Genomic scans for selective sweeps through haplotype homozygosity and allelic fixation in 14 indigenous sheep breeds from Middle East and South Asia

AbstractThe performance and productivity of livestock have consistently improved by natural and artificial selection over the centuries. Both these selections are expected to leave patterns on the genome and lead to changes in allele frequencies, but natural selection has played the major role among indigenous populations. Detecting selective sweeps in livestock may assist in understanding the processes involved in domestication, genome evolution and discovery of genomic regions associated with economically important traits. We investigated population genetic diversity and selection signals in this study using SNP genotype data of 14 indigenous sheep breeds from Middle East and South Asia, including six breeds from Iran, namely Iranian Balochi, Afshari, Moghani, Qezel, Zel, and Lori-Bakhtiari, three breeds from Afghanistan, namely Afghan Balochi, Arabi, and Gadik, three breeds from India, namely Indian Garole, Changthangi, and Deccani, and two breeds from Bangladesh, namely Bangladeshi Garole and Bangladesh East. The SNP genotype data were generated by the Illumina OvineSNP50 Genotyping BeadChip array. To detect genetic diversity and population structure, we used principal component analysis (PCA), admixture, phylogenetic analyses, and Runs of homozygosity. We applied four complementary statistical tests, FST (fixation index), xp-EHH (cross-population extended haplotype homozygosity), Rsb (extended haplotype homozygosity between-populations), and FLK (the extension of the Lewontin and Krakauer) to detect selective sweeps. Our results not only confirm the previous studies but also provide a suite of novel candidate genes involved in different traits in sheep. On average, FST, xp-EHH, Rsb, and FLK detected 128, 207, 222, and 252 genomic regions as candidates for selective sweeps, respectively. Furthermore, nine overlapping candidate genes were detected by these four tests, especially TNIK, DOCK1, USH2A, and TYW1B which associate with resistance to diseases and climate adaptation. Knowledge of candidate genomic regions in sheep populations may facilitate the identification and potential exploitation of the underlying genes in sheep breeding.

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Genomic Scans for Selective Sweeps With Four Complementary Statistical Tests on 14 Indigenous Sheep Breeds From Middle East and South Asia

10.21203/rs.3.rs-124388/v1 ◽

2020 ◽

Author(s):

Sirous Eydivandi ◽

Mohammad Osman Karimi ◽

Mahmood Amiri Roudbar ◽

Goutam Sahana

Keyword(s):

Middle East ◽

South Asia ◽

Candidate Genes ◽

Statistical Tests ◽

Genotype Data ◽

Extended Haplotype Homozygosity ◽

Selective Sweeps ◽

Extended Haplotype ◽

Indigenous Sheep ◽

Genomic Regions

Abstract The performance and productivity of livestock have consistently improved by natural and artificial selection over the centuries. Both these selections are expected to leave patterns on the genome and lead to changes in allele frequencies, but natural selection has played the major role among indigenous populations. Detecting selective sweeps in livestock may assist in understanding the processes involved in domestication, genome evolution and discovery of genomic regions associated with economically important traits. We investigated selection signals in this study using SNP genotype data of 14 indigenous sheep breeds from Middle East and South Asia, including six breeds from Iran, namely Iranian Balochi, Afshari, Moghani, Qezel, Zel, and Lori-Bakhtiari, three breeds from Afghanistan, namely Afghan Balochi, Arabi, and Gadik, three breeds from India, namely Indian Garole, Changthangi, and Deccani, and two breeds from Bangladesh, namely Bangladeshi Garole and Bangladesh East. The SNP genotype data were generated by the Illumina OvineSNP50 Genotyping BeadChip array. We applied four complementary statistical tests, FST (fixation index), xp-EHH (cross-population extended haplotype homozygosity), Rsb (extended haplotype homozygosity between-populations), and FLK (the extension of the Lewontin and Krakauer) to detect selective sweeps. Our results not only confirm the previous studies but also provide a suite of novel candidate genes involved in different traits in sheep. On average, FST, xp-EHH, Rsb, and FLK detected 128, 207, 222, and 252 genomic regions as candidates for selective sweeps, respectively. Furthermore, overlapping candidate genes were detected by these four tests, including; TNIK, DOCK1, SFMBT1, SPO11, USH2A, TYW1B, NELL2, EML5, and IQCE. The first six of these genes, especially TNIK, DOCK1, and SPO11 were enriched by Gene Ontology (GO) and are involved in embryonic development, immune response, and fertility respectively. Knowledge of candidate genomic regions in sheep populations may facilitate the identification and potential exploitation of the underlying genes in sheep breeding.

