Genome-wide selection signal analysis of Australian Boer goat reveals artificial selection imprinting on candidate genes related to muscle development

Genomic insights into demographic history, structural variation landscape, and complex traits from 514 Hu sheep genomes

Hu sheep is an indigenous breed from the Taihu Lake Plain in China, known for its high fertility. Although Hu sheep belong to the Mongolian group, their demographic history and genetic architecture remain inconclusive. Here, we analyze 697 sheep genomes from representatives of Mongolian sheep breeds. Our study suggests that the ancestral Hu sheep first separated from the Mongolian group approximately 3000 years ago. As Hu sheep migrated from the north and flourished in the Taihu Lake Plain around 1000 years ago, they developed a unique genetic foundation and phenotypic characteristics, which are evident in the genomic footprints of selective sweeps and structural variation landscape. Genes associated with reproductive traits (BMPR1B and TDRD10) and horn phenotype (RXFP2) exhibit notable selective sweeps in the genome of Hu sheep. A genome-wide association analysis reveals that structural variations at LOC101110773, MAST2, and ZNF385B may significantly impact polledness, teat number, and early growth in Hu sheep, respectively. Our study offers insights into the evolutionary history of Hu sheep and may serve as a valuable genetic resource to enhance the understanding of complex traits in Hu sheep.

Genomic evidence of improved fertility and adaptation in Iranian domestic sheep attributed to introgression from Asiatic Mouflon and urial

Due to the diverse climate in Iran, there has been an opportunity for the emergence of different domestic sheep breeds. On the other hand, two of the seven wild sheep species have settled in the broad areas of Iran. This study investigated the introgression between wild and domestic Iranian sheep using the whole genome sequencing data for 55 domestic and 19 wild sheep. The study reveals introgression signals from Asiatic mouflon and urial in Iranian domestic breeds. The results of Treemix unveiled the introgression from the common ancestor of Iranian domestic sheep to Asiatic mouflons, which sheds light on the dynamics of gene flow between domestic and wild sheep in Iran. There were 36 genomic regions (containing 26 protein coding genes) introgressed from both Asiatic mouflon and urial into the genome of their domestic relatives. In the genomic windows containing 19 of the mentioned genes, we observed a noticeable drop in the dxy value of the urial vs. domestic and Asiatic mouflon vs. domestic sheep. Also, a decrease in nucleotide diversity was observed in these regions for wild and domestic sheep, suggesting the occurrence of a selective sweep in the mentioned genomic regions. The study found important genes in these regions that are involved in fertility (TTC29, STPG2), spatial memory and learning (CAMK1G), taste perception (OTOP1), visual system (DYRK2) and olfactory (LOC101110674). The results demonstrate that most genes affected by introgression between wild and domestic sheep are related to survival, reproduction and adaptation. This information can enhance our understanding of the impact of wild species on domesticated livestocks, providing us with clearer insights for management, breeding, and conservation of these species.

Transcriptome Analysis of Myocardial Ischemic-Hypoxic Injury in Rats and Hypoxic H9C2 Cells

AIMS

This study aimed to address inconsistencies in results between the H9C2 myocardial hypoxia (MH) cell line and myocardial infarction (MI) rat models used in MI research. We identified differentially expressed genes (DEGs) and underlying molecular mechanisms using RNA sequencing technology.

METHODS

RNA sequencing was used to analyse DEGs in MI rat tissues and H9C2 cells exposed to hypoxia for 24 h. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were used to identify key biological processes and pathways. Weighted correlation network analysis [weighted gene co-expression network analysis (WGCNA)] was used to construct gene co-expression networks, and hub genes were compared with published MI datasets [Gene Expression Omnibus (GEO)] for target identification.

RESULTS

GO analysis revealed enrichment of immune inflammation and mitochondrial respiration processes among 5139 DEGs in MI tissues and 2531 in H9C2 cells. KEGG analysis identified 537 overlapping genes associated with metabolism and oxidative stress pathways. Cross-analyses using the published GSE35088 and GSE47495 datasets identified 40 and 16 overlapping genes, respectively, with nine genes overlapping across all datasets and our models. WGCNA identified a key module in the MI model enriched for mRNA processing and protein binding. GO analysis revealed enrichment of mRNA processing, protein binding and mitochondrial respiratory chain complex I assembly in MI and H9C2 MH models. Five relevant hub genes were identified via a cross-analysis between the 92 hub genes that showed a common expression trend in both models.

