Revealing new candidate genes for reproductive traits in pigs: combining Bayesian GWAS and functional pathways

Comparative whole-genome resequencing to uncover selection signatures linked to litter size in Hu Sheep and five other breeds

Hu sheep (HS), a breed of sheep carrying the FecB mutation gene, is known for its "year-round estrus and multiple births" and is an ideal model for studying the high fecundity mechanisms of livestock. Through analyzing and comparing the genomic selection features of Hu sheep and other sheep breeds, we identified a series of candidate genes that may play a role in Hu sheep's high fecundity mechanisms. In this study, we conducted whole-genome resequencing on six breeds and screened key mutations significantly correlated with high reproductive traits in sheep. Notably, the CC2D1B gene was selected by the fixation index (FST) and the cross-population composite likelihood ratio (XP-CLR) methods in HS and other five breeds. It was worth noting that the CC2D1B gene in HS was different from that in other sheep breeds, and seven missense mutations have been identified. Furthermore, the linkage disequilibrium (LD) analysis revealed a strong linkage disequilibrium in this specific gene region. Subsequently, by performing different grouping based on FecB genotypes in Hu sheep, genome-wide selective signal analysis screened several genes related to reproduction, such as BMPR1B and PPM1K. Besides, FST analysis identified functional genes related to reproductive traits, including RHEB, HSPA2, PPP1CC, HVCN1, and CCDC63. Additionally, a missense mutation was found in the CCDC63 gene and the haplotype was different between the high reproduction (HR) group and low reproduction (LR) group in HS. In summary, we discovered genetic differentiation among six distinct breeding sheep breeds at the whole genome level. Additionally, we identified a set of genes which were associated with reproductive performance in Hu sheep and visualized how these genes differed in different breeds. These findings laid a theoretical foundation for understanding genetic mechanisms behind high prolific traits in sheep.

Characterization of runs of homozygosity islands in American mink using whole-genome sequencing data

The genome-wide analysis of runs of homozygosity (ROH) islands can be an effective strategy for identifying shared variants within a population and uncovering important genomic regions related to complex traits. The current study performed ROH analysis to characterize the genome-wide patterns of homozygosity, identify ROH islands and annotated genes within these candidate regions using whole-genome sequencing data from 100 American mink (Neogale vison). After sequence processing, variants were called using GATK and Samtools pipelines. Subsequent to quality control, 8,373,854 bi-allelic variants identified by both pipelines remained for further analysis. A total of 34,652 ROH segments were identified in all individuals, among which shorter segments (0.3-1 Mb) were abundant throughout the genome, approximately accounting for 84.39% of all ROH. Within these segments, we identified 63 ROH islands housing 156 annotated genes. The genes located in ROH islands were associated with fur quality (EDNRA, FGF2, FOXA2 and SLC24A4), body size/weight (MYLK4, PRIM2, FABP2, EYS and PHF3), immune capacity (IL2, IL21, PTP4A1, SEMA4C, JAK2, CCNA2 and TNIP3) and reproduction (ADAD1, KHDRBS2, INSL6, PGRMC2 and HSPA4L). Furthermore, Gene Ontology and KEGG pathway enrichment analyses revealed 56 and 9 significant terms (FDR-corrected p-value < 0.05), respectively, among which cGMP-PKG signalling pathway, regulation of actin cytoskeleton, and calcium signalling pathway were highlighted due to their functional roles in growth and fur characteristics. This is the first study to present ROH islands in American mink. The candidate genes from ROH islands and functional enrichment analysis suggest possible signatures of selection in response to the mink breeding targets, such as increased body length, reproductive performance and fur quality. These findings contribute to our understanding of genetic characteristics, and provide complementary information to assist with implementation of breeding strategies for genetic improvement in American mink.

Revelation of genetic diversity and genomic footprints of adaptation in Indian pig breeds

In the present study, the genetic diversity measures among four Indian domestic breeds of pig namely Agonda Goan, Ghurrah, Ghungroo, and Nicobari, of different agro-climatic regions of country were explored and compared with European commercial breeds, European wild boar and Chinese domestic breeds. The double digest restriction site-associated DNA sequencing (ddRADseq) data of Indian pigs (102) and Landrace (10 animals) were generated and whole genome sequencing data of exotic pigs (60 animals) from public data repository were used in the study. The principal component analysis (PCA), admixture analysis and phylogenetic analysis revealed that Indian breeds were closer in ancestry to Chinese breeds than European breeds. European breeds exhibited highest genetic diversity measures among all the considered breeds. Among Indian breeds, Agonda Goan and Ghurrah were found to be more genetically diverse than Nicobari and Ghungroo. The selection signature regions in Indian pigs were explored using iHS and XP-EHH, and during iHS analysis, it was observed that genes related to growth, reproduction, health, meat quality, sensory perception and behavior were found to be under selection pressure in Indian pig breeds. Strong selection signatures were recorded in 24.25-25.25 Mb region of SSC18, 123.25-124 Mb region of SSC15 and 118.75-119.5 Mb region of SSC2 in most of the Indian breeds upon pairwise comparison with European commercial breeds using XP-EHH. These regions were harboring some important genes such as EPHA4 for thermotolerance, TAS2R16, FEZF1, CADPS2 and PTPRZ1 for adaptability to scavenging system of rearing, TRIM36 and PGGT1B for disease resistance and CCDC112, PIAS1, FEM1B and ITGA11 for reproduction.

Genome-Wide Association Study Meta-Analysis Elucidates Genetic Structure and Identifies Candidate Genes of Teat Number Traits in Pigs

The teat number is a pivotal reproductive trait that significantly influences the survival rate of piglets. A meta-analysis is a robust instrument, enhancing the universality of research findings and improving statistical power by increasing the sample size. This study aimed to identify universal candidate genes associated with teat number traits using a genome-wide association study (GWAS) meta-analysis with three breeds. We identified 21 chromosome threshold significant single-nucleotide polymorphisms (SNPs) associated with five teat number traits in single-breed and cross-breed meta-GWAS analyses. Using a co-localization analysis of expression quantitative trait loci and GWAS loci, we detected four unique genes that were co-localized with cross-breed GWAS loci associated with teat number traits. Through a meta-analysis and integrative analysis, we identified more reliable candidate genes associated with multiple-breed teat number traits. Our research provides new information for exploring the genetic mechanism affecting pig teat number for breeding selection and improvement.

Genome-wide association study using a single-step approach for teat number in Duroc, Landrace and Yorkshire pigs in Korea

We investigated the genetic basis of teat number in sows, which is an important factor in their reproductive performance. We collected genotyping data from 20 353 pigs of three breeds (Duroc, Landrace and Yorkshire) using the Porcine SNP60K Bead Chip, and analyzed phenotypic data from 240 603 pigs. The heritability values of total teat number were 0.33 ± 0.02, 0.51 ± 0.01 and 0.50 ± 0.01 in Duroc, Landrace and Yorkshire pigs, respectively. A genome-wide association study was used to identify significant chromosomal regions associated with teat number in SSC7 and SSC9 in Duroc pig, SSC3, SSC7 and SSC18 in Landrace pig, and SSC7, SSC8 and SSC10 in Yorkshire pig. Among the markers, MARC0038565, located between the vertnin (VRTN) and synapse differentiation-inducing 1-like (SYNDIG1L) genes, showed the strongest association in the Duroc pig and was significant in all breeds. In Landrace and Yorkshire pigs, the most significant markers were located within the apoptosis resistant E3 ubiquitin protein ligase 1 (AREL1) and latent transforming growth factor beta-binding protein 2 (LTBP2) genes in SSC7, respectively. VRTN is a candidate gene regulating the teat number. Most markers were located in SSC7, indicating their significance in determining teat number and their potential as valuable genomic selection targets for improving this trait. Extensive linkage disequilibrium blocks were identified in SSC7, supporting their use in genomic selection strategies. Our study provides valuable insights into the genetic architecture of teat numbers in pigs, and helps identify candidate genes and genomic regions that may contribute to this economically important trait.

CYP24A1 is associated with fetal mummification in pigs

Mummified piglets are among the leading causes of fertility loss and severely hamper reproductive performance in pigs. However, the contributions of genomic variation to the emergence of mummified piglets (MUM) have rarely been studied. This study aims to (1) elucidate the genetic architecture of MUM in sows of parity 1 - 3 using a single-step genome-wide association study (ssGWAS). The ssGWAS involved genotyping-by-sequencing of Large White and Landrace pig breeds. (2) Explore the biological role of the candidate genes at the cellular level. A total of 185 and 48 genome-wide significant SNPs are associated with MUM in Large White and Landrace pigs, explaining 0.01-36.52% genetic variance for different significant loci, respectively. All the significant SNPs are parity-specific, and the numerous, consecutive significant loci likely generated the nine significant peaks in different parities. Multiple candidate genes (including CYP24A1, FBXO30, and ARHGEF28) are associated with fetal congenital and maternal diseases. Collectively, CYP24A1 regulation contributes to steady-state levels of embryo development genes. CYP24A1 is involved in reproduction and, immune and gestational disorders. Thus, it is associated with known newborn death traits and MUM in Large White sows. Altogether, these results improve the current understanding of the genetic architecture of MUM and expand the knowledge on genetic variations for selecting against mummified piglets in pig breeding.

