scholarly journals Whole genome sequences reveal multiple functions of PAT1 gene on environment adaptation and coat coloration in Tibetan sheep populations

2019 ◽  
Author(s):  
Jianbin Liu ◽  
Xuezhi Ding ◽  
Chao Yuan ◽  
Yufeng Zeng ◽  
Tingting Guo ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Coat Color ◽  
Body Height ◽  
Multiple Traits ◽  
Adaptive Traits ◽  
Environment Adaptation ◽  
Tibetan Sheep ◽  
Genomic Regions ◽  
The Tropics ◽  
Productive Trait

Abstract Background: Most sheep breeding programs designed for the tropics and sub-tropics have to take into account the impacts of both productive and adaptive traits. However, the genetic mechanism regulating the multiple biological process remain unclear. Results: In this study, we report a novel PAT1 gene that simultaneously explained the variations of productive trait (coat color), adaptive traits (altitude and geography response) in 15 indigenous Tibetan sheep populations. Overlapped genomic regions harboring 6 candidate genes across three traits were identified at 27 chromosomes, with the top 1% of Fst and |Zph| values. The SNP/INDELs and expression of these candidate genes were further analyzed, and we find that only PAT1 gene, a CSDE1 homologue was consistent with the variation of multiple traits regarding. Haplotype analysis of PAT1 reveal that Tibetan sheep breeds with C-type of PAT1 have significantly greater body weight, shear amount, chest width and body length, but have lower body height, than those with CA-type of PAT1. Conclusions: We emphasized that PAT1 gene could be a potentially selective target used for the improvements of environmental adaption and coat coloration in the future. These results contribute to the knowledge of adaptive response in Tibetan sheep populations and will help to guide future conservation programs for Tibetan sheep native to Qinghai-Tibetan Plateau.

scholarly journals Genomic Scan for Selection Signature Reveals Fat Deposition in Chinese Indigenous Sheep with Extreme Tail Types

Animals ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 773 ◽  
Author(s):  
Fuping Zhao ◽  
Tianyu Deng ◽  
Liangyu Shi ◽  
Wenwen Wang ◽  
Qin Zhang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Coat Color ◽  
Reproductive Traits ◽  
Bioinformatic Analysis ◽  
Selection Signatures ◽  
Selection Signature ◽  
Positional Candidate ◽  
Indigenous Sheep ◽  
Tibetan Sheep ◽  
Genomic Regions

It is a unique feature that fat can be deposited in sheep tails and rumps. To elucidate the genetic mechanism underlying this trait, we collected 120 individuals from three Chinese indigenous sheep breeds with extreme tail types, namely large fat-tailed sheep (n = 40), Altay sheep (n = 40), and Tibetan sheep (n = 40), and genotyped them using the Ovine Infinium HD SNP BeadChip. Then genomic scan for selection signatures was performed using the hapFLK. In total, we identified 25 genomic regions exhibiting evidence of having been under selection. Bioinformatic analysis of the genomic regions showed that selection signatures related to multiple candidate genes had a demonstrated role in phenotypic variation. Nine genes have documented association with sheep tail types, including WDR92, TBX12, WARS2, BMP2, VEGFA, PDGFD, HOXA10, ALX4, and ETAA1. Moreover, a number of genes were of particular interest, including RXFP2 associated with the presence/absence and morphology of horns; MITF involved in coat color; LIN52 and SYNDIG1L related to the number of teats; MSRB3 gene associated with ear sizes; LTBP2 considered as a positional candidate genes for number of ribs; JAZF1 regulating lipid metabolism; PGRMC2, SPAG17, TSHR, GTF2A1, and LARP1B implicated with reproductive traits. Our findings provide insights into fat tail formation and a reference for carrying out molecular breeding and conservation in sheep.

scholarly journals Genetic signatures of high-altitude adaptation and geographic distribution in Tibetan sheep

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Jianbin Liu ◽  
Chao Yuan ◽  
Tingting Guo ◽  
Fan Wang ◽  
Yufeng Zeng ◽  
...  
Keyword(s):  
Bos Taurus ◽  
Body Height ◽  
Hypoxia Tolerance ◽  
Adaptive Responses ◽  
Sheep Breeds ◽  
Tibetan Sheep ◽  
Altitude Adaptation ◽  
Genomic Regions ◽  
The Tropics ◽  
Indel Variation