CONCLUSIONS

This study reveals both shared and distinct transcriptomic responses in the MI and H9C2 models, highlighting the importance of model selection for studying myocardial ischaemia and hypoxia.

Whole-genome resequencing reveals new mutations in candidate genes for Beichuan-white goat prolificacya

In this study, we evaluated the copy number variation in the genomes of two groups of Beichuan-white goat populations with large differences in litter size by FST method, and identified 1739 genes and 485 missense mutations in the genes subject to positive selection. Through functional enrichment, ITGAV, LRP4, CDH23, TPRN, RYR2 and CELSR1 genes, involved in embryonic morphogenesis, were essential for litter size trait, which received intensive attention. In addition, some mutation sites of these genes have been proposed (ITGAV: c.38C > T; TPRN: c.133A > T, c.1192A > G, c.1250A > C; CELSR1: c.7640T > C), whose allele frequencies were significantly changed in the high fecundity goat group. Besides, we found that new mutations at these sites altered the hydrophilicity and 3D structure of the protein. Candidate genes related to litter size in this study and their missense mutation sites were identified. These candidate genes are helpful to understand the genetic mechanism of fecundity in Beichuan white goat, and have important significance for future goat breeding.

Genetic Diversity and Selection Signal Analysis of Hu Sheep Based on SNP50K BeadChip

This research is designed to examine the genetic diversity and kinship among Hu sheep, as well as to discover genes associated with crucial economic traits. A selection of 50 unrelated adult male Hu sheep underwent genotyping with the SNP50K BeadChip. Seven indicators of genetic diversity were assessed based on high-quality SNP data: effective population size (Ne), polymorphic information content (PIC), polymorphic marker ratio (PN), expected heterozygosity (He), observed heterozygosity (Ho), effective number of alleles, and minor allele frequency (MAF). Plink software was employed to compute the IBS genetic distance matrix and detect runs of homozygosity (ROHs), while the G matrix and principal component analysis were performed using GCTA software. Selective sweep analysis was carried out using ROH, Pi, and Tajima's D methodologies. This study identified a total of 64,734 SNPs, of which 56,522 SNPs remained for downstream analysis after quality control. The population displayed relatively high genetic diversity. The 50 Hu sheep were ultimately grouped into 12 distinct families, with families 6, 8, and 10 having the highest numbers of individuals, each consisting of 6 sheep. Furthermore, a total of 294 ROHs were detected, with the majority having lengths between 1 and 5 Mb, and the inbreeding coefficient FROH was 0.01. In addition, 41, 440, and 994 candidate genes were identified by ROH, Pi, and Tajima's D methods, respectively, with 3 genes overlapping (BMPR1B, KCNIP4, and FAM13A). These results offer valuable insights for future Hu sheep breeding, genetic assessment, and population management.

Genome-wide association studies of egg production traits by whole genome sequencing of Laiwu Black chicken

