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.

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.

46 Footprints of Selection in Angus and Hanwoo Beef Cattle Using Imputed Whole Genome Sequence Data

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 25-25
Author(s):  
Muhammad Yasir Nawaz ◽  
Rodrigo Pelicioni Savegnago ◽  
Cedric Gondro
Keyword(s):  
Beef Cattle ◽  
Genome Sequence ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Fixation Index ◽  
Whole Genome ◽  
Extended Haplotype Homozygosity ◽  
Extended Haplotype ◽  
Genome Sequence Data ◽  
Genomic Regions

Abstract In this study, we detected genome wide footprints of selection in Hanwoo and Angus beef cattle using different allele frequency and haplotype-based methods based on imputed whole genome sequence data. Our dataset included 13,202 Angus and 10,437 Hanwoo animals with 10,057,633 and 13,241,550 imputed SNPs, respectively. A subset of data with 6,873,624 common SNPs between the two populations was used to estimate signatures of selection parameters, both within (runs of homozygosity and extended haplotype homozygosity) and between (allele fixation index, extended haplotype homozygosity) the breeds in order to infer evidence of selection. We observed that correlations between various measures of selection ranged between 0.01 to 0.42. Assuming these parameters were complementary to each other, we combined them into a composite selection signal to identify regions under selection in both beef breeds. The composite signal was based on the average of fractional ranks of individual selection measures for every SNP. We identified some selection signatures that were common between the breeds while others were independent. We also observed that more genomic regions were selected in Angus as compared to Hanwoo. Candidate genes within significant genomic regions may help explain mechanisms of adaptation, domestication history and loci for important traits in Angus and Hanwoo cattle. In the future, we will use the top SNPs under selection for genomic prediction of carcass traits in both breeds.

scholarly journals Whole-Genome Signatures of Selection in Sport Horses Revealed Selection Footprints Related to Musculoskeletal System Development Processes

Animals ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 53 ◽  
Author(s):  
Siavash Salek Ardestani ◽  
Mehdi Aminafshar ◽  
Mohammad Bagher Zandi Baghche Maryam ◽  
Mohammad Hossein Banabazi ◽  
Mehdi Sargolzaei ◽  
...  
Keyword(s):  
Musculoskeletal System ◽  
Limb Development ◽  
System Development ◽  
Enrichment Analysis ◽  
Sport Performance ◽  
Functional Enrichment ◽  
Fixation Index ◽  
Whole Genome ◽  
Selective Pressures ◽  
Genomic Regions

Selective breeding has led to gradual changes at the genome level of horses. Deciphering selective pressure patterns is progressive to understand how breeding strategies have shaped the sport horse genome; although, little is known about the genomic regions under selective pressures in sport horse breeds. The major goal of this study was to shed light on genomic regions and biological pathways under selective pressures in sport horses. In this study, whole-genome sequences of 16 modern sport and 35 non-sport horses were used to investigate the genomic selective signals of sport performance, by employing fixation index, nucleotide diversity, and Tajima’s D approaches. A total number of 49 shared genes were identified using these approaches. The functional enrichment analysis for candidate genes revealed novel significant biological processes related to musculoskeletal system development, such as limb development and morphogenesis, having been targeted by selection in sport breeds.

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.

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 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.

Identification of genomic islands in Synechococcus sp. WH8102 using genomic barcode and whole-genome microarray analyses

2020 ◽  
Vol 15 ◽  
Author(s):  
Jiahui Pan ◽  
Xizi Luo ◽  
Tong Shao ◽  
Chaoying Li ◽  
Tingting Zhao ◽  
...  
Keyword(s):  
Genomic Islands ◽  
Whole Genome ◽  
Photosynthetic Organisms ◽  
Depth Study ◽  
Whole Genome Microarray ◽  
Integrated Methods ◽  
Synechococcus Sp ◽  
Intuitive View ◽  
Genomic Regions ◽  
Different Origins

Background: Synechococcus sp. WH8102 is one of the most abundant photosynthetic organisms in many ocean regions. Objective: The aim of this study is to identify genomic islands (GIs) in Synechococcus sp. WH8102 with integrated methods. Methods: We have applied genomic barcode to identify the GIs in Synechococcus sp. WH8102, which could make genomic regions of different origins visually apparent. The gene expression data of the predicted GIs was analyzed through microarray data which was collected for functional analysis of the relevant genes. Results: Seven GIs were identified in Synechococcus sp. WH8102. Most of them are involved in cell surface modification, photosynthesis and drug resistance. In addition, our analysis also revealed the functions of these GIs, which could be used for in-depth study on the evolution of this strain. Conclusion: Genomic barcodes provide us with a comprehensive and intuitive view of the target genome. We can use it to understand the intrinsic characteristics of the whole genome and identify GIs or other similar elements.

scholarly journals Assessing genomic diversity and signatures of selection in Jiaxian Red cattle using whole-genome sequencing data

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xiaoting Xia ◽  
Shunjin Zhang ◽  
Huaju Zhang ◽  
Zijing Zhang ◽  
Ningbo Chen ◽  
...  
Keyword(s):  
Population Structure ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
System Response ◽  
Whole Genome ◽  
Population Structure Analysis ◽  
Native Cattle ◽  
Genomic Regions

