2015, Aliloo, H, Pryce, J E, Gozalez-Recio, O, Cocks, B G, Hayes, B J

It has been suggested that traits associated with fitness, such as fertility, may have proportionately more genetic variation arising from non-additive effects than traits with higher heritability, such as milk yield. Here, we performed a large genome scan with 408,255 single nucleotide polymorphism (SNP) markers to identify chromosomal regions associated with dominance and epistatic (pairwise additive × additive) variability in milk yield and fertility (measured by calving interval), using 7,055 genotyped and phenotyped Holstein cows. The results were subsequently replicated in an independent set of 3,795 Jersey cows. We identified genome regions with replicated dominance effects for milk yield on Bos taurus autosomes (BTA) 2, 3, 5, 26 and 27 whereas SNPs with replicated dominance effects for fertility were found on BTA 1, 2, 3, 7, 23, 25 and 28. A number of significant epistatic effects for milk yield on BTA 14 were found across breeds. However, these were likely to be associated with the mutation in the diacylglycerol O-acyltransferase 1 (DGAT1) gene, given that the associations were no longer significant when the full additive effect of the DGAT1 mutation was included in the epistatic model. The results of our study suggest that individual non-additive effects make a small contribution to the genetic variation of milk yield and fertility.

2023-07-26, Samaraweera, A M, Aliloo, H, Byrne, A, Duff, C J, Clark, S A

Animals with sleeker coats are commonly considered to have better heat tolerance, tick resistance, and a lower incidence of dags in feedlot environments. The objective of this study was to estimate genetic parameters for coat type traits and to estimate genetic correlations between coat type and scan and carcass weight traits using single-step methods. Two coat type traits were defined based on the month of scoring where scores recorded in April to October were considered as coat type 1 (CT1) and those recorded in November to March were categorized as coat type 2 (CT2). The coat type traits were moderately heritable, and the heritability of CT1 (0.36 ± 0.04) was higher than CT2 (0.32 ± 0.03). Genetic correlations between coat type traits and steer and heifer ultrasound scan traits (eye muscle area, intramuscular fat) were either low to moderate in strength, but favourable in direction. The outcomes of this study suggest selection for sleeker coat type is possible without any associated detrimental effect on scan and carcase traits.

2020-11-04, Gebrehiwot, Netsanet Zergaw, Gibson, John, Strucken, Eva, Mrode, Raphael, Aliloo, Hassan

In developing countries, the livestock sector plays an important role in achieving food security and alleviating poverty for the rapidly growing human population. Cattle populations are an important part of these resources and have significant socio-economic and cultural importance to the livelihood of farmers in Africa. The advances in genotyping technology, such as high-density marker arrays or even whole-genome sequencing, provide unique opportunities for in-depth assessments of genetic structure and genetic diversity of indigenous cattle populations. Understanding population sub-structures plays an important role in several allied fields, including conservation genetics, association studies, and quantitative genetics. Genomic markers also allow breeders to trace relationships between animals accurately and can thus be useful for facilitating genetic improvement and breeding decisions.

This thesis focuses on providing important insights into the genetic diversity and structure of African cattle populations and presents methods and tools for genetic improvement in smallholder crossbred dairy systems in Africa. A brief description of the research chapters of the thesis follows:

Chapter 1 presents a general introduction to cattle domestication and a description of African cattle breeds, followed by a review of smallholder dairy farming based on crossbred cattle in Africa. The chapter also discusses linkage disequilibrium and several statistical approaches that are used for genetic diversity estimation, selection of informative SNP panels for breed proportion and parentage assignment, and methods for genotype imputation.

In Chapter 2, the genetic diversity and structure of the African indigenous and dairy breed proportions of crossbred cattle populations were studied in relation to Bos indicus, European Bos taurus, and African Bos taurus reference populations using medium-density SNP data. I found that all African indigenous cattle populations are hybrids between Bos indicus and African Bos taurus except some West African pure Bos taurus breeds, with West African and South African populations showing a lower Bos indicus content than East African populations. Estimates of effective population sizes declined for all African cattle breeds from a large population at 2,000 generations ago. The largest European dairy proportions found in Kenyan and Tanzanian crossbreds were Holstein/Friesian and Ayrshire with some influence also from Jersey and Guernsey. In Uganda and Ethiopia, the dairy ancestry was mostly from Holstein/Friesian and in Senegal, the dairy proportion were mostly from Monbeliarde and Holstein.

