Genome-wide association analysis reveals genetic loci and candidate genes for feeding behavior and eating efficiency in Duroc boars

Ascertaining the genetic background of the Celtic-Iberian pig strain: A signatures of selection approach

Celtic-Iberian pig breeds were majority in Spain and Portugal until the first half of the 20th century. In the 1990s, they were nearly extinct as a result of the introduction of foreign improved pig breeds. Despite its historical importance, the genetic background of the Celtic-Iberian pig strain is poorly documented. In this study, we have identified genomic regions that might contain signatures of selection peculiar of the Celtic-Iberian genetic lineage. A total of 153 DNA samples of Celtic-Iberian pigs (Spanish Gochu Asturcelta and Portuguese Bísara breeds), Iberian pigs (Spanish Iberian and Portuguese Alentejano breeds), Cinta Senese pig, Korean local pig and Cosmopolitan pig (Hampshire, Landrace and Large White individuals) were analysed. A pairwise-comparison approach was applied: the Gochu Asturcelta and the Bísara samples as test populations and the five other pig populations as reference populations. Three different statistics (XP-EHH, FST and ΔDAF) were computed on each comparison. Strict criteria were used to identify selection sweeps in order to reduce the noise brought on by the Gochu Asturcelta and Bísara breeds' severe population bottlenecks. Within test population, SNPs used to construct potential candidate genomic areas under selection were only considered if they were identified in four of ten two-by-two pairwise comparisons and in at least two of three statistics. Genomic regions under selection constructed within test population were subsequently overlapped to construct candidate regions under selection putatively unique to the Celtic-Iberian pig strain. These genomic regions were finally used for enrichment analyses. A total of 39 candidate regions, mainly located on SSC5 and SSC9 and covering 3130.5 kb, were identified and could be considered representative of the ancient genomic background of the Celtic-Iberian strain. Enrichment analysis allowed to identify a total of seven candidate genes (NOL12, LGALS1, PDXP, SH3BP1, GGA1, WIF1, and LYPD6). Other studies reported that the WIF1 gene is associated with ear size, one of the characteristic traits of the Celtic-Iberian pig strain. The function of the other candidate genes could be related to reproduction, adaptation and immunity traits, indirectly fitting with the rusticity of a non-improved pig strain traditionally exploited under semi-extensive conditions.

Genome-Wide Association Study for Somatic Skeletal Traits in Duroc × (Landrace × Yorkshire) Pigs

The pig bone weight trait holds significant economic importance in southern China. To expedite the selection of the pig bone weight trait in pig breeding, we conducted molecular genetic research on these specific traits. These traits encompass the bone weight of the scapula (SW), front leg bone weight (including humerus and ulna) (FLBW), hind leg bone weight (including femur and tibia) (HLBW), and spine bone weight (SBW). Up until now, the genetic structure related to these traits has not been thoroughly explored, primarily due to challenges associated with obtaining the phenotype data. In this study, we utilized genome-wide association studies (GWAS) to discern single nucleotide polymorphisms (SNPs) and genes associated with four bone weight traits within a population comprising 571 Duroc × (Landrace × Yorkshire) hybrid pigs (DLY). In the analyses, we employed a mixed linear model, and for the correction of multiple tests, both the false discovery rate and Bonferroni methods were utilized. Following functional annotation, candidate genes were identified based on their proximity to the candidate sites and their association with the bone weight traits. This study represents the inaugural application of GWAS for the identification of SNPs associated with individual bone weight in DLY pigs. Our analysis unveiled 26 SNPs and identified 12 promising candidate genes (OPRM1, SLC44A5, WASHC4, NOPCHAP1, RHOT1, GLP1R, TGFB3, PLCB1, TLR4, KCNJ2, ABCA6, and ABCA9) associated with the four bone weight traits. Furthermore, our findings on the genetic mechanisms influencing pig bone weight offer valuable insights as a reference for the genetic enhancement of pig bone traits.

