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| 2. |
- Tarekegn, Getinet Mekuriaw
(författare)
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Ethiopian indigenous goats offer insights into past and recent demographic dynamics and local adaptation in sub-Saharan African goats
- 2021
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Ingår i: Evolutionary applications. - : Wiley. - 1752-4571. ; 14, s. 1716-1731
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Tidskriftsartikel (refereegranskat)abstract
- Knowledge on how adaptive evolution and human socio-cultural and economic interests shaped livestock genomes particularly in sub-Saharan Africa remains limited. Ethiopia is in a geographic region that has been critical in the history of African agriculture with ancient and diverse human ethnicity and bio-climatic conditions. Using 52K genome-wide data analysed in 646 individuals from 13 Ethiopian indigenous goat populations, we observed high levels of genetic variation. Although runs of homozygosity (ROH) were ubiquitous genome-wide, there were clear differences in patterns of ROH length and abundance and in effective population sizes illustrating differences in genome homozygosity, evolutionary history, and management. Phylogenetic analysis incorporating patterns of genetic differentiation and gene flow with ancestry modelling highlighted past and recent intermixing and possible two deep ancient genetic ancestries that could have been brought by humans with the first introduction of goats in Africa. We observed four strong selection signatures that were specific to Arsi-Bale and Nubian goats. These signatures overlapped genomic regions with genes associated with morphological, adaptation, reproduction and production traits due possibly to selection under environmental constraints and/or human preferences. The regions also overlapped uncharacterized genes, calling for a comprehensive annotation of the goat genome. Our results provide insights into mechanisms leading to genome variation and differentiation in sub-Saharan Africa indigenous goats.
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| 3. |
- Tarekegn, Getinet Mekuriaw, et al.
(författare)
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Genetic parameters of endocrine fertility traits based on in-line milk progesterone profiles in Swedish Red and Holstein dairy cows
- 2019
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Ingår i: Journal of Dairy Science. - : American Dairy Science Association. - 0022-0302 .- 1525-3198. ; 102, s. 11207-11216
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Tidskriftsartikel (refereegranskat)abstract
- Evaluating fertility traits based on endocrine progesterone profiles is becoming a promising option to improve dairy cow fertility. Several studies have been conducted on endocrine fertility traits, mainly in the Holstein breed. In this study, focusing also on the Swedish Red (SR) breed, genetic parameters were estimated for classical and endocrine fertility traits, the latter based on in-line milk progesterone records obtained for 14 Swedish herds using DeLaval Herd Navigator (DeLaval International, Tumba, Sweden). A total of 210,403 observations from 3,437 lactations of 1,107 SR and 1,538 Holstein cows were used. Mixed linear animal models were used for estimation of genetic parameters. Least squares means analysis showed that Holstein cows had a 2.5-d-shorter interval from calving to commencement of luteal activity (C-LA) and longer length of first inter-ovulatory interval (IOI) than SR cows. The highest mean interval for C-LA, IOI, and first luteal phase length (LPL) was observed in the fourth parity. The incidence of short (<18 d), normal, (18-24 d), and long (>24 d) IOI was 29.3, 40.7, and 30%, respectively. Genetic analysis indicated moderate heritability (h(2)) for C-LA (h(2) = 0.24), luteal activity during the first 60 d in milk (LA60, h(2) = 0.15), proportion of samples with luteal activity (PLA, h(2) = 0.13), and calving to first heat (CFH, h(2) = 0.18), and low heritability estimates for LPL (h(2) = 0.08) and IOI (h(2) = 0.03) in the combined data set for both breeds. Similar heritability estimates were obtained for each breed separately except for IOI and LPL in SR cows, for which heritability was estimated to be zero. Swedish Red cows had 0.01 to 0.06 higher heritability estimates for C-LA, LA60, and PLA than did Holstein cows. Calving interval had moderate heritability among the classical traits for Holstein and the combined data set, but h(2) was zero for SR. Commencement of luteal activity had a strong genetic correlation with LA60 (mean +/- SE; -0.88 +/- 0.06), PLA (-0.72 +/- 0.11), and CFH (0.90 +/- 0.04). Similarly, CFH had a strong genetic correlation with IOI (0.98 +/- 0.20). Number of inseminations per series showed a weak genetic correlation with all endocrine traits except IOI. Overall, endocrine traits had higher heritability estimates than classical traits in both breeds, and may have a better potential to explain the actual reproductive status of dairy cows than classical traits. This might favor inclusion of some endocrine fertility traits-especially those related to commencement of luteal activity as selection criteria and breeding goal traits if recording becomes more common in herds. Further studies on genetic and genomic evaluations for endocrine fertility traits may help to provide firm conclusions. A prerequisite is that the data from automatic devices be made available to recording and breeding organizations in the future and included in a central database.
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| 4. |
- Tarekegn, Getinet Mekuriaw, et al.
