A genome-wide association study for prolificacy in three Polish sheep breeds

Genome-Wide DNA Methylation Analysis and Functional Validation of Litter Size Traits in Jining Grey Goats

DNA methylation (DNAm) is associated with the reproductive system. However, the genetic mechanism through which DNAm regulates gene expression and thus affects litter size in goats is unclear. Therefore, in the present work, genome-wide DNAm profiles of HP and LP Jining Grey goat ovary tissues were comprehensively analyzed via WGBS, and RNA-Seq data were combined to identify candidate genes associated with litter size traits in the Jining Grey goat. Finally, BSP and RT-qPCR were used to verify the sequencing results of the key genes. Notably, the DNMT genes were downregulated at the expression level in the HP group. Both groups exhibited comparable levels of methylation. A total of 976 differentially methylated regions (DMRs) (973 DMRs for CG and 3 DMRs for CHG) and 310 differentially methylated genes (DMGs) were identified in this study. Through integration of WGBS and RNA-Seq data, we identified 59 differentially methylated and differentially expressed genes (DEGs) and ultimately screened 8 key DMGs (9 DMRS) associated with litter size traits in Jining Grey goats (SERPINB2: chr24_62258801_62259000, NDRG4: chr18_27599201_27599400, CFAP43: chr26_27046601_27046800, LRP1B. chr2_79720201_79720400, EPHA6: chr1_40088601_40088800, TTC29: chr17_59385801_59386000, PDE11A: chr2_117418601_117418800 and PGF: chr10_ 16913801_16914000 and chr10_16916401_16916600). In summary, our research comprehensively analyzed the genome-wide DNAm profiles of HP and LP Jining Grey goat ovary tissues. The data findings suggest that DNAm in goat ovaries may play an important role in determining litter size.

Runs of Homozygosity Detection and Selection Signature Analysis for Local Goat Breeds in Yunnan, China

Runs of Homozygosity (ROH) are continuous homozygous DNA segments in diploid genomes, which have been used to estimate the genetic diversity, inbreeding levels, and genes associated with specific traits in livestock. In this study, we analyzed the resequencing data from 10 local goat breeds in Yunnan province of China and five additional goat populations obtained from a public database. The ROH analysis revealed 21,029 ROH segments across the 15 populations, with an average length of 1.27 Mb, a pattern of ROH, and the assessment of the inbreeding coefficient indicating genetic diversity and varying levels of inbreeding. iHS (integrated haplotype score) was used to analyze high-frequency Single-Nucleotide Polymorphisms (SNPs) in ROH regions, specific genes related to economic traits such as coat color and weight variation. These candidate genes include OCA2 (OCA2 melanosomal transmembrane protein) and MLPH (melanophilin) associated with coat color, EPHA6 (EPH receptor A6) involved in litter size, CDKAL1 (CDK5 regulatory subunit associated protein 1 like 1) and POMC (proopiomelanocortin) linked to weight variation and some putative genes associated with high-altitude adaptability and immune. This study uncovers genetic diversity and inbreeding levels within local goat breeds in Yunnan province, China. The identification of specific genes associated with economic traits and adaptability provides actionable insights for utilization and conservation efforts.

Identifying Candidate Genes for Litter Size and Three Morphological Traits in Youzhou Dark Goats Based on Genome-Wide SNP Markers

This study aimed to reveal the potential genetic basis for litter size, coat colour, black middorsal stripe and skin colour by combining genome-wide association analysis (GWAS) and selection signature analysis and ROH detection within the Youzhou dark (YZD) goat population (n = 206) using the Illumina GoatSNP54 BeadChip. In the GWAS, we identified one SNP (snp54094-scaffold824-899720) on chromosome 11 for litter size, two SNPs on chromosome 26 (snp11508-scaffold142-1990450, SORCS3) and chromosome 12 (snp55048-scaffold842-324525, LOC102187779) for coat colour and one SNP on chromosome 18 (snp56013-scaffold873-22716, TCF25) for the black middorsal stripe. In contrast, no SNPs were identified for skin colour. In selection signature analysis, 295 significant iHS genomic regions with a mean |iHS| score > 2.66, containing selection signatures encompassing 232 candidate genes were detected. In particular, 43 GO terms and one KEGG pathway were significantly enriched in the selected genes, which may contribute to the excellent environmental adaptability and characteristic trait formation during the domestication of YZD goats. In ROH detection, we identified 4446 ROH segments and 282 consensus ROH regions, among which nine common genes overlapped with those detected using the iHS method. Some known candidate genes for economic traits such as reproduction (TSHR, ANGPT4, CENPF, PIBF1, DACH1, DIS3, CHST1, COL4A1, PRKD1 and DNMT3B) and development and growth (TNPO2, IFT80, UCP2, UCP3, GHRHR, SIM1, CCM2L, CTNNA3 and CTNNA1) were revealed by iHS and ROH detection. Overall, this study is limited by the small population size, which affects the results of GWAS to a certain extent. Nevertheless, our findings could provide the first overview of the genetic mechanism underlying these important traits and provide novel insights into the future conservation and utilisation of Chinese goat germplasm resources.