Chapter 3 focused on the selection of informative SNP markers for estimation of total dairy breed proportion and parentage assignment in African crossbred dairy cattle. For estimation of dairy breed proportion, small SNP panels performed better when the highest proportion of markers was selected to differentiate African Bos taurus from European Bos taurus ancestral populations, compared to markers distinguishing Bos indicus from Bos taurus. In all African crossbred populations, unambiguous parentage assignment was possible with ≥300 SNPs for the majority of the panels when parents were sought among all animals with known genotypes, and ≥200 SNPs when parents were sought only among animals known to be a parent of at least one progeny.

Chapter 4 investigated the inference of local and global ancestry and estimated the heterozygosity proportions in West African crossbreds, and genotype imputation accuracies in African indigenous and crossbred cattle populations. Two approaches were tested to estimate the admixture of crossbred cattle, assuming either two or three ancestral populations. Estimates from both the LAMP-LD and ADMIXTURE approaches were highly correlated (r ≥0.981) and showed an average European Bos taurus content of ~49.7% with SD of ±19.8%. The observed heterozygosity proportions in putative F1 crosses were much higher than for other crossbred and pure breed individuals. The imputation accuracy was generally higher when the reference data came from the same geographical region as the target population, and when crossbred reference data was used to impute crossbred genotypes. The lowest imputation accuracies were observed for indigenous breeds.

Finally, Chapter 5 summarises the overall conclusion of all the research chapters and a general perspective on the findings and their relevance to the field, and highlighting the main findings of the thesis.

2015, Aliloo, Hassan, Pryce, Jennie E, Gonzalez-Recio, Oscar, Cocks, Benjamin G, Hayes, Ben J

Background: It has been suggested that traits with low heritability, such as fertility, may have proportionately more genetic variation arising from non-additive effects than traits with higher heritability, such as milk yield. Here, we performed a large genome scan with 408,255 single nucleotide polymorphism (SNP) markers to identify chromosomal regions associated with additive, dominance and epistatic (pairwise additive x additive) variability in milk yield and a measure of fertility, calving interval, using records from a population of 7,055 Holstein cows. The results were subsequently validated in an independent set of 3,795 Jerseys. Results: We identified genomic regions with validated additive effects on milk yield on Bos taurus autosomes (BTA) 5, 14 and 20, whereas SNPs with suggestive additive effects on fertility were observed on BTA 5, 9, 11, 18, 22, 27, 29 and the X chromosome. We also confirmed genome regions with suggestive dominance effects for milk yield (BTA 2, 3, 5, 26 and 27) and for fertility (BTA 1, 2, 3, 7, 23, 25 and 28). A number of significant epistatic effects for milk yield on BTA 14 were found across breeds. However on close inspection, these were likely to be associated with the mutation in the diacylglycerol O-acyltransferase 1 (DGAT1) gene, given that the associations were no longer significant when the additive effect of the DGAT1 mutation was included in the epistatic model. Conclusions: In general, we observed a low statistical power (high false discovery rates and small number of significant SNPs) for non-additive genetic effects compared with additive effects for both traits which could be an artefact of higher dependence on linkage disequilibrium between markers and causative mutations or smaller size of non-additive effects relative to additive effects. The results of our study suggest that individual non-additive effects make a small contribution to the genetic variation of milk yield and fertility. Although we found no individual mutation with large dominance effect for both traits under investigation, a contribution to genetic variance is still possible from a large number of small dominance effects, so methods that simultaneously incorporate genotypes across all loci are suggested to test the variance explained by dominance gene actions.

