Detection of whole genome selection signatures of Pakistani Teddy goat

2021 ◽  
Author(s):  
Rashid Saif ◽  
Jan Henkel ◽  
Tania Mahmood ◽  
Aniqa Ejaz ◽  
Fraz Ahmad ◽  
...  
Keyword(s):  
Whole Genome ◽  
Selection Signatures ◽  
Genome Selection

scholarly journals Detection of Whole Genome Selection Signatures of Pakistani Teddy Goat

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.

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

2019 ◽  
Vol 42 (2) ◽  
pp. 203-215
Author(s):  
Hasan Moradian ◽  
Ali Esmailizadeh Koshkoiyeh ◽  
Mohammadreza Mohammadabadi ◽  
Masood Asadi Fozi
Keyword(s):  
Whole Genome ◽  
Selection Signatures ◽  
Taurine Breed ◽  
Recent Selection

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

2019 ◽  
Vol 10 ◽  
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

Whole-Genome Selection in Livestock

2019 ◽  
pp. 349-364 ◽  
Author(s):  
Birbal Singh ◽  
Gorakh Mal ◽  
Sanjeev K. Gautam ◽  
Manishi Mukesh
Keyword(s):  
Whole Genome ◽  
Genome Selection

scholarly journals Genomic Uniqueness of Local Sheep Breeds From Morocco

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.

scholarly journals Indigenous ancestry and admixture in the Uruguayan population

2021 ◽  
Author(s):  
Lucia Spangenberg ◽  
Maria Ines Fariello ◽  
Dario Arce ◽  
Gabriel Illanes ◽  
Gonzalo Greif ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Indigenous Peoples ◽  
European Ancestry ◽  
Whole Genome ◽  
Historical Records ◽  
Selection Signatures ◽  
Franciscan Missions ◽  
Colonial Contact ◽  
The City ◽  
Genomic Similarity

The Amerindian group known as the Charrúas inhabited Uruguay at the timing of European colonial contact. Even though they were extinguished as an ethnic group as a result of a genocide, Charrúan heritage is part of the Uruguayan identity both culturally and genetically. While mitochondrial DNA studies have shown evidence of Amerindian ancestry in living Uruguayans, here we undertake whole-genome sequencing of 10 Uruguayan individuals with Charruan heritage. We detect chromosomal segments of Amerindian ancestry supporting the presence of indigenous genetic ancestry in living descendants. Specific haplotypes were found to be enriched in 'Charrúas' and rare in the rest of the Amerindian groups studied. Some of these we interpret as the result of positive selection, as we identified selection signatures and they were located mostly within genes related to the infectivity of specific viruses. Historical records describe contacts of the Charrúas with other Amerindians, such as Guaraní, and patterns of genomic similarity observed here concur with genomic similarity between these groups. Less expected, we found a high genomic similarity of the Charrúas to Diaguita from Argentinian and Chile, which could be explained by geographically proximity. Finally, by fitting admixture models of Amerindian and European ancestry for the Uruguayan population, we were able to estimate the timing of the first pulse of admixture between European and Uruguayan indigenous peoples in 1658 and the second migration pulse in 1683. Both dates roughly concurring with the Franciscan missions in 1662 and the foundation of the city of Colonia in 1680 by the Spanish.

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