Integrated Single-Trait and Multi-Trait GWASs Reveal the Genetic Architecture of Internal Organ Weight in Pigs

Internal organ weight is an essential indicator of growth status as it reflects the level of growth and development in pigs. However, the associated genetic architecture has not been well explored because phenotypes are difficult to obtain. Herein, we performed single-trait and multi-trait genome-wide association studies (GWASs) to map the genetic markers and genes associated with six internal organ weight traits (including heart weight, liver weight, spleen weight, lung weight, kidney weight, and stomach weight) in 1518 three-way crossbred commercial pigs. In summation, single-trait GWASs identified a total of 24 significant single- nucleotide polymorphisms (SNPs) and 5 promising candidate genes, namely, TPK1, POU6F2, PBX3, UNC5C, and BMPR1B, as being associated with the six internal organ weight traits analyzed. Multi-trait GWAS identified four SNPs with polymorphisms localized on the APK1, ANO6, and UNC5C genes and improved the statistical efficacy of single-trait GWASs. Furthermore, our study was the first to use GWASs to identify SNPs associated with stomach weight in pigs. In conclusion, our exploration of the genetic architecture of internal organ weights helps us better understand growth traits, and the key SNPs identified could play a potential role in animal breeding programs.

Genome-wide association study to identify SNPs and candidate genes associated with body size traits in donkeys

The Yangyuan donkey is a domestic animal breed mainly distributed in the northwest region of Hebei Province. Donkey body shape is the most direct production index, can fully reflect the donkey's growth status, and is closely related to important economic traits. As one of the main breeding selection criteria, body size traits have been widely used to monitor animal growth and evaluate the selection response. Molecular markers genetically linked to body size traits have the potential to accelerate the breeding process of animals via marker-assisted selection. However, the molecular markers of body size in Yangyuan donkeys have yet to be explored. In this study, we performed a genome-wide association study to identify the genomic variations associated with body size traits in a population of 120 Yangyuan donkeys. We screened 16 single nucleotide polymorphisms that were significantly associated with body size traits. Some genes distributed around these significant SNPs were considered candidates for body size traits, including SMPD4, RPS6KA6, LPAR4, GLP2R, BRWD3, MAGT1, ZDHHC15, and CYSLTR1. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses indicated that these genes were mainly involved in the P13K-Akt signaling pathway, Rap1 signaling pathway, regulation of actin cytoskeleton, calcium signaling pathway, phospholipase D signaling pathway, and neuroactive ligand-receptor interactions. Collectively, our study reported on a list of novel markers and candidate genes associated with body size traits in donkeys, providing useful information for functional gene studies and offering great potential for accelerating Yangyuan donkey breeding.

Application of Genetic, Genomic and Biological Pathways in Improvement of Swine Feed Efficiency

Despite the significant improvement of feed efficiency (FE) in pigs over the past decades, feed costs remain a major challenge for producers profitability. Improving FE is a top priority for the global swine industry. A deeper understanding of the biology underlying FE is crucial for making progress in genetic improvement of FE traits. This review comprehensively discusses the topics related to the FE in pigs including: measurements, genetics, genomics, biological pathways and the advanced technologies and methods involved in FE improvement. We first provide an update of heritability for different FE indicators and then characterize the correlations of FE traits with other economically important traits. Moreover, we present the quantitative trait loci (QTL) and possible candidate genes associated with FE in pigs and outline the most important biological pathways related to the FE traits in pigs. Finally, we present possible ways to improve FE in swine including the implementation of genomic selection, new technologies for measuring the FE traits, and the potential use of genome editing and omics technologies.

