Evaluation of female fertility in dairy cattle enterprises – A review

The aim of this article was to review the state of fertility of female dairy cattle in South Africa and to compare it with international efforts at improving fertility. Fertility in dairy cows is defined as the ability to conceive from first insemination soon after calving and to carry the calf full term to calving. It is one of the main profit drivers in the dairy industry and is a complex trait that is influenced by the environment, genetics, and their interaction. Generally, there has been a decline in dairy cow fertility across breeds worldwide because of intense selection for milk yield, milk components, and body conformation traits. In addition, most fertility traits are negatively correlated to milk production traits. Milk production has been the focal point of selection programmes as it is linked directly to the profitability of the dairy enterprise. The low heritability of fertility traits is one of the factors that discouraged efforts to include fertility in genetic evaluations. However, owing to its economic importance, female fertility was later included in the breeding objectives for dairy cattle in several countries. Although most fertility traits are heritable to a low degree, some additive genetic variability can be exploited

Genome-wide identification of breed-informative single-nucleotide polymorphisms in three South African indigenous cattle breeds

Access to genotyping assays enables the identification of informative markers that discriminate between cattle breeds. Identification of these markers can assist in breed assignment, improvement and conservation. The objective of this study was to identify breed informative markers to discriminate between three South African indigenous cattle breeds. Data from BovineSNP50 and GeneSeek Genomic Profiler (GGP-80K) assays were generated for Afrikaner, Drakensberger and Nguni, and were analysed for their genetic differentiation. Hereford and Angus were included as outgroups. Breeds were differentiated using principal component analysis (PCA). Single-nucleotide polymorphisms (SNPs) within the breeds were determined when minor allele frequency (MAF) was ≥ 0.05. Breed-specific SNPs were identified using Reynolds Fst and extended Lewontin and Krakauer's (FLK) statistics. These SNPs were validated using three African breeds, namely N’Dama, Kuri and Zebu from Madagascar. PCA discriminated among the breeds. A larger number of polymorphic SNPs was detected in Drakensberger (73%) than in Afrikaner (56%) and Nguni (65%). No substantial numbers of informative SNPs (Fst ≥ 0.6) were identified among indigenous breeds. Eleven SNPs were validated as discriminating the indigenous breeds from other African breeds. This is because the SNPs on BovineSNP50 and GGP-80K assays were ascertained as being common in European taurine breeds. Lower MAF and SNP informativeness observed in this study limits the application of these assays in breed assignment, and could have other implications for genome-wide studies in South African indigenous breeds. Sequencing should therefore be considered to discover new SNPs that are common among indigenous South African breeds and also SNPs that discriminate among these indigenous breeds

Gene-set enrichment analysis of selective sweeps reveals phenotypic traits in Nguni cattle

Adaptation of animals to different environments is typically associated with structural and functional genomic variations. High throughput SNP genotyping and next-generation sequencing (NGS) have made it possible to study positive selection footprints and adaptation traits. Nguni is a small frame-size breed, mostly horned, and well known for being adapted to diverse South African environmental conditions. This study used previously identified selective sweeps to perform functional analysis of genes related to phenotypic characteristics in Nguni. Two hundred and sixty-four candidate selective sweeps were used for gene-set enrichment analysis in molecular functional categories (KEGG pathways) using the database for annotation, visualization, and integrated discovery (DAVID). In total, 107 genes were identified across all the chromosomes with 74 genes associated with eight phenotype queries, including fat content, milk production, walking ability, heat tolerance, meat production, reproduction, and bone and muscle development. Gene CRHR2 was associated with meat quality (juiciness and flavour). The IRAK3 gene was associated with decreased body size, feed intake and fatness in cattle, and CARD15 with disease resistance. Gene annotation using phenotype queries identified four genes (SPI, YWHAZ, RGS4, and RGS5) that were associated with myometrial relaxation in cattle. Genes such as NOD2 and IL21R were associated with inflammatory bowel diseases in cattle, whereas CPLS gene was associated with fat content. These genes are important to the phenotypic and adaptive characteristics present in South African Nguni cattle and hold potential for selection for traits of economic importance.The Red Meat Research and Development of South Africa (RMRDSA) and the National Research Foundation (NRF).http://www.sasas.co.zaam2022Animal and Wildlife Science