Abstract Background Native cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and tough feeding conditions. Jiaxian Red, a Chinese native cattle breed, is reported to have originated from crossbreeding between taurine and indicine cattle; their history as a draft and meat animal dates back at least 30 years. Using whole-genome sequencing (WGS) data of 30 animals from the core breeding farm, we investigated the genetic diversity, population structure and genomic regions under selection of Jiaxian Red cattle. Furthermore, we used 131 published genomes of world-wide cattle to characterize the genomic variation of Jiaxian Red cattle. Results The population structure analysis revealed that Jiaxian Red cattle harboured the ancestry with East Asian taurine (0.493), Chinese indicine (0.379), European taurine (0.095) and Indian indicine (0.033). Three methods (nucleotide diversity, linkage disequilibrium decay and runs of homozygosity) implied the relatively high genomic diversity in Jiaxian Red cattle. We used θπ, CLR, FST and XP-EHH methods to look for the candidate signatures of positive selection in Jiaxian Red cattle. A total number of 171 (θπ and CLR) and 17 (FST and XP-EHH) shared genes were identified using different detection strategies. Functional annotation analysis revealed that these genes are potentially responsible for growth and feed efficiency (CCSER1), meat quality traits (ROCK2, PPP1R12A, CYB5R4, EYA3, PHACTR1), fertility (RFX4, SRD5A2) and immune system response (SLAMF1, CD84 and SLAMF6). Conclusion We provide a comprehensive overview of sequence variations in Jiaxian Red cattle genomes. Selection signatures were detected in genomic regions that are possibly related to economically important traits in Jiaxian Red cattle. We observed a high level of genomic diversity and low inbreeding in Jiaxian Red cattle. These results provide a basis for further resource protection and breeding improvement of this breed.

scholarly journals Genome-Wide Analyses Identifies Known and New Markers Responsible of Chicken Plumage Color

Animals ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 493
Author(s):  
Salvatore Mastrangelo ◽  
Filippo Cendron ◽  
Gianluca Sottile ◽  
Giovanni Niero ◽  
Baldassare Portolano ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Snp Array ◽  
Fixation Index ◽  
Phenotypic Traits ◽  
Plumage Color ◽  
Phenotypic Marker ◽  
Genome Wide ◽  
A Genome ◽  
The Difference ◽  
Genomic Regions

Through the development of the high-throughput genotyping arrays, molecular markers and genes related to phenotypic traits have been identified in livestock species. In poultry, plumage color is an important qualitative trait that can be used as phenotypic marker for breed identification. In order to assess sources of genetic variation related to the Polverara chicken breed plumage colour (black vs. white), we carried out a genome-wide association study (GWAS) and a genome-wide fixation index (FST) scan to uncover the genomic regions involved. A total of 37 animals (17 white and 20 black) were genotyped with the Affymetrix 600 K Chicken single nucleotide polymorphism (SNP) Array. The combination of results from GWAS and FST revealed a total of 40 significant markers distributed on GGA 01, 03, 08, 12 and 21, and located within or near known genes. In addition to the well-known TYR, other candidate genes have been identified in this study, such as GRM5, RAB38 and NOTCH2. All these genes could explain the difference between the two Polverara breeds. Therefore, this study provides the basis for further investigation of the genetic mechanisms involved in plumage color in chicken.

149 Integration of Selection Signatures Analyses and Weighted Single-step GWAS to Prioritize Candidate Genes for Body Conformation Traits in Pigs

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 76-77
Author(s):  
Seyed Milad Vahedi ◽  
Siavash Salek Ardestani ◽  
Duy Ngoc Do ◽  
Karim Karimi ◽  
Younes Miar
Keyword(s):  
Candidate Genes ◽  
Complex Traits ◽  
Body Height ◽  
Single Step ◽  
Fixation Index ◽  
Nucleotide Polymorphisms ◽  
Selection Signatures ◽  
Body Conformation ◽  
Yorkshire Pigs ◽  
Estimated Breeding Values

Abstract Body conformation traits such as body height (BH) and body length (BL) have been included in the swine industry’s selection criteria. The objective of this study was to identify the quantitative trait loci (QTLs) and candidate genes for pig conformation traits using an integration of selection signatures analyses and weighted single-step GWAS (WssGWAS). Body measurement records of 5,593 Yorkshire pigs of which 598 animals were genotyped with Illumina 50K panel were used. Estimated breeding values (EBVs) for BH and BL were computed using univariate animal models. Genotyped animals were grouped into top 5% and bottom 5% based on their EBVs, and selection signatures analyses were performed using fixation index (Fst), FLK, hapFLK, and Rsb statistics, which were then combined as a Mahalanobis distance (Md) framework. The WssGWAS was conducted to detect the single nucleotide polymorphisms (SNPs) associated with the studied traits. The top 1% SNPs (n=530) from Md distribution that overlapped with the top 1% SNPs from WssGWAS (n = 530) were used to detect the candidate genes. A total of 31 and six overlapped SNPs were found to be associated with BH and BL, respectively. Several candidate genes were identified for BH (PARVA, DCDC1, SYT1, CASTOR2, RGSL1, RGS8, RBMS3, TGFBR2, and HS6ST1) and BL (SNTB1, AK7, PAPOLA, KSR1, CHODL, and BMP2), explaining 2.58% and 0.42% of the trait’s genetic variation, respectively. Our results indicated that integrating data from the signatures of selection tests with WssGWAS could help elucidate genomic regions underlying complex traits.

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