DIA-Based Proteomic Analysis Reveals MYOZ2 as a Key Protein Affecting Muscle Growth and Development in Hybrid Sheep.

Hybridization of livestock can be used to improve varieties, and different hybrid combinations produce unique breeding effects. In this study, male Southdown and Suffolk sheep were selected to hybridize with female Hu sheep to explore the effects of male parentage on muscle growth and the development of offspring. Using data-independent acquisition technology, we identified 119, 187, and 26 differentially abundant proteins (DAPs) between Hu × Hu (HH) versus Southdown × Hu (NH), HH versus Suffolk × Hu (SH), and NH versus SH crosses. Two DAPs, MYOZ2 and MYOM3, were common to the three hybrid groups and were mainly enriched in muscle growth and development-related pathways. At the myoblast proliferation stage, MYOZ2 expression decreased cell viability and inhibited proliferation. At the myoblast differentiation stage, MYOZ2 expression promoted myoblast fusion and enhanced the level of cell fusion. These findings provide new insights into the key proteins and metabolic pathways involved in the effect of male parentage on muscle growth and the development of hybrid offspring in sheep.

Single-Cell Transcriptome Sequence Profiling on the Morphogenesis of Secondary Hair Follicles in Ordos Fine-Wool Sheep.

The Ordos fine-wool sheep is a high-quality breed in China that produces superior natural textiles and raw materials such as wool and lamb meat. However, compared to the Australian Merino sheep, there is still a gap in terms of the wool fiber fineness and wool yield. The hair follicle is the main organ that controls the type of wool fiber, and the morphological changes in the secondary hair follicle are crucial in determining wool quality. However, the process and molecular mechanisms of hair follicle morphogenesis in Ordos fine-wool sheep are not yet clear. Therefore, analyzing the molecular mechanisms underlying the process of follicle formation is of great significance for improving the fiber diameter and wool production of Ordos fine-wool sheep. The differential expressed genes, APOD, POSTN, KRT5, and KRT15, which related to primary hair follicles and secondary hair follicles, were extracted from the dermal papillae. Based on pseudo-time analysis, the differentiation trajectories of dermal lineage cells and epidermal lineage cells in the Ordos fine-wool sheep were successfully constructed, providing a theoretical basis for breeding research in Ordos fine-wool sheep.

Genome-wide detection of structural variation in some sheep breeds using whole-genome long-read sequencing data.

Genomic structural variants (SVs) constitute a significant proportion of genetic variation in the genome. The rapid development of long-reads sequencing has facilitated the detection of long-fragment SVs. There is no published study to detect SVs using long-read data from sheep. We applied a long-read mapping approach to detect SVs and characterized a total of 30,771 insertions, deletions, inversions and translocations. We identified 716, 916, 842 and 303 specific SVs in Southdown sheep, Alpine merino sheep, Qilian White Tibetan sheep and Oula sheep, respectively. We annotated these SVs and found that these SV-related genes were primarily enriched in the well-established pathways involved in the regulation of the immune system, growth and development and environmental adaptability. We detected and annotated SVs based on NGS resequencing data to validate the accuracy based on third-generation detection. Moreover, five candidate SVs were verified using the PCR method in 50 sheep. Our study is the first to use a long-reads sequencing approach to construct a novel structural variation map in sheep. We have completed a preliminary exploration of the potential effects of SVs on sheep.

Genomic Selection for Live Weight in the 14th Month in Alpine Merino Sheep Combining GWAS Information.

