Genome-Wide Survey of Selection Signatures in Pakistani Cattle Breeds

Mustafa, Hiba J.

doi:10.29261/pakvetj/2018.051

Cited by 8 publications

(6 citation statements)

References 28 publications

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“…Other studies on signatures of selection in the crossbred cattle reported a region that coincided with our study and is associated with milk production (Li et al, 2010;Singh et al, 2020). In our study, additionally one more candidate gene located on BTA 9 and related to milk production was observed (Mustafa et al, 2018). Multi-trait meta-analysis in Nordic cattle detected several loci with pleiotropic effects on milk production and mastitis resistance (Cai et al, 2020).…”

Section: Milk and Related Traitssupporting

confidence: 87%

“…Selection signatures in Sahiwal were identified by the DCMS method, which combined the p-values from five different statistics into a new statistic, in contrast to the studies that considered the overlap in the genomic regions among the different methods. One earlier study utilized two complementary tests such as iHS and F ST (Mustafa et al, 2018) to detect the loci under selection in Sahiwal cattle. However, the compound measure of DCMS gives precise and unbiased information about the genomic regions under selection by integrating the univariate statistic p-values (Grossman et al, 2010;Ma et al, 2015;Lotterhos et al, 2017).…”

Section: Discussionmentioning

confidence: 99%

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Genome-Wide Scanning for Signatures of Selection Revealed the Putative Genomic Regions and Candidate Genes Controlling Milk Composition and Coat Color Traits in Sahiwal Cattle

et al. 2021

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BackgroundIn the evolutionary time scale, selection shapes the genetic variation and alters the architecture of genome in the organisms. Selection leaves detectable signatures at the genomic coordinates that provide clues about the protein-coding regions. Sahiwal is a valuable indicine cattle adapted to tropical environments with desirable milk attributes. Insights into the genomic regions under putative selection may reveal the molecular mechanisms affecting the quantitative and other important traits. To understand this, the present investigation was undertaken to explore signatures of selection in the genome of Sahiwal cattle using a medium-density genotyping INDUS chip.ResultDe-correlated composite of multiple selection signals (DCMS), which combines five different univariate statistics, was computed in the dataset to detect the signatures of selection in the Sahiwal genome. Gene annotations, Quantitative Trait Loci (QTL) enrichment, and functional analyses were carried out for the identification of significant genomic regions. A total of 117 genes were identified, which affect a number of important economic traits. The QTL enrichment analysis highlighted 14 significant [False Discovery Rate (FDR)-corrected p-value ≤ 0.05] regions on chromosomes BTA 1, 3, 6, 11, 20, and 21. The top three enriched QTLs were found on BTA 6, 20, and 23, which are associated with exterior, health, milk production, and reproduction traits. The present study on selection signatures revealed some key genes related with coat color (PDGFRA, KIT, and KDR), facial pigmentation (LEF), milk fat percent (MAP3K1, HADH, CYP2U1, and SGMS2), sperm membrane integrity (OSTC), lactation persistency (MRPS30, NNT, CCL28, HMGCS1, NIM1K, ZNF131, and CCDC152), milk yield (GHR and ZNF469), reproduction (NKX2-1 and DENND1A), and bovine tuberculosis susceptibility (RNF144B and PAPSS1). Further analysis of candidate gene prioritization identified four hub genes, viz., KIT, KDR, MAP3K1, and LEF, which play a role in coat color, facial pigmentation, and milk fat percentage in cattle. Gene enrichment analysis revealed significant Gene ontology (GO) terms related to breed-specific coat color and milk fat percent.ConclusionThe key candidate genes and putative genomic regions associated with economic traits were identified in Sahiwal using single nucleotide polymorphism data and the DCMS method. It revealed selection for milk production, coat color, and adaptability to tropical climate. The knowledge about signatures of selection and candidate genes affecting phenotypes have provided a background information that can be further utilized to understand the underlying mechanism involved in these traits in Sahiwal cattle.

