Management practices, reproductive performances, and production constraints of indigenous cattle in north-western parts of Ethiopia

Description of the production condition and level of performance is the first step in improving production performance. The study described the indigenous cattle reproductive performances, management practices and production limitations in north-western Ethiopia. Multistage purposive and random sampling methods were used to select the study sites/districts and households. A semi-structured questionnaire (320 interviewees), focus group discussions (12) and personal observations were used for data collection. Chi-square (χ2) test, the least squares mean and the ranking indexes were the statistical methods employed for data analysis. Livestock composition, reproductive performance and production constraints of cattle showed significant differences (p &lt; 0.001) between agro-ecological zones. Cattle were the dominant livestock species, with mean numbers of 18.3 ± 9.9, 8.1 ± 3.2 and 5.4 ± 2.5 heads in the lowland, midland and highland agro-ecological zones, respectively. The mean ages at first mating of bulls, first service of heifers, first calving and calving interval of cows were best in the highlands, while the midland agro-ecology had the worst performance. Feed shortage (Index = 0.4) and disease prevalence (Index = 0.25) were the main cattle production problems. Natural pasture was the main feed source for cattle in the study areas. The study revealed a significant effect agro-ecology on landholding, cattle management practices, species composition; cattle herd structure, reproductive performances and cattle production constraints. This implies that the socioeconomic characteristics, management-level constraints for production and performance level of the livestock stock are important for developing improvement strategies for smallholder livestock production in different agro-ecological zones.</p

Typology and characteristics of indigenous goats and production systems in different agro-ecological zones of Tanzania

Tanzania has a goat population of about 24.8 million most of which belong to the Small East African breed distributed in almost all agro-ecological zones. The different goat populations and the production system in which they are raised are not well characterized depriving animal breeders useful information in designing and running improvement and conservation programs. Therefore, the study was conducted in all agro-ecological zones in Tanzania to characterize the indigenous goats and the production system in which they are raised. Data on animals were collected from 688 randomly selected adult female goats and for production system description; 220 households were interviewed. Analysis of variance and discriminant analysis were used on quantitative data, while frequency analysis was used on qualitative data. Income generation and meat production were the primary goat rearing objectives. More than 55% of respondents grazed their animals freely in communal lands where natural pasture was the chief feed resource. Mating was mainly uncontrolled with apron and castration being used by goat keepers as mating control methods. Common diseases were contagious caprine pleural pneumonia and helminthiasis. Feed shortage, prevalence of diseases, and water scarcity were the major goat production constraints. There were morphological variations between and within these goat populations, and based on quantitative data, the goats were categorized into two groups. High twinning was observed in Ujiji and Lindi goats and low for Sukuma. The dominant coat color was plain white in Pare, Gogo, Maasai, and Tanga. Other coat color patterns were mixed black and white for Sukuma, reddish-brown for Lindi, black and reddish-brown for Ujiji, and white and reddish-brown for Pwani and Maasai. High within population variation is observed which is important as it can be used as a basis for genetic improvement through selection

Whole-Genome Resequencing Reveals Selection Signatures of Abigar Cattle for Local Adaptation

Over time, indigenous cattle breeds have developed disease resistance, heat tolerance, and adaptability to harsh environments. Deciphering the genetic mechanisms underlying adaptive traits is crucial for their improvement and sustainable utilization. For the first time, we performed whole-genome sequencing to unveil the genomic diversity, population structure, and selection signatures of Abigar cattle living in a tropical environment. The population structure analysis revealed that Abigar cattle exhibit high nucleotide diversity and heterozygosity, with low runs of homozygosity and linkage disequilibrium, suggesting a genetic landscape less constrained by inbreeding and enriched by diversity. Using nucleotide diversity (Pi) and population differentiation (FST) selection scan methods, we identified 83 shared genes that are likely associated with tropical adaption. The functional annotation analysis revealed that some of these genes are potentially linked to heat tolerance (HOXC13, DNAJC18, and RXFP2), immune response (IRAK3, MZB1, and STING1), and oxidative stress response (SLC23A1). Given the wider spreading impacts of climate change on cattle production, understanding the genetic mechanisms of adaptation of local breeds becomes crucial to better respond to climate and environmental changes. In this context, our finding establishes a foundation for further research into the mechanisms underpinning cattle adaptation to tropical environments.</p

