CRP Livestock genetics flagship

Permanent URI for this collectionhttps://hdl.handle.net/10568/80104

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    Activity report: Stakeholder meeting for Kilimanjaro and Arusha: African Dairy Genetic Gains Data platform
    (Report, 2021-10-30) Lyatuu, Eliamoni T.R.; Nguluma, A.; Kitalyi, Aichi; Komwihangilo, Daniel M.; Mashingo, M.; Msuta, G.; Kelya, N.; Urasa, A.
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    Whole-genome resequencing of worldwide wild and domestic sheep elucidates genetic diversity, introgression and agronomically important loci
    (Journal Article, 2022-02-03) Feng-Hua Lv; Yin-Hong Cao; Guang-Jian Liu; Ling-Yun Luo; Ran Lu; Ming-Jun Liu; Wen-Rong Li; Ping Zhou; Xin-Hua Wang; Min Shen; Lei Gao; Jing-Quan Yang; Hua Yang; Yong-Lin Yang; Chang-Bin Liu; Peng-Cheng Wan; Yun-Sheng Zhang; Wen-Hui Pi; Yan-Ling Ren; Zhi-Qiang Shen; Feng Wang; Yu-Tao Wang; Jin-Quan Li; Salehian-Dehkordi, H.; Eer Hehua; Yong-Gang Liu; Jian-Fei Chen; Jian-Kui Wang; Xue-Mei Deng; Esmailizadeh, A.; Dehghani-Antezana, M.; Charati, H.; Nosrati, M.; Štěpánek, O.; Rushdi, H.E.; Olsaker, I.; Curik, I.; Gorkhali, N.A.; Paiva, S.R.; Caetano, A.R.; Ciani, E.; Amills, M.; Weimann, C.; Erhardt, G.; Amane, A.; Mwacharo, Joram M.; Han Jianlin; Hanotte, Olivier H.; Periasamy, K.; Johansson, A.M.; Hallsson, J.H.; Kantanen, J.; Coltman, D.W.; Bruford, M.W.; Lenstra, J.A.; Meng-Hua Li
    Domestic sheep and their wild relatives harbor substantial genetic variants that can form the backbone of molecular breeding, but their genome landscapes remain understudied. Here, we present a comprehensive genome resource for wild ovine species, landraces and improved breeds of domestic sheep, comprising high-coverage (∼16.10×) whole genomes of 810 samples from 7 wild species and 158 diverse domestic populations. We detected, in total, ∼121.2 million single nucleotide polymorphisms, ∼61 million of which are novel. Some display significant (P < 0.001) differences in frequency between wild and domestic species, or are private to continent-wide or individual sheep populations. Retained or introgressed wild gene variants in domestic populations have contributed to local adaptation, such as the variation in the HBB associated with plateau adaptation. We identified novel and previously reported targets of selection on morphological and agronomic traits such as stature, horn, tail configuration, and wool fineness. We explored the genetic basis of wool fineness and unveiled a novel mutation (chr25: T7,068,586C) in the 3′-UTR of IRF2BP2 as plausible causal variant for fleece fiber diameter. We reconstructed prehistorical migrations from the Near Eastern domestication center to South-and-Southeast Asia and found two main waves of migrations across the Eurasian Steppe and the Iranian Plateau in the Early and Late Bronze Ages. Our findings refine our understanding of genome variation as shaped by continental migrations, introgression, adaptation, and selection of sheep.
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    Biobanking African poultry breeds for the future
    (Brief, 2021-10-30) Tiambo, Christian K.; McGrew, M.
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    Introduction to bioinformatics and population genomics applied to livestock
    (Report, 2021-11-01) Rudloff, E.B.; Johansson, A.M.; Damme, R. van; Utsunomiya, Y.