(författare)
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Genetic parameters of forage dry matter intake and milk produced from forage in Swedish Red and Holstein dairy cows
- 2021
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Ingår i: Journal of Dairy Science. - : American Dairy Science Association. - 0022-0302 .- 1525-3198. ; 104, s. 4424-4440
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Tidskriftsartikel (refereegranskat)abstract
- High-yielding dairy cows are often fed high proportions of cereal grain and pulses. For several reasons, it would be desirable to replace these feed sources with forage, which is not suitable for human consumption. Feeding large amounts of forage to dairy cows could also make dairy production more publicly acceptable in the future. In this study, we estimated genetic parameters for total dry matter intake (DMI), DMI from forage (DMIFor), energy-corrected milk (ECM), and ECM produced from forage (ECMFor). A total of 1,177 lactations from 575 cows of Swedish Red (SR) and Holstein (HOL) dairy breeds were included in the study. Mixed linear animal random regression models were used, with fixed effect of calving season and lactation week nested within parity 1 and 2+, fixed effect of calving year, and random regression coefficients for breeding value (up to linear) and permanent environmental effect (up to quadratic) of the cow. Heritability for DMI and DMIFor was generally higher for HOL than for SR in all-parity data and in later parities; however, the opposite was true for first parity. Heritability for DMI and DMIFor during the first 8 wk averaged 0.11 and 0.15, respectively, in all-parity data for the 2 breeds. Corresponding values for ECMFor and ECM were 0.21 and 0.29, respectively. In first parity, values were 0.32, 0.36, 0.28, and 0.51, respectively. The genetic correlation between DMI and DMIFor was high, above 0.83, and fairly constant across the lactation. The genetic correlation between ECMFor and ECM was close to unity in the later part of lactation for both breeds, but was around 0.8 in the early lactation for both breeds; it decreased for HOL to 0.54 in wk 17. The genetic correlations between DMI and ECMFor and between DMIFor and ECMFor were low and negative for HOL (absolute value similar to 0.2-0.3), but changed for SR from weakly positive in early lactation to negative values and back to positive toward the end of lactation. For most traits, the correlation between wk 1 and wk 8 into the lactation was very high; the lowest value was for DMI in HOL at 0.81. The genetic correlation between parities was rather high in the first part of the lactation. During the first 8 wk, the correlation was lower for HOL than for SR, except for ECM. We found that DMIFor and ECMFor showed reasonably large heritability, and future work should explore the possibility of genomic evaluations.
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| 5. |
- Tarekegn, Getinet Mekuriaw
(författare)
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Genome-wide association study for the level of prolificacy in Cameroon's native goat
- 2024
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Ingår i: Journal of Applied Animal Research. - 0971-2119 .- 0974-1844. ; 52
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Tidskriftsartikel (refereegranskat)abstract
- Income from goats highly depends on prolificacy, which is difficult to improve by traditional breeding methods. The study aimed to identify SNP markers for prolificacy, using a case-control genome-wide association study (GWAS) on 111 genotyped Cameroon native goat (CNG) does, based on the 50 K single nucleotide polymorphism (SNP) chip panel. None of the top SNPs reached the significant p-value of 5 x 10-8. The highest p-value was 0.0009. Despite the number of cases being about a quarter of the number of controls, the highest allele frequency of some of the top 20 variants in the cases was indicative of their potential role in the trait. These top variants included the following 15: rs268285661, rs268235169, rs268236449, rs268235135, rs268240394 in Sphingosine-1-phosphate phosphatase 2 (SGPP2) gene, rs268283635 in Solute carrier family 24 member 2 (SLC24A2) gene, rs268251678 in Androgen-induced gene 1 (AIG1) gene, rs268267018, rs268239617, rs268281364, rs268273029, rs268286941, rs268236144, rs268233233 in CEP126 gene and rs268278159, respectively. Our findings indicate that GWAS enable the identification of some loci within genes, with known biological functions and pathways in human being and mice animal model but far-ranging to what was previously hypothesized and tested in goat.
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| 6. |
- Tarekegn, Getinet Mekuriaw, et al.
(författare)
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Genome-wide diversity and demographic dynamics of Cameroon goats and their divergence from east African, north African, and Asian conspecifics
- 2019
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- Indigenous goats make significant contributions to Cameroon's national and local economy, but little effort has been devoted to identifying the populations. Here, we assessed the genetic diversity and demographic dynamics of Cameroon goat populations using mitochondrial DNA (two populations) and autosomal markers (four populations) generated with the Caprine 50K SNP chip. To infer genetic relationships at continental and global level, genotype data on six goat populations from Ethiopia and one population each from Egypt, Morocco, Iran, and China were included in the analysis. The mtDNA analysis revealed 83 haplotypes, all belonging to haplogroup A, in Cameroon goats. Four haplotypes were shared between goats found in Cameroon, Mozambique, Namibia, Zimbabwe, Kenya, and Ethiopia. Analysis of autosomal SNPs in Cameroon goats revealed the lowest H-O (0.335 +/- 0.13) and H-E (0.352 +/- 0.15) in the North-west Highland and Central Highland populations, respectively. Overall, the highest H-O (0.401 +/- 0.12) and H-E (0.422 +/- 0.12) were found for Barki and Iranian goats, respectively. Barki goats had the highest average MAF, while Central Highland Cameroon goats had the lowest. Overall, Cameroon goats demonstrated high F-IS. AMOVA revealed that 13.29% of the variation was explained by genetic differences between the six population groups. Low average F-ST (0.01) suggests intermixing among Cameroon goats. All measures indicated that Cameroon goats are closer to Moroccan goats than to other goat populations. PCA and STRUCTURE analyses poorly differentiated the Cameroon goats, as did genetic distance, Neighbor-Net network, and neighbor-joining tree analyses. The haplotype analysis of mtDNA showed the initial dispersion of goats to Cameroon and central Africa from north-east Africa following the Nile Delta. Whereas, the approximate Bayesian computation indicated Cameroon goats were separated from Moroccan goats after 506 generations in later times (similar to 1518 YA), as supported by the phylogenetic net-work and admixture outputs. Overall, indigenous goats in Cameroon show weak phylogenetic structure, suggesting either extensive intermixing.
