Whole genome detection of recent selection signatures in Sarabi cattle: a unique Iranian taurine breed

The Dwarf Lagune and the Savannah Somba cattle in Benin are typical representatives of the endangered West African indigenous Shorthorn taurine. The Lagune was previously exported to African and European countries and bred as Dahomey cattle, whereas the Somba contributed to the formation of two indigenous hybrids known as Borgou and Pabli cattle. These breeds are affected by demographic, economic, and environmental pressures in local production systems. Considering current and historical genomic data, we applied a formal test of admixture, estimated admixture proportions, and computed genomic inbreeding coefficients to characterize the five breeds. Subsequently, we unraveled the most recent selection signatures using the cross-population extended haplotype homozygosity approach, based on the current and historical genotypes. Results from principal component analyses and high proportion of Lagune ancestry confirm the Lagune origin of the European Dahomey cattle. Moreover, the Dahomey cattle displayed neither indicine nor European taurine (EUT) background, but they shared on average 40% of autozygosity from common ancestors, dated approximately eight generations ago. The Lagune cattle presented inbreeding coefficients larger than 0.13; however, the Somba and the hybrids (Borgou and Pabli) were less inbred (≤0.08). We detected evidence of admixture in the Somba and Lagune cattle, but they exhibited a similar African taurine (AFT) ancestral proportion (≥96%) to historical populations, respectively. A moderate and stable AFT ancestral proportion (62%) was also inferred for less admixed hybrid cattle including the Pabli. In contrast, the current Borgou samples displayed a lower AFT ancestral proportion (47%) than historical samples (63%). Irrespective of the admixture proportions, the hybrid populations displayed more selection signatures related to economic traits (reproduction, growth, and milk) than the taurine. In contrast, the taurine, especially the Somba, presented several regions known to be associated with adaptive traits (immunity and feed efficiency). The identified subregion of bovine leukocyte antigen (BoLA) class IIb (including DSB and BOLA-DYA) in Somba cattle is interestingly uncommon in other African breeds, suggesting further investigations to understand its association with specific adaptation to endemic diseases in Benin. Overall, our study provides deeper insights into recent evolutionary processes in the Beninese indigenous cattle and their aptitude for conservation and genetic improvement.

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Whole Genome Resequencing Reveals Selection Signatures Associated With Important Traits in Ethiopian Indigenous Goat Populations

Frontiers in Genetics ◽

10.3389/fgene.2019.01190 ◽

2019 ◽

Vol 10 ◽

Cited By ~ 1

Author(s):

Haile Berihulay ◽

Yefang Li ◽

Berihu Gebrekidan ◽

Gebremedhin Gebreselassie ◽

Xuexue Liu ◽

...

Keyword(s):

Whole Genome ◽

Selection Signatures ◽

Genome Resequencing ◽

Indigenous Goat ◽

Whole Genome Resequencing

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Whole genome characterization of autochthonous Bos taurus brachyceros and introduced Bos indicus indicus cattle breeds in Cameroon regarding their adaptive phenotypic traits and pathogen resistance

10.21203/rs.2.20033/v1 ◽

2020 ◽

Author(s):

Archile Eric paguem ◽

Babette Abanda ◽

Mbunkah Daniel Achukwi ◽

Praveen Baskaran ◽

Stefan Czemmel ◽

...

Keyword(s):

Bos Taurus ◽

Bos Indicus ◽

Cattle Breed ◽

Phenotypic Traits ◽

Zebu Cattle ◽

Whole Genome ◽

Genetic Traits ◽

Cattle Breeds ◽

Taurine Breed ◽

Taurine Cattle

Abstract BackgroundWest African indigenous taurine cattle display unique adaptive traits shaped by husbandry management, regional climate and exposure to endemic pathogens. They are less productive with respect to milk and meat production which has been associated with a number of factors, amongst others small size, traditional beliefs and husbandry practices. This resulted in the severe dwindling of their populations size rendering them vulnerable to extinction. The Namchi (Doayo) taurine cattle breed has documented resistance traits against trypanosome infection and exposure to tick infestation. Nonetheless, the historically later introduced Zebu cattle are the main cattle breeds in Africa today, even though they suffer more from locally prevailing pathogens. By using a reference-based whole genome sequencing approach, we sequenced for the first time the genomes of five cattle breeds from Cameroon: the Namchi (Doayo), an endangered trypanotolerant taurine breed, the Kapsiki, an indigenous trypanosusceptible taurine breed, and three Zebu (Bos indicus indicus) breeds: Ngaoundere Gudali, White Fulani and Red Fulani.ResultsApproximately 167 Giga bases of raw sequencing data were generated and mapped to the cattle reference genome UMD3.1. The coverage was 22 to 30-fold. The single nucleotide polymorphisms (SNPs) were compared with reference genomes of European Bos taurus Holstein and of Asian Bos indicus Brahman and the African trypanotolerant N’Dama breeds.Of a total of 50 million SNPs identified, 3.43 million were breed-specific ranging from 0.37 to 0.47 million SNPs in the domestic Cameroonian breeds and approximately 0.58 million constituted of small insertions and deletions. We identified breed specific-non-synonymous variants as genetic traits that could explain certain cattle-breed specific phenotypes such as increased tolerance against trypanosome parasites in the Namchi (Doayo) breed, heat tolerance in the Kapsiki breed, and growth, metabolism and meat quality in the Gudali breeds. Phylogenetic comparison grouped Namchi (Doayo) to the African Zebu clade indicating a hybrid status of the selected animal with a Zebu breed, albeit it showed the Namchi breed’s phenotype.ConclusionsThe findings provide the first comprehensive set of full genome variant data of the most important Cameroonian cattle breeds. The genomic data shall constitute a foundation for breed amelioration whilst exploiting the heritable traits and support conservation efforts for the endangered local cattle breeds.

