- Moreover, they were found to have descended from unique ancestors (K = 2 and K = 3) according to the structure analysis. - Conclusions: The comprehensive genome-wide characterization provided the fundamental footprints for breeding and management of the Chaka sheep and confirmed that they harbor unique genetic resources.. - The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. - If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. - Full list of author information is available at the end of the article. - Salinity in the lake increased by 7.2 cal ka BP (calibrated kilo years be- fore present) [1]. - Chaka sheep, a natural inhabitant of the lake, have naturally adapted to the hypersaline envir- onment and plateau habitat. - Sheep are ruminants and one of the main sources of wool, hide, and meat for humans. - Geographically, the Kazakh lineage is mainly concen- trated in the Xinjiang area, while the Tibetan lineage (TL) group inhabits the Yunnan-Guizhou plateau. - TAN and BYK sheep are within the Mongolian lineage, OLA is within the Tibetan lineage, and the lineage of CKA sheep has not yet been identified.. - To characterize the Chaka sheep’s genome, it could be compared to the genomes of Mongolian (TAN and BYK sheep) and Tibetan lineage sheep (OLA sheep). - Although SNP arrays have been extensively used to identify genetic variations [3–6], the results are limited by low probe density. - However, to our knowledge, a survey of the genome-wide genetic features of CKA sheep has not been conducted. - To investigate genetic di- versity and population structure of CKA sheep, genomes of 40 sheep, including 10 each of the CKA, TAN, BAK,. - and OLA breeds, were assembled to the sheep reference genome (REF). - Our analyses provided new insights into the genetic diversity, population structure, and selective signature of the CKA breed compared to the other three breeds, which will improve the conservation programs for CKA sheep.. - Three metrics were used to estimate the genetic diver- sities of the sheep breeds in the current study. - The expected heterozygosity of CKA sheep was much higher than that of other breeds on average. - Furthermore, approximately 65% of the single nucleotide polymorphisms (SNPs) were highly variable with a minor allele frequency (MAF) >. - The total length of ROH in CKA sheep, in the range of <. - 0.5 Mb, was lowest, suggesting CKA sheep have higher genetic diversity (Fig. - 1c) was nearly consistent with those from the ROH profile, in which the lowest genetic diversity was found in the OLA breed. - The effective population sizes of the four breeds 1000 years before present were OLA sheep >. - TAN sheep >. - CKA sheep >. - The distribution of the length and number of ROH in different individuals. - CKA, Chaka sheep. - Population structure. - Most of the sheep breeds included in this study origi- nated from western China. - 2a), explaining 4.43% of the total variance, which indicated a considerable genetic distance between the CKA breed and the other three breeds.. - Among these four breeds, OLA sheep were differenti- ated from the other breeds in the second component, explaining 3.30% of the total variance (Fig. - K changed progressively from 02 to 03 in the four analyzed breeds, providing evidence of admixture,. - At K = 3, TAN sheep represented clear evidence of genetic heterogen- eity with shared genome ancestry with BYK sheep, which both belong to the Mongolian lineage.. - Specific SNPs and Indels in CKA sheep. - 2 Analysis of the population structure in four sheep breeds. - The cross-population composite likelihood ratio (XP- CLR) was used to detect the selective signal by compar- ing CKA with other three breeds grouped together, and Fst detected positive selection signatures in CKA sheep compared with the other three sheep breeds as per the results of population structure (Fig. - 4a and Supplementary Table 5).. - Notably, the genes were significantly enriched in the MAPK signaling pathway (hsa04010) and supramolecu- lar fiber organization (GO:0097435) (Fig. - The results suggested the enrichment of muscle-related genes including MDS1 and EVI1 com- plex locus (MECOM), Neurofibromin 1 (NF1), trans- forming growth factor beta 2 (TGFB2), phospholipase A2 group IVF (PLA2G4F), phosphatidylinositol-3,4,5- trisphosphate dependent Rac exchange factor 1 (PRex1) and myomesin 1 (MYOM1) which are crucial in the gen- ome selection of CKA sheep.. - 3 Specific SNP and indel in CKA sheep and the GO and KEGG analysis of its host gene. - Supplementary Table 7). - 4d and Supplementary Table 8).. - CKA sheep are well known for their diverse alleles, more so than any of their commercial counterparts, and they have been a valuable genetic resource, potentially har- boring unique gene pools resulting from long-term adaptation to the Chaka Salt Lake environment. - To ex- plore the genetic resources and to preserve the diverse gene pools of CKA sheep, we reported the genome-wide population structure, genetic diversity, and candidate signatures of positive selection in CKA sheep breeds for the first time using next-generation sequencing.. - Combining the length of the ROH with LD decay, the CKA and TAN sheep were found to have higher genetic diversity than