Alpine Merino Sheep is a novel breed reared from Australian Merino Sheep as the father and Gansu Alpine Fine-Wool Sheep as the mother, living all year in cold and arid alpine areas with exceptional wool quality and meat performance. Body weight is an important economic trait of the Alpine Merino Sheep, but there is limited research on identifying the genes associated with live weight in the 14th month for improving the accuracy of the genomic prediction of this trait. Therefore, this study's sample comprised 1310 Alpine Merino Sheep ewes, and the Fine Wool Sheep 50K Panel was used for genome-wide association study (GWAS) analysis to identify candidate genes. Moreover, the trial population (1310 ewes) in this study was randomly divided into two groups. One group was used as the population for GWAS analysis and screened for the most significant top 5%, top 10%, top 15%, and top 20% SNPs to obtain prior marker information. The other group was used to estimate the genetic parameters based on the weight assigned by heritability combined with different prior marker information. The aim of this study was to compare the accuracy of genomic breeding value estimation when combined with prior marker information from GWAS analysis with the optimal linear unbiased prediction method for genome selection (GBLUP) for the breeding value of target traits. Finally, the accuracy was evaluated using the five-fold cross-validation method. This research provides theoretical and technical support to improve the accuracy of sheep genome selection and better guide breeding. The results demonstrated that eight candidate genes were associated with GWAS analysis, and the gene function query and literature search results suggested that FAM184B, NCAPG, MACF1, ANKRD44, DCAF16, FUK, LCORL, and SYN3 were candidate genes affecting live weight in the 14th month (WT), which regulated the growth of muscle and bone in sheep. In genome selection analysis, the heritability of GBLUP to calculate the WT was 0.335-0.374, the accuracy after five-fold cross-verification was 0.154-0.190, and after assigning different weights to the top 5%, top 10%, top 15%, and top 20% of the GWAS results in accordance with previous information to construct the G matrix, the accuracy of the WT in the GBLUP model was improved by 2.59-7.79%.

Transcriptomics and metabolomics reveal improved performance of Hu sheep on hybridization with Southdown sheep.

Consumers are increasingly demanding high-quality mutton. Cross breeding can improve meat quality and is widely used in sheep breeding. However, little is known about the molecular mechanism of cross breeding sheep meat quality. In this study, male Southdown and female Hu sheep were hybridized. The slaughter performance and longissimus dorsi quality of the 6-month-old hybrid offspring were measured, and the longissimus dorsi of the hybrid offspring was analyzed by transcriptomics and metabolomics to explore the effect of cross breeding on meat quality. The results showed that the production performance of Southdown × Hu F1 sheep was significantly improved, the carcass fat content was significantly decreased, and the eating quality of Southdown × Hu F1 sheep were better. Compared with the HS group (Hu × Hu), the NH group (Southdown × Hu) had 538 differentially expressed genes and 166 differentially expressed metabolites (P < 0.05), which were significantly enriched in amino acid metabolism and other related pathways. Up-regulated genes METTL21C, PPARGC1A and down-regulated gene WFIKKN2 are related to muscle growth and development. Among them, the METTL21C gene, which is related to muscle development, was highly correlated with carnosine, a metabolite related to meat quality (correlation > 0.6 and P < 0.05). Our results provide further understanding of the molecular mechanism of cross breeding for sheep muscle growth and meat quality optimization.

Global DNA Methylation, miRNA, and mRNA Profiles in Sheep Skeletal Muscle Promoted by Hybridization.

With the development of high-throughput sequencing technology, several nongenetic variations, including noncoding RNAs such as miRNAs, and DNA methylation, have been found to play an important role in animal muscle development and fat metabolism. In this study, Southdown and Suffolk were selected as male parents for hybridization with Hu sheep (Southdown × Hu (NH), Suffolk × Hu (SH), and Hu × Hu (HH)). RNA sequencing, bisulfite sequencing, and small-RNA sequencing were used to study the methylation patterns and differences in miRNA and mRNA expression in the F1 sheep longissimus dorsi muscle tissue. We identified 765 differentially expressed genes (DEGs), 10,161 differentially methylated regions (DMRs), and 164 differentially expressed miRNAs, which were significantly enriched in AMPK signaling, fatty acid degradation, metabolism, and other related pathways (P < 0.05). In addition, we constructed a DNA methylation-mRNA and miRNA-mRNA coexpression network. A total of 42 common genes were identified from DMRs and DEGs. Importantly, we predicted that 33 differentially expressed miRNAs directly or indirectly targeted the SLC27A6. The data obtained in this study provide useful information and evidence to support further understanding of the miRNA and DNA methylation of key genes regulating muscle growth and fat metabolism in hybrid sheep populations.

Effects of Sheep Sires on Muscle Fiber Characteristics, Fatty Acid Composition and Volatile Flavor Compounds in F1 Crossbred Lambs.