Transcriptome analysis reveals mRNAs and long non-coding RNAs associated with fecundity in the hypothalamus of high-and low-fecundity goat

As an important organ that coordinates the neuroendocrine system, the hypothalamus synthesizes and secretes reproductive hormones that act on the goat organism, thereby precisely regulating follicular development and reproductive processes in goats. However, it is still elusive to explore the mechanism of hypothalamic effects on goat fertility alone. Therefore, RNA-seq was used to analyze the gene expression in hypothalamic tissues of goats in high fertility group (HFG: litter size per litter ≥2) and low fertility group (LFG: litter size per litter = 1), and identified the differential lncRNAs and mRNAs and their associated pathways related to their fertility. The results showed that a total of 23 lncRNAs and 57 mRNAs were differentially expressed in the hypothalamic tissue of high and low fertility goats. GO terms and KEGG functional annotation suggest that DE lncRNAs and DE mRNAs were significantly enriched in hormone-related pathways regulating ovarian development, hormone synthesis and secretion, regulation of reproductive processes, Estrogen signaling pathway, Oxytocin signaling pathway and GnRH signaling pathway. And we constructed a co-expression network of lncRNAs and target genes, and identified reproduction-related genes such as NMUR2, FEZF1, and WT1. The sequencing results of the hypothalamic transcriptome have broadened our understanding of lncRNA and mRNA in goat hypothalamic tissue and provided some new insights into the molecular mechanisms of follicle development and regulation of its fertility in goats.

Novel genomic markers and genes related to reproduction in prolific Chios dairy sheep: a genome-wide association study

Genetic architecture of sheep reproduction is increasingly gaining scientific interest due to the major impact on sheep production systems. In the present study, we conducted pedigree-based analyses and genome-wide association studies using the Illumina Ovine SNP50K BeadChip to explore the genetic mechanisms underlying the reproduction of the highly prolific Chios dairy sheep. First lambing age, total prolificacy and maternal lamb survival were selected as representative reproductive traits and estimated as significantly heritable (h² = 0.07-0.21) with no evident genetic antagonism among traits. We identified novel genome-wide and suggestive significant single-nucleotide polymorphisms (SNPs) on chromosomes 2 and 12 associated with age at first lambing. The new variants detected on chromosome 2 span a region of 357.79 kb with high pairwise linkage disequilibrium estimates (r² = 0.8-0.9). Functional annotation analysis revealed candidate genes, such as the collagen-type genes and the Myostatin gene, that participate in osteogenesis, myogenesis, skeletal and muscle mass development resembling the functionality of major genes affecting the ovulation rate and prolificacy. Additional functional enrichment analysis associated the collagen-type genes with multiple uterine-related disfunctions, such as cervical insufficiency, uterine prolapse and abnormalities of the uterine cervix. Several genes (e.g., KAZN, PRDM2, PDPN, LRRC28) localised close to the SNP marker on chromosome 12 were grouped in annotation enrichment clusters majorly involved in developmental and biosynthetic pathways, apoptosis, and nucleic acid-templated transcription. Our findings may further contribute to unravel the genomic regions that are important for sheep reproduction and could be incorporated into future selective breeding programmes.

Molecular markers for thermo-tolerance are associated with reproductive and physiological traits in Pelibuey ewes raised in a semiarid environment