Typology, management and smallholder farmer-preferred traits for selection of indigenous goats (Capra hisrcus) in three agro-ecological zones in the Democratic Republic of Congo

The present study aimed to assess the typology, production management, and smallholder farmer-preferred traits in selecting indigenous goats in three agro-ecological zones (AEZs) in the Democratic Republic of Congo (DR Congo). Based on a structured survey, baseline data were recorded on 320 adults and unrelated does from 202 goat farms. Hierarchical clustering on principal components revealed three clusters in the goats studied well distinguished by double and triple kidding. Prolific goats mostly clustered into cluster two and three more represented by goats of South Kivu while 82.69% of goats in Tshopo were clustered into cluster one characterized by low reproductive performances. The Canonical Discriminant Analysis revealed that the body length was an important variable both to discriminate and to classify goats from the three AEZs. Goats from Kinshasa and South Kivu were not distanced while large distance was observed between goats from Kinshasa and Tshopo (F-stat, p < 0.001). While not subjected to any good management practices, goats were considered as a source of income and saving method in smallholder farmers' households. Adaptability, resistance to disease and prolificacy were preferred traits by farmers in selecting goats. These results give the first step in the decision-making towards goat improvement in DR Congo

The mosaic genome of indigenous African cattle as a unique genetic resource for African pastoralism

© 2020, The Author(s), under exclusive licence to Springer Nature America, Inc. Cattle pastoralism plays a central role in human livelihood in Africa. However, the genetic history of its success remains unknown. Here, through whole-genome sequence analysis of 172 indigenous African cattle from 16 breeds representative of the main cattle groups, we identify a major taurine × indicine cattle admixture event dated to circa 750–1,050 yr ago, which has shaped the genome of today’s cattle in the Horn of Africa. We identify 16 loci linked to African environmental adaptations across crossbred animals showing an excess of taurine or indicine ancestry. These include immune-, heat-tolerance- and reproduction-related genes. Moreover, we identify one highly divergent locus in African taurine cattle, which is putatively linked to trypanotolerance and present in crossbred cattle living in trypanosomosis-infested areas. Our findings indicate that a combination of past taurine and recent indicine admixture-derived genetic resources is at the root of the present success of African pastoralism

Morphological Characterization of Goat Populations in Central Zone of Tigray, Ethiopia

Ethiopia has huge livestock resource, but poor in their productivity. It stated national small ruminant breeding policy and strategy focused on genetic improvement. This is intended to design appropriate breeding programs based on the indigenous breeds status. Study of phenotypic variation is among the prerequisite activities of genetic improvement that is limited in this study area. The objective of this study was to describe morphological characteristics and variations of goat populations in the Central zone of Tigray. Qualitative and quantitative data of 403 young to matured goats (326 lactating does and 77 bucks) were used to analyze by frequency procedure, GLM procedure, Pearson correlation, and multivariate analysis of SAS version 9.4. The study revealed that goats in Adwa district were distinct in coat colors and pattern, horn shape, ear orientation, head profile and ruff, significantly heavier (p&lt;0.01) and larger (p&lt;0.001) in height at withers and in height at pelvic than those in Tanqua Abergele (TA) and Kola Tembien (KT) districts. Goats found in Adwa district were morphologically distinct from those found in TA and KT districts with the higher discriminating values in female goats

Mitochondrial DNA D-loop sequence analysis reveals high variation and multiple maternal origins of indigenous Tanzanian goat populations