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Whole genome characterization of autochthonous Bos taurus brachyceros and introduced Bos indicus indicus cattle breeds in Cameroon regarding their adaptive phenotypic traits and pathogen resistance

10.21203/rs.2.20033/v2 ◽

2020 ◽

Author(s):

Archile Eric Paguem ◽

Babette Abanda ◽

Mbunkah Daniel Achukwi ◽

Praveen Baskaran ◽

Stefan Czemmel ◽

...

Keyword(s):

Bos Taurus ◽

Bos Indicus ◽

Cattle Breed ◽

Phenotypic Traits ◽

Whole Genome ◽

Genetic Traits ◽

Cattle Breeds ◽

Taurine Breed ◽

Taurine Cattle ◽

Reference Genomes

Abstract Background:West African indigenous taurine cattle display unique adaptive traits shaped by husbandry management, regional climate and exposure to endemic pathogens. They are less productive with respect to milk and meat production which has been associated with amongst others, small size, traditional beliefs and husbandry practices. This resulted in the severe dwindling of their population size rendering them vulnerable to extinction. The Namchi taurine cattle breed is referred to as [Namchi (Doayo)] and shows resistance traits against trypanosome infection and exposure to tick infestation. Nonetheless, the historically later introduced Zebu cattle are the main cattle breeds in Africa today, even though they suffer more from locally prevailing pathogens. By using a reference-based whole genome sequencing approach, we sequenced with high depth for the first time the genomes of five cattle breeds from Cameroon in order to provide a valuable genetic resource for future African cattle breeding: the Namchi , an endangered trypano-tolerant taurine breed, the Kapsiki, an indigenous trypano-susceptible taurine breed, and three Zebu (Bos indicus indicus) breeds: Ngaoundere Gudali, White Fulani and Red Fulani.Results: Approximately 167 Gigabases of raw sequencing data were generated for each breed and mapped to the cattle reference genomes ARS-UCD1.2 and UMD3.1.The coverage was 103 to 140-fold when aligning the reads to ARS-UCD1.2 with an average mapping rate of ~99%, and 22 to 30-fold when aligning the reads to UMD3.1 with an average mapping rate of ~64%. The single nucleotide polymorphisms (SNPs) obtained from analysis using the genome ARS-UCD1.2 were compared with reference genomes of European Bos taurus Holstein, the Asian Bos indicus Brahman, and the African trypanotolerant N’Dama breeds.A total of ~100 million (M) SNPs were identified and 7.7 M of those were breed-specific. Approximately 11.1 M constituted of small insertions and deletions. By using only breed-specific non-synonymous variants we identified genes as genetic traits and associated Gene Ontology (GO) terms that could explain certain cattle-breed specific phenotypes such as increased tolerance against trypanosome parasites in the Namchi breed and heat tolerance in the Kapsiki breed. Phylogenetic analysis grouped, except for Namchi, the Bos taurus breeds Kapsiki, N’Dama and Holstein together while the B. indicus breeds White and Red Fulani, Gudali and Brahman clustered separately. The deviating result for Namchi indicates a hybrid status of the selected animal with a recent introgression of Zebu genes into its genome.Conclusions:The findings provide the first comprehensive set of genome-wide variant data of the most important Cameroonian cattle breeds. The genomic data shall constitute a foundation for breed amelioration whilst exploiting the heritable traits and support conservation efforts for the endangered local cattle breeds.