Pelibuey sheep exhibit reproductive activity through the year, but warm weather lowers their fertility and demonstrates physiological limitations of environmental heat stress. Single nucleotide polymorphisms (SNPs) associated with heat stress tolerance in sheep have been reported previously. The objective was to validate the association of seven thermo-tolerance SNP markers with reproductive and physiological traits in Pelibuey ewes raised in a semiarid region. Pelibuey ewes were assigned to a cool (January 1st^.- March 31st^.; n = 101) or warm (April 1st^.- August 31st^.; n = 104) experimental group. All ewes were exposed to fertile rams and assessed for pregnancy diagnosis 90 days later; lambing day was reported at birth. These data served to calculate the reproductive traits of services per conception, prolificacy, days to estrus, days to conception, conception rate and lambing rate. Rectal temperature, rump/leg skin temperature and respiratory rate were measured and reported as physiological traits. Blood samples were collected and processed to extract DNA, which was genotyped using the TaqMan allelic discrimination method and qPCR. A mixed effects statistical model was used to validate associations between SNP genotypes and phenotypic traits. The SNPs rs421873172, rs417581105 and rs407804467 were confirmed as markers associated with reproductive and physiological traits (P < 0.05), and these SNPs were in the genes PAM, STAT1 and FBXO11, respectively. Interestingly, these SNP markers resulted as predictors for the evaluated traits but only in ewes from the warm group, which indicated their association with heat-stress tolerance. An additive SNP effect was confirmed with the highest contribution (P < 0.01) of the SNP rs417581105 for the evaluated traits. Reproductive performance improved (P < 0.05) and physiological parameters decreased in ewes carrying favorable SNP genotypes. In conclusion, three thermo-tolerance SNP markers were associated with improved reproductive and physiological traits in a prospective population of heat-stressed ewes raised in a semiarid environment.

Single nucleotide polymorphisms in the 3′ UTR of follistatin-like 4 and scavenger receptor class B member 1 are associated with Dazu black goat litter size

The untranslated regions (UTR) of genes play crucial roles in regulating gene expression at the post-transcriptional level such as affecting mRNA stabilization. In this study, 26 single nucleotide polymorphisms (SNPs) and one deletion located in UTR were genotyped from 186 Dazu black goats via SNaPshot, and the correlation between genotype and litter size was analyzed. Results indicated that two SNP loci, SNP_chr17-20182525 and SNP_chr7-65652612, which are located at the 3′UTR of scavenger receptor class B member 1 and follistatin-like 4, are significantly (p<0.05) correlated with the litter size of first parity goats. SNP_chr7-65652612 is also significantly associated with the total litter size of first and second parity offspring (p<0.05). In conclusion, SNP_chr7-65652612 and SNP_chr17-20182525 have correlation with the litter size of Dazu black goat and they are potential genetic markers for litter size breeding.

A genome-wide association study of mare fertility in the Pura Raza Español horse

Despite the economic importance of fertility for the horse industry, few efforts have been made to achieve a better understanding of the genetic mechanisms underlying its control. This is probably due to the difficulty of obtaining reliable phenotypes and the complexity of modelling the environmental and management factors. This work is novel in that we propose to use reproductive efficiency (RE) as an indicator of mare fertility. To achieve this, we performed a genome-wide association study in the Pura Raza Español horse aimed at identifying genomic variants, regions, and candidate genes associated with fertility in mares. The dataset included 819 animals genotyped with the Affymetrix Axiom™ Equine 670 K single-nucleotide polymorphisms (SNPs) Genotyping Array and the deregressed breeding values for RE trait, obtained using a ssBLUP model, employed as pseudo-phenotypic data. Our results showed 28 SNPs potentially associated with RE, which explained 87.19% of the genetic variance and 6.61% of the phenotypic variance. Those results were further validated in BayesB, showing a correlation between observed and predicted RE of 0.57. In addition, 15 candidate genes (HTRA3, SPIRE1, APOE, ERCC1, FOXA3, NECTIN-2, KLC3, RSPH6A, PDPK1, MEIOB, PAQR4, NM3, PKD1, PRSS21, IFT140) previously related to fertility in mammals were associated with the markers and genomic regions significantly associated with RE. To our knowledge, this is the first genome-wide association study performed on mare fertility.

Meta-analysis of genome-wide association studies for litter size in sheep

Litter size and ovulation rate are important reproduction traits in sheep and have important impacts on the profitability of farm animals. To investigate the genetic architecture of litter size, we report the first meta-analysis of genome-wide association studies (GWAS) using 522 ewes and 564,377 SNPs from six sheep breeds. We identified 29 significant associations for litter size which 27 of which have not been reported in individual GWAS for each population. However, we could confirm the role of BMPR1B in prolificacy. Our gene set analysis discovered biological pathways related to cell signaling, communication, and adhesion. Functional clustering and enrichment using protein databases identified epidermal growth factor-like domain affecting litter size. Through analyzing protein-protein interaction data, we could identify hub genes like CASK, PLCB4, RPTOR, GRIA2, and PLCB1 that were enriched in most of the significant pathways. These genes have a role in cell proliferation, cell adhesion, cell growth and survival, and autophagy. Notably, identified SNPs were scattered on several different chromosomes implying different genetic mechanisms underlying variation of prolificacy in each breed. Given the different layers that make up the follicles and the need for communication and transfer of hormones and nutrients through these layers to the oocyte, the significance of pathways related to cell signaling and communication seems logical. Our results provide genetic insights into the litter size variation in different sheep breeds.