OLA and BYK sheep. - a The XP-CLR of CKA sheep based on other three sheep b The Fst on four breeds c. - GO and KEGG heatmap selected analyzed by XP-CLR. - The top 5% was chosen as the significant threshold for Fst and XP-CLR. - The estimated relative effective population size of the breeds 1000 years before present was OLA >. - The results of PCA, NJ-tree, and STRUCTURE suggest that the four sheep breeds could be subdivided into three genetic clusters: the CKA group, the Mongolian lineage group, and the Tibetan lineage group. - In general, the partitioning of the breeds was consistent with their geographic distributions and breed properties. - The PCA showed that CKA sheep completely separated from OLA, TAN, and BYK sheep. - Furthermore, CKA sheep represented distinctive ancestry in the structure analysis.. - In the current analysis, BYK and TAN sheep were observed to originate from Xinjiang and Ningxia provinces, respectively. - The current data set provides strong evidence of the different population structures between CKA and the other three breeds. - Further analyses are needed to develop an in-depth understanding of the relationships between the CKA sheep and Mongolian or Tibetan lineage groups.. - Additionally, CKA sheep accounted for of total mutations. - The expression of the CAPN3 gene is involved in progressive muscular dystro- phies during early human development [18]. - For adult skeletal muscle fibers, the supramolecular organization of the subsarcolemmal cytoskeleton is also a crucial factor in influencing meat quality [25].. - The PCA, STRUCTURE, and NJ-tree analyses revealed that CKA sheep are distinct from BYK, TAN, and OLA sheep, and this breed has descended from a unique an- cestor. - The host genes annotated by specific missense mutations, including SNPs and indels of CKA sheep enriched muscle structure development (GO:0061061), which included IGF1, GDF3, HDAC9, TGFBR2, and CAPN3, genes, among others. - This study was conducted according to the Faculty Ani- mal Policy and Welfare Committee of Northwest A&F University (FAPWC-NWAFU).. - We randomly selected CKA sheep (n = 10) for the study from 305 individuals scattered on the prairie [26].. - spectrophotometry (IMPLEN, CA, USA), and the Qubit®. - 15 Avgqual:20 Minlen:35 Tophred:33) was used to trim the sequencing reads, and FASTQC was used to assess the quality of the raw sequencing data. - The average sequencing depth was obtained for the 10 CKA sheep was 7.68×. - To assess the genetic diversity of CKA sheep, the genomes of the four sheep breeds (Table 2) were assem- bled and genotyped using GATK (version 3.6–0- g89b7209) [28]. - and the filtered data were used for the subsequent analyses.. - PC1 and PC2 were plotted using the ggplot2 package in the R 3.6.1 software.. - To accurately identify the ancestral components of the four sheep breeds, the study used ADMIXTURE to esti- mate the ancestral composition of each individual with genome-wide unlinked sites. - The cross-population composite likelihood ratio (XP-CLR) is another method for the determination of the selection signal based on the differentiation of al- lele frequency across populations. - 1.6 million indels [37, 38], and the selective signatures. - Additional file 1: Supplementary Table 1. - The genetic variation information of SNPs and indels in sheep breeds. - Supplementary Table 2. - The level of genetic diversity in the four populations.. - Supplementary Table 3. - Supplementary Table 4. - Supplementary Table 5.. - Summary of candidate genes in the Chaka sheep population detected by XP-CLR statistics. - Supplementary Table 6. - The list of GO and KEGG ana- lyses for genes with high selection signature by XP-CLR. - Supplementary Table 7. - Supplementary Table 8. - Supplementary Table 11. - Geographic distribution of the four Chinese sheep breeds. - XP-CLR: Cross- population composite likelihood ratio. - Thanks to the Laboratory for Agricultural Genomic Big Data in the College of Animal Science and Technology, Northwest A&F University.. - HZ and NC were responsible for data analysis and the creation of new software used in the analyses. - XC and QH assisted in the interpretation of data and modifying the manuscript. - LP, LH, and BC made substantial contributions to the acquisition data of CKA sheep and performed preliminary analysis. - Genetic diversity and population structure of six Chinese indigenous pig breeds in the Taihu Lake region revealed by sequencing data. - Whole-genome sequences of 89 Chinese sheep suggest role of RXFP2 in the development of unique horn phenotype as response to semi- feralization. - Genome-wide analysis reveals population structure and selection in Chinese indigenous sheep breeds. - Genghis Khan: the history of the world conqueror.. - The role of the insulin-like growth factor 1 (IGF-1) in skeletal muscle physiology. - Mapping signatures of positive selection in the genome of livestock. - Supramolecular organization of the subsarcolemmal cytoskeleton of adult skeletal muscle fibers. - Regions of homozygosity in the porcine genome: consequence of demography and the recombination landscape.. - A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain
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