Crossbreeding significantly improves meat production performance in sheep; however, whether hybridization changes the meat quality characteristics of lambs is uncertain. We analyzed the effects of three different hybrid sires on muscle fiber characteristics (MFCs), fatty acid composition (FAC), and volatile flavor compounds (VFCs) in lambs under identical feeding conditions. Compared with those of purebred lambs, the muscle fiber diameter and cross-sectional areas of the crossbred lambs were significantly decreased (p < 0.05), and the collagen fiber content was significantly increased (p < 0.05). The numbers and area ratios of the fast and slow muscle fibers did not significantly differ between the purebred and crossbred lambs, but the expressions of four MyHC gene types differed significantly (p < 0.05). Twenty-three fatty acids were identified in both the purebred and crossbred lambs, of which thirteen were differentially expressed (p < 0.05). Saturated fatty acid (SFA) contents in the crossbred lambs were significantly increased (p < 0.05), whereas the monounsaturated fatty acid content was significantly decreased (p < 0.05). Polyunsaturated fatty acid/SFA and n-6/n-3 ratios were significantly lower in the crossbred lambs than in the purebred lambs (p < 0.05). Twenty-five VFCs were identified among the three hybrids, and aldehydes were the main VFCs. Eleven VFCs were differentially expressed in the crossbred lambs (p < 0.05). Hybrid sires affected the MFCs, FAC, and VFCs of the F1 lambs, thus providing a reference for high-quality mutton production.

Transcriptome-metabolome analysis reveals how sires affect meat quality in hybrid sheep populations.

Crossbreeding improves and enhances meat quality and is widely used in sheep production; however, the molecular mechanisms underlying the meat quality of various crossbred sheep remain unknown. In this study, male Southdown, Suffolk and Hu sheep were crossbred with female Hu sheep, and the transcriptomes and metabolomes of the longissimus dorsi muscle of the F1 generation were sequenced to explore how different sire breeds affect meat quality. The results showed that 631 differentially expressed genes and 119 significantly altered metabolites contributed to muscle development characteristics and meat quality-related diversity (P < 0.05). These genes and metabolites were significantly enriched in lipid metabolism pathways, including arachidonic acid metabolism and PPAR signaling. Several candidate genes were associated with muscle growth, such as MYLK3, MYL10, FIGN, MYH8, MYOM3, LMCD1, and FLRT1. Among these, MYH8 and MYL10 participated in regulating muscle growth and development and were correlated with meat quality-related fatty acid levels (|r| > 0.5 and p < 0.05). We selected mRNA from four of these genes to verify the accuracy of the sequencing data via qRT-PCR. Our findings provide further insight into the key genes and metabolites involved in muscle growth and meat quality in hybrid sheep populations.

The Transcriptional Cell Atlas of Testis Development in Sheep at Pre-Sexual Maturity.

Sheep testes undergo a dramatic rate of development with structural changes during pre-sexual maturity, including the proliferation and maturation of somatic niche cells and the initiation of spermatogenesis. To explore this complex process, 12,843 testicular cells from three males at pre-sexual maturity (three-month-old) were sequenced using the 10× Genomics ChromiumTM single-cell RNA-seq (scRNA-seq) technology. Nine testicular somatic cell types (Sertoli cells, myoid cells, monocytes, macrophages, Leydig cells, dendritic cells, endothelial cells, smooth muscle cells, and leukocytes) and an unknown cell cluster were observed. In particular, five male germ cell types (including two types of undifferentiated spermatogonia (Apale and Adark), primary spermatocytes, secondary spermatocytes, and sperm cells) were identified. Interestingly, Apale and Adark were found to be two distinct states of undifferentiated spermatogonia. Further analysis identified specific marker genes, including UCHL1, DDX4, SOHLH1, KITLG, and PCNA, in the germ cells at different states of differentiation. The study revealed significant changes in germline stem cells at pre-sexual maturation, paving the way to explore the candidate factors and pathways for the regulation of germ and somatic cells, and to provide us with opportunities for the establishment of livestock stem cell breeding programs.

Evaluation of Mutton Quality Characteristics of Dongxiang Tribute Sheep Based on Membership Function and Gas Chromatography and Ion Mobility Spectrometry.