Genome-wide association studies identified loci associated with both feed conversion ratio and residual feed intake in Yorkshire pigs

Feed occupies a significant proportion in the production cost of pigs, and the feed efficiency (FE) in pigs are of utmost economic importance. Hence, the objective of this study is to identify single nucleotide polymorphisms (SNPs) and candidate genes associated with FE related traits, including feed conversion ratio (FCR) and residual feed intake (RFI). A genome-wide association study (GWAS) was conducted for FCR and RFI in 169 Yorkshire pigs using whole-genome sequencing data. A total of 23 and 33 suggestive significant SNPs (P<1×10^(-6)) were detected for FCR and RFI, respectively. However, none of the SNPs achieved the genome-wide significance threshold (P<5×10^(-8)). Importantly, three common SNPs (SSC7:7987268, SSC13:42350250, and SSC13:42551718) were associated with both FCR and RFI. Additionally, the NEDD9 gene related to FCR and RFI traits was overlapped. This study detected novel SNPs on SSC7 and SSC13 common for FCR and RFI. These results provide new insights into the genetic mechanisms and candidate genes of FE-related traits in pigs.

Genome-wide association studies reveals polygenic genetic architecture of litter traits in Duroc pigs

With continuous improvement of sow litter size, breeders are gradually paying more attention to the quality of litter traits that directly impact the production efficiency of pig companies, such as the rate of piglets born alive (RBA) and the rate of healthy births (RHB). The objectives of this study are to dissect the genetic basis of litter traits in pig and to identify valuable genes and genetic markers, especially pleiotropic, for pig breeding. Herein, 1140 Duroc pigs and 2046 reproduction records, 5 litter traits, including the number of healthy births (NHB), number of deformed fetuses (NDF), number of stillborn (NSB), RBA, and RHB, were used in this study. Subsequently, a genome-wide association study (GWAS) was performed for the five litter traits in the first two parities from two Duroc populations. A total of 76 significantly related SNPs and 10 potential candidate genes (CAV1, DAB2, FGF12, FHOD3, DYNC2H1, GRHL1, TCTN3, PYROXD2, MMP8, MMP13, and PGR) were detected, including 13 pleiotropic SNPs that affected more than one litter trait. Finally, the functional enrichment analysis of functional genes that were closest to these significant SNPs indicated that most of the significant pathways were associated with hormone secretion and embryo and organ development. This study advances our understanding of the genetic mechanisms of litter traits, especially the survival rate of piglets born, and provides an opportunity to increase the quality of litter using marker-assisted selection or genomic selection in pigs.

Accurate prediction and genome-wide association analysis of digital intramuscular fat content in longissimus muscle of pigs

Intramuscular fat (IMF) content is a critical indicator of pork quality that affects directly the purchasing desire of consumers. However, to measure IMF content is both laborious and costly, preventing our understanding of its genetic determinants and improvement. In the present study, we constructed an accurate and fast image acquisition and analysis system, to extract and calculate the digital IMF content, the proportion of fat areas in the image (PFAI) of the longissimus muscle of 1709 animals from multiple pig populations. PFAI was highly significantly correlated with marbling scores (MS; 0.95, r²  = 0.90), and also with IMF contents chemically defined for 80 samples (0.79, r²  = 0.63; more accurate than direct analysis between IMF contents and MS). The processing time for one image is only 2.31 s. Genome-wide association analysis on PFAI for all 1709 animals identified 14 suggestive significant SNPs and 1 genome-wide significant SNP. On MS, we identified nine suggestive significant SNPs, and seven of them were also identified in PFAI. Furthermore, the significance (-log P) values of the seven common SNPs are higher in PFAI than in MS. Novel candidate genes of biological importance for IMF content were also discovered. Our imaging systems developed for prediction of digital IMF content is closer to IMF measured by Soxhlet extraction and slightly more accurate than MS. It can achieve fast and high-throughput IMF phenotype, which can be used in improvement of pork quality.