Compared to high-yield commercial laying hens, Chinese indigenous chicken breeds have poor egg laying capacity due to the lack of intensive selection. However, as these breeds have not undergone systematic selection, it is possible that there is a greater abundance of genetic variations related to egg laying traits. In this study, we assessed 5 egg number (EN) traits at different stages of the egg-laying period: EN1 (from the first egg to 23 wk), EN2 (from 23 to 35 wk), EN3 (from 35 to 48 wk), EN4 (from the first egg to 35 wk), and EN5 (from the first egg to 48 wk). To investigate the molecular mechanisms underlying egg number traits in a Chinese local chicken breed, we conducted a genome-wide association study (GWAS) using data from whole-genome sequencing (WGS) of 399 Laiwu Black chickens. We obtained a total of 3.01 Tb of raw data with an average depth of 7.07 × per individual. A total of 86 genome-wide suggestive or significant single-nucleotide polymorphisms (SNP) contained within a set of 45 corresponding candidate genes were identified and found to be associated with stages EN1-EN5. The genes vitellogenin 2 (VTG2), lipase maturation factor 1 (LMF1), calcium voltage-gated channel auxiliary subunit alpha2delta 3 (CACNA2D3), poly(A) binding protein cytoplasmic 1 (PABPC1), programmed cell death 11 (PDCD11) and family with sequence similarity 213 member A (FAM213A) can be considered as the candidate genes associated with egg number traits, due to their reported association with animal reproduction traits. Noteworthy, results suggests that VTG2 and PDCD11 are not only involved in the regulation of EN3, but also in the regulation of EN5, implies that VTG2 and PDCD11 have a significant influence on egg production traits. Our study offers valuable genomic insights into the molecular genetic mechanisms that govern egg number traits in a Chinese indigenous egg-laying chicken breed. These findings have the potential to enhance the egg-laying performance of chickens.

Genome-wide association analysis explores the genetic loci of amino acid content in duck's breast muscle

BACKGROUND

Amino acids are the basic components of protein and an important index to evaluate meat quality. With the rapid development of genomics, candidate regions and genes affecting amino acid content in livestock and poultry have been gradually revealed. Hence, genome-wide association study (GWAS) can be used to screen candidate loci associated with amino acid content in duck meat.

RESULT

In the current study, the content of 16 amino acids was detected in 358 duck breast muscles. The proportion of Glu to the total amino acid content was relatively high, and the proportion was 0.14. However, the proportion of Met content was relatively low, at just 0.03. By comparative analysis, significant differences were found between males and females in 3 amino acids, including Ser, Met, and Phe. In addition, 12 SNPs were significantly correlated with Pro content by GWAS analysis, and these SNPs were annotated by 7 protein-coding genes; 8 significant SNPs were associated with Tyr content, and these SNPs were annotated by 6 protein-coding genes. At the same time, linkage disequilibrium (LD) analysis was performed on these regions with significant signals. The results showed that three SNPs in the 55-56 Mbp region of chromosome 3 were highly correlated with the leader SNP (chr3:55526954) that affected Pro content (r2 > 0.6). Similarly, LD analysis showed that there were three SNPs in the 21.2-21.6 Mbp region of chromosome 13, which were highly correlated with leader SNP (chr13:21421661) (r2 > 0.6). Moreover, Through functional enrichment analysis of all candidate genes. The results of GO enrichment analysis showed that several significant GO items were associated with amino acid transport function, including amino acid transmembrane transport and glutamine transport. The results further indicate that these candidate genes are closely associated with amino acid transport. Among them, key candidate genes include SLC38A1. For KEGG enrichment analysis, CACNA2D3 and CACNA1D genes were covered by significant pathways.

CONCLUSION

In this study, GWAS analysis found a total of 28 significant SNPs affecting amino acid content. Through gene annotation, a total of 20 candidate genes were screened. In addition, Through LD analysis and enrichment analysis, we considered that SERAC1, CACNA2D3 and SLC38A1 genes are important candidate genes affecting amino acid content in duck breast muscle.

An Identification of Functional Genetic Variants in B4GALNT2 Gene and Their Association with Growth Traits in Goats