Single-step genome-wide association studies and post-GWAS analyses for the number of oocytes and embryos in Gir cattle

Genome-Wide Association Studies (GWAS) are used for identification of quantitate trait loci (QTL) and genes associated with several traits. We aimed to identify genomic regions, genes, and biological processes associated with number of total and viable oocytes, and number of embryos in Gir dairy cattle. A dataset with 17,526 follicular aspirations, including the following traits: number of viable oocytes (VO), number of total oocytes (TO), and number of embryos (EMBR) from 1641 Gir donors was provided by five different stock farms. A genotype file with 2093 animals and 395,524 SNP markers was used to perform a single-step GWAS analysis for each trait. The top 10 windows with the highest percentage of additive genetic variance explained by 100 adjacent SNPs were selected. The genomic regions identified in our work were overlapped with QTLs from QTL database on chromosomes 1, 2, 5, 6, 7, 8, 9, 13, 17, 18, 20, 21, 22, 24, and 29. These QTLs were classified as External, Health, Meat and carcass, Production or Reproduction traits, and about 38% were related to Reproduction. In total, 117 genes were identified, of which 111 were protein-coding genes. Exclusively associations were observed for 42 genes with EMBR, and 1 with TO. Also, 42 genes were in common between VO and TO, 28 between VO and EMBR, and four genes were in common among all traits. In conclusion, great part of the identified genes plays a functional role in initial embryo development or general cell functions. The protein-coding genes ARNT, EGR1, HIF1A, AHR, and PAX2 are good markers for the production of oocytes and embryos in Gir cattle.

Genetic Diversity and Selection Signatures in Jianchang Black Goats Revealed by Whole-Genome Sequencing Data

Understanding the genetic composition of indigenous goats is essential to promote the scientific conservation and sustainable utilization of these breeds. The Jianchang Black (JC) goat, a Chinese native breed, is solid black and exhibits crude feed tolerance, but is characterized by a low growth rate and small body size. Based on the whole-genome sequencing data for 30 JC, 41 Jintang Black (JT), and 40 Yunshang Black (YS) goats, and 21 Bezoar ibexes, here, we investigated the genetic composition of JC goats by conducting analyses of the population structure, runs of homozygosity (ROH), genomic inbreeding, and selection signature. Our results revealed that JT and YS showed a close genetic relationship with a non-negligible amount of gene flows but were genetically distant from JC, apart from Bezoars. An average of 2039 ROHs were present in the autosomal genome per individual. The ROH-based inbreeding estimates in JC goats generally showed moderate values ranging from 0.134 to 0.264, mainly due to rapid declines in the effective population size during recent generations. The annotated genes (e.g., IL2, IL7, and KIT) overlapping with ROH islands were significantly enriched in immune-related biological processes. Further, we found 61 genes (e.g., STIM1, MYO9A, and KHDRBS2) under positive selection in JC goats via three complementary approaches, which may underly genetic adaptations to local environmental conditions. Our findings provided references for the conservation and sustainable utilization of JC goats.

Genome-Wide Association Study Reveals Additive and Non-Additive Effects on Growth Traits in Duroc Pigs

Growth rate plays a critical role in the pig industry and is related to quantitative traits controlled by many genes. Here, we aimed to identify causative mutations and candidate genes responsible for pig growth traits. In this study, 2360 Duroc pigs were used to detect significant additive, dominance, and epistatic effects associated with growth traits. As a result, a total number of 32 significant SNPs for additive or dominance effects were found to be associated with various factors, including adjusted age at a specified weight (AGE), average daily gain (ADG), backfat thickness (BF), and loin muscle depth (LMD). In addition, the detected additive significant SNPs explained 2.49%, 3.02%, 3.18%, and 1.96% of the deregressed estimated breeding value (DEBV) variance for AGE, ADG, BF, and LMD, respectively, while significant dominance SNPs could explain 2.24%, 13.26%, and 4.08% of AGE, BF, and LMD, respectively. Meanwhile, a total of 805 significant epistatic effects SNPs were associated with one of ADG, AGE, and LMD, from which 11 sub-networks were constructed. In total, 46 potential genes involved in muscle development, fat deposition, and regulation of cell growth were considered as candidates for growth traits, including CD55 and NRIP1 for AGE and ADG, TRIP11 and MIS2 for BF, and VRTN and ZEB2 for LMD, respectively. Generally, in this study, we detected both new and reported variants and potential candidate genes for growth traits of Duroc pigs, which might to be taken into account in future molecular breeding programs to improve the growth performance of pigs.

A genome-wide association study of important reproduction traits in large white pigs

Augmenting the reproductive efficiency of sows remains the predominant challenge in the swine industry. This work was aimed at scrutinizing vital genetic markers for reproductive traits in this animal. This entailed probing of the records of vital attributes of Large White pigs (n = 695) inclusive of the total number of born (TNB), number of born alive (NBA), number of weaned pigs (NWP), number of healthy births (NHS), total litter weight of piglets born alive (BALWT), weaning litter weight (WNWT), and corrected litter weight at 21 days (W21). A genome-wide association study (GWAS) for the four litter traits and three traits of litter weight in the Denmark Large White population then ensued. We discovered seven significantly related SNPs and eleven potential candidate genes (e.g., TUSC3, THRB for TNB; STT3B for NBA). The subsequent functional enrichment analysis of these genes showed that the significant gene were associated with steroid hormone receptor activity. Our findings indicated that the genes TUSC3, THRB and STT3B probably contribute to litter traits in this population. This work reveals genetic mechanisms of reproduction traits and also supports ensuing genetic improvement employing marker-assisted selection in Large White pigs.

Genomic evaluation and genome-wide association studies for total number of teats in a combined American and Danish Yorkshire pig populations selected in China

Joint genomic evaluation by combining data recordings and genomic information from different pig herds and populations is of interest for pig breeding companies because the efficiency of genomic selection (GS) could be further improved. In this work, an efficient strategy of joint genomic evaluation combining data from multiple pig populations is investigated. Total Teat Number (TTN), a trait that is equally recorded on 13 060 American Yorkshire (AY) populations (~14.68 teats) and 10 060 Danish Yorkshire (DY) pigs (~14.29 teats), was used to explore the feasibility and accuracy of GS combining datasets from different populations. We first estimated the genetic correlation (rg) of TTN between AY and DY pig populations (rg=0.79, se=0.23). Then we employed the genome-wide association study (GWAS) to identify QTL regions that are significantly associated with TTN and investigate the genetic architecture of TTN in different populations. Our results suggested that the genomic regions controlling TTN are slight different in the two Yorkshire populations, where the candidate QTL regions were on SSC 7 and SSC 8 for AY population and on SSC 7 for DY population. Finally, we explored an optimal way of genomic prediction for TTN via three different Genomic Best Linear Unbiased Prediction (GBLUP) models and we concluded that when TTN across populations are regarded as different, but correlated, traits in a multi-trait model, predictive abilities for both Yorkshire populations improve. As a conclusion, joint genomic evaluation for target traits in multiple pig populations is feasible in practice and more accurate, provided a proper model is used.

Genome-wide association study of three litter traits in Yorkshire pigs

Litter traits are important in the development of production and economic profits of pigs. The object of this study was to perform genome-wide association studies (GWASs) for the total number born (TNB), number born alive (NBA) and number born healthy (NBH) traits in a Yorkshire population. By mixed model, we conducted GWASs with gcta software, and in total identified 3, 7 and 12 significant SNPs associated with TNB, NBA and NBH respectively: one on Sus scrofa chromosome (SSC) 2 (p = 7.03 × 10^-5 ), one on SSC4 (p = 8.53 × 10^-5 ), two on SSC 6 (p = 9.27 × 10^-5 to 9.64 × 10^-5 ), nine on SSC 8 (p = 1.53 × 10^-5 to 8.52 × 10^-5 ), four on SSC 14 (p = 2.17 × 10^-5 to 6.79 × 10^-5 ), and one on SSC 15 (p = 9.30 × 10^-5 ). We screened for flanking regions ±1 Mb nearby or within the significant SNPs, and found 203 candidate genes, including 53 for TNB, 71 for NBA and 112 for NBH. In conclusion, our findings show the significant SNPs with candidate genes for the TNB, NBA and NBH traits in Yorkshire pigs.