A combined GWAS approach reveals key loci for socially-affected traits in Yorkshire pigs

Socially affected traits in pigs are controlled by direct genetic effects and social genetic effects, which can make elucidation of their genetic architecture challenging. We evaluated the genetic basis of direct genetic effects and social genetic effects by combining single-locus and haplotype-based GWAS on imputed whole-genome sequences. Nineteen SNPs and 25 haplotype loci are identified for direct genetic effects on four traits: average daily feed intake, average daily gain, days to 100 kg and time in feeder per day. Nineteen SNPs and 11 haplotype loci are identified for social genetic effects on average daily feed intake, average daily gain, days to 100 kg and feeding speed. Two significant SNPs from single-locus GWAS (SSC6:18,635,874 and SSC6:18,635,895) are shared by a significant haplotype locus with haplotype alleles 'GGG' for both direct genetic effects and social genetic effects in average daily feed intake. A candidate gene, MT3, which is involved in growth, nervous, and immune processes, is identified. We demonstrate the genetic differences between direct genetic effects and social genetic effects and provide an anchor for investigating the genetic architecture underlying direct genetic effects and social genetic effects on socially affected traits in pigs.

Transcriptomic Profiling of Skeletal Muscle Reveals Candidate Genes Influencing Muscle Growth and Associated Lipid Composition in Portuguese Local Pig Breeds

Simple Summary

Screening and interpretation of differentially expressed genes and associated biological pathways was conducted among experimental groups with divergent phenotypes providing valuable information about the metabolic events occurring and identification of candidate genes with major regulation roles. This comparative transcriptomic analysis includes the first RNA-seq analysis of the Longissimus lumborum muscle tissue from two Portuguese autochthonous pig breeds with different genetic backgrounds, Alentejano and Bísaro. Moreover, a complementary candidate gene approach was employed to analyse, by real time qPCR, the expression profile of relevant genes involved in lipid metabolism, and therefore with potential impacts on meat composition. This study contributes to explaining the biological basis of phenotypical differences occurring between breeds, particularly the ones related to meat quality traits that affect consumer interest.

Abstract

Gene expression is one of the main factors to influence meat quality by modulating fatty acid metabolism, composition, and deposition rates in muscle tissue. This study aimed to explore the transcriptomics of the Longissimus lumborum muscle in two local pig breeds with distinct genetic background using next-generation sequencing technology and Real-Time qPCR. RNA-seq yielded 49 differentially expressed genes between breeds, 34 overexpressed in the Alentejano (AL) and 15 in the Bísaro (BI) breed. Specific slow type myosin heavy chain components were associated with AL (MYH7) and BI (MYH3) pigs, while an overexpression of MAP3K14 in AL may be associated with their lower loin proportion, induced insulin resistance, and increased inflammatory response via NFkB activation. Overexpression of RUFY1 in AL pigs may explain the higher intramuscular (IMF) content via higher GLUT4 recruitment and consequently higher glucose uptake that can be stored as fat. Several candidate genes for lipid metabolism, excluded in the RNA-seq analysis due to low counts, such as ACLY, ADIPOQ, ELOVL6, LEP and ME1 were identified by qPCR as main gene factors defining the processes that influence meat composition and quality. These results agree with the fatter profile of the AL pig breed and adiponectin resistance can be postulated as responsible for the overexpression of MAP3K14′s coding product NIK, failing to restore insulin sensitivity.

A Systematic Review of Genomic Regions and Candidate Genes Underlying Behavioral Traits in Farmed Mammals and Their Link with Human Disorders

Simple Summary

This study is a comprehensive review of genomic regions associated with animal behavior in farmed mammals (beef and dairy cattle, pigs, and sheep) which contributes to a better understanding of the biological mechanisms influencing the target indicator trait and to gene expression studies by suggesting genes likely controlling the trait, and it will be useful in optimizing genomic predictions of breeding values incorporating biological information. Behavioral mechanisms are complex traits, genetically controlled by multiple genes spread across the whole genome. The majority of the genes identified in cattle, pigs, and sheep in association with a plethora of behavioral measurements (e.g., temperament, terrain use, milking speed, tail biting, and sucking reflex) are likely controlling stimuli reception (e.g., olfactory), internal recognition of stimuli (e.g., neuroactive ligand–receptor interaction), and body response to a stimulus (e.g., blood pressure, fatty acidy metabolism, hormone signaling, and inflammatory pathways). Six genes were commonly identified between cattle and pigs. About half of the genes for behavior identified in farmed mammals were also identified in humans for behavioral, mental, and neuronal disorders. Our findings indicate that the majority of the genes identified are likely controlling animal behavioral outcomes because their biological functions as well as potentially differing allele frequencies between two breed groups (subjectively) clustered based on their temperament characteristics.