Genetic association between longevity and linear type traits of Holstein cows

Longevity is a desirable trait in the dairy industry because of its relationship to profitability. The aim of this study was to estimate genetic parameters for longevity measurements related to productive life, or life in the herd, and linear type traits of Brazilian Holstein cows born between the years 1990 and 2008. The (co) variance components were estimated by the restricted maximum likelihood method. The heritability for measurements of longevity and linear type traits ranged from 0.05 to 0.07 and 0.08 to 0.39, respectively. The genetic correlations between measurements of longevity and linear type traits ranged from -0.39 to 0.31. Direct selection for longevity does not necessarily lead to long-lived cows, due to low heritability. Indirect genetic selection for udder depth, bone quality, udder height, rear teat placement and conformation traits showed the highest genetic correlations with measurements of time between birth and last milk record and time from first calving to last milk record

Genetic relationships between calving interval and linear type traits in

Genetic correlations between first calving interval (CI) and linear type traits in South African Holstein and Jersey cattle were estimated to assess the possibility of using type information as selection criteria for CI. All linear type traits routinely evaluated under the National Genetic Evaluation Programme (18 for Jersey and 17 for Holstein) were considered. Data were obtained from the National Dairy Animal Recording Scheme and comprised records of 30 503 Holstein cows in 640 herds and 27 360 Jersey cows in 460 herds. Multiple-trait animal models were used to estimate parameters, based on the restricted maximum likelihood (REML) methodology. Fixed effects in the model varied depending on the individual trait. Linear type traits reflecting body size generally had much higher correlations with CI than udder characteristics. Genetic correlations of CI with body size traits were mostly positive in both breeds, ranging from 0.04 ± 0.16 with bone structure to 0.51 ± 0.08 with body depth, dairy strength and rear leg set. Correlations between CI and body depth (0.51 ± 0.08), angularity (0.32 ± 0.08) and rump angle (0.32 ± 0.12) indicate that cows with deep, more angular bodies and low pins have longer CI. Genetic correlations with udder type traits were generally low, ranging from -0.01 ± 0.20 with udder width to 0.25 ± 0.11 with rear teat placement. The highest genetic correlations with CI were for rear leg rear view (-0.70 ± 0.34), body depth (0.51 ± 0.08), dairy strength (0.51 ± 0.09), rear leg set (0.51 ± 0.06), foot angle (-0.44 ± 0.04) and rump angle (0.32 ± 0.05) in the Jersey and rump height (0.31 ± 0.08), angularity (0.32 ± 0.08) and body depth in the Holstein (0.51 ± 0.08). These traits may therefore be used in the analysis of CI to carry out early prediction of fertility and increase the accuracy of evaluation

Use of SNP genotyping to determine pedigree and breed composition of dairy cattle in Kenya

High levels of inbreeding in East African dairy cattle are a potential concern because of use of a limited range of imported germplasm coupled with strong selection, especially by disease, and sparse performance recording. To address this, genetic relationships and breed composition in an admixed population of Kenyan dairy cattle were estimated by means of a 50K SNP scan. Genomic DNA from 3 worldwide Holstein and 20 Kenyan bulls, 71 putative cow-calf pairs, 25 cows from a large ranch and 5 other Kenyan animals were genotyped for 37 238 informative SNPs. Sires were predicted and 89% of putative dam-calf relationships were supported by genotype data. Animals were clustered with the HapMap population using Structure software to assess breed composition. Cows from a large ranch primarily clustered with Holsteins, while animals from smaller farms were generally crosses between Holstein and Guernsey. Coefficients of relatedness were estimated and showed evidence of heavy use of one AI bull. We conclude that little native germplasm exists within the genotyped populations and mostly European ancestry remains

Correlações genéticas entre algumas características de tipo e intervalo de partos em vacas da raça Holandesa

Estimaram-se correlações genéticas entre algumas características de tipo e intervalo de partos (IP) em vacas da raça Holandesa no Estado do Paraná. Foram analisados registros de conformação de 23.014 vacas, classificadas no período de 2000 a 2010, oriundas de 248 rebanhos, filhas de 797 touros. Os componentes de variância necessários para obtenção das estimativas das herdabilidades e das correlações genéticas foram obtidos pelo método da Máxima Verossimilhança Restrita (REML), utilizando-se o procedimento MIXED do pacote estatístico SAS. As estimativas de herdabilidade para as características de tipo variaram de 0,09 a 0,24 e para IP foi 0,05. As estimativas de correlação genética entre as características de tipo foram, em geral, de pequena magnitude, sendo o maior valor observado entre largura de peito e profundidade corporal (0,52). As estimativas de correlação genética entre as características de tipo e IP foram, em sua maioria, de pequena magnitude. A baixa correlação genética entre ângulo de garupa e IP (0,02) sugere que a seleção para ângulo de garupa pode não ser efetiva em determinar ganho genético para fertilidade