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    Technical efficiency of traditional village chicken production in Africa: Entry points for sustainable transformation and improved livelihood
    (Journal Article, 2021-07-30) Yitayih, Mulugeta; Alemayehu, T.; Bruno, J.E.; Kebede, F.G.; Sonaiya, E.B.; Goromela, E.H.; Bamidele, O.; Dessie, Tadelle
    Increasing poultry product consumption trends have attracted researchers and development practitioners to look for interventions that transform the low-input low-output-based village chicken production to a high yielding production system. However, due to the intricate nature of the production system, there is a dearth of evidence that helps design comprehensive interventions at the smallholder level. Using national-level representative data collected from 3555 village chicken producers in Ethiopia, Nigeria, and Tanzania, this study examines the technical efficiency of village chicken production and investigates the main factors that explain the level of inefficiency. We applied a stochastic frontier analysis to simultaneously quantify the level of technical efficiency and identify factors associated with heterogeneity in inefficiency. We found that the level of technical efficiency is extremely low in the three countries, suggesting enormous opportunities to enhance productivity using available resources. The heterogeneity in technical efficiency is strongly associated with producers’ experience in breed improvements and flock management, limited technical knowledge and skills, limited access to institutions and markets, smaller flock size, gender disparities, and household livelihood orientation. We argue the need to adopt an integrated approach to enhance village producers’ productivity and transform the traditional subsistence-based production system into a commercially oriented semi-intensive production system.
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    Species and phenotypic distribution models reveal population differentiation in Ethiopian indigenous chickens
    (Journal Article, 2021-09-08) Getachew, Fasil; Komen, Hans; Dessie, Tadelle; Worku, Setegn; Hanotte, Olivier H.; Bastiaansen, John W.M.
    Smallholder poultry production dominated by indigenous chickens is an important source of livelihoods for most rural households in Ethiopia. The long history of domestication and the presence of diverse agroecologies in Ethiopia create unique opportunities to study the effect of environmental selective pressures. Species distribution models (SDMs) and Phenotypic distribution models (PDMs) can be applied to investigate the relationship between environmental variation and phenotypic differentiation in wild animals and domestic populations. In the present study we used SDMs and PDMs to detect environmental variables related with habitat suitability and phenotypic differentiation among nondescript Ethiopian indigenous chicken populations. 34 environmental variables (climatic, soil, and vegetation) and 19 quantitative traits were analyzed for 513 adult chickens from 26 populations. To have high variation in the dataset for phenotypic and ecological parameters, animals were sampled from four spatial gradients (each represented by six to seven populations), located in different climatic zones and geographies. Three different ecotypes are proposed based on correlation test between habitat suitability maps and phenotypic clustering of sample populations. These specific ecotypes show phenotypic differentiation, likely in response to environmental selective pressures. Nine environmental variables with the highest contribution to habitat suitability are identified. The relationship between quantitative traits and a few of the environmental variables associated with habitat suitability is non-linear. Our results highlight the benefits of integrating species and phenotypic distribution modeling approaches in characterization of livestock populations, delineation of suitable habitats for specific breeds, and understanding of the relationship between ecological variables and quantitative traits, and underlying evolutionary processes.
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    Effects of breed exoticness and agroecological zones on selected production and fertility traits in multibreed dairy cattle in Kenya
    (Poster, 2021-09) Oloo, Richard Dooso; Ekine-Dzivenu, Chinyere C.; Ojango, Julie M.K.; Mrode, Raphael A.; Okeyo Mwai, Ally; Chagunda, Mizeck G.G.