β-1,4-N-acetylgalactosamine transferase 2 (B4GALNT2) is a vital candidate gene that affects the growth traits in sheep. However, whether it has the same function in goats remains to be investigated further. This study selected 348 Nanjiang Yellow goats, screened all exons, and conserved non-coding regions of the B4GALNT2 gene for single-nucleotide polymorphisms (SNPs). Our results revealed the presence of a synonymous mutation, rs672215506, within the exon of the B4GALNT2 gene in the Nanjiang Yellow goat population. The mutation resulted in a decrease in the mRNA stability of the B4GALNT2 gene. The results of SNP detection of the conserved non-coding region of the B4GALNT2 gene showed five potential regulatory SNPs in the Nanjiang Yellow goat population. Except for rs66095343, the ~500 bp fragments of the other four SNPs (rs649127714, rs649573228, rs652899012, and rs639183528) significantly increased the luciferase activity both in goat skeletal muscle satellite cells (MuSCs) and 293T cells. The genetic diversity indexes indicated low or intermediate levels for all six SNPs analyzed, and the genotype frequencies were in Hardy-Weinberg equilibrium. Association analysis showed that rs660965343, rs649127714, and rs649573228 significantly correlate with growth traits in the later stage of growth and development of Nanjiang Yellow goats. The haplotype combinations of H2H3 and H2H2 had higher body weight and greater body size. Moreover, H2H2 haplotype combinations significantly correlated with the litter size of the Nanjiang Yellow goats. The results of our study demonstrate the potential role of the B4GALNT2 gene as a functional genetic marker in the breeding programs of Nanjiang Yellow goats.

Identification of genomic characteristics and selective signals in Guizhou black goat

BACKGROUND

Guizhou black goat is one of the indigenous black goat breeds in the southwest region of Guizhou, China, which is an ordinary goat for mutton production. They are characterized by moderate body size, black coat, favorite meat quality with tender meat and lower odor, and tolerance for cold and crude feed. However, little is known about the genetic characteristics or variations underlying their important economic traits.

RESULTS

Here, we resequenced the whole genome of Guizhou black goat from 30 unrelated individuals breeding in the five core farms. A total of 9,835,610 SNPs were detected, and 2,178,818 SNPs were identified specifically in this breed. The population structure analysis revealed that Guizhou black goat shared a common ancestry with Shaanbei white cashmere goat (0.146), Yunshang black goat (0.103), Iran indigenous goat (0.054), and Moroccan goat (0.002). However, Guizhou black goat showed relatively higher genetic diversity and a lower level of linkage disequilibrium than the other seven goat breeds by the analysis of the nucleotide diversity, linkage disequilibrium decay, and runs of homozygosity. Based on FST and θπ values, we identified 645, 813, and 804 selected regions between Guizhou black goat and Yunshang black goat, Iran indigenous goat, and cashmere goats. Combined with the results of XP-EHH, there were 286, 322, and 359 candidate genes, respectively. Functional annotation analysis revealed that these genes are potentially responsible for the immune response (e.g., CD28, CD274, IL1A, TLR2, and SLC25A31), humility-cold resistance (e.g., HBEGF, SOSTDC1, ARNT, COL4A1/2, and EP300), meat quality traits (e.g., CHUK, GAB2, PLAAT3, and EP300), growth (e.g., GAB2, DPYD, and CSF1), fertility (e.g., METTL15 and MEI1), and visual function (e.g., PANK2 and NMNAT2) in Guizhou black goat.

CONCLUSION

Our results indicated that Guizhou black goat had a high level of genomic diversity and a low level of linkage disequilibrium in the whole genome. Selection signatures were detected in the genomic regions that were mainly related to growth and development, meat quality, reproduction, disease resistance, and humidity-cold resistance in Guizhou black goat. These results would provide a basis for further resource protection and breeding improvement of this very local breed.

Transcriptome analysis of mRNAs, lncRNAs, and miRNAs in the skeletal muscle of Tibetan chickens at different developmental stages