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

Journal of Animal Science ◽

10.1093/jas/skab235.042 ◽

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.

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Genome-Wide Runs of Homozygosity, Effective Population Size, and Detection of Positive Selection Signatures in Six Chinese Goat Breeds

Genes ◽

10.3390/genes10110938 ◽

2019 ◽

Vol 10 (11) ◽

pp. 938 ◽

Cited By ~ 4

Author(s):

Islam ◽

Li ◽

Liu ◽

Berihulay ◽

Abied ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Differentiation ◽

Positive Selection ◽

Candidate Genes ◽

Runs Of Homozygosity ◽

Selection Signatures ◽

Effective Population ◽

Signature Of Selection ◽

Genomic Regions ◽

Insight Into

: Detection of selection footprints provides insight into the evolution process and the underlying mechanisms controlling the phenotypic diversity of traits that have been exposed to selection. Selection focused on certain characters, mapping certain genomic regions often shows a loss of genetic diversity with an increased level of homozygosity. Therefore, the runs of homozygosity (ROHs), homozygosity by descent (HBD), and effective population size (Ne) are effective tools for exploring the genetic diversity, understanding the demographic history, foretelling the signature of directional selection, and improving the breeding strategies to use and conserve genetic resources. We characterized the ROH, HBD, Ne, and signature of selection of six Chinese goat populations using single nucleotide polymorphism (SNP) 50K Illumina beadchips. Our results show an inverse relationship between the length and frequency of ROH. A long ROH length, higher level of inbreeding, long HBD segment, and smaller Ne in Guangfeng (GF) goats suggested intensive selection pressure and recent inbreeding in this breed. We identified six reproduction-related genes within the genomic regions with a high ROH frequency, of which two genes overlapped with a putative selection signature. The estimated pair-wise genetic differentiation (FST) among the populations is 9.60% and the inter- and intra-population molecular variations are 9.68% and 89.6%, respectively, indicating low to moderate genetic differentiation. Our selection signatures analysis revealed 54 loci harboring 86 putative candidate genes, with a strong signature of selection. Further analysis showed that several candidate genes, including MARF1, SYCP2, TMEM200C, SF1, ADCY1, and BMP5, are involved in goat fecundity. We identified 11 candidate genes by using cross-population extended haplotype homozygosity (XP-EHH) estimates, of which MARF1 and SF1 are under strong positive selection, as they are differentiated in high and low reproduction groups according to the three approaches used. Gene ontology enrichment analysis revealed that different biological pathways could be involved in the variation of fecundity in female goats. This study provides a new insight into the ROHs patterns for maintenance of within breed diversity and suggests a role of positive selection for genetic variation influencing fecundity in Chinese goat.

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Genetic Diversity and Signatures of Selection for Thermal Stress in Cattle and Other Two Bos Species Adapted to Divergent Climatic Conditions

Frontiers in Genetics ◽

10.3389/fgene.2021.604823 ◽

2021 ◽

Vol 12 ◽

Author(s):

Pedro H. F. Freitas ◽

Yachun Wang ◽

Ping Yan ◽

Hinayah R. Oliveira ◽

Flavio S. Schenkel ◽

...

Keyword(s):