Dongxiang tribute sheep have a history of use in food dishes such as "Dongxiang Handgrip," which dates back hundreds of years and is a favorite halal food in northwestern China. However, little is known about the mutton quality characteristics of Dongxiang tribute sheep. Here, we measured the sensory characteristics, nutritional quality, and flavor substances to comprehensively evaluate the mutton quality characteristics of these sheep. The mutton qualities of Dongxiang tribute, Tibetan, Ujumqin, and Hu sheep were comprehensively evaluated by membership function. Subsequently, the volatile components in mutton samples from 30 Dongxiang tribute sheep were detected via gas chromatography and ion mobility spectrometry (GC-IMS), and their fingerprints were established. The result of meat quality revealed that the shear force, the contents of protein, essential amino acid (EAA), non-essential amino acid (NEAA), and n-6/n-3 ratio of Dongxiang tribute mutton were better than the other three breeds. Membership functions were calculated for 10 physical and chemical indexes of mutton quality, and the comprehensive membership function values of the four breeds in order of highest to lowest mutton quality were Tibetan sheep (0.76) > Dongxiang tribute sheep (0.49) > Hu sheep (0.46) > Ujumqin sheep (0.33). Thirty volatile compounds were identified via GC-IMS: seven alcohols, eight aldehydes, five ketones, two esters, two phenols, one ether, one furan, one acid, two hydrocarbons, and one pyrazine. Ketones, aldehydes, and alcohols were the main volatile compounds forming the flavor of Dongxiang tribute sheep mutton. The reliability of the results was validated by PCA (principal component analysis) and similarity analyses. Our results provide reference value for consumers of mutton in China.

Genetic Basis of Dorper Sheep (Ovis aries) Revealed by Long-Read De Novo Genome Assembly.

Dorper sheep (Ovis aries) (DPS), developed in the 1930s by crossing Dorset Horn and Blackhead Persian sheep in South Africa, is a world-famous composite breed for mutton production. The genetic basis underlying this breed is yet to be elucidated. Here, we report the sequencing and assembly of a highly contiguous Dorper sheep genome via integration of Oxford Nanopore Technology (ONT) sequencing and Hi-C (chromatin conformation capture) approaches. The assembled genome was around 2.64 Gb with a contig N50 of 73.33 Mb and 140 contigs in total. More than 99.5% of the assembled sequences could be anchored to 27 chromosomes and they were annotated with 20,450 protein-coding genes. Allele-specific expression (ASE) genes of Dorper sheep were revealed through ASE analysis and they were involved in the immune system, lipid metabolism, and environmental adaptation. A total of 5,701 and 456 allelic sites were observed in the SNP and indels loci identified from relevant whole-genome resequencing data. These allelic SNP and INDEL sites were annotated in 1,002 and 294 genes, respectively. Moreover, we calculated the number of variant sites and related genes derived from the maternal and paternal ancestors, revealing the genetic basis of outstanding phenotypic performance of Dorper sheep. In conclusion, this study reports the first reference genome of Dorper sheep and reveals its genetic basis through ASE. This study also provides a pipeline for mining genetic information of composite breeds, which has an implication for future hybrid-breeding practices.

Genome-Wide Selective Signatures Reveal Candidate Genes Associated with Hair Follicle Development and Wool Shedding in Sheep.

Hair follicle development and wool shedding in sheep are poorly understood. This study investigated the population structures and genetic differences between sheep with different wool types to identify candidate genes related to these traits. We used Illumina ovine SNP 50K chip genotyping data of 795 sheep populations comprising 27 breeds with two wool types, measuring the population differentiation index (Fst), nucleotide diversity (θπ ratio), and extended haplotype homozygosity among populations (XP-EHH) to detect the selective signatures of hair sheep and fine-wool sheep. The top 5% of the Fst and θπ ratio values, and values of XP-EHH < -2 were considered strongly selected SNP sites. Annotation showed that the PRX, SOX18, TGM3, and TCF3 genes related to hair follicle development and wool shedding were strongly selected. Our results indicated that these methods identified important genes related to hair follicle formation, epidermal differentiation, and hair follicle stem cell development, and provide a meaningful reference for further study on the molecular mechanisms of economically important traits in sheep.