Introduction: As a valuable genetic resource, native birds can contribute to the sustainable development of animal production. Tibetan chickens, known for their special flavor, are one of the important local poultry breeds in the Qinghai-Tibet Plateau. However, Tibetan chickens have a slow growth rate and poor carcass traits compared with broilers. Although most of the research on Tibetan chickens focused on their hypoxic adaptation, there were fewer studies related to skeletal muscle development. Methods: Here, we performed the transcriptional sequencing of leg muscles from Tibetan chicken embryos at E (embryonic)10, E14, and E18. Results: In total, 1,600, 4,610, and 2,166 DE (differentially expressed) mRNAs, 210, 573, and 234 DE lncRNAs (long non-coding RNAs), and 52, 137, and 33 DE miRNAs (microRNAs) were detected between E10 and E14, E10 and E18, and E14 and E18, respectively. Functional prediction showed several DE mRNAs and the target mRNAs of DE lncRNAs and DE miRNAs were significantly enriched in sarcomere organization, actin cytoskeleton organization, myofibril, muscle fiber development, and other terms and pathways related to muscle growth and development. Finally, a lncRNA-miRNA-mRNA ceRNA (competing endogenous RNA) network associated with muscle growth and development, which contained 6 DE lncRNAs, 13 DE miRNAs, and 50 DE mRNAs, was constructed based on the screened DE RNAs by Gene Ontology (GO) enrichment. These DE RNAs may play a critical regulatory role in the skeletal muscle development of chickens. Discussion: The results provide a genomic resource for mRNAs, lncRNAs, and miRNAs potentially involved in the skeletal muscle development of chickens, which lay the foundation for further studies of the molecular mechanisms underlying skeletal muscle growth and development in Tibetan chickens.

Whole-genome resequencing reveals genetic diversity and selection characteristics of dairy goat

The dairy goat is one of the earliest dairy livestock species, which plays an important role in the economic development, especially for developing countries. With the development of agricultural civilization, dairy goats have been widely distributed across the world. However, few studies have been conducted on the specific characteristics of dairy goat. In this study, we collected the whole-genome data of 89 goat individuals by sequencing 48 goats and employing 41 publicly available goats, including five dairy goat breeds (Saanen, Nubian, Alpine, Toggenburg, and Guanzhong dairy goat; n = 24, 15, 11, 6, 6), and three goat breeds (Guishan goat, Longlin goat, Yunshang Black goat; n = 6, 15, 6). Through compared the genomes of dairy goat and non-dairy goat to analyze genetic diversity and selection characteristics of dairy goat. The results show that the eight goats could be divided into three subgroups of European, African, and Chinese indigenous goat populations, and we also found that Australian Nubian, Toggenburg, and Australian Alpine had the highest linkage disequilibrium, the lowest level of nucleotide diversity, and a higher inbreeding coefficient, indicating that they were strongly artificially selected. In addition, we identified several candidate genes related to the specificity of dairy goat, particularly genes associated with milk production traits (GHR, DGAT2, ELF5, GLYCAM1, ACSBG2, ACSS2), reproduction traits (TSHR, TSHB, PTGS2, ESR2), immunity traits (JAK1, POU2F2, LRRC66). Our results provide not only insights into the evolutionary history and breed characteristics of dairy goat, but also valuable information for the implementation and improvement of dairy goat cross breeding program.

Identification and Characterization of lncRNAs Expression Profile Related to Goat Skeletal Muscle at Different Development Stages

LncRNAs are essential for regulating skeletal muscle. However, the expression profile and function of lncRNAs in goat muscle remains unclear. Here, an average of ~14.58 Gb high-quality reads were obtained from longissimus dorsi tissues of 1-month-old (n = 3) and 9-month-old (n = 3) Wu'an black goats using RNA sequencing. Of a total of 3441 lncRNAs, 1281 were lincRNAs, 805 were antisense lncRNAs, and 1355 were sense_overlapping lncRNAs. These lncRNAs shared some properties with goats, such as fewer exons, shorter transcript, and open reading frames (ORFs) length. Among them, 36 differentially expressed lncRNAs (DE lncRNA) were identified, and then 10 random lncRNAs were validated by RT-qPCR. Furthermore, 30 DE lncRNAs were neighboring 71 mRNAs and several genes were functionally enriched in muscle development-related pathways, such as APC, IFRD1, NKX2-5, and others. Additionally, 36 DE lncRNAs and 2684 mRNAs were included in co-expression interactions. A lncRNA-miRNA-mRNA network containing 4 lncRNAs, 3 miRNAs, and 8 mRNAs was finally constructed, of which XR_001296113.2 might regulate PDLIM7 expression by interaction with chi-miR-1296 to affect skeletal muscle development. This study revealed the expression profile of goat lncRNAs for further investigative studies and provides a fuller understanding of skeletal muscle development.