Genetic Diversity ◽

Candidate Genes ◽

Thermal Tolerance ◽

Climatic Conditions ◽

Biological Processes ◽

Biological Mechanisms ◽

Cattle Breeds ◽

Signatures Of Selection ◽

Selection For ◽

Genomic Regions

Understanding the biological mechanisms of climatic adaptation is of paramount importance for the optimization of breeding programs and conservation of genetic resources. The aim of this study was to investigate genetic diversity and unravel genomic regions potentially under selection for heat and/or cold tolerance in thirty-two worldwide cattle breeds, with a focus on Chinese local cattle breeds adapted to divergent climatic conditions, Datong yak (Bos grunniens; YAK), and Bali (Bos javanicus) based on dense SNP data. In general, moderate genetic diversity levels were observed in most cattle populations. The proportion of polymorphic SNP ranged from 0.197 (YAK) to 0.992 (Mongolian cattle). Observed and expected heterozygosity ranged from 0.023 (YAK) to 0.366 (Sanhe cattle; SH), and from 0.021 (YAK) to 0.358 (SH), respectively. The overall average inbreeding (±SD) was: 0.118 ± 0.028, 0.228 ± 0.059, 0.194 ± 0.041, and 0.021 ± 0.004 based on the observed versus expected number of homozygous genotypes, excess of homozygosity, correlation between uniting gametes, and runs of homozygosity (ROH), respectively. Signatures of selection based on multiple scenarios and methods (FST, HapFLK, and ROH) revealed important genomic regions and candidate genes. The candidate genes identified are related to various biological processes and pathways such as heat-shock proteins, oxygen transport, anatomical traits, mitochondrial DNA maintenance, metabolic activity, feed intake, carcass conformation, fertility, and reproduction. This highlights the large number of biological processes involved in thermal tolerance and thus, the polygenic nature of climatic resilience. A comprehensive description of genetic diversity measures in Chinese cattle and YAK was carried out and compared to 24 worldwide cattle breeds to avoid potential biases. Numerous genomic regions under positive selection were detected using three signature of selection methods and candidate genes potentially under positive selection were identified. Enriched function analyses pinpointed important biological pathways, molecular function and cellular components, which contribute to a better understanding of the biological mechanisms underlying thermal tolerance in cattle. Based on the large number of genomic regions identified, thermal tolerance has a complex polygenic inheritance nature, which was expected considering the various mechanisms involved in thermal stress response.

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

Animals ◽

10.3390/ani10050773 ◽

2020 ◽

Vol 10 (5) ◽

pp. 773 ◽

Cited By ~ 1

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.

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Evolution of the bread wheat D-subgenome and enriching it with diversity from Aegilops tauschii

10.1101/2021.01.31.428788 ◽

2021 ◽

Author(s):

Kumar Gaurav ◽

Sanu Arora ◽

Paula Silva ◽

Javier Sánchez-Martín ◽

Richard Horsnell ◽

...

Keyword(s):

Genetic Diversity ◽

Association Mapping ◽

Candidate Genes ◽

Bread Wheat ◽

Aegilops Tauschii ◽

Pest Resistance ◽

Wild Progenitor ◽

Genomic Regions ◽

Synthetic Hexaploids ◽

Diploid Ancestor

AbstractAegilops tauschii, the diploid wild progenitor of the D-subgenome of bread wheat, constitutes a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. To better define and understand this diversity, we sequenced 242 Ae. tauschii accessions and compared them to the wheat D-subgenome. We characterized a rare, geographically-restricted lineage of Ae. tauschii and discovered that it contributed to the wheat D-subgenome, thereby elucidating the origin of bread wheat from at least two independent hybridizations. We then used k-mer-based association mapping to identify discrete genomic regions with candidate genes for disease and pest resistance and demonstrated their functional transfer into wheat by transgenesis and wide crossing, including the generation of a library of ‘synthetic’ hexaploids incorporating diverse Ae. tauschii genomes. This pipeline permits rapid trait discovery in the diploid ancestor through to functional genetic validation in a hexaploid background amenable to breeding.

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Multiple selection signatures in farmed Atlantic salmon adapted to different environments across Hemispheres

10.1101/525550 ◽

2019 ◽

Author(s):

M.E. López ◽

T. Linderoth ◽

A. Norris ◽

J.P. Lhorente ◽

R. Neira ◽

...

Keyword(s):