Abstract

The main objectives of this study were to perform a systematic review of genomic regions associated with various behavioral traits in the main farmed mammals and identify key candidate genes and potential causal mutations by contrasting the frequency of polymorphisms in cattle breeds with divergent behavioral traits (based on a subjective clustering approach). A total of 687 (cattle), 1391 (pigs), and 148 (sheep) genomic regions associated with 37 (cattle), 55 (pigs), and 22 (sheep) behavioral traits were identified in the literature. In total, 383, 317, and 15 genes overlap with genomic regions identified for cattle, pigs, and sheep, respectively. Six common genes (e.g., NR3C2, PITPNM3, RERG, SPNS3, U6, and ZFAT) were found for cattle and pigs. A combined gene-set of 634 human genes was produced through identified homologous genes. A total of 313 out of 634 genes have previously been associated with behavioral, mental, and neurologic disorders (e.g., anxiety and schizophrenia) in humans. Additionally, a total of 491 candidate genes had at least one statistically significant polymorphism (p-value < 0.05). Out of those, 110 genes were defined as having polymorphic regions differing in greater than 50% of exon regions. Therefore, conserved genomic regions controlling behavior were found across farmed mammal species and humans.

Genes and SNPs Involved with Scrotal and Umbilical Hernia in Pigs

Hernia is one of the most common defects in pigs. The most prevalent are the scrotal (SH), inguinal (IH) and umbilical (UH) hernias. We compared the inguinal ring transcriptome of normal and SH-affected pigs with the umbilical ring transcriptome of normal and UH-affected pigs to discover genes and pathways involved with the development of both types of hernia. A total of 13,307 transcripts was expressed in the inguinal and 13,302 in the umbilical ring tissues with 94.91% of them present in both tissues. From those, 35 genes were differentially expressed in both groups, participating in 108 biological processes. A total of 67 polymorphisms was identified in the inguinal ring and 76 in the umbilical ring tissue, of which 11 and 14 were novel, respectively. A single nucleotide polymorphism (SNP) with deleterious function was identified in the integrin α M (ITGAM) gene. The microtubule associated protein 1 light chain 3 γ (MAP1LC3C), vitrin (VIT), aggrecan (ACAN), alkaline ceramidase 2 (ACER2), potassium calcium-activated channel subfamily M α 1 (KCNMA1) and synaptopodin 2 (SYNPO2) genes are highlighted as candidates to trigger both types of hernia. We generated the first comparative study of the pig umbilical and inguinal ring transcriptomes, contributing to the understanding of the genetic mechanism involved with these two types of hernia in pigs and probably in other mammals.

A meta-analysis of genome-wide association studies for average daily gain and lean meat percentage in two Duroc pig populations

Background

Average daily gain (ADG) and lean meat percentage (LMP) are the main production performance indicators of pigs. Nevertheless, the genetic architecture of ADG and LMP is still elusive. Here, we conducted genome-wide association studies (GWAS) and meta-analysis for ADG and LMP in 3770 American and 2090 Canadian Duroc pigs.