Evaluation of Bayesian alphabet and GBLUP based on different marker density for genomic prediction in Alpine Merino sheep.

The marker density, the heritability level of trait and the statistical models adopted are critical to the accuracy of genomic prediction (GP) or selection (GS). If the potential of GP is to be fully utilized to optimize the effect of breeding and selection, in addition to incorporating the above factors into simulated data for analysis, it is essential to incorporate these factors into real data for understanding their impact on GP accuracy, more clearly and intuitively. Herein, we studied the GP of six wool traits of sheep by two different models, including Bayesian Alphabet (BayesA, BayesB, BayesCπ, and Bayesian LASSO) and genomic best linear unbiased prediction (GBLUP). We adopted fivefold cross-validation to perform the accuracy evaluation based on the genotyping data of Alpine Merino sheep (n = 821). The main aim was to study the influence and interaction of different models and marker densities on GP accuracy. The GP accuracy of the six traits was found to be between 0.28 and 0.60, as demonstrated by the cross-validation results. We showed that the accuracy of GP could be improved by increasing the marker density, which is closely related to the model adopted and the heritability level of the trait. Moreover, based on two different marker densities, it was derived that the prediction effect of GBLUP model for traits with low heritability was better; while with the increase of heritability level, the advantage of Bayesian Alphabet would be more obvious, therefore, different models of GP are appropriate in different traits. These findings indicated the significance of applying appropriate models for GP which would assist in further exploring the optimization of GP.

Whole-genome re-sequencing association study on yearling wool traits in Chinese fine-wool sheep.

To investigate single nucleotide polymorphism (SNP) loci associated with yearling wool traits of fine-wool sheep for optimizing marker-assisted selection and dissection of the genetic architecture of wool traits, we conducted a genome-wide association study (GWAS) based on the fixed and random model circulating probability unification (FarmCPU) for yearling staple length (YSL), yearling mean fiber diameter (YFD), yearling greasy fleece weight (YGFW), and yearling clean fleece rate (YCFR) by using the whole-genome re-sequenced data (totaling 577 sheep) from the following four fine-wool sheep breeds in China: Alpine Merino sheep (AMS), Chinese Merino sheep (CMS), Qinghai fine-wool sheep (QHS), and Aohan fine-wool sheep (AHS). A total of 16 SNPs were detected above the genome-wise significant threshold (P = 5.45E-09), and 79 SNPs were located above the suggestive significance threshold (P = 5.00E-07) from the GWAS results. For YFD and YGFW traits, 7 and 9 SNPs reached the genome-wise significance thresholds, whereas 10 and 12 SNPs reached the suggestive significance threshold, respectively. For YSL and YCFR traits, none of the SNPs reached the genome-wise significance thresholds, whereas 57 SNPs exceeded the suggestive significance threshold. We recorded 14 genes located at the region of ±50-kb near the genome-wise significant SNPs and 59 genes located at the region of ±50-kb near the suggestive significant SNPs. Meanwhile, we used the Average Information Restricted Maximum likelihood algorithm (AI-REML) in the "HIBLUP" package to estimate the heritability and variance components of the four desired yearling wool traits. The estimated heritability values (h2) of YSL, YFD, YGFW, and YCFR were 0.6208, 0.7460, 0.6758, and 0.5559, respectively. We noted that the genetic parameters in this study can be used for fine-wool sheep breeding. The newly detected significant SNPs and the newly identified candidate genes in this study would enhance our understanding of yearling wool formation, and significant SNPs can be applied to genome selection in fine-wool sheep breeding.

Selective Sweeps Uncovering the Genetic Basis of Horn and Adaptability Traits on Fine-Wool Sheep in China.