2019, Gebrehiwot, N Z, Strucken, E M, Aliloo, H, Marshall, K, Gibson, J P

African taurine cattle populations are widely distributed in humid and sub-humid zones of West and Central Africa. We assessed the genetic structure and differentiation within and across 8 African Bos taurus populations: 4 N’Dama populations (N’Dama, N’Dama1, N’Dama2, N’Dama3), Lagunaire, Lagune, Somba, and Baoule. A total of 38k autosomal SNPs were used for principal component analyses (PCA), estimation of pairwise FST values and within population heterozygosity (FIS), and neighbour-joining (NJ) tree construction. The first PC clearly differentiated Lagune and Lagunaire from N’Dama; PC2 separated Lagunaire, Lagune and one N’Dama population from the rest of taurine breeds; and PC3 separated N’Dama3 from Somba and Baoule. Estimates of pairwise FST values among the majority of populations ranged from 0.03 to 0.149, indicating low to moderate genetic differentiations, while a high genetic divergence between N’Dama3 and Lagune (FST =0.178), and N’Dama3 and Lagunaire (FST =0.168) was observed. No genetic subdivision was found between N’Dama and N’Dama1, and Lagune and Lagunaire. A higher heterozygosity (FIS value from -0.011 to 0.025) was found in N’Dama, N’Dama1, N’Dama2, Lagune, Lagunaire, and Baoule breeds. The NJ tree clearly separated Lagune and Lagunaire as well as Somba and Baoule with a 100% and around 31% bootstrap value, respectively, from the other taurine populations. We highlighted that African taurine populations are diverse and genetic differences between sampling locations exists even within a breed. Therefore, choice of an African taurine breed to anchor African indigenous breeds should be carefully considered.

2022, Lynn, A M, McGilchrist, P, Aliloo, H, van der Werf, J H J, Polkinghorne, R, Clark, S A

Consumer satisfaction influences purchasing habits and ultimately the premiums consumers are willing to pay for beef. There are four criteria currently used to describe consumer satisfaction: tenderness, juiciness, flavour and overall liking. While previous studies have focused on the traits associated with consumer satisfaction such as marbling and shear force, few have analysed consumer traits directly. The aim of this study was to determine if genomic regions affecting consumer satisfaction could be discovered using a genome-wide association study. Phenotypic data including consumer sensory scores were collected for 1,924 animals from a breed diverse population of cattle genotyped for a minimum of 50k single nucleotide polymorphisms. A single region linked to the CAST gene on chromosome 7 (BTA7) was associated with tenderness. The CAST gene is responsible for muscle proteolysis after slaughter and has been well documented as impacting on the mechanical tenderness measurement of Warner-Bratzler shear force.

2019, Al kalaldeh, M, Gaundare, Y, Swaminathan, M, Joshi, S, Aliloo, H, Strucken, E M, Ducrocq, V, Gibson, J P

We report the results of the first large scale milk recording and genetic evaluation for crossbred cows in a smallholder dairy production system in India. Preliminary results represented 8,144 smallholder crossbred cows with a total of 140,214 daily milk records, of which 2,946 animals were genotyped with the GGP Bovine and Illumina SNP assays. Data were adjusted for fixed effects and analysed with a random regression (RR) model with the 1st degree Legendre polynomial and heterogeneous variance. Heritabilities of milk yield ranged from 0.14 to 0.22 throughout the lactation period, with an average value of 0.19. Genomic Estimated breeding values (GEBV) for the genotyped animals including the smallholder crossbred cows and the bulls and dams from the BAIF bull stud ranged from +1.9 to -1.4 kg/day. The moderate heritability of the milk yield found in our results together with the wide range of GEBV, indicate that a good response to genomic selection for milk yield can be expected for smallholder dairy farms in India.

2021, Aliloo, Hassan, Clark, Samuel A

Context. Genotype imputation is an effective method to increase the number of SNP markers available for an animal and thereby increase the overall power of genome-wide associations and accuracy of genomic predictions. It is also the key to achieve a common set of markers for all individuals when the original genotypes are obtained using multiple genotyping platforms. High accuracy of imputed genotypes is crucial to their utility.

Aims. In this study, we propose a method for the construction of a common set of medium density markers for imputation, which relies on keeping as much information as possible. We also investigated the impact of changing marker coordinates on the basis of the new bovine genome assembly, ARS-UCD 1.2, on imputation accuracy.

Methods. In total, 49 754 animals with 45 364 single nucleotide polymorphism markers were used in a 10-fold cross-validation to compare four different imputation scenarios. The four scenarios were based on two alternative designs for the reference datasets. (1) A traditional reference panel that was created using the overlapping SNP from five medium density arrays and (2) a composite reference panel created by combining SNPs across the five arrays. Each of the reference datasets was used to test imputation accuracy when the SNPs were aligned on the basis of two genome assemblies (UMD 3.1 and ARS-UCD 1.2).