Genome-Wide Association Study for Body Length, Body Height, and Total Teat Number in Large White Pigs

Body length, body height, and total teat number are economically important traits in pig breeding, as these traits are usually associated with the growth, reproductivity, and longevity potential of piglets. Here, we report a genetic analysis of these traits using a population comprising 2,068 Large White pigs. A genotyping-by-sequencing (GBS) approach was used to provide high-density genome-wide SNP discovery and genotyping. Univariate and bivariate animal models were used to estimate heritability and genetic correlations. The results showed that heritability estimates for body length, body height, and total teat number were 0.25 ± 0.04, 0.11 ± 0.03, and 0.22 ± 0.04, respectively. The genetic correlation between body length and body height exhibited a strongly positive correlation (0.63 ± 0.15), while a positive but low genetic correlation was observed between total teat number and body length. Furthermore, we used two different genome-wide association study (GWAS) approaches: single-locus GWAS and weighted single-step GWAS (WssGWAS), to identify candidate genes for these traits. Single-locus GWAS detected 76, 13, and 29 significant single-nucleotide polymorphisms (SNPs) associated with body length, body height, and total teat number. Notably, the most significant SNP (S17_15781294), which is located 20 kb downstream of the BMP2 gene, explained 9.09% of the genetic variance for body length traits, and it also explained 9.57% of the genetic variance for body height traits. In addition, another significant SNP (S7_97595973), which is located in the ABCD4 gene, explained 8.92% of the genetic variance for total teat number traits. GWAS results for these traits identified some candidate genomic regions, such as SSC6: 14.96–15.02 Mb, SSC7: 97.18–98.18 Mb, SSC14: 128.29–131.15 Mb, SSC17: 15.39–17.27 Mb, and SSC17: 22.04–24.15 Mb, providing a starting point for further inheritance research. Most quantitative trait loci were detected by single-locus GWAS and WssGWAS. These findings reveal the complexity of the genetic mechanism of the three traits and provide guidance for subsequent genetic improvement through genome selection.

Host Genetics of Response to Porcine Reproductive and Respiratory Syndrome in Sows: Reproductive Performance

Porcine Reproductive and Respiratory Syndrome (PRRS) is historically the most economically important swine disease worldwide that severely affects the reproductive performance of sows. However, little is still known about the genetic basis of reproductive performance in purebred herds during a PRRS outbreak through the comparison of maternal and terminal breeds. Thus, the objective of this work was to explore the host genetics of response to PRRS in purebred sows from two breeds. Reproductive data included 2546 Duroc and 2522 Landrace litters from 894 and 813 purebred sows, respectively, which had high-density genotype data available (29,799 single nucleotide polymorphisms; SNPs). The data were split into pre-PRRS, PRRS, and post-PRRS phases based on standardized farrow-year-week estimates. Heritability estimates for reproductive traits were low to moderate (≤0.20) for Duroc and Landrace across PRRS phases. On the other hand, genetic correlations of reproductive traits between PRRS phases were overall moderate to high for both breeds. Several associations between MARC0034894, a candidate SNP for response to PRRS, with reproductive performance were identified (P-value < 0.05). Genomic analyses detected few QTL for reproductive performance across all phases, most explaining a small percentage of the additive genetic variance (≤8.2%, averaging 2.1%), indicating that these traits are highly polygenic. None of the identified QTL within a breed and trait overlapped between PRRS phases. Overall, our results indicate that Duroc sows are phenotypically more resilient to PRRS than Landrace sows, with a similar return to PRRS-free performance between breeds for most reproductive traits. Genomic prediction results indicate that genomic selection for improved reproductive performance under a PRRS outbreak is possible, especially in Landrace sows, by training markers using data from PRRS-challenged sows. On the other hand, the high genetic correlations with reproductive traits between PRRS phases suggest that selection for improved reproductive performance in a clean environment could improve performance during PRRS, but with limited efficiency due to their low heritability estimates. Thus, we hypothesize that an indicator trait that could be indirectly selected to increase the response to selection for these traits would be desirable and would also improve the reproductive performance of sows during a PRRS outbreak.

Single-marker and haplotype-based genome-wide association studies for the number of teats in two heavy pig breeds

The number of teats is a reproductive‐related trait of great economic relevance as it affects the mothering ability of the sows and thus the number of properly weaned piglets. Moreover, genetic improvement of this trait is fundamental to parallelly help the selection for increased litter size. We present the results of single‐marker and haplotypes‐based genome‐wide association studies for the number of teats in two large cohorts of heavy pig breeds (Italian Large White and Italian Landrace) including 3990 animals genotyped with the 70K GGP Porcine BeadChip and other 1927 animals genotyped with the Illumina PorcineSNP60 BeadChip. In the Italian Large White population, genome scans identified three genome regions (SSC7, SSC10, and SSC12) that confirmed the involvement of the VRTN gene (as we previously reported) and highlighted additional loci known to affect teat counts, including the FRMD4A and HOXB1 gene regions. A different picture emerged in the Italian Landrace population, with a total of 12 genome regions in eight chromosomes (SSC3, SSC6, SSC8, SSC11, SSC13, SSC14, SSC15, and SSC16) mainly detected via the haplotype‐based genome scan. The most relevant QTL was close to the ARL4C gene on SSC15. Markers in the VRTN gene region were not significant in the Italian Landrace breed. The use of both single‐marker and haplotype‐based genome‐wide association analyses can be helpful to exploit and dissect the genome of the pigs of different populations. Overall, the obtained results supported the polygenic nature of the investigated trait and better elucidated its genetic architecture in Italian heavy pigs.

Revealing New Candidate Genes for Teat Number Relevant Traits in Duroc Pigs Using Genome-Wide Association Studies

Simple Summary

Number of teats is very important for lactating sows. We conducted genome-wide association studies (GWAS) and estimated the genetic parameters for traits related to teat number. Results showed that there were nine and 22 SNPs exceeding genome-wide significance and suggestive significance levels, respectively. Eighteen genes annotated near them were concentrated on chromosomes 7 and 10. Among them, three new candidate genes were located on the genomic regions around the significant SNPs. Our findings provide new insight into investigating the complex genetic mechanism of traits related to teat number in pigs.

Abstract

The number of teats is related to the nursing ability of sows. In the present study, we conducted genome-wide association studies (GWAS) for traits related to teat number in Duroc pig population. Two mixed models, one for counted and another for binary phenotypic traits, were employed to analyze seven traits: the right (RTN), left (LTN), and total (TTN) teat numbers; maximum teat number on a side (MAX); left minus right side teat number (LR); the absolute value of LR (ALR); and the presence of symmetry between left and right teat numbers (SLR). We identified 11, 1, 4, 13, and 9 significant SNPs associated with traits RTN, LTN, MAX, TTN, and SLR, respectively. One significant SNP (MARC0038565) was found to be simultaneous associated with RTN, LTN, MAX and TTN. Two annotated genes (VRTN and SYNDIG1L) were located in genomic region around this SNP. Three significant SNPs were shown to be associated with TTN, RTN and MAX traits. Seven significant SNPs were simultaneously detected in two traits of TTN and RTN. Other two SNPs were only identified in TTN. These 13 SNPs were clustered in the genomic region between 96.10—98.09 Mb on chromosome 7. Moreover, nine significant SNPs were shown to be significantly associated with SLR. In total, four and 22 SNPs surpassed genome-wide significance and suggestive significance levels, respectively. Among candidate genes annotated, eight genes have documented association with the teat number relevant traits. Out of them, DPF3 genes on Sus scrofa chromosome (SSC) 7 and the NRP1 gene on SSC 10 were new candidate genes identified in this study. Our findings demonstrate the genetic mechanism of teat number relevant traits and provide a reference to further improve reproductive performances in practical pig breeding programs.

Goat Genomic Resources: The Search for Genes Associated with Its Economic Traits

Goat plays a crucial role in human livelihoods, being a major source of meat, milk, fiber, and hides, particularly under adverse climatic conditions. The goat genomics related to the candidate gene approach is now being used to recognize molecular mechanisms that have different expressions of growth, reproductive, milk, wool, and disease resistance. The appropriate literature on this topic has been reviewed in this article. Several genetic characterization attempts of different goats have reported the existence of genotypic and morphological variations between different goat populations. As a result, different whole-genome sequences along with annotated gene sequences, gene function, and other genomic information of different goats are available in different databases. The main objective of this review is to search the genes associated with economic traits in goats. More than 271 candidate genes have been discovered in goats. Candidate genes influence the physiological pathway, metabolism, and expression of phenotypes. These genes have different functions on economically important traits. Some genes have pleiotropic effect for expression of phenotypic traits. Hence, recognizing candidate genes and their mutations that cause variations in gene expression and phenotype of an economic trait can help breeders look for genetic markers for specific economic traits. The availability of reference whole-genome assembly of goats, annotated genes, and transcriptomics makes comparative genomics a useful tool for systemic genetic upgradation. Identification and characterization of trait-associated sequence variations and gene will provide powerful means to give positive influences for future goat breeding program.