Long-term natural and artificial selection leads to change in certain regions of the genome, resulting in selection signatures that can reveal genes associated with selected traits, such as horns (i.e., polled/horned), high-quality wool traits, and high-altitude hypoxia adaptability. These are complex traits determined by multiple genes, regulatory pathways, and environmental factors. A list of genes with considerable effects on horn and adaptability traits has not been found, although multiple quantitative trait loci (QTL) have been identified. Selection signatures could be identified using genetic differentiation (F ST ), polymorphism levels θπ, and Tajima's D. This study aimed to identify selection signatures in fine-wool sheep and to investigate the genes annotated in these regions, as well as the biological pathways involved in horn and adaptability traits. For this purpose, the whole-genome sequence of 120 individuals from four breeds, which come from different elevations and habitats in China, was used to analyze selection signatures for horn and adaptability traits. Annotation of the consensus regions of F ST and θπ ratios revealed a list of identified genes associated with polled/horned and high-altitude hypoxia adaptability traits, such as RXPF2, EERFC4, MSH6, PP1R12A, THBS1, ATP1B2, RYR2, and PLA2G2E. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified genes related primarily to mismatch repair, metabolism, vascular smooth muscle contraction, and cardiac muscle contraction. This is the first study to demonstrate that selection signatures play an important role in the polled/horned and high-altitude hypoxia adaptability traits of fine-wool sheep breeds that have undergone high-intensity selection and adapted to different ecological environments in China. Changes observed in the genome of fine-wool sheep may have acted on genomic regions that affect performance traits and provide a reference for genome design and breeding.

Quantitative proteomic analysis identified differentially expressed proteins with tail/rump fat deposition in Chinese thin- and fat-tailed lambs.

Tail adipose as one of the important functional tissues can enhance hazardous environments tolerance for sheep. The objective of this study was to gain insight into the underlying development mechanisms of this trait. A quantitative analysis of protein abundance in ovine tail/rump adipose tissue was performed between Chinese local fat- (Kazakh, Hu and Lanzhou) and thin-tailed (Alpine Merino, Tibetan) sheep in the present study by using lable-free approach. Results showed that 3400 proteins were identified in the five breeds, and 804 were differentially expressed proteins, including 638 up regulated proteins and 83 down regulated proteins in the tail adipose tissues between fat- and thin-tailed sheep, and 8 clusters were distinguished for all the DEPs' expression patterns. The differentially expressed proteins are mainly associated with metabolism pathways and peroxisome proliferator activated receptor signaling pathway. Furthermore, the proteomics results were validated by quantitative real-time PCR and Western Blot. Our research has also suggested that the up-regulated proteins ACSL1, HSD17ß4, FABP4 in the tail adipose tissue might contribute to tail fat deposition by facilitating the proliferation of adipocytes and fat accumulation in tail/rump of sheep. Particularly, FABP4 highly expressed in the fat-tail will play an important role for tail fat deposition. Our study might provide a novel view to understanding fat accumulation in special parts of the body in sheep and other animals.

Genome-wide association studies detects candidate genes for wool traits by re-sequencing in Chinese fine-wool sheep.

BACKGROUND: The quality and yield of wool determine the economic value of the fine-wool sheep. Therefore, discovering markers or genes relevant to wool traits is the cornerstone for the breeding of fine-wool sheep. In this study, we used the Illumina HiSeq X Ten platform to re-sequence 460 sheep belonging to four different fine-wool sheep breeds, namely, Alpine Merino sheep (AMS), Chinese Merino sheep (CMS), Aohan fine-wool sheep (AHS) and Qinghai fine-wool sheep (QHS). Eight wool traits, including fiber diameter (FD), fiber diameter coefficient of variance (FDCV), fiber diameter standard deviation (FDSD), staple length (SL), greasy fleece weight (GFW), clean wool rate (CWR), staple strength (SS) and staple elongation (SE) were examined. A genome-wide association study (GWAS) was performed to detect the candidate genes for the eight wool traits. RESULTS: A total of 8.222 Tb of raw data was generated, with an average of approximately 8.59X sequencing depth. After quality control, 12,561,225 SNPs were available for analysis. And a total of 57 genome-wide significant SNPs and 30 candidate genes were detected for the desired wool traits. Among them, 7 SNPs and 6 genes are related to wool fineness indicators (FD, FDCV and FDSD), 10 SNPs and 7 genes are related to staple length, 13 SNPs and 7 genes are related to wool production indicators (GFW and CWR), 27 SNPs and 10 genes associated with staple elongation. Among these candidate genes, UBE2E3 and RHPN2 associated with fiber diameter, were found to play an important role in keratinocyte differentiation and cell proliferation. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment results, revealed that multitude significant pathways are related to keratin and cell proliferation and differentiation, such as positive regulation of canonical Wnt signaling pathway (GO:0090263). CONCLUSION: This is the first GWAS on the wool traits by using re-sequencing data in Chinese fine-wool sheep. The newly detected significant SNPs in this study can be used in genome-selective breeding for the fine-wool sheep. And the new candidate genes would provide a good theoretical basis for the fine-wool sheep breeding.

