Whole genome sequencing reveals a complex introgression history and the basis of adaptation to subarctic climate in wild sheep

Upadhyay, Maulik; Kunz, Elisabeth; Sandoval‐Castellanos, Edson; Hauser, Andreas; Krebs, Stefan; Graf, Alexander; Blum, Helmut; Dotsev, Arsen V; Охлопков, И. М.; Shakhin, Alexey; Багиров, В. А.; Brem, Gottfried; Fries, R.; Zinovieva, N. A.; Međugorac, Ivica

doi:10.1111/mec.16184

Cited by 15 publications

(14 citation statements)

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“…We further implemented sliding window statistics analysis using the Dsuite v0.5r50 41 to quantify the introgressions. We calculated f dM values using a sliding window of 50 SNPs with a step of 25 SNPs across the genomes with the defined trios (MEN, SSA, O. gmelini _2), where SSA represents the four South-and-Southeast Asian sheep populations suggested to be the introgressed populations by the D -statistics and f 4 -ratio tests.…”

Section: Methodsmentioning

confidence: 99%

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Genomic analyses of Asiatic Mouflon in Iran provide insights into the domestication and evolution of sheep

Wang,

Orozco-terWengel,

et al. 2023

Preprint

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The wild ancestor of domestic sheep, Asiatic mouflon (O. gmelini), consists of several subspecies mainly distributed in Iran nowadays. However, the impact of the Asiatic mouflon subspecies in Iran on sheep domestication remains unclear. Here, we conducted a comprehensive population genomics analysis of Asiatic mouflons in Iran with 780 whole-genome sequences, 767 whole mitogenomes, and 239 Y chromosomes. Whole-genome sequence analyses revealed two subpopulations of the Asiatic mouflons in Iran:O. gmelini_2 limited in Kabudan andO. gmelini_1 over a wide geographic area. Phylogenetic analyses of the Asiatic mouflons in Iran based on uniparental variants revealed a monophyletic lineage with the mitochondrial haplogroups C+E, and clustered into a monophyletic with Y-chromosomal lineage HY2 of sheep. Additionally, introgression tests detected significant signals of genetic introgression fromO. gmelini_2 to four sheep populations (e.g., Garut, Garole, Bangladeshi, and Sumatra) in South and Southeast Asia. In the four sheep populations, selective tests and introgression signals revealed that the wild introgression could have contributed to their small body size and local adaptation to the hot and humid environments in the Indian Peninsula. Our results suggested that the maternal haplogroups C+E and paternal lineage HY2 could have originated from the Asiatic mouflon in Iran. Also, our findings provide new insights into sheep domestication and subsequent introgressions from wild ancestors to domestic populations.

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Section: Methodsmentioning

confidence: 99%

“…The analysis was performed using the GTR + GAMMA (4) + I site model and the strict clock model. The most recent common ancestor (MRCA) of Asiatic mouflon and domestic sheep was set to be 0.653 million years [41]. The chain length was set to be 40,000,000 with a burn-in of 2,000,000.…”

Section: Demographics and Divergence Time Inferencementioning

confidence: 99%

Genomic analyses of Asiatic Mouflon in Iran provide insights into the domestication and evolution of sheep

Wang,

Orozco-terWengel,

et al. 2023

Preprint

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“…One of the possible reasons for the selection of this gene in IB camels may be related to the composition of soil and vegetation in the habitat of camels; however, to confirm this claim we need accurate information about these parameters. Previous studies have found that the OPA1 gene, as one of the candidate genes under selection for IB camels, is involved in the adaptation of snow and Tibetan sheep to survive at high altitudes with low oxygen and temperature 47 , 48 , that is somewhat similar to the habitat of IB camels. Also, Tang et al 49 reported that OPA1 potentially enhances the ability of Tibetan chicken to survive under the hypoxic condition of the Qinghai-Tibet Plateau.…”

Section: Discussionmentioning

confidence: 99%

Identification of selection signatures in Iranian dromedary and Bactrian camels using whole genome sequencing data