Identification and Functional Annotation of Genes Related to Horses' Performance: From GWAS to Post-GWAS

Simple Summary

It is assumed that the athletic performance of horses is influenced by a large number of genes; however, to date, not many genomic studies have been performed to identify candidate genes. In this study we performed a systematic review of genome-wide association studies followed by functional analyses aiming to identify the most candidate genes for horse performance. We were successful in identifying 669 candidate genes, from which we built biological process networks. Regulatory elements (transcription factors, TFs) of these genes were identified and used to build a gene–TF network. Genes and TFs presented in this study are suggested to play a role in the studied traits through biological processes related with exercise performance, for example, positive regulation of glucose metabolism, regulation of vascular endothelial growth factor production, skeletal system development, cellular response to fatty acids and cellular response to lipids. In general, this study may provide insights into the genetic architecture underlying horse performance in different breeds around the world.

Abstract

Integration of genomic data with gene network analysis can be a relevant strategy for unraveling genetic mechanisms. It can be used to explore shared biological processes between genes, as well as highlighting transcription factors (TFs) related to phenotypes of interest. Unlike other species, gene–TF network analyses have not yet been well applied to horse traits. We aimed to (1) identify candidate genes associated with horse performance via systematic review, and (2) build biological processes and gene–TF networks from the identified genes aiming to highlight the most candidate genes for horse performance. Our systematic review considered peer-reviewed articles using 20 combinations of keywords. Nine articles were selected and placed into groups for functional analysis via gene networks. A total of 669 candidate genes were identified. From that, gene networks of biological processes from each group were constructed, highlighting processes associated with horse performance (e.g., regulation of systemic arterial blood pressure by vasopressin and regulation of actin polymerization and depolymerization). Transcription factors associated with candidate genes were also identified. Based on their biological processes and evidence from the literature, we identified the main TFs related to horse performance traits, which allowed us to construct a gene–TF network highlighting TFs and the most candidate genes for horse performance.

Genome-wide association analysis reveals the genetic locus for high reproduction trait in Chinese Arbas Cashmere goat

BACKGROUND

Litter size is the most important reproductive trait which plays a crucial role in goat production. Therefore, improvement of litter size trait has been of increasing interest in goat industry as small improvement in litter size may lead to large profit. The recent Cashmere goat breeding program produced a high-reproductive genetic line of Arbas Cashmere goat. But the genetic mechanism of high reproduction rate remains largely unknown in this Chinese native goat breed. To address this question, we performed a genome-wide association studies (GWAS) using two groups of goats varying in fecundity.

OBJECTIVES

Our study was aimed to investigate the significant SNPs and genes associated with high reproduction trait in Inner Mongolia Arbas Cashmere Goat.

METHODS

We used logistic model association to perform GWAS using 47 goats from high fecundity group (~ 190%) and 314 goats from low fecundity group (~ 130%) of the Arbas Cashmere goat breed.

RESULTS

We identified 66 genomic regions associated with genome wide significant level wherein six loci were found to be associated with reproduction traits. Further analysis showed that five key candidate genes including KISS1, KHDRBS2, WNT10B, SETDB2 and PPP3CA genes are involved in goat fecundity trait. Gene ontology enrichment analysis revealed that several biological pathways could be involved in the variation of fecundity in female goats.

CONCLUSIONS

The identified significant SNPs or genes provide useful information about the underlying genetic control of fecundity trait which will be helpful to use them in goat breeding programs for improving the reproductive efficiency of goats.

Polymorphisms in 5' proximal regulating region of THRSP gene are associated with fat production in pigs

Chinese and imported pig breeds differ in fat production potential, which is associated with the polymorphisms in the 5' proximal regulating region (5'PRR) of thyroid hormone responsive gene (THRSP). In three Chinese breeds (Dingyuan, CDY; Wannanhua, CWH; and Jixi, CJX) and one introduced breed (Yorkshire, YKS), three variant sites were located at T/C-400, A/G-376, and G/A-98 in the 5'PRR. Chinese pig breeds had higher C-400 allele frequencies than YKS. The frequencies of A-376 in CDY and G-376 in CWH were about 0.8. G-98 allele frequencies in CWH and YKS were 0.8617 and 0.8149, respectively. TGG was the dominant haplotype in YKS, CGG in CWH and CJX, and CAA in CDY. According to haplotype frequency, four breeds were clustered into three types, which was consistent with the geographical distribution of the breeds. In CDY, the average backfat thickness (BFT) was the highest with the CC-400 genotype, followed by CT-400 and TT-400 genotypes. In YKS, the pigs with CC-400 or CT-400 genotypes had higher BFT and average daily weight gain, whereas those with CC-400 or TT-400 genotypes had larger lion-eye area. No significant difference was observed in carcass traits among different genotypes at the A/G-376 and G/A-98 loci. The mRNA abundance of THRSP expression for the CCAGAG genotype was significantly higher than that for CTAGAG or TTAGAG genotype. These results indicated that the polymorphisms and genotype distribution of THRSP were closely related to the potential for fat production in pig breeds, which were the result of adaptation to artificial selection and natural selection.

Genome-wide association analyses identify known and novel loci for teat number in Duroc pigs using single-locus and multi-locus models

BACKGROUND

More teats are necessary for sows to nurse larger litters to provide immunity and nutrient for piglets prior to weaning. Previous studies have reported the strong effect of an insertion mutation in the Vertebrae Development Associated (VRTN) gene on Sus scrofa chromosome 7 (SSC7) that increased the number of thoracic vertebrae and teat number in pigs. We used genome-wide association studies (GWAS) to map genetic markers and genes associated with teat number in two Duroc pig populations with different genetic backgrounds. A single marker method and several multi-locus methods were utilized. A meta-analysis that combined the effects and P-values of 34,681 single nucleotide polymorphisms (SNPs) that were common in the results of single marker GWAS of American and Canadian Duroc pigs was conducted. We also performed association tests between the VRTN insertion and teat number in the same populations.

RESULTS

A total of 97 SNPs were found to be associated with teat number. Among these, six, eight and seven SNPs were consistently detected with two, three and four multi-locus methods, respectively. Seven SNPs were concordantly identified between single marker and multi-locus methods. Moreover, 26 SNPs were newly found by multi-locus methods to be associated with teat number. Notably, we detected one consistent quantitative trait locus (QTL) on SSC7 for teat number using single-locus and meta-analysis of GWAS and the top SNP (rs692640845) explained 8.68% phenotypic variance of teat number in the Canadian Duroc pigs. The associations between the VRTN insertion and teat number in two Duroc pig populations were substantially weaker. Further analysis revealed that the effect of VRTN on teat number may be mediated by its LD with the true causal mutation.

CONCLUSIONS

Our study suggested that VRTN insertion may not be a strong or the only candidate causal mutation for the QTL on SSC7 for teat number in the analyzed Duroc pig populations. The combination of single-locus and multi-locus GWAS detected additional SNPs that were absent using only one model. The identified SNPs will be useful for the genetic improvement of teat number in pigs by assigning higher weights to associated SNPs in genomic selection.

Genome Wide Assessment of Genetic Variation and Population Distinctiveness of the Pig Family in South Africa

Genetic diversity is of great importance and a prerequisite for genetic improvement and conservation programs in pigs and other livestock populations. The present study provides a genome wide analysis of the genetic variability and population structure of pig populations from different production systems in South Africa relative to global populations. A total of 234 pigs sampled in South Africa and consisting of village (n = 91), commercial (n = 60), indigenous (n = 40), Asian (n = 5) and wild (n = 38) populations were genotyped using Porcine SNP60K BeadChip. In addition, 389 genotypes representing village and commercial pigs from America, Europe, and Asia were accessed from a previous study and used to compare population clustering and relationships of South African pigs with global populations. Moderate heterozygosity levels, ranging from 0.204 for Warthogs to 0.371 for village pigs sampled from Capricorn municipality in Eastern Cape province of South Africa were observed. Principal Component Analysis of the South African pigs resulted in four distinct clusters of (i) Duroc; (ii) Vietnamese; (iii) Bush pig and Warthog and (iv) a cluster with the rest of the commercial (SA Large White and Landrace), village, Wild Boar and indigenous breeds of Koelbroek and Windsnyer. The clustering demonstrated alignment with genetic similarities, geographic location and production systems. The PCA with the global populations also resulted in four clusters that where populated with (i) all the village populations, wild boars, SA indigenous and the large white and landraces; (ii) Durocs (iii) Chinese and Vietnamese pigs and (iv) Warthog and Bush pig. K = 10 (The number of population units) was the most probable ADMIXTURE based clustering, which grouped animals according to their populations with the exception of the village pigs that showed presence of admixture. AMOVA reported 19.92%-98.62% of the genetic variation to be within populations. Sub structuring was observed between South African commercial populations as well as between Indigenous and commercial breeds. Population pairwise F ST analysis showed genetic differentiation (P ≤ 0.05) between the village, commercial and wild populations. A per marker per population pairwise F ST analysis revealed SNPs associated with QTLs for traits such as meat quality, cytoskeletal and muscle development, glucose metabolism processes and growth factors between both domestic populations as well as between wild and domestic breeds. Overall, the study provided a baseline understanding of porcine diversity and an important foundation for porcine genomics of South African populations.