A global analysis of CNVs in Chinese indigenous fine-wool sheep populations using whole-genome resequencing.

BACKGROUND: Copy number variation (CNV) is an important source of genetic variation that has a significant influence on phenotypic diversity, economically important traits and the evolution of livestock species. In this study, the genome-wide CNV distribution characteristics of 32 fine-wool sheep from three breeds were analyzed using resequencing. RESULTS: A total of 1,747,604 CNVs were detected in this study, and 7228 CNV regions (CNVR) were obtained after merging overlapping CNVs; these regions accounted for 2.17% of the sheep reference genome. The average length of the CNVRs was 4307.17 bp. "Deletion" events took place more frequently than "duplication" or "both" events. The CNVRs obtained overlapped with previously reported sheep CNVRs to variable extents (4.39-55.46%). Functional enrichment analysis showed that the CNVR-harboring genes were mainly involved in sensory perception systems, nutrient metabolism processes, and growth and development processes. Furthermore, 1855 of the CNVRs were associated with 166 quantitative trait loci (QTL), including milk QTLs, carcass QTLs, and health-related QTLs, among others. In addition, the 32 fine-wool sheep were divided into horned and polled groups to analyze for the selective sweep of CNVRs, and it was found that the relaxin family peptide receptor 2 (RXFP2) gene was strongly influenced by selection. CONCLUSIONS: In summary, we constructed a genomic CNV map for Chinese indigenous fine-wool sheep using resequencing, thereby providing a valuable genetic variation resource for sheep genome research, which will contribute to the study of complex traits in sheep.

Comprehensive Analysis of Long Non-coding RNA and mRNA Transcriptomes Related to Hypoxia Adaptation in Tibetan Sheep.

Tibetan sheep have lived on the Qinghai-Tibet Plateau for a long time, and after long-term natural selection, they have shown stable genetic adaptability to high-altitude environments. However, little is known about the molecular mechanisms of the long non-coding (lnc)RNAs involved in the adaptation of Tibetan sheep to hypoxia. Here, we collected lung tissues from high-altitude Tibetan sheep and low-altitude Hu sheep for RNA sequencing to study the regulatory mechanisms of the lncRNAs and mRNAs in the adaptation of Tibetan sheep to hypoxia. We identified 254 differentially expressed lncRNAs and 1,502 differentially expressed mRNAs. We found 20 pairs of cis-regulatory relationships between 15 differentially expressed lncRNAs and 14 protein-coding genes and two pairs of trans-regulatory relationships between two differentially expressed lncRNAs and two protein-coding genes. These differentially expressed mRNAs and lncRNA target genes were mainly enriched in pathways related to lipid metabolism and immune function. Interaction network analysis showed that 17 differentially expressed lncRNAs and 15 differentially expressed mRNAs had an interactive relationship. Additionally, we used six differentially expressed lncRNAs and mRNAs to verify the accuracy of the sequencing data via qRT-PCR. Our results provide a comprehensive overview of the expression patterns of the lncRNAs and mRNAs involved in the adaptation of Tibetan sheep to hypoxia, laying a foundation for further analysis of the adaptations of plateau animals.

The complete mitochondrial genome sequence and phylogenetic analysis of Alpine Merino sheep (Ovis aries).

Alpine Merino sheep is one of the most important fine-wool sheep breeds in China. In this study, we present the complete mitogenome of Alpine Merino sheep for the first time. The genome has a length of 16,619bp, containing 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region (D-loop). Phylogenetically, the Alpine Merino sheep is closer to Oula Tibetan sheep and Tashkurgan sheep. This report provided new data for the phylogeny of Alpine Merino sheep.