Atlantic Salmon ◽

Candidate Genes ◽

Complex Traits ◽

Score Test ◽

Selection Signatures ◽

Biological Mechanisms ◽

Extended Haplotype ◽

Selection Strategies ◽

Farmed Atlantic Salmon ◽

Genomic Regions

1.ABSTRACTDomestication of Atlantic salmon started approximately forty years ago, using both artificial and natural selection strategies. Such selection methods are likely to have imposed distinctive selection signatures on the salmon genome. Therefore, identifying differences in selection signatures may give insights into the mechanism of selection and candidate genes of biological and productive interest. Here, we used two complementary haplotype-based statistics, the within-population integrated Haplotype Score test (|iHS|) and the cross-population Extended Haplotype Homozygosity test (XP-EHH) to compare selection signatures in four populations of Atlantic salmon with a common genetic origin. Using |iHS| we found 24, 14, 16 and 26 genomic regions under selection in Pop-A, Pop-B, Pop-C, and Pop-D, respectively. While using the XP-EHH test we identified 27, 25 and 15 potential selection regions in Pop-A/Pop-B, Pop-A/Pop-C and Pop-A/Pop-D, respectively. These genomic regions harbor important genes such igf1r and sh3rf1 which have been associated with growth related traits in other species. Our results contribute to the detection of candidate genes of interest and help to understand the evolutionary and biological mechanisms for controlling complex traits under selection in Atlantic salmon.

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Genomics of Indian SARS-CoV-2: Implications in genetic diversity, possible origin and spread of virus

10.1101/2020.04.25.20079475 ◽

2020 ◽

Cited By ~ 9

Author(s):

Mainak Mondal ◽

Ankita Lawarde ◽

Kumaravel Somasundaram

Keyword(s):

Genetic Diversity ◽

Middle East ◽

South Asia ◽

World Health ◽

Initial Examination ◽

Synonymous Mutations ◽

Viral Virulence ◽

Depth Analysis ◽

Cluster A ◽

Health Organization

AbstractWorld Health Organization (WHO) declared COVID-19 as a pandemic disease on March 11, 2020. Comparison of genome sequences from diverse locations allows us to identify the genetic diversity among viruses which would help in ascertaining viral virulence, disease pathogenicity, origin and spread of the SARS-CoV-2 between countries. The aim of this study is to ascertain the genetic diversity among Indian SARS-CoV-2 isolates. Initial examination of the phylogenetic data of SARS-CoV-2 genomes (n=3123) from different continents deposited at GISAID (Global Initiative on Sharing All Influenza Data) revealed multiple origin for Indian isolates. An in-depth analysis of 449 viral genomes derived from samples representing countries from USA, Europe, China, East Asia, South Asia, Oceania, Middle East regions and India revealed that most Indian samples are divided into two clusters (A and B) with cluster A showing more similarity to samples from Oceania and Kuwait and the cluster B grouping with countries from Europe, Middle East and South Asia. Diversity analysis of viral clades, which are characterized by specific non-synonymous mutations in viral proteins, discovered that the cluster A Indian samples belong to I clade (V378I in ORF1ab), which is an Oceania clade with samples having Iran connections and the cluster B Indian samples belong to G clade (D614G in Spike protein), which is an European clade. Thus our study identifies that the Indian SARS-CoV-2 viruses belong to I and G clades with potential origin to be countries mainly from Oceania, Europe, Middle East and South Asia regions, which strongly implying the spread of virus through most travelled countries. The study also emphasizes the importance of pathogen genomics through phylogenetic analysis to discover viral genetic diversity and understand the viral transmission dynamics with eventual grasp on viral virulence and disease pathogenesis.

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«Имперский синдром»: концепция османского халифата на Ближнем Востоке и в Южной Азии (первая четверть XX в.)

Istoricheskii vestnik ◽

10.35549/hr.2019.2019.47860 ◽

2019 ◽

Author(s):

S.A. Kirillina ◽

A.L. Safronova ◽

V.V. Orlov

Keyword(s):