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Selection signatures of litter size in Dazu black goats based on a whole genome sequencing mixed pools strategy

Molecular Biology Reports ◽

10.1007/s11033-019-04904-6 ◽

2019 ◽

Vol 46 (5) ◽

pp. 5517-5523 ◽

Cited By ~ 4

Author(s):

Guang-Xin E ◽

Yong-Ju Zhao ◽

Yong-Fu Huang

Keyword(s):

Whole Genome Sequencing ◽

Litter Size ◽

Genome Sequencing ◽

Whole Genome ◽

Selection Signatures

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Whole-genome resequencing reveals selection signatures associated with milk production traits in African Kenana dairy zebu cattle

Genomics ◽

10.1016/j.ygeno.2019.06.002 ◽

2020 ◽

Vol 112 (1) ◽

pp. 880-885

Author(s):

Hojjat Asadollahpour Nanaei ◽

Mostafa Dehghani Qanatqestani ◽

Ali Esmailizadeh

Keyword(s):

Milk Production ◽

Zebu Cattle ◽

Whole Genome ◽

Production Traits ◽

Selection Signatures ◽

Milk Production Traits ◽

Genome Resequencing ◽

Whole Genome Resequencing

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Whole-genome scan for signatures of recent selection reveals loci associated with important traits in White Leghorn chickens

Poultry Science ◽

10.3382/ps.2012-02275 ◽

2012 ◽

Vol 91 (8) ◽

pp. 1804-1812 ◽

Cited By ~ 10

Author(s):

D.F. Li ◽

W.B. Liu ◽

J.F. Liu ◽

G.Q. Yi ◽

L. Lian ◽

...

Keyword(s):

Genome Scan ◽

Whole Genome ◽

White Leghorn ◽

Whole Genome Scan ◽

Recent Selection

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Genomic Uniqueness of Local Sheep Breeds From Morocco

Frontiers in Genetics ◽

10.3389/fgene.2021.723599 ◽

2021 ◽

Vol 12 ◽

Author(s):

Abdessamad Ouhrouch ◽

Simon Boitard ◽

Frédéric Boyer ◽

Bertrand Servin ◽

Anne Da Silva ◽

...

Keyword(s):

Genetic Diversity ◽

Demographic History ◽

Large Set ◽

Whole Genome ◽

Selection Signatures ◽

Effective Population ◽

High Genetic Diversity ◽

Sheep Breeds ◽

Genome Data ◽

Genomic Regions

Sheep farming is a major source of meat in Morocco and plays a key role in the country’s agriculture. This study aims at characterizing the whole-genome diversity and demographic history of the main Moroccan sheep breeds, as well as to identify selection signatures within and between breeds. Whole genome data from 87 individuals representing the five predominant local breeds were used to estimate their level of neutral genetic diversity and to infer the variation of their effective population size over time. In addition, we used two methods to detect selection signatures: either for detecting selective sweeps within each breed separately or by detecting differentially selected regions by contrasting different breeds. We identified hundreds of genomic regions putatively under selection, which related to several biological terms involved in local adaptation or the expression of zootechnical performances such as Growth, UV protection, Cell maturation or Feeding behavior. The results of this study revealed selection signatures in genes that have an important role in traits of interest and increased our understanding of how genetic diversity is distributed in these local breeds. Thus, Moroccan local sheep breeds exhibit both a high genetic diversity and a large set of adaptive variations, and therefore, represent a valuable genetic resource for the conservation of sheep in the context of climate change.

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Detection of Whole Genome Selection Signatures of Pakistani Teddy Goat

10.20944/preprints202012.0421.v1 ◽

2020 ◽

Author(s):

Rashid Saif ◽

Jan Henkel ◽

Tania Mahmood ◽

Aniqa Ejaz ◽

Fraz Ahmed ◽

...

Keyword(s):

Positive Selection ◽

Reference Genome ◽

Sequence Data ◽

Body Height ◽

Whole Genome ◽

Selection Signatures ◽

Genome Selection ◽

Reference Genome Assembly ◽

Genetic Potential ◽

Productive Traits

Whole genome pooled sequence data of 12 Pakistani Teddy goats is analyzed for positive selection signatures as their breed defining characteristics. Selection imprints left in the Teddy genome are unveiled by genomic differentiation after the successful paired-end alignment of 635,357,043 reads with (ARS1) reference genome assembly. Pooled-heterozygosity ( ) and Tajima’s D (TD) are applied for validation and getting better hits of selection signals, while pairwise FST statistics is conducted on Teddy vs. Bezoar (wild goat ancestor) for genomic differentiation. Annotation of regions under positive selection reveals 59 genes underlying production and adaptive traits. score ≥ 5 detected six windows having highest scores on Chr. 29, 9, 25, 15 and 14 that harbor HRASLS5, LACE1 and AXIN1 genes which are candidate for embryonic development, lactation and body height. Secondly, TD value of ≤ -2.2 showed 4 windows with very strong hits on Chr.5 & 9 harbor STIM1 and ADM genes related to body mass and weight. Lastly, FST analysis generated three strong signals with threshold ≤ 0.42 on Chr.12 & 5 harbor ITGB1 gene associated with milk production & lactation traits. Other significant selection signatures encompass genes associated with wool production, prolificacy, immunity and coat colors. In brief, this study identified the genes under selection in this Pakistani goat breed that will be helpful to refining future breeding policies and converging required productive traits within and across other goat breeds and to explore full genetic potential of this valued livestock species.

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