Genomic Scan for Selection Signature Reveals Fat Deposition in Chinese Indigenous Sheep with Extreme Tail Types

Simple Summary

According to the tail types, sheep can be briefly classified into three groups (fat-tailed, fat-rumped, and thin-tailed sheep). In this study, we used these three typical breeds from Chinese indigenous sheep breeds to perform a genome scan for selective sweeps using Ovine Infinium HD SNP BeadChip genotype data. Results showed that 25 genomic regions exhibited selection signals and harbored 73 positional candidate genes. These genes were documented not only to be associated with tail fat formation, but also be related to reproduction, body conformation, and appearance. Our findings contributed to understanding genetic basis of fat deposition in sheep tail and provide a reference for developing new sheep breeds with an ideal tail type.

Abstract

It is a unique feature that fat can be deposited in sheep tails and rumps. To elucidate the genetic mechanism underlying this trait, we collected 120 individuals from three Chinese indigenous sheep breeds with extreme tail types, namely large fat-tailed sheep (n = 40), Altay sheep (n = 40), and Tibetan sheep (n = 40), and genotyped them using the Ovine Infinium HD SNP BeadChip. Then genomic scan for selection signatures was performed using the hapFLK. In total, we identified 25 genomic regions exhibiting evidence of having been under selection. Bioinformatic analysis of the genomic regions showed that selection signatures related to multiple candidate genes had a demonstrated role in phenotypic variation. Nine genes have documented association with sheep tail types, including WDR92, TBX12, WARS2, BMP2, VEGFA, PDGFD, HOXA10, ALX4, and ETAA1. Moreover, a number of genes were of particular interest, including RXFP2 associated with the presence/absence and morphology of horns; MITF involved in coat color; LIN52 and SYNDIG1L related to the number of teats; MSRB3 gene associated with ear sizes; LTBP2 considered as a positional candidate genes for number of ribs; JAZF1 regulating lipid metabolism; PGRMC2, SPAG17, TSHR, GTF2A1, and LARP1B implicated with reproductive traits. Our findings provide insights into fat tail formation and a reference for carrying out molecular breeding and conservation in sheep.

Artificial selection reveals the role of transcriptional constraints in the maintenance of life history variation

The trade-off between reproduction and self-maintenance is a cornerstone of life history theory, yet its proximate underpinnings are elusive. Here, we used an artificial selection approach to create replicated lines of Japanese quail (Coturnix japonica) that differ genetically in their reproductive investment. Whole transcriptome sequencing revealed that females from lines selected for high reproductive output show a consistent upregulation of genes associated with reproduction but a simultaneous downregulation of immune genes. Concordant phenotypic differences in immune function (i.e., specific antibody response against keyhole limpet hemocyanin) were observed between the selection lines, even in males who do not provide parental care. Our findings demonstrate the key role of obligate transcriptional constraints in the maintenance of life history variation. These constraints set fundamental limits to productivity and health in natural and domestic animal populations.

Assembly of hundreds of novel bacterial genomes from the chicken caecum

Background

Chickens are a highly important source of protein for a large proportion of the human population. The caecal microbiota plays a crucial role in chicken nutrition through the production of short-chain fatty acids, nitrogen recycling, and amino acid production. In this study, we sequence DNA from caecal content samples taken from 24 chickens belonging to either a fast or a slower growing breed consuming either a vegetable-only diet or a diet containing fish meal.

Results

We utilise 1.6 T of Illumina data to construct 469 draft metagenome-assembled bacterial genomes, including 460 novel strains, 283 novel species, and 42 novel genera. We compare our genomes to data from 9 European Union countries and show that these genomes are abundant within European chicken flocks. We also compare the abundance of our genomes, and the carbohydrate active enzymes they produce, between our chicken groups and demonstrate that there are both breed- and diet-specific microbiomes, as well as an overlapping core microbiome.

Conclusions

This data will form the basis for future studies examining the composition and function of the chicken caecal microbiota.

Genome-wide association study for backfat thickness at 100 kg and loin muscle thickness in domestic pigs based on genotyping by sequencing

Both backfat thickness at 100 kg (B100) and loin muscle thickness (LMT) are economically important traits in pigs. In this study, a total of 1,200 pigs (600 Landrace and 600 Yorkshire pigs) were examined with genotyping by sequencing. A total of 345,570 single nucleotide polymorphisms (SNPs) were obtained from 1,200 pigs. Then, a single marker regression test was used to conduct a genome-wide association study for B100 and LMT. A total of 8 and 90 significant SNPs were detected for LMT and B100, respectively. Interestingly, two shared significant loci [located at Sus scrofa chromosome (SSC) 6: 149876694 and SSC12: 46226580] were detected in two breeds for B100. Furthermore, three potential candidate genes were found for LMT and B100. The positional candidate gene FAM3C (SSC18: 25573656, P = 2.48 × 10^-9), which controls the survival, growth, and differentiation of tissues and cells, was found for LMT in Landrace pigs. At SSC9: 6.78-6.82 Mb in Landrace pigs, the positional candidate gene, INPPL1, which has a negative regulatory effect on diet-induced obesity and is involved in the regulation of insulin function, was found for B100. The candidate gene, RAB35, which regulates the adipocyte glucose transporter SLC2A4/GLUT4, was identified at approximately SSC14: 40.09-40.13 Mb in Yorkshire pigs. The results of this GWAS will greatly advance our understanding of the genetic architecture of the LMT and B100 traits. However, these identified loci and genes need to be further verified in more pig populations, and their functions also need to be validated by more biological experiments in pigs.

An Epigenome-Wide DNA Methylation Map of Testis in Pigs for Study of Complex Traits

Epigenetic changes are important for understanding complex trait variation and inheritance in pigs that are also a valuable biomedical model for human health research. Testis is the main organ for reproduction and boar taint in pigs; however, there have been no studies to-date on adult pig testis epigenome. The main objective of this study was to establish a genome-wide DNA methylation map of pig testis that would help identify candidate epigenetic biomarkers and methylated genes for complex traits such as male reproduction, fertility or boar taint. Reduced Representation Bisulfite Sequencing (RRBS) was used to study methylation levels of cytosine in nine pig testis samples. The results showed that genome-wide methylation status of nine samples overlapped greatly and their variation among pigs were low. The methylation levels of promoter, exon, intron, cytosine and guanine dinucleotide (CpG) islands and CpG island shores regions were 0.15, 0.47, 0.55, 0.39, and 0.53, respectively. Cytosines binding to CpG islands showed different methylation levels between exon and intron regions. All methylation levels of CpG islands were lower than CpG island shores in different genic features. The distribution of 12,738 differentially methylated cytosines (DMCs) within CpG islands, CpG island shores and other regions was 36.86, 21.65, and 41.49%, respectively, and was 0.33, 1.71, 5.95, and 92.01% in promoter, exon, intron and intergenic regions, respectively. Methylation levels of DMCs in promoter, exon and intron regions were significantly different between CpG islands and CpG island shores (P < 0.05). A total of 898 genes with 2089 DMCs were enriched in 112 Gene Ontology (GO) terms. Fifteen methylated genes from our study were associated with fertility or boar taint traits. Our analysis revealed the methylation patterns in different genic features and CpG island regions of testis in pigs, and summarized several candidate genes associated with DMCs and the involved GO terms. These findings are helpful to understand the relationship between DNA methylation and genic CpG islands, to provide candidate epigenetic regions or biomarkers for pig production and welfare and for translational epigenomic studies that use pigs as an animal model for human research.