The Small East African (SEA) goat are widely distributed in different agro-ecological zones of Tanzania. We report the genetic diversity, maternal origin, and phylogenetic relationship among the 12 Tanzanian indigenous goat populations, namely Fipa, Songwe, Tanga, Pwani, Iringa, Newala, Lindi, Gogo, Pare, Maasai, Sukuma, and Ujiji, based on the mitochondrial DNA (mtDNA) D-loop. High haplotype (H-d = 0.9619-0.9945) and nucleotide (pi = 0.0120-0.0162) diversities were observed from a total of 389 haplotypes. The majority of the haplotypes (n = 334) belonged to Haplogroup A which was consistent with the global scenario on the genetic pattern of maternal origin of all goat breeds in the world. Haplogroup G comprised of 45 haplotypes drawn from all populations except the Ujiji goat population while Haplogroup B with 10 haplotypes was dominated by Ujiji goats (41%). Tanzanian goats shared four haplotypes with the Kenyan goats and two with goats from South Africa, Namibia, and Mozambique. There was no sharing of haplotypes observed between individuals from Tanzanian goat populations with individuals from North or West Africa. The indigenous goats in Tanzania have high genetic diversity defined by 389 haplotypes and multiple maternal origins of haplogroup A, B, and G. There is a lot of intermixing and high genetic variation within populations which represent an abundant resource for selective breeding in the different agro-ecological regions of the country

Single-step genome-wide association study uncovers known and novel candidate genomic regions for endocrine and classical fertility traits in Swedish Red and Holstein dairy cows

In a study aiming to identify candidate genomic regions associated with endocrine and classical fertility traits in Swedish Red (SR) and Holstein cows, data on 3955 lactations in 1164 SR and 1672 Holstein cows were examined. The dataset comprised milk progesterone (P4) levels (n = 341,212) in 14 Swedish herds, automatically collected and analyzed in-line using the DeLaval Herd NavigatorTM. Endocrine traits studied were: days from calving to commencement of luteal activity (C-LA), first luteal phase length (LPL), length of first inter-luteal interval, length of first inter-ovulatory interval (IOI), luteal activity during the first 60 DIM, and proportion of samples with luteal activity during the first 60 DIM. Classical fertility traits based on insemination data were also investigated, such as days from calving to last insemination and calving interval. A total of 180 SR and 312 Holstein cows were genotyped with a low-density SNP chip and imputed to 50 K. Single-step genome-wide association (ssGWAS) was used to explore candidate genomic regions associated with fertility traits. A mixed linear single-trait animal model was fitted, considering season and parity as fixed effects and animal and permanent environment as random effects. The results revealed 990 and 415 SNPs above the threshold (-log (p-value) >= 4) for SR and Holstein cows, respectively. The breeds shared only eight SNPs significantly associated with fertility traits. Annotation analysis revealed 281 SNPs located in 241 genes. Functional enrichment analysis using DAVID tools reduced the number to 80 genes, which were mediated in various biological processes and KEGG pathways in multiple functions, including folliculogenesis, embryogenesis, uterine growth and development, immune response, and ovarian cysts. Of the 80 genes, 67 were associated with fertility traits in SR cows and 13 in Holstein. Most genes were associated with LPL and IOI in SR cows, but in Holstein the only association with an endocrine trait was with C-LA. Twenty QTL regions that embedded 40 genes were associated with fertility traits in both breeds. All the QTLs detected, except at BTA2 and BTA19 are novel QTL regions that were not reported previously. These novel QTL regions embedded the candidate genes that include ARHGAP20, PHLDB1, CACNA1D, ATG7, CCNE1, GPI, CDH13, ECT2, PLD1, FBN2, KIF3A, FGF12, KCNMB2, GJA1, MAN1A1, KCNN2, SMAD6, MAPK8IP1, PHF21A, LPXN, MMRN1, KCNIP4, NID2, PCDHGA8, GRIA1, PCDHGB4, PHLDB2, STXBP5L, PPP3CA, PTPRR, SRGAP1, SNX27, SPTA1, S100A10, TBC1D20 and ITCH. The candidate regions may help to improve genetic progress in female fertility if used in selection decisions. A challenge for future research is to determine why different regions seem relevant for different traits and breeds, and the practical implications for genomic selection