Genome-Wide Selective Analysis of Boer Goat to Investigate the Dynamic Heredity Evolution under Different Stages

Boer goats, as kemp in meat-type goats, are selected and bred from African indigenous goats under a long period of artificial selection. Their advantages in multiple economic traits, particularly their plump growth, have attracted worldwide attention. The current study displayed the genome-wide selection signature analyses of South African indigenous goat (AF), African Boer (BH), and Australian Boer (AS) to investigate the hereditary basis of artificial selection in different stages. Four methods (principal component analysis, nucleotide diversity, linkage disequilibrium decay, and neighbor-joining tree) implied the genomic diversity changes with different artificial selection intensities in Boer goats. In addition, the θπ, FST, and XP-CLR methods were used to search for the candidate signatures of positive selection in Boer goats. Consequently, 339 (BH vs. AF) and 295 (AS vs. BH) candidate genes were obtained from SNP data. Especially, 10 genes (e.g., BMPR1B, DNER, ITGAL, and KIT) under selection in both groups were identified. Functional annotation analysis revealed that these genes are potentially responsible for reproduction, metabolism, growth, and development. This study used genome-wide sequencing data to identify inheritance by artificial selection. The results of the current study are valuable for future molecular-assisted breeding and genetic improvement of goats.

Genomic analysis of 10 years of artificial selection in community‐based breeding programs in two Ethiopian indigenous sheep breeds

In recent times, community-based breeding programs (CBBPs) have been advocated as the best strategy for genetic improvement of local breeds in smallholder farms in developing countries. Since 2009, CBBPs have been implemented for Ethiopian Bonga and Menz sheep to improve growth rates resulting in significant genetic gains in 6-month weights. With the hypothesis that selection could be impacting their genomes, we systematically screened for possible genome changes in the two breeds by analyzing 600K BeadChip genotype data of 151 individuals (with the highest breeding values for 6-month weights) from CBBP flocks against 98 individuals from non-CBBP flocks. We observed no differences in genetic diversity and demographic dynamics between CBBP and non-CBBP flocks. Selection signature analysis employing ROH, logistic regression genome-wide association study , F_ST , XP-EHH and iHS revealed 5 (Bonga) and 11 (Menz) overlapping regions under selection, that co-localized with QTLs for production (body size/weight, growth, milk yield), meat/milk quality, and health/parasite resistance, suggesting that the decade-long selection has likely started to impact their genomes. However, genome-wide genetic differentiation between the CBBP and non-CBBP flocks is not yet clearly evident.

Genome-Wide Association Study of Body Conformation Traits by Whole Genome Sequencing in Dazu Black Goats

Simple Summary

Body conformation traits are economically important in the goat meat industry. Good growth performance in goats, including an accelerated growth rate, can improve carcass weight and meat yield. The identification of genetic variants associated with these traits provides a basis for the genetic improvement of growth performance. In this study, we measured six body conformation traits, including body height, body length, cannon circumference, chest depth, chest width, and heart girth. By a genome-wide association study of a Chinese meat goat breed, 53 significant single nucleotide polymorphisms and 42 candidate genes associated with these traits were detected. These findings improve our understanding of the genetic basis of body conformation traits in goats.

Abstract

Identifying associations between genetic markers and economic traits has practical benefits for the meat goat industry. To better understand the genomic regions and biological pathways contributing to body conformation traits of meat goats, a genome-wide association study was performed using Dazu black goats (DBGs), a Chinese indigenous goat breed. In particular, 150 DBGs were genotyped by whole-genome sequencing, and six body conformation traits, including body height (BH), body length (BL), cannon circumference (CC), chest depth (CD), chest width (CW), and heart girth (HG), were examined. In total, 53 potential SNPs were associated with these body conformation traits. A bioinformatics analysis was performed to evaluate the genes located close to the significant SNPs. Finally, 42 candidate genes (e.g., PSTPIP2, C7orf57, CCL19, FGF9, SGCG, FIGN, and SIPA1L) were identified as components of the genetic architecture underlying body conformation traits. Our results provide useful biological information for the improvement of growth performance and have practical applications for genomic selection in goats.