A QTL for Number of Teats Shows Breed Specific Effects on Number of Vertebrae in Pigs: Bridging the Gap Between Molecular and Quantitative Genetics

Modern breeding schemes for livestock species accumulate a large amount of genotype and phenotype data which can be used for genome-wide association studies (GWAS). Many chromosomal regions harboring effects on quantitative traits have been reported from these studies, but the underlying causative mutations remain mostly undetected. In this study, we combine large genotype and phenotype data available from a commercial pig breeding scheme for three different breeds (Duroc, Landrace, and Large White) to pinpoint functional variation for a region on porcine chromosome 7 affecting number of teats (NTE). Our results show that refining trait definition by counting number of vertebrae (NVE) and ribs (RIB) helps to reduce noise from other genetic variation and increases heritability from 0.28 up to 0.62 NVE and 0.78 RIB in Duroc. However, in Landrace, the effect of the same QTL on NTE mainly affects NVE and not RIB, which is reflected in reduced heritability for RIB (0.24) compared to NVE (0.59). Further, differences in allele frequencies and accuracy of rib counting influence genetic parameters. Correction for the top SNP does not detect any other QTL effect on NTE, NVE, or RIB in Landrace or Duroc. At the molecular level, haplotypes derived from 660K SNP data detects a core haplotype of seven SNPs in Duroc. Sequence analysis of 16 Duroc animals shows that two functional mutations of the Vertnin (VRTN) gene known to increase number of thoracic vertebrae (ribs) reside on this haplotype. In Landrace, the linkage disequilibrium (LD) extends over a region of more than 3 Mb also containing both VRTN mutations. Here, other modifying loci are expected to cause the breed-specific effect. Additional variants found on the wildtype haplotype surrounding the VRTN region in all sequenced Landrace animals point toward breed specific differences which are expected to be present also across the whole genome. This Landrace specific haplotype contains two missense mutations in the ABCD4 gene, one of which is expected to have a negative effect on the protein function. Together, the integration of largescale genotype, phenotype and sequence data shows exemplarily how population parameters are influenced by underlying variation at the molecular level.

Whole-genome sequencing identifies potential candidate genes for reproductive traits in pigs

Reproductive performance is a complex quantitative trait, that is determined by multiple genes, regulatory pathways and environmental factors. A list of major genes with large effect have been detected, although multiple QTLs are identified. To identify candidate genes for pig prolificacy, whole genome variants from five high- and five low-prolificacy Yorkshire sows were collected using whole-genome resequencing. A total of 13,955,609 SNPs and 2,666,366 indels were detected across the genome. Common differential SNPs and indels were identified between the two groups of sows. Genes encoding components of the TGF-beta signaling pathway were enriched with the variations, including BMP5, BMP6, BMP7, ACVR1, INHBA, ZFYVE9, TGFBR2, DCN, ID4, BAMBI, and ACVR2A. Several differential variants within these genes related to reproductive traits were identified to be associated with litter size. A comparison of selective regions and published QTL data suggests that NEDD9, SLC39A11, SNCA, and UNC5D are candidate genes for reproduction traits.

A genome-wide detection of selection signatures in conserved and commercial pig breeds maintained in Poland

BACKGROUND

Identification of selection signatures can provide a direct insight into the mechanism of artificial selection and allow further disclosure of the candidate genes related to the animals' phenotypic variation. Domestication and subsequent long-time selection have resulted in extensive phenotypic changes in domestic pigs, involving a number of traits, like behavior, body composition, disease resistance, reproduction and coat color. In this study, based on genotypes obtained from PorcineSNP60 Illumina assay we attempt to detect both diversifying and within-breed selection signatures in 530 pigs belonging to four breeds: Polish Landrace, Puławska, Złotnicka White and Złotnicka Spotted, of which the last three are a subject of conservative breeding and substantially represent the native populations.

RESULTS

A two largely complementary statistical methods were used for signatures detection, including: pairwise F_ST and relative extended haplotype homozygosity (REHH) test. Breed-specific diversifying selection signals included several genes involved in processes connected with fertility, growth and metabolism which are potentially responsible for different phenotypes of the studied breeds. The diversifying selection signals also comprised PPARD gene that was previously found to have a large effect on the shape of the external ear in pigs or two genes encoding neuropeptide Y receptors (Y2 and Y5) involved in fat deposition and stress response which are important features differentiating the studied breeds. REHH statistics allowed detecting several within-breed selection signatures overlapping with genes connected with a range of functions including, among others: metabolic pathways, immune system response or implantation and development of the embryo.

CONCLUSIONS

The study provides many potential candidate genes with implication for traits selected in the individual breeds and gives strong basis for further studies aiming at identification of sources of variation among the studied pig breeds.

Genome-wide association studies for tick resistance in Bos taurus × Bos indicus crossbred cattle: A deeper look into this intricate mechanism

Rhipicephalus (Boophilus) microplus is the main cattle ectoparasite in tropical areas. Gir × Holstein crossbred cows are well adapted to different production systems in Brazil. In this context, we performed genome-wide association study (GWAS) and post-GWAS analyses for R. microplus resistance in an experimental Gir × Holstein F₂ population. Single nucleotide polymorphisms (SNP) identified in GWAS were used to build gene networks and to investigate the breed of origin for its alleles. Tick artificial infestations were performed during the dry and rainy seasons. Illumina BovineSNP50 BeadChip (Illumina Inc., San Diego, CA) and single-step BLUP procedure was used for GWAS. Post-GWAS analyses were performed by gene ontology terms enrichment and gene transcription factors networks, generated from enriched transcription factors, identified from the promoter sequences of selected gene sets. The genetic origin of marker alleles in the F₂ population was assigned using the breed of origin of alleles approach. Heritability estimates for tick counts were 0.40 ± 0.11 in the rainy season and 0.54 ± 0.11 in the dry season. The top ten 0.5-Mbp windows with the highest percentage of genetic variance explained by SNP markers were found in chromosomes 10 and 23 for both the dry and rainy seasons. Gene network analyses allowed the identification of genes involved with biological processes relevant to immune system functions (TREM1, TREM2, and CD83). Gene-transcription factors network allowed the identification of genes involved with immune functions (MYO5A, TREML1, and PRSS16). In resistant animals, the average proportion of animals showing significant SNPs with paternal and maternal alleles originated from Gir breed was 44.8% whereas the proportion of animals with both paternal and maternal alleles originated from Holstein breed was 11.3%. Susceptible animals showing both paternal and maternal alleles originated from Holstein breed represented 44.6% on average, whereas both paternal and maternal alleles originated from Gir breed animals represented 9.3%. This study allowed us to identify candidate genes for tick resistance in Gir × Holstein crossbreds in both rainy and dry seasons. According to the origin of alleles analysis, we found that most animals classified as resistant showed 2 alleles from Gir breed, while the susceptible ones showed alleles from Holstein. Based on these results, the identified genes may be thoroughly investigated in additional experiments aiming to validate their effects on tick resistance phenotype in cattle.

Whole-genome sequencing reveals selection signatures associated with important traits in six goat breeds

Comparative population genomics analysis is an effective approach to identify selection signatures in farm animals. In this study, we systematically investigated the selection signatures in six phenotypically diverse goat breeds using SNPs obtained from pooled whole-genome resequencing data. More than 95.5% of 446–642 million clean reads were mapped to the latest reference goat genome, which generated a sequencing depth ranging from 22.30 to 31.75-fold for each breed. A total of 5,802,307, 6,794,020, 7,562,312, 5,325,119, 8,764,136, and 9,488,057 putative SNPs were detected in Boer, Meigu, Jintang Black, Nanjiang Yellow, Tibetan, and Tibetan cashmere goats, respectively. Based on the genome-wide F_ST and expected heterozygosity scores along 100-kb sliding windows, 68, 89, 44, 44, 19, and 35 outlier windows were deemed as the selection signatures in the six goat breeds. After genome annotation, several genes within the selection signals were found to be possibly associated with important traits in goats, such as coat color (IRF4, EXOC2, RALY, EIF2S2, and KITLG), high-altitude adaptation (EPAS1), growth (LDB2), and reproduction traits (KHDRBS2). In summary, we provide an improved understanding of the genetic diversity and the genomic footprints under positive selection or the adaptations to the local environments in the domestic goat genome.

Genome-wide association study for reproductive traits in a Large White pig population

Using the PorcineSNP80 BeadChip, we performed a genome‐wide association study for seven reproductive traits, including total number born, number born alive, litter birth weight, average birth weight, gestation length, age at first service and age at first farrowing, in a population of 1207 Large White pigs. In total, we detected 12 genome‐wide significant and 41 suggestive significant SNPs associated with six reproductive traits. The proportion of phenotypic variance explained by all significant SNPs for each trait ranged from 4.46% (number born alive) to 11.49% (gestation length). Among them, 29 significant SNPs were located within known QTL regions for swine reproductive traits, such as corpus luteum number, stillborn number and litter size, of which one QTL region associated with litter size contained the ALGA0098819 SNP for total number born. Subsequently, we found that 376 functional genes contained or were near these significant SNPs. Of these, 14 genes—BHLHA15, OCM2, IL1B2, GCK, SMAD2, HABP2, PAQR5, GRB10, PRELID2, DMKN, GPI, GPIHBP1, ADCY2 and ACVR2B—were considered important candidates for swine reproductive traits based on their critical roles in embryonic development, energy metabolism and growth development. Our findings contribute to the understanding of the genetic mechanisms for reproductive traits and could have a positive effect on pig breeding programs.

