevalences of 12.7% for T. congolense savannah (95% CI: 10.6–14.8), 7.7% for T. brucei brucei (CI: 6.0–9.4), 8.7% for T. vivax (CI: 6.9–10.5), and 1.3% for T. theileri (CI: 0.6–2.0). About 2.4% of cattle had mixed infections (CI: 1.4–3.41). No human-infective trypanosomes were found. Infections clustered across villages but were not associated with animal age, sex, herd size, and distance from the park. Approximately 85% of infections occurred within 2 km of the park. These findings add to evidence that previous interventions eliminated human trypanosomosis but not bovine trypanosomosis. Risk-tailored intervention within 2 km of Ruma Park, especially in the north and south ends, coupled with stringent screening with molecular tools, could significantly reduce bovine trypanosomosis.

Geographical Distribution of Zebu Breeds in Brazil And Their Relationship With Environmental Variables and Human Development Indicator

The aim of this study was to evaluate the geographical distribution of zebu breeds in Brazil and correlate their occurrence with environmental variables and human development indicator. The herds of purebred zebu cattle in Brazil were classified as beef breeds (Brahman, Polled Brahman, Nelore, Polled Nelore and Tabapuã), dairy breeds (Gir and Polled Gir), and dual-purpose breeds (Guzerá, Indubrasil, Polled Indubrasil, Sindhi and Polled Sindhi), all breeds being spatialized in ArcGIS program. Variables examined included environmental and human development indicator. The statistical analysis included analysis and logistic regression.The lower distribution of zebu cattle in the states of Northeast compared to other locations is probably due to its extreme climate, highly susceptible to long periods of high temperatures and lower precipitation, which directly affects local livestock. The beef breeds were evenly spread throughout the country. The location occupied for beef breeds was influenced by environmental variables, showing a higher incidence with increased precipitation, normalized difference vegetation index (NDVI), temperature, relative humidity and temperature humidity index (THI), as well as establishments without family agriculture and rivers and streams with forest protection. The location used for dual-purpose and dairy breeds was influenced by areas with cultivated cutting forages, areas with integrated crop-livestock forest systems and areas with rotational grazing system, indicating a higher occupation in fertile lands. The Gir breed, the only one with dairy exploration in this study, showed herds in establishments with family agriculture, characterized by small to medium farms, and in regions with higher altitude.

PSXI-4 Genome-Wide association study for muscle visual score in Nellore cattle raised in pasture-based systems

Visual scoring traits have been proposed as an alternative to evaluate body composition of Zebu cattle near the slaughter season when phenotyping technologies are not available. Considering the increased demand for high-quality animal protein in developing countries, there is a need to genetically improve body muscle (MUSC) in Zebu cattle (Bos taurus indicus), especially in animals raised in pasture-based systems. Therefore, our main objectives were to estimate genetic parameters, perform a genome-wide association study based on the single-step GBLUP approach (ssGWAS), and identify candidate genes and metabolic pathways related to MUSC in Nellore cattle. A total of 20,808 Nellore animals born between 2009 and 2018 were visually score at 18 months of age and 2,775 of these animals were also genotyped using the GGP-Indicus 35K SNP panel (33,247 SNPs after quality control). Heritability was estimated based on the REML approach and the model included the effects of age at measurement as covariable and the contemporary group (farm, birth season, management group and sex). The ssGWAS was performed using the BLUPF90 family programs. The identification of candidate genes was performed through the Ensembl database incorporated in the BioMart tool. MUSC is heritable (0.38) and can be improved through selection. Nineteen genomic regions (explaining 38.12% of the total additive genetic variance) located on BTA1, BTA7, BTA9, BTA16, and BTA21 and harboring 19 candidate genes were identified. The main genes identified were SEMA6A, TIAM2, UNC5A, and UIMC1, which are related to the metabolism of energy, growth, homeostasis and axonogenesis, and therefore, muscle development. These findings contribute to a better understanding of the molecular mechanisms over the gene expression of muscle visual score in Nellore cattle, and the polymorphisms located in these genes can be incorporated in commercial genotyping platforms to improve the accuracy of imputation and genomic evaluations for body and carcass traits.