Abstract Most sheep breeding programs designed for the tropics and sub-tropics have to take into account the impacts of environmental adaptive traits. However, the genetic mechanism regulating the multiple biological processes driving adaptive responses remains unclear. In this study, we applied a selective sweep analysis by combing 1% top values of Fst and ZHp on both altitude and geographic subpopulations (APS) in 636 indigenous Tibetan sheep breeds. Results show that 37 genes were identified within overlapped genomic regions regarding Fst significantly associated with APS. Out of the 37 genes, we found that 8, 3 and 6 genes at chromosomes (chr.) 13, 23 and 27, respectively, were identified in the genomic regions with 1% top values of ZHp. We further analyzed the INDEL variation of 6 genes at chr.27 (X chromosome) in APS together with corresponding orthologs of 6 genes in Capra, Pantholops, and Bos Taurus. We found that an INDEL was located within 5′UTR region of HAG1 gene. This INDEL of HAG1 was strongly associated with the variation of APS, which was further confirmed by qPCR. Sheep breeds carrying “C-INDEL” of HAG1 have significantly greater body weight, shear amount, corpuscular hemoglobin and globulin levels, but lower body height, than those carrying “CA-INDEL” of HAG1. We concluded that “C-INDEL” variation of HAG1 gene confers better hypoxia tolerance in the highlands of Tibetan and explains well geographic distributions in this population. These results contribute to our understanding of adaptive responses to altitude and geographic adaptation in Tibetan sheep populations and will help to guide future conservation programs for Tibetan sheep native to Qinghai-Tibetan Plateau.

scholarly journals Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Jingya Xu ◽  
Yuhua Fu ◽  
Yan Hu ◽  
Lilin Yin ◽  
Zhenshuang Tang ◽  
...  
Keyword(s):  
Body Weight ◽  
Candidate Genes ◽  
Complex Traits ◽  
Coat Color ◽  
Body Height ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Pig Breeds ◽  
Genome Variants

Abstract Background A large number of pig breeds are distributed around the world, their features and characteristics vary among breeds, and they are valuable resources. Understanding the underlying genetic mechanisms that explain across-breed variation can help breeders develop improved pig breeds. Results In this study, we performed GWAS using a standard mixed linear model with three types of genome variants (SNP, InDel, and CNV) that were identified from public, whole-genome, sequencing data sets. We used 469 pigs of 57 breeds, and we identified and analyzed approximately 19 million SNPs, 1.8 million InDels, and 18,016 CNVs. We defined six biological phenotypes by the characteristics of breed features to identify the associated genome variants and candidate genes, which included coat color, ear shape, gradient zone, body weight, body length, and body height. A total of 37 candidate genes was identified, which included 27 that were reported previously (e.g., PLAG1 for body weight), but the other 10 were newly detected candidate genes (e.g., ADAMTS9 for coat color). Conclusion Our study indicated that using GWAS across a modest number of breeds with high density genome variants provided efficient mapping of complex traits.

scholarly journals Genome-wide comparative analyses reveal selection signatures underlying adaptation and production in Tibetan and Poll Dorset sheep

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yingyue Zhang ◽  
Xianglan Xue ◽  
Yue Liu ◽  
Adam Abied ◽  
Yangyang Ding ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Coat Color ◽  
Genomic Diversity ◽  
Mean Corpuscular Hemoglobin ◽  
Nucleotide Polymorphisms ◽  
Production Traits ◽  
Selection Signatures ◽  
Corpuscular Hemoglobin ◽  
Genome Wide ◽  
Tibetan Sheep

AbstractThe identification of genome-wide selection signatures can provide insights on the mechanisms of natural and/or artificial selection and uncover genes related to biological functions and/or phenotypes. Tibetan sheep are an important livestock in Tibet, providing meat and wool for Tibetans who are renown for breeding livestock that adapt well to high altitudes. Using whole-genome sequences with an effective sequencing depth of 5×, we investigated the genomic diversity and structure and, identified selection signatures of White Tibetan, Oula and Poll Dorset sheep. We obtained 30,163,679 Single Nucleotide Polymorphisms (SNPs) and 5,388,372 indels benchmarked against the ovine Oar_v4.0 genome assembly. Next, using FST, ZHp and XP-EHH approaches, we identified selection signatures spanning a set of candidate genes, including HIF1A, CAPN3, PRKAA1, RXFP2, TRHR and HOXA10 that are associated with pathways and GO categories putatively related to hypoxia responses, meat traits and disease resistance. Candidate genes and GO terms associated with coat color were also identified. Finally, quantification of blood physiological parameters, revealed higher levels of mean corpuscular hemoglobin measurement and mean corpuscular hemoglobin concentration in Tibetan sheep compared with Poll Dorset, suggesting a greater oxygen-carrying capacity in the Tibetan sheep and thus better adaptation to high-altitude hypoxia. In conclusion, this study provides a greater understanding of genome diversity and variations associated with adaptive and production traits in sheep.