Multiple-trait genomewide mapping and gene network analysis for scrotal circumference growth curves in Brahman cattle

Fertility traits are economically important in cattle breeding programs. Scrotal circumference (SC) measures are repeatable, easily obtained, highly heritable, and positively correlated with female fertility traits and sperm quality traits in males. A useful approach to summarize SC measures over time is using nonlinear models, which summarize specific measures of SC in a few parameters with biological interpretation. This approach facilitates the selection of bulls with larger SC and maturity index (K), that is, early maturing animals. Because SC is a sex-limited trait, identifying the underlying genomics of growth curve parameters will allow selection across both males and females. We reported the first multitrait genomewide association study (GWAS) of estimated growth curve parameters for SC data in Brahman cattle. Five widely used nonlinear models were tested to fit a total of 3,612 SC records, measured at 6, 12, 18, and 24 mo of age. The von Bertalanffy model, individually fitted for each animal, best fit this SC data. Parameter estimates SC at maturity (A) and K as well as SC at all ages were jointly analyzed in a GWAS to identify 1-Mb regions most strongly associated with each trait. Heritabilities were 0.25 for K and 0.32 for A and ranged from 0.51 to 0.72 for SC at 6 (SC6), 12 (SC12), 18 (SC18), and 24 mo of age (SC24). An overlapping window on chromosome 14 explaining around 0.8% of genetic variance for K, SC12, SC18, and SC24 was observed. The major positional candidate genes within 1 Mb upstream and downstream of this overlapping window were , , , and . Windows of 1 Mb explaining more than 0.4% of each trait on chromosomes 1, 3, 6, 7, 14, 17, 18, 24, 25, and 26 were identified. Pathways and net-work analyses were indicated through transcription factors playing a role on fertility traits: , , , , , , and . Further validation studies on larger populations or other breeds are required to validate these findings and to improve our understanding of the biology and complex genetic architecture of traits associated with scrotal growth and male fertility in cattle.

A systematic survey to identify lethal recessive variation in highly managed pig populations

BACKGROUND

Lethal recessive variation can cause prenatal death of homozygous offspring. Although usually present at low-frequency in populations, the impact on individual fitness can be substantial. Until recently, the presence of recessive embryonic lethal variation could only be measured indirectly through reduced fertility. In this study, we estimate the presence of genetic loci associated with both early and late termination of development during gestation in pigs from the wealth of genome data routinely generated by a commercial breeding company.

RESULTS

We examined three commercial pig (Sus scrofa) populations for potentially deleterious genetic variation based on 80 K SNP-chip genotypes, and estimate the effects on reproductive traits. 24,000 pigs from three populations were analyzed for missing or depletion of homozygous haplotypes. We identified 145 haplotypes (ranging from 0.5-4 Mb in size) in the genome with complete absence or depletion of homozygous animals. Thirty-five haplotypes show a negative effect on at least one of the analysed reproductive traits (total number born, number of stillborn, and number of mummified piglets). One variant in particular appeared to result in relative late termination of development of fetuses, responsible for a significant fraction of observed stillborn piglets ('mummies'), as they die mid-gestation. Moreover, we identified the BMPER gene as a likely candidate underlying this phenomenon.

CONCLUSIONS

Our study shows that although lethal recessive variation is present, the frequency of these alleles is invariably low in these highly managed populations. Nevertheless, due to cumulative effects of deleterious variants, large numbers of affected offspring are produced. Furthermore, our study demonstrates the use of a large-scale commercial genetic experiment to systematically screen for 'natural knockouts' that can increase understanding of gene function.

Whole-genome association and genome partitioning revealed variants and explained heritability for total number of teats in a Yorkshire pig population

Objective

The study was designed to perform a genome-wide association (GWA) and partitioning of genome using Illumina’s PorcineSNP60 Beadchip in order to identify variants and determine the explained heritability for the total number of teats in Yorkshire pig.

Methods

After screening with the following criteria: minor allele frequency, MAF≤0.01; Hardy-Weinberg equilibrium, HWE≤0.000001, a pair-wise genomic relationship matrix was produced using 42,953 single nucleotide polymorphisms (SNPs). A genome-wide mixed linear model-based association analysis (MLMA) was conducted. And for estimating the explained heritability with genome- or chromosome-wide SNPs the genetic relatedness estimation through maximum likelihood approach was used in our study.

Results

The MLMA analysis and false discovery rate p-values identified three significant SNPs on two different chromosomes (rs81476910 and rs81405825 on SSC8; rs81332615 on SSC13) for total number of teats. Besides, we estimated that 30% of variance could be explained by all of the common SNPs on the autosomal chromosomes for the trait. The maximum amount of heritability obtained by partitioning the genome were 0.22±0.05, 0.16±0.05, 0.10±0.03 and 0.08±0.03 on SSC7, SSC13, SSC1, and SSC8, respectively. Of them, SSC7 explained the amount of estimated heritability along with a SNP (rs80805264) identified by genome-wide association studies at the empirical p value significance level of 2.35E-05 in our study. Interestingly, rs80805264 was found in a nearby quantitative trait loci (QTL) on SSC7 for the teat number trait as identified in a recent study. Moreover, all other significant SNPs were found within and/or close to some QTLs related to ovary weight, total number of born alive and age at puberty in pigs.

Conclusion

The SNPs we identified unquestionably represent some of the important QTL regions as well as genes of interest in the genome for various physiological functions responsible for reproduction in pigs.

Gene networks for total number born in pigs across divergent environments

For reproductive traits such as total number born (TNB), variance due to different environments is highly relevant in animal breeding. In this study, we aimed to perform a gene-network analysis for TNB in pigs across different environments using genomic reaction norm models. Thus, based on relevant single-nucleotide polymorphisms and linkage disequilibrium blocks across environments obtained from GWAS, different sets of candidate genes having biological roles linked to TNB were identified. Network analysis across environment levels resulted in gene interactions consistent with known mammal's fertility biology, captured relevant transcription factors for TNB biology and pointing out different sets of candidate genes for TNB in different environments. These findings may have important implication for animal production, as optimal breeding may vary depending on later environments. Based on these results, genomic diversity was identified and inferred across environments highlighting differential genetic control in each scenario.

Using markers with large effect in genetic and genomic predictions

The first attempts of applying marker-assisted selection (MAS) in animal breeding were not very successful because the identification of markers closely linked to QTL using low-density microsatellite panels was difficult. More recently, the use of high-density SNP panels in genome-wide association studies (GWAS) have increased the power and precision of identifying markers linked to QTL, which offer new possibilities for MAS. However, when GWAS started to be performed, the focus of many breeders had already shifted from the use of MAS to the application of genomic selection (using all available markers without any preselection of markers linked to QTL). In this study, we aimed to evaluate the prediction accuracy of a MAS approach that accounts for GWAS findings in the prediction models by including the most significant SNP from GWAS as a fixed effect in the marker-assisted BLUP (MA-BLUP) and marker-assisted genomic BLUP (MA-GBLUP) prediction models. A second aim was to compare the prediction accuracies from the marker-assisted models with those obtained from a Bayesian variable selection (BVS) model. To compare the prediction accuracies of traditional BLUP, MA-BLUP, genomic BLUP (GBLUP), MA-GBLUP, and BVS, we applied these models to the trait "number of teats" in 4 distinct pig populations, for validation of the results. The most significant SNP in each population was located at approximately 103.50 Mb on chromosome 7. Applying MAS by accounting for the most significant SNP in the prediction models resulted in improved prediction accuracy for number of teats in all evaluated populations compared with BLUP and GBLUP. Using MA-BLUP instead of BLUP, the increase in prediction accuracy ranged from 0.021 to 0.124, whereas using MA-GBLUP instead of GBLUP, the increase in prediction accuracy ranged from 0.003 to 0.043. The BVS model resulted in similar or higher prediction accuracies than MA-GBLUP. For the trait number of teats, BLUP resulted in the lowest prediction accuracies whereas the highest were observed when applying MA-GBLUP or BVS. In the same data set, MA-BLUP can yield similar or superior accuracies compared with GBLUP. The superiority of MA-GBLUP over traditional GBLUP is more pronounced when training populations are smaller and when relationships between training and validation populations are smaller. Marker-assisted GBLUP did not outperform BVS but does have implementation advantages in large-scale evaluations.