Key results. Our results showed that a composite reference panel can achieve higher imputation accuracies than does a traditional overlap reference. Incorporating mapping information on the basis of the recent genome build slightly improved the imputation accuracies, especially for lower density chips.

Conclusions. Markers with unreliable mapping information and animals with low connectedness to the imputation reference dataset benefited the most from the ARS-UCD 1.2 assembly and composite reference respectively.

Implications. The presented method is straightforward and can be used to setup an optimal imputation for accurate inference of genotypes in Australian Angus cattle.

2021-03, Gebrehiwot, Netsanet Z, Aliloo, Hassan, Strucken, Eva M, Marshall, Karen, Al Kalaldeh, Mohammad, Missohou, Ayao, Gibson, John P

Several studies have evaluated computational methods that infer the haplotypes from population genotype data in European cattle populations. However, little is known about how well they perform in African indigenous and crossbred populations. This study investigates: (1) global and local ancestry inference; (2) heterozygosity proportion estimation; and (3) genotype imputation in West African indigenous and crossbred cattle populations. Principal component analysis (PCA), ADMIXTURE, and LAMP-LD were used to analyse a medium-density single nucleotide polymorphism (SNP) dataset from Senegalese crossbred cattle. Reference SNP data of East and West African indigenous and crossbred cattle populations were used to investigate the accuracy of imputation from low to medium-density and from medium to high-density SNP datasets using Minimac v3. The first two principal components differentiated Bos indicus from European Bos taurus and African Bos taurus from other breeds. Irrespective of assuming two or three ancestral breeds for the Senegalese crossbreds, breed proportion estimates from ADMIXTURE and LAMP-LD showed a high correlation (r ≥ 0.981). The observed ancestral origin heterozygosity proportion in putative F1 crosses was close to the expected value of 1.0, and clearly differentiated F1 from all other crosses. The imputation accuracies (estimated as correlation) between imputed and the real data in crossbred animals ranged from 0.142 to 0.717 when imputing from low to medium-density, and from 0.478 to 0.899 for imputation from medium to high-density. The imputation accuracy was generally higher when the reference data came from the same geographical region as the target population, and when crossbred reference data was used to impute crossbred genotypes. The lowest imputation accuracies were observed for indigenous breed genotypes. This study shows that ancestral origin heterozygosity can be estimated with high accuracy and will be far superior to the use of observed individual heterozygosity for estimating heterosis in African crossbred populations. It was not possible to achieve high imputation accuracy in West African crossbred or indigenous populations based on reference data sets from East Africa, and population-specific genotyping with high-density SNP assays is required to improve imputation.

2014-09, Aliloo, H, Miraie-Ashtiani, S R, Moradi Shahrbabak, M, Urioste, J I, Sadeghi, M

First lactation milk yield data consisting of 1,576,102 test-day records for 221,862 Iranian Holstein cows having lactations between 1983 and 2008 were used to study the existence and effect of heterogeneity of variance (HOV) on estimated breeding values and the performance of random regression models (RRMs) with different orders of fit. A pre-correction method based on phenotypic variance, assuming equal heritability for different levels of herd-test date classes and a genetic correlation of one between them, was used to correct for HOV. RRMs with Legendre polynomial functions were used to analyze adjusted and unadjusted records. Some re-ranking of animals occurred from the adjustment, but the correction method only had slight effects on the overall ranking and rank correlations of animals. Data correction had considerable effects on top animals, such that 10% and 17% of top sires and dams, respectively, were replaced from the list of top 1% animals when compared to the homogeneous variance scenario. Application of the adjustment method resulted in slightly higher heritabilities, which may be due to the more accurate estimation of additive genetic effects when HOV is considered. An index consisting of different comparison criteria was used to investigate the effect of HOV on fitting orders of Legendre polynomials and to compare RRMs. In general, the rank of models was improved by increasing the order of fit, but models with smaller orders of fit and correction for HOV performed better than models with higher orders of fit without correction for variance heterogeneity. The results of this research indicate that the accuracy of estimated breeding values may be increased and the genetic progress of the herds could be affected by accounting for HOV as part of genetic evaluations in Iran.