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| 7. |
- Tarekegn, Getinet Mekuriaw
(författare)
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Genome-wide insights of Ethiopian indigenous sheep populations reveal the population structure related to tail morphology and phylogeography
- 2020
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Ingår i: Genes and Genomics. - : Springer Science and Business Media LLC. - 1976-9571 .- 2092-9293. ; 42, s. 1169-1178
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Tidskriftsartikel (refereegranskat)abstract
- Background Ethiopian sheep living in different climatic zones and having contrasting morphologies are a most promising subject of molecular-genetic research. Elucidating their genetic diversity and genetic structure is critical for designing appropriate breeding and conservation strategies. Objective The study was aimed to investigate genome-wide genetic diversity and population structure of eight Ethiopian sheep populations. Methods A total of 115 blood samples were collected from four Ethiopian sheep populations that include Washera, Farta and Wollo (short fat-tailed) and Horro (long fat-tailed). DNA was extracted using Quick-DNA (TM) Miniprep plus kit. All DNA samples were genotyped using Ovine 50 K SNP BeadChip. To infer genetic relationships of Ethiopian sheep at national, continental and global levels, genotype data on four Ethiopian sheep (Adilo, Arsi-Bale, Menz and Black Head Somali) and sheep from east, north, and south Africa, Middle East and Asia were included in the study as reference. Results Mean genetic diversity of Ethiopian sheep populations ranged from 0.352 +/- 0.14 for Horro to 0.379 +/- 0.14 for Arsi-Bale sheep. Population structure and principal component analyses of the eight Ethiopian indigenous sheep revealed four distinct genetic cluster groups according to their tail phenotype and geographical distribution. The short fat-tailed sheep did not represent one genetic cluster group. Ethiopian fat-rump sheep share a common genetic background with the Kenyan fat-tailed sheep. Conclusion The results of the present study revealed the principal component and population structure follows a clear pattern of tail morphology and phylogeography. There is clear signature of admixture among the study Ethiopian sheep populations
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| 8. |
- Tarekegn, Getinet Mekuriaw
(författare)
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Haplotype analysis of the mitochondrial DNA d-loop region reveals the maternal origin and historical dynamics among the indigenous goat populations in east and west of the Democratic Republic of Congo
- 2022
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Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- This study aimed at assessing haplotype diversity and population dynamics of three Congolese indigenous goat populations that included Kasai goat (KG), small goat (SG), and dwarf goat (DG) of the Democratic Republic of Congo (DRC). The 1169 bp d-loop region of mitochondrial DNA (mtDNA) was sequenced for 339 Congolese indigenous goats. The total length of sequences was used to generate the haplotypes and evaluate their diversities, whereas the hypervariable region (HVI, 453 bp) was analyzed to define the maternal variation and the demographic dynamic. A total of 568 segregating sites that generated 192 haplotypes were observed from the entire d-loop region (1169 bp d-loop). Phylogenetic analyses using reference haplotypes from the six globally defined goat mtDNA haplogroups showed that all the three Congolese indigenous goat populations studied clustered into the dominant haplogroup A, as revealed by the neighbor-joining (NJ) tree and median-joining (MJ) network. Nine haplotypes were shared between the studied goats and goat populations from Pakistan (1 haplotype), Kenya, Ethiopia and Algeria (1 haplotype), Zimbabwe (1 haplotype), Cameroon (3 haplotypes), and Mozambique (3 haplotypes). The population pairwise analysis (F-ST) indicated a weak differentiation between the Congolese indigenous goat populations. Negative and significant (p-value <.05) values for Fu's Fs (-20.418) and Tajima's (-2.189) tests showed the expansion in the history of the three Congolese indigenous goat populations. These results suggest a weak differentiation and a single maternal origin for the studied goats. This information will contribute to the improvement of the management strategies and long-term conservation of indigenous goats in DRC.
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| 10. |
- Tarekegn, Getinet Mekuriaw
(författare)
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Mitochondrial DNA D-loop sequence analysis reveals high variation and multiple maternal origins of indigenous Tanzanian goat populations
- 2021
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Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 11, s. 15961-15971
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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