Genome-wide association study and accuracy of genomic prediction for teat number in Duroc pigs using genotyping-by-sequencing

Background

The number of teats in pigs is related to a sow’s ability to rear piglets to weaning age. Several studies have identified genes and genomic regions that affect teat number in swine but few common results were reported. The objective of this study was to identify genetic factors that affect teat number in pigs, evaluate the accuracy of genomic prediction, and evaluate the contribution of significant genes and genomic regions to genomic broad-sense heritability and prediction accuracy using 41,108 autosomal single nucleotide polymorphisms (SNPs) from genotyping-by-sequencing on 2936 Duroc boars.

Results

Narrow-sense heritability and dominance heritability of teat number estimated by genomic restricted maximum likelihood were 0.365 ± 0.030 and 0.035 ± 0.019, respectively. The accuracy of genomic predictions, calculated as the average correlation between the genomic best linear unbiased prediction and phenotype in a tenfold validation study, was 0.437 ± 0.064 for the model with additive and dominance effects and 0.435 ± 0.064 for the model with additive effects only. Genome-wide association studies (GWAS) using three methods of analysis identified 85 significant SNP effects for teat number on chromosomes 1, 6, 7, 10, 11, 12 and 14. The region between 102.9 and 106.0 Mb on chromosome 7, which was reported in several studies, had the most significant SNP effects in or near the PTGR2, FAM161B, LIN52, VRTN, FCF1, AREL1 and LRRC74A genes. This region accounted for 10.0% of the genomic additive heritability and 8.0% of the accuracy of prediction. The second most significant chromosome region not reported by previous GWAS was the region between 77.7 and 79.7 Mb on chromosome 11, where SNPs in the FGF14 gene had the most significant effect and accounted for 5.1% of the genomic additive heritability and 5.2% of the accuracy of prediction. The 85 significant SNPs accounted for 28.5 to 28.8% of the genomic additive heritability and 35.8 to 36.8% of the accuracy of prediction.

Conclusions

The three methods used for the GWAS identified 85 significant SNPs with additive effects on teat number, including SNPs in a previously reported chromosomal region and SNPs in novel chromosomal regions. Most significant SNPs with larger estimated effects also had larger contributions to the total genomic heritability and accuracy of prediction than other SNPs.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-017-0311-8) contains supplementary material, which is available to authorized users.

Whole-genome association analysis of pork meat pH revealed three significant regions and several potential genes in Finnish Yorkshire pigs

Background

One of the most commonly used quality measurements of pork is pH measured 24 h after slaughter. The most probable mode of inheritance for this trait is oligogenic with several known major genes, such as PRKAG3. In this study, we used whole-genome SNP genotypes of over 700 AI boars; after a quality check, 42,385 SNPs remained for association analysis. All the boars were purebred Finnish Yorkshire. To account for relatedness of the animals, a pedigree-based relationship matrix was used in a mixed linear model to test the effect of SNPs on pH measured from loin. A bioinformatics analysis was performed to identify the most promising genes in the significant regions related to meat quality.

Results

Genome-wide association study (GWAS) revealed three significant chromosomal regions: one on chromosome 3 (39.9 Mb–40.1 Mb) and two on chromosome 15 (58.5 Mb–60.5 Mb and 132 Mb–135 Mb including PRKAG3). A conditional analysis with a significant SNP in the PRKAG3 region, MARC0083357, as a covariate in the model retained the significant SNPs on chromosome 3. Even though linkage disequilibrium was relatively high over a long distance between MARC0083357 and other significant SNPs on chromosome 15, some SNPs retained their significance in the conditional analysis, even in the vicinity of PRKAG3. The significant regions harbored several genes, including two genes involved in cyclic AMP (cAMP) signaling: ADCY9 and CREBBP. Based on functional and transcription factor-gene networks, the most promising candidate genes for meat pH are ADCY9, CREBBP, TRAP1, NRG1, PRKAG3, VIL1, TNS1, and IGFBP5, and the key transcription factors related to these genes are HNF4A, PPARG, and Nkx2-5.

Conclusions

Based on SNP association, pathway, and transcription factor analysis, we were able to identify several genes with potential to control muscle cell homeostasis and meat quality. The associated SNPs can be used in selection for better pork. We also showed that post-GWAS analysis reveals important information about the genes’ potential role on meat quality. The gained information can be used in later functional studies.

Genome-wide association study for conformation traits in three Danish pig breeds

Background

Selection for sound conformation has been widely used as a primary approach to reduce lameness and leg weakness in pigs. Identification of genomic regions that affect conformation traits would help to improve selection accuracy for these lowly to moderately heritable traits. Our objective was to identify genetic factors that underlie leg and back conformation traits in three Danish pig breeds by performing a genome-wide association study followed by meta-analyses.

Methods

Data on four conformation traits (front leg, back, hind leg and overall conformation) for three Danish pig breeds (23,898 Landrace, 24,130 Yorkshire and 16,524 Duroc pigs) were used for association analyses. Estimated effects of single nucleotide polymorphisms (SNPs) from single-trait association analyses were combined in two meta-analyses: (1) a within-breed meta-analysis for multiple traits to examine if there are pleiotropic genetic variants within a breed; and (2) an across-breed meta-analysis for a single trait to examine if the same quantitative trait loci (QTL) segregate across breeds. SNP annotation was implemented through Sus scrofa Build 10.2 on Ensembl to search for candidate genes.

Results

Among the 14, 12 and 13 QTL that were detected in the single-trait association analyses for the three breeds, the most significant SNPs explained 2, 2.3 and 11.4% of genetic variance for back quality in Landrace, overall conformation in Yorkshire and back quality in Duroc, respectively. Several candidate genes for these QTL were also identified, i.e. LRPPRC, WRAP73, VRTN and PPARD likely control conformation traits through the regulation of bone and muscle development, and IGF2BP2, GH1, CCND2 and MSH2 can have an influence through growth-related processes. Meta-analyses not only confirmed many significant SNPs from single-trait analyses with higher significance levels, but also detected several additional associated SNPs and suggested QTL with possible pleiotropic effects.

Conclusions

Our results imply that conformation traits are complex and may be partly controlled by genes that are involved in bone and skeleton development, muscle and fat metabolism, and growth processes. A reliable list of QTL and candidate genes was provided that can be used in fine-mapping and marker assisted selection to improve conformation traits in pigs.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-017-0289-2) contains supplementary material, which is available to authorized users.

Genetic analysis of teat number in pigs reveals some developmental pathways independent of vertebra number and several loci which only affect a specific side

Background

Number of functional teats is an important trait in commercial swine production. As litter size increases, the number of teats must also increase to supply nutrition to all piglets. Therefore, a genome-wide association analysis was conducted to identify genomic regions that affect this trait in a commercial swine population. Genotypic data from the Illumina Porcine SNP60v1 BeadChip were available for 2951 animals with total teat number (TTN) records. A subset of these animals (n = 1828) had number of teats on each side recorded. From this information, the following traits were derived: number of teats on the left (LTN) and right side (RTN), maximum number of teats on a side (MAX), difference between LTN and RTN (L − R) and absolute value of L − R (DIF). Bayes C option of GENSEL (version 4.61) and 1-Mb windows were implemented. Identified regions that explained more than 1.5% of the genomic variation were tested in a larger group of animals (n = 5453) to estimate additive genetic effects.

Results

Marker heritabilities were highest for TTN (0.233), intermediate for individual side counts (0.088 to 0.115) and virtually nil for difference traits (0.002 for L − R and 0.006 for DIF). Each copy of the VRTN mutant allele increased teat count by 0.35 (TTN), 0.16 (LTN and RTN) and 0.19 (MAX). 15, 18, 13 and 18 one-Mb windows were detected that explained more than 1.0% of the genomic variation for TTN, LTN, RTN, and MAX, respectively. These regions cumulatively accounted for over 50% of the genomic variation of LTN, RTN and MAX, but only 30% of that of TTN. Sus scrofa chromosome SSC10:52 Mb was associated with all four count traits, while SSC10:60 and SSC14:54 Mb were associated with three count traits. Thirty-three SNPs accounted for nearly 39% of the additive genetic variation in the validation dataset. No effect of piglet sex or percentage of males in litter was detected, but birth weight was positively correlated with TTN.

Conclusions

Teat number is a heritable trait and use of genetic markers would expedite selection progress. Exploiting genetic variation associated with teat counts on each side would enhance selection focused on total teat counts. These results confirm QTL on SSC4, seven and ten and identify a novel QTL on SSC14.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-016-0282-1) contains supplementary material, which is available to authorized users.