Khalkhali-Evrigh

Hedayat

Liang

et al. 2022

Sci Rep

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The Old World camels play an important role as one of the main food sources in large parts of Asia and Africa. Natural selection combined with artificial selection by human has affected parts of the domestic animal genome for adapting them to their habitats and meeting human needs. Here, we used whole genome sequencing data of 34 camels (including 14 dromedaries and 20 Bactrian camels) to identify the genomic signature of selection in the Iranian dromedary (ID) and Bactrian camels (IB). To detect the mentioned regions, we used two methods including population differentiation index (Fst) and cross-population extended haplotype homozygosity (XP-EHH) with 50 kb sliding window and 25 kb step size. Based on gene ontology analysis on the candidate genes identified for IB camels, we found GO terms associated with lung development, nervous system development, immune system and behavior. Also, we identified several genes related to body thermoregulation (ZNF516), meat quality (ANK1 and HSPA13), and high-altitude adaptation (OPA1) for IB camels. In the list of detected candidate genes under selection in ID camels, the genes related to energy metabolism (BDH1), reproduction (DLG1, IMMP2L and FRASI), long-term memory (GRIA1), kidney (SLC12A1), lung development (EMILIN2 and FBN1) and immunity (SOCS2, JAK1, NRROS and SENP1) were found. Our findings, along with further studies in this field, will strengthen our knowledge about the effect of selection on the camelid genome under different geographical, climatic and even cultural conditions.

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“…Understanding and then maintaining the genetic diversity that exists in domestic livestock breeds is important for the future of agriculture ( Rexroad et al, 2019 ). Recent studies have used WGS to understand and preserve diversity and specific biological traits in breeds that are economically and culturally relevant, including Snow sheep in Siberia and native sheep breeds in Greece ( Upadhyay et al 2021 , and Kominakis et al, 2021). Studies that have used bead array genotypes to analyze diversity between global sheep breeds have demonstrated the geographical distribution and differences of breeds from Europe, Asia, and Africa ( Kijas et al, 2009 and Kijas et al, 2012 ).…”

Section: Introductionmentioning

confidence: 99%

Using whole genome sequence to compare variant callers and breed differences of US sheep

et al. 2023

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As whole genome sequence (WGS) data sets have become abundant and widely available, so has the need for variant detection and scoring. The aim of this study was to compare the accuracy of commonly used variant calling programs, Freebayes and GATK HaplotypeCaller (GATK-HC), and to use U.S. sheep WGS data sets to identify novel breed-associated SNPs. Sequence data from 145 sheep consisting of 14 U.S. breeds were filtered and biallelic single nucleotide polymorphisms (SNPs) were retained for genotyping analyses. Genotypes from both programs were compared to each other and to genotypes from bead arrays. The SNPs from WGS were compared to the bead array data with breed heterozygosity, principal component analysis and identifying breed associated SNPs to analyze genetic diversity. The average sequence read depth was 2.78 reads greater with 6.11% more SNPs being identified in Freebayes compared to GATK-HC. The genotype concordance of the variant callers to bead array data was 96.0% and 95.5% for Freebayes and GATK-HC, respectively. Genotyping with WGS identified 10.5 million SNPs from all 145 sheep. This resulted in an 8% increase in measured heterozygosity and greater breed separation in the principal component analysis compared to the bead array analysis. There were 1,849 SNPs identified in only the Romanov sheep where all 10 rams were homozygous for one allele and the remaining 135 sheep from 13 breeds were homozygous for the opposite allele. Both variant calling programs had greater than 95% concordance of SNPs with bead array data, and either was suitably accurate for ovine WGS data sets. The use of WGS SNPs improved the resolution of PCA analysis and was critical for identifying Romanov breed-associated SNPs. Subsets of such SNPs could be used to estimate germplasm composition in animals without pedigree information.

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Whole genome sequencing reveals a complex introgression history and the basis of adaptation to subarctic climate in wild sheep

Abstract: This is an open access article under the terms of the Creat ive Commo ns Attri bution-NonCo mmercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

Cited by 15 publications

References 93 publications

Genomic analyses of Asiatic Mouflon in Iran provide insights into the domestication and evolution of sheep

Genomic analyses of Asiatic Mouflon in Iran provide insights into the domestication and evolution of sheep

Identification of selection signatures in Iranian dromedary and Bactrian camels using whole genome sequencing data

Using whole genome sequence to compare variant callers and breed differences of US sheep

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