Results

In the American Duroc pigs, one novel pleiotropic quantitative trait locus (QTL) on Sus scrofa chromosome 1 (SSC1) was identified to be associated with ADG and LMP, which spans 2.53 Mb (from 159.66 to 162.19 Mb). In the Canadian Duroc pigs, two novel QTLs on SSC1 were detected for LMP, which were situated in 3.86 Mb (from 157.99 to 161.85 Mb) and 555 kb (from 37.63 to 38.19 Mb) regions. The meta-analysis identified ten and 20 additional SNPs for ADG and LMP, respectively. Finally, four genes (PHLPP1, STC1, DYRK1B, and PIK3C2A) were detected to be associated with ADG and/or LMP. Further bioinformatics analysis showed that the candidate genes for ADG are mainly involved in bone growth and development, whereas the candidate genes for LMP mainly participated in adipose tissue and muscle tissue growth and development.

Conclusions

We performed GWAS and meta-analysis for ADG and LMP based on a large sample size consisting of two Duroc pig populations. One pleiotropic QTL that shared a 2.19 Mb haplotype block from 159.66 to 161.85 Mb on SSC1 was found to affect ADG and LMP in the two Duroc pig populations. Furthermore, the combination of single-population and meta-analysis of GWAS improved the efficiency of detecting additional SNPs for the analyzed traits. Our results provide new insights into the genetic architecture of ADG and LMP traits in pigs. Moreover, some significant SNPs associated with ADG and/or LMP in this study may be useful for marker-assisted selection in pig breeding.

Identification of functional candidate variants and genes for feed efficiency in Holstein and Jersey cattle breeds using RNA-sequencing

The identification of functional genetic variants and associated candidate genes linked to feed efficiency may help improve selection for feed efficiency in dairy cattle, providing economic and environmental benefits for the dairy industry. This study used RNA-sequencing data obtained from liver tissue from 9 Holstein cows [n = 5 low residual feed intake (RFI), n = 4 high RFI] and 10 Jersey cows (n = 5 low RFI, n = 5 high RFI), which were selected from a single population of 200 animals. Using RNA-sequencing, 3 analyses were performed to identify: (1) variants within low or high RFI Holstein cattle; (2) variants within low or high RFI Jersey cattle; and (3) variants within low or high RFI groups, which are common across both Holstein and Jersey cattle breeds. From each analysis, all variants were filtered for moderate, modifier, or high functional effect, and co-localized quantitative trait loci (QTL) classes, enriched biological processes, and co-localized genes related to these variants, were identified. The overlapping of the resulting genes co-localized with functional SNP from each analysis in both breeds for low or high RFI groups were compared. For the first two analyses, the total number of candidate genes associated with moderate, modifier, or high functional effect variants fixed within low or high RFI groups were 2,810 and 3,390 for Holstein and Jersey breeds, respectively. The major QTL classes co-localized with these variants included milk and reproduction QTL for the Holstein breed, and milk, production, and reproduction QTL for the Jersey breed. For the third analysis, the common variants across both Holstein and Jersey breeds, uniquely fixed within low or high RFI groups were identified, revealing a total of 86,209 and 111,126 functional variants in low and high RFI groups, respectively. Across all 3 analyses for low and high RFI cattle, 12 and 31 co-localized genes were overlapping, respectively. Among the overlapping genes across breeds, 9 were commonly detected in both the low and high RFI groups (INSRR, CSK, DYNC1H1, GAB1, KAT2B, RXRA, SHC1, TRRAP, PIK3CB), which are known to play a key role in the regulation of biological processes that have high metabolic demand and are related to cell growth and regeneration, metabolism, and immune function. The genes identified and their associated functional variants may serve as candidate genetic markers and can be implemented into breeding programs to help improve the selection for feed efficiency in dairy cattle.

A Genome-Wide Association Study on Feed Efficiency Related Traits in Landrace Pigs

Feed efficiency (FE) traits in pigs are of utmost economic importance. Genetic improvement of FE related traits in pigs might significantly reduce production cost and energy consumption. Hence, our study aimed at identifying SNPs and candidate genes associated with FE related traits, including feed conversion ratio (FCR), average daily gain (ADG), average daily feed intake (ADFI), and residual feed intake (RFI). A genome-wide association study (GWAS) was performed for the four FE related traits in 296 