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Section: Milk and Related Traitssupporting

confidence: 87%

Section: Discussionmentioning

confidence: 99%

Genome-Wide Scanning for Signatures of Selection Revealed the Putative Genomic Regions and Candidate Genes Controlling Milk Composition and Coat Color Traits in Sahiwal Cattle

et al. 2021

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“…It is preferred for genetic diversity, population structure, geography and animal evolution studies (Ankel-Simons and Cummins, 1996;Merwad et al, 2014). There are some related studies in our region for different species (Mustafa et al, 2018;Firyal et al, 2013). We have analyzed genetic diversity of donkey from Pakistani on the base of D-loop region of mtDNA.…”

Section: Resultsmentioning

confidence: 99%

Mitochondrial DNA diversity and maternal origins of Pakistani donkey

et al. 2024

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Domestic donkey plays a key role as a draft animal in rural economy of Pakistan where its population is increasing every year. The complete mtDNA control region of forty randomly sampled donkeys was PCR- amplified and sequenced bi-directionally using specific primers. Distinct mtDNA haplotypes obtained in the current study (KY446001−KY446011) were subjected to haplotype (h) and nucleotide diversity (π) measures using DnaS as well as to phylogenetic, Network, and AMOVA analyses. There were a total 27 polymorphic sites present within 11 unique mtDNA haplotypes from the studied 40 animals from different regions. Neighbor-joining network and median-joining network both illustrated the splitting of all these haplotypes into two well-defined Nubian and Somali lineages, confirming African maternal origin of Pakistani domestic donkey. Diversity parameters h (0.967± 0.037) and π (0.02917± 0.00307) were found to reveal high levels of genetic diversity in Pakistani donkeys. AMOVA demonstrated only 1% of genetic differences between two mtDNA maternal lineages, pointing to lack of population substructure in Pakistani donkeys as is the case with worldwide domestic donkey population. Pakistani donkeys have African maternal origin and high levels of mtDNA diversity. High genetic diversity may be due to non-selective breeding and heteroplasmy. We herein provide the first report on mtDNA diversity of control region in Pakistani domestic donkey.

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“…CNV в этом гене ассоциирована с иммунным ответом у яка (Zhang X. et al, 2016). Сообщалось, что гены AUH, CXCL14, IL1RL2 и EPB42 влияют на толерантность к паразитам у различных пород скота (Mustafa et al, 2018). Ряд генов, в том числе A2M, BLA-DQB, HSPA9, IFNA16, IL15, IL2, PROCR, SP3, VAMP7 и TLR4, связаны, по данным многочисленных исследований, с иммунным ответом (Mei et al, 2016;Randhawa et al, 2016).…”

Section: гены иммунного ответаunclassified

Signatures of selection and candidate genes for adaptation to extreme environmental factors in the genomes of Turano-Mongolian cattle breeds

2021

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Changes in the environment force populations of organisms to adapt to new conditions, either through phenotypic plasticity or through genetic or epigenetic changes. Signatures of selection, such as specific changes in the frequency of alleles and haplotypes, as well as the reduction or increase in genetic diversity, help to identify changes in the cattle genome in response to natural and artificial selection, as well as loci and genetic variants directly affecting adaptive and economically important traits. Advances in genetics and biotechnology enable a rapid transfer of unique genetic variants that have originated in local cattle breeds in the process of adaptation to local environments into the genomes of cosmopolitan high-performance breeds, in order to preserve their outstanding performance in new environments. It is also possible to use genomic selection approach to increase the frequency of already present adaptive alleles in cosmopolitan breeds. The review examines recent work on the origin and evolution of Turano-Mongolian cattle breeds, adaptation of Turano-Mongolian cattle to extreme environments, and summarizes available information on potential candidate genes for climate adaptation of Turano-Mongolian breeds, including cold resistance genes, immune response genes, and high-altitude adaptation genes. The authors conclude that the current literature data do not provide preference to one of the two possible scenarios of Turano-Mongolian breed origins: as a result of the domestication of a wild aurochs at East Asia or as a result of the migration of taurine proto-population from the Middle East. Turano-Mongolian breeds show a high degree of adaptation to extreme climatic conditions (cold, heat, lack of oxygen in the highlands) and parasites (mosquitoes, ticks, bacterial and viral infections). As a result of high-density genotyping and sequencing of genomes and transcriptomes, prospective candidate genes and genetic variants involved in adaptation to environmental factors have recently been identified.

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Genome-Wide Survey of Selection Signatures in Pakistani Cattle Breeds

Cited by 8 publications

References 28 publications

Genome-Wide Scanning for Signatures of Selection Revealed the Putative Genomic Regions and Candidate Genes Controlling Milk Composition and Coat Color Traits in Sahiwal Cattle

Genome-Wide Scanning for Signatures of Selection Revealed the Putative Genomic Regions and Candidate Genes Controlling Milk Composition and Coat Color Traits in Sahiwal Cattle

Mitochondrial DNA diversity and maternal origins of Pakistani donkey

Signatures of selection and candidate genes for adaptation to extreme environmental factors in the genomes of Turano-Mongolian cattle breeds

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