Middle East ◽

South Asia ◽

South Asian ◽

Political Role ◽

The Social ◽

The Difference ◽

Aspect Interaction ◽

Muhammad Rashid Rida ◽

Political Actions

Аннотация В статье изучены общие и специфические черты идейных воззрений, пропагандистской риторики и политических действий представителей халифатистского движения на Ближнем Востоке и в Южной Азии. В ретроспективном ключе прослеживается эволюция представлений о сущности и необходимости возрождения института халифата в трудах исламских идеологов, реформаторов и политиков Джамал ад-Дина ал-Афгани, Абд ар-Рахмана ал-Кавакиби, Мухаммада Рашида Риды, Абул Калама Азада. Внимание авторов сосредоточено на общественно-политических дискуссиях 2030-х годов XX столетия, а также на повестке дня халифатистских конгрессов и конференций этого периода. На них вырабатывались первые представления современников о пост-османском формате мусульманского единства и идейно-политической роли будущего халифата. Авторы демонстрируют различие между моделями реакции мусульман Ближнего Востока и Южной Азии на упразднение османского халифата республиканским руководством Турции. Установлена многоаспектная взаимосвязь между халифатистскими ценностями, проосманскими настроениями и формами самоотождествления, которые сложились в арабских и южноазиатских обществах. Отдельно намечено соотношение между подъемом халифатистских настроений и радикализацией антиколониальных действий мусульман Индостана.Abstract The article deals with analysis of common and specific features of ideas, propaganda, rhetoric and political actions taken by representatives of the movement for defense of the Caliphate in the Middle East and South Asia. The retrospection showing the transformation of conception of the Caliphate and the necessity of its revival in the works of eminent ideologists and politicians of the Muslim world Jamal al-Din al-Afghani, Abd al-Rahman al-Kawakibi, Muhammad Rashid Rida and Abul Kalam Azad, is also given in the article. The authors also focus on the social and political discussions of the 1920s 1930s, as well as on the agenda of Caliphatist congresses and conferences of this period. They helped to elaborate the early representations of post-Ottoman pattern of the Muslim unity and the ideological and political role of the future Caliphate. The authors demonstrate the difference between the forms of reaction of Muslims in the Middle East and South Asia to the repudiation of the Caliphate by the Republican leaders of Turkey. The article establishes a multi-aspect interaction between the Caliphatist values and forms of self-identification, emerged in Arab and South Asian societies. The correlation between the rise of Caliphatist attitudes and radicalization of anti-colonial actions of South Asian Muslims is also outlined.

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Identification of Genomic Regions Associated with Concentrations of Milk Fat, Protein, Urea and Efficiency of Crude Protein Utilization in Grazing Dairy Cows

Genes ◽

10.3390/genes12030456 ◽

2021 ◽

Vol 12 (3) ◽

pp. 456

Author(s):

Hewa Bahithige Pavithra Chathurangi Ariyarathne ◽

Martin Correa-Luna ◽

Hugh Thomas Blair ◽

Dorian John Garrick ◽

Nicolas Lopez-Villalobos

Keyword(s):

Gene Ontology ◽

New Zealand ◽

Dairy Cows ◽

Candidate Genes ◽

Milk Fat ◽

Crude Protein ◽

Single Locus ◽

Protein Utilization ◽

Grazing Dairy Cows ◽

Genomic Regions

The objective of this study was to identify genomic regions associated with milk fat percentage (FP), crude protein percentage (CPP), urea concentration (MU) and efficiency of crude protein utilization (ECPU: ratio between crude protein yield in milk and dietary crude protein intake) using grazing, mixed-breed, dairy cows in New Zealand. Phenotypes from 634 Holstein Friesian, Jersey or crossbred cows were obtained from two herds at Massey University. A subset of 490 of these cows was genotyped using Bovine Illumina 50K SNP-chips. Two genome-wise association approaches were used, a single-locus model fitted to data from 490 cows and a single-step Bayes C model fitted to data from all 634 cows. The single-locus analysis was performed with the Efficient Mixed-Model Association eXpedited model as implemented in the SVS package. Single nucleotide polymorphisms (SNPs) with genome-wide association p-values ≤ 1.11 × 10−6 were considered as putative quantitative trait loci (QTL). The Bayes C analysis was performed with the JWAS package and 1-Mb genomic windows containing SNPs that explained > 0.37% of the genetic variance were considered as putative QTL. Candidate genes within 100 kb from the identified SNPs in single-locus GWAS or the 1-Mb windows were identified using gene ontology, as implemented in the Ensembl Genome Browser. The genes detected in association with FP (MGST1, DGAT1, CEBPD, SLC52A2, GPAT4, and ACOX3) and CPP (DGAT1, CSN1S1, GOSR2, HERC6, and IGF1R) were identified as candidates. Gene ontology revealed six novel candidate genes (GMDS, E2F7, SIAH1, SLC24A4, LGMN, and ASS1) significantly associated with MU whose functions were in protein catabolism, urea cycle, ion transportation and N excretion. One novel candidate gene was identified in association with ECPU (MAP3K1) that is involved in post-transcriptional modification of proteins. The findings should be validated using a larger population of New Zealand grazing dairy cows.

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