scholarly journals A chromosomal inversion drives evolution of multiple adaptive traits in deer mice

2021 ◽  
Author(s):  
Emily R. Hager ◽  
Olivia S. Harringmeyer ◽  
T. Brock Wooldridge ◽  
Shunn Theingi ◽  
Jacob T. Gable ◽  
...  
Keyword(s):  
Local Adaptation ◽  
Evolutionary Biology ◽  
Coat Color ◽  
Tail Length ◽  
Chromosomal Inversion ◽  
Deer Mice ◽  
Strong Linkage Disequilibrium ◽  
Multiple Traits ◽  
Adaptive Traits ◽  
Genetic Mechanisms

AbstractA long-standing question in evolutionary biology is how differences in multiple traits can evolve quickly and be maintained together during local adaptation. Using forest and prairie ecotypes in deer mice, which differ in both tail length and coat color, we discovered a 41 Mb chromosomal inversion that is strongly linked to variation in both traits. The inversion maintains highly divergent loci in strong linkage disequilibrium and likely originated ~170 kya, long before the forest-prairie divergence ~10 kya. Consistent with a role in local adaptation, inversion frequency is associated with phenotype and habitat across both a local transect and the species range. Still, although eastern and western forest subspecies share similar phenotypes, the inversion is absent in eastern North America. This work highlights the significance of inversion polymorphisms for the establishment and maintenance of multiple locally adaptive traits in mammals, and demonstrates that, even within a species, parallel phenotypes may evolve through nonparallel genetic mechanisms.

scholarly journals 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

2021 ◽  
Vol 12 ◽  
Author(s):  
Satish Kumar Illa ◽  
Sabyasachi Mukherjee ◽  
Sapna Nath ◽  
Anupama Mukherjee
Keyword(s):  
Candidate Genes ◽  
Milk Production ◽  
Milk Fat ◽  
Coat Color ◽  
Enrichment Analysis ◽  
Background Information ◽  
Economic Traits ◽  
Sahiwal Cattle ◽  
Signatures Of Selection ◽  
Genomic Regions

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.

scholarly journals Whole Genome Selective Sweeps Analysis in Pakistani Kamori Goat

2021 ◽  
Author(s):  
Rashid Saif ◽  
Jan Henkel ◽  
Tania Mahmood ◽  
Aniqa Ejaz ◽  
Saeeda Zia
Keyword(s):  
Coat Color ◽  
Body Height ◽  
Fixation Index ◽  
Whole Genome ◽  
Genetic Potential ◽  
Mapping Process ◽  
Quality Checks ◽  
Breed Improvement ◽  
Genomic Regions ◽  
Initial Process

Abstract Natural and artificial selection fix certain genomic regions of reduce heterozygosity which is an initial process in breed development. Primary goal of the current study is to identify these genomic selection signatures under positive selection and harbor genes in Pakistani Kamori goat breed. High throughput whole genome pooled-seq of Kamori (n = 12) and Bezoar (n = 8) was carried out. Raw fastq files were undergone quality checks, trimming and mapping process against ARS1 reference followed by calling variant allele frequencies. Selection sweeps were identified by applying pooled heterozygosity (Hp) and Tajima’s D (TD) on Kamori while regions under divergent selection between Kamori & Bezoar were observed by Fixation Index (FST) analysis. Genome sequencing yielded 619,031,812 reads of which, 616,624,284 were successfully mapped. Total 98,574 autosomal selection signals were detected; 32,838 from Hp and 32,868 from each FST & TD statistics. Annotation of the regions with threshold (-ZHp ≥ 5, TD ≤ -2.72 & FST ≤ 0.09) detected 60 candidate genes. The top hits harbor Chr.1, 6, 8 & 21 having genes associated with body weight (GLIS3, ASTE1), coat color (DOCK8, MIPOL1) & body height (SLC25A21). Other significant windows harbor milk production, wool production, immunity, adaptation and reproduction trait related genes. Current finding highlighted the under-selection genomic regions of Kamori breed and likely to be associated with its vested traits and further useful in breed improvement, and may be also propagated to other undefined goat breeds by adopting targeted breeding policies to improve the genetic potential of this valued species.