    The aim of this study was to evaluate the effect of degree of exoticness of multi-breed dairy cattle on production and fertility traits in 3 different agroecological zones of Kenya. Test-day milk yield (MY) records (n = 62321) together with fertility-trait records on age at first calving (AFC) (n = 1490) and calving interval (CI) (n = 2640) from a total of 1490 dairy cattle performing in semi-arid arable, semi-arid pasture-based, and semi-humid agroecological zones were analyzed. Animals were grouped into two breed classes based on the proportion of exoticness in their breed composition. These groups were, Exotic Class 1 (EC1) (≤50% exotic, n = 481) and EC2 (>50% exotic, n = 1009). A multiple linear regression model was fitted for AFC and a mixed-repeatability model for test-day MY and CI to determine the effect of exoticness on these traits and to assess whether this effect changed in the different agroecological zones. Overall, EC2 cows had lower AFC than EC1 cows (32.4, se = 0.2 vs. 34.0, se = 0.2 months). However, EC1 cows had a shorter CI than EC2 cows (452, se = 6 vs 466, se = 7 days). Within breed group comparison showed that EC1 had a larger AFC of 36.7 months (se = 0.4) in the semi-arid pasture-based agroecological zone compared to 31.0 (se=0.6) in the semi-humid environment. This denotes delayed puberty in the semi-arid pasture-based agroecological zone. For the EC2, however, it was in the semi-arid arable agroecological zone where cows had the higher AFC compared to the semi-humid environment (34.7, se=0.2 vs. 28.9, se=0.3). In both breed groups, MY was highest in semi-humid and lowest in semi-arid pasture-based environment. Although the semi-humid agroecological zone seemed to favor the onset of puberty and high milk yield, this environment had the longest CI for both breed groups (478, se=9 days for EC1 and 484, se= 7 for EC2). Genotype by environment interaction was significant for AFC and MY (P<0.01). These findings demonstrated that biophysical variation in different agroecological zones affects production and fertility traits in multibreed dairy cattle differently and hence, it is an important factor to consider when designing genetic improvement programs.
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    Demographic expansion and high level of matrilineal diversity in two populations of East African Baggara cattle
    (Journal Article, 2022-03) Kambal, Sumaya; Abdelrahim, A.E.; Hanotte, Olivier H.; Nakao, R.; Alkhaibari, A.M.; Salim, B.
    Western Baggara cattle breed (WBCB) is an East African zebu inhabiting Sudan, well‐known as beef‐producing cattle. We investigated herein two phenotypically and geographically distinct populations of this breed, namely Nyalawi and Daeinawi, which are renowned for their unique meat production capabilities and adaptation attributes, with the aim to contribute to our understanding of their maternal genetic diversity and demography dynamics. Genetic polymorphism analysis of the full‐length D‐loop mtDNA region revealed 44 and 35 polymorphic sites defining 28 and 24 distinct haplotypes in the Nyalawi and the Daeinawi, respectively. Observed genetic diversity is high within the population with a low level of genetic differentiation between populations. Approximate Bayesian computation via the calculation of Bayesian skyline plots and neutrality tests support past expansion with a higher maternal effective population size (Ne) in Nyalawi compared with the Daeinawi population and a population expansion beginning around 4,500 YBP and 3,500 YBP, respectively, before the arrival of zebu into the continent.
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    Evaluation of Bayesian alphabet and GBLUP based on different marker density for genomic prediction in Alpine Merino Sheep
    (Journal Article, 2021-10-19) Shaohua Zhu; Tingting Guo; Chao Yuan; Jianbin Liu; Jianye Li; Mei Han; Hongchang Zhao; Yi Wu; Weibo Sun; Xijun Wang; Tianxiang Wang; Jigang Liu; Tiambo, Christian K.; Yaojing Yue; Bohui Yang
    The marker density, the heritability level of trait and the statistical models adopted are critical to the accuracy of genomic prediction (GP) or selection (GS). If the potential of GP is to be fully utilized to optimize the effect of breeding and selection, in addition to incorporating the above factors into simulated data for analysis, it is essential to incorporate these factors into real data for understanding their impact on GP accuracy, more clearly and intuitively. Herein, we studied the GP of six wool traits of sheep by two different models, including Bayesian Alphabet (BayesA, BayesB, BayesCπ, and Bayesian LASSO) and genomic best linear unbiased prediction (GBLUP). We adopted fivefold cross-validation to perform the accuracy evaluation based on the genotyping data of Alpine Merino sheep (n = 821). The main aim was to study the influence and interaction of different models and marker densities on GP accuracy. The GP accuracy of the six traits was found to be between 0.28 and 0.60, as demonstrated by the cross-validation results. We showed that the accuracy of GP could be improved by increasing the marker density, which is closely related to the model adopted and the heritability level of the trait. Moreover, based on two different marker densities, it was derived that the prediction effect of GBLUP model for traits with low heritability was better; while with the increase of heritability level, the advantage of Bayesian Alphabet would be more obvious, therefore, different models of GP are appropriate in different traits. These findings indicated the significance of applying appropriate models for GP which would assist in further exploring the optimization of GP.
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    Genome-wide association study of trypanosome prevalence and morphometric traits in purebred and crossbred Baoulé cattle of Burkina Faso
    (Journal Article, 2021-08-05) Yougbaré, B.; Soudré, A.; Ouédraogo, D.; Zoma, B.L.; Tapsoba, A.S.R.; Sanou, M.; Ouédraogo-Koné, S.; Burger, P.A.; Wurzinger, Maria; Khayatzadeh, N.; Tamboura, H.H.; Okeyo Mwai, Ally; Traoré, A.; Sölkner, J.; Mészáros, Gábor
    In this study, single-SNP GWAS analyses were conducted to find regions affecting tolerance against trypanosomosis and morphometrics traits in purebred and crossbred Baoulé cattle of Burkina Faso. The trypanosomosis status (positive and negative) and a wide set of morphological traits were recorded for purebred Baoulé and crossbred Zebu x Baoulé cattle, and genotyped with the Illumina Bovine SNP50 BeadChip. After quality control, 36,203 SNPs and 619 animals including 343 purebred Baoulé and 279 crossbreds were used for the GWAS analyses. Several important genes were found that can influence morphological parameters. Although there were no genes identified with a reported strong connection to size traits, many of them were previously identified in various growth-related studies. A re-occurring theme for the genes residing in the regions identified by the most significant SNPs was pleiotropic effect on growth of the body and the cardiovascular system. Regarding trypanosomosis tolerance, two potentially important regions were identified in purebred Baoulé on chromosomes 16 and 24, containing the CFH, CRBN, TRNT1 and, IL5RA genes, and one additional genomic region in Baoulé, x Zebu crossbreds on chromosome 5, containing MGAT4C and NTS. Almost all of these regions and genes were previously related to the trait of interest, while the CRBN gene was to our knowledge presented in the context of trypanosomiasis tolerance for the first time.
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    Overview of the ADGG Data Platform
    (Presentation, 2021-05-20) Ojango, Julie M.K.; Mrode, Raphael A.; Ekine, C.; Oyieng, Edwin P.; Mogaka, David; Okeyo Mwai, Ally
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    Origin and genetic diversity of Nepalese indigenous goats (Capra hircus)
    (Journal Article, 2021-05-11) Gorkhali, N.A.; Lin, J.; Sapkota, Suraj; Pokhrel, B.R.; Ma, Y.H.; Han Jianlin
    Background: A very little study has been conducted on the phylogenetic diversity of Nepalese indigenous goats where four breeds, Khari, Chyangra, Terai and Sinhal, have been identified. Methods: The 625-bp long sequences of the mitochondrial DNA hyper-variable region obtained from 93 goats in this study revealed high haplotype diversity among breeds, which come under four haplogroups (A-D).Result: The study demonstrated a certain level of gene flow among the neighboring goat populations exhibiting no correspondence between the geographic regions of origin and relationships among breeds. The complex mtDNA diversity and structure identified among indigenous Nepalese goats can be explained by gene flow through ancient trading and the current ‘free’ movement of goats across the geographic vicinities in India and China. Furthermore, HapG B showed the southward direction of gene flow which does not cross the Himalayas, whereas HapG B1 revealed the South-West gene flow from the claimed domestication center for HapG B, China, to Nepal.
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    ADGG dairy tool: Raising healthy calves 2 - Routine management practices
    (Extension Material, 2021-05) Ojango, Julie M.K.; Rao, E.J.O.; Mwirigi, J.; Gitau, J.; Richardson, F.; Okeyo Mwai, Ally