scholarly journals Molecular characterization of two candidate genes associated with coat color in Tibetan sheep (Ovis arise)

2015 ◽  
Vol 14 (7) ◽  
pp. 1390-1397 ◽  
Author(s):  
Ji-long HAN ◽  
Min YANG ◽  
Ting-ting GUO ◽  
Yao-jing YUE ◽  
Jian-bin LIU ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Molecular Characterization ◽  
Coat Color ◽  
Tibetan Sheep

scholarly journals Review on Genomic Regions and Candidate Genes Associated with Economically Important Production and Reproduction Traits in Sheep (Ovies aries)

Animals ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 33 ◽  
Author(s):  
Gebremedhin Gebreselassie ◽  
Haile Berihulay ◽  
Lin Jiang ◽  
Yuehui Ma
Keyword(s):  
Candidate Genes ◽  
Production Efficiency ◽  
Genome Wide Association Study ◽  
Coat Color ◽  
Ovis Aries ◽  
Phenotypic Traits ◽  
Comprehensive Information ◽  
Reproduction Traits ◽  
Development And Utilization ◽  
Genomic Regions

Sheep (Ovis aries) is one of the most economically, culturally, and socially important domestic animals. They are reared primarily for meat, milk, wool, and fur production. Sheep were reared using natural selection for a long period of time to offer these traits. In fact, this production system has been slowing the productivity and production potential of the sheep. To improve production efficiency and productivity of this animal through genetic improvement technologies, understanding the genetic background of traits such as body growth, weight, carcass quality, fat percent, fertility, milk yield, wool quality, horn type, and coat color is essential. With the development and utilization of animal genotyping technologies and gene identification methods, many functional genes and genetic variants associated with economically important phenotypic traits have been identified and annotated. This is useful and presented an opportunity to increase the pace of animal genetic gain. Quantitative trait loci and genome wide association study have been playing an important role in identifying candidate genes and animal characterization. This review provides comprehensive information on the identified genomic regions and candidate genes associated with production and reproduction traits, and gene function in sheep.

scholarly journals Whole Genome Selective Sweeps Analysis in Pakistani Kamori Goat

2021 ◽  
Author(s):  
Rashid Saif ◽  
Jan Henkel ◽  
Tania Mahmood ◽  
Aniqa Ejaz ◽  
Saeeda Zia
Keyword(s):  
Coat Color ◽  
Body Height ◽  
Fixation Index ◽  
Whole Genome ◽  
Genetic Potential ◽  
Mapping Process ◽  
Quality Checks ◽  
Breed Improvement ◽  
Genomic Regions ◽  
Initial Process

AbstractNatural and artificial selection fix certain genomic regions of reduce heterozygosity which is an initial process in breed development. Primary goal of the current study is to identify these genomic selection signatures under positive selection and harbor genes in Pakistani Kamori goat breed. High throughput whole genome pooled-seq of Kamori (n = 12) and Bezoar (n = 8) was carried out. Raw fastq files were undergone quality checks, trimming and mapping process against ARS1 reference followed by calling variant allele frequencies. Selection sweeps were identified by applying pooled heterozygosity (Hp) and Tajima’s D (TD) on Kamori while regions under divergent selection between Kamori & Bezoar were observed by Fixation Index (FST) analysis. Genome sequencing yielded 619,031,812 reads of which, 616,624,284 were successfully mapped. Total 98,574 autosomal selection signals were detected; 32,838 from Hp and 32,868 from each FST & TD statistics. Annotation of the regions with threshold (−ZHp ≥ 5, TD ≤ −2.72 & FST ≤ 0.09) detected 60 candidate genes. The top hits harbor Chr.1, 6, 8 & 21 having genes associated with body weight (GLIS3, ASTE1), coat color (DOCK8, MIPOL1) & body height (SLC25A21). Other significant windows harbor milk production, wool production, immunity, adaptation and reproduction trait related genes. Current finding highlighted the under-selection genomic regions of Kamori breed and likely to be associated with its vested traits and further useful in breed improvement, and may be also propagated to other undefined goat breeds by adopting targeted breeding policies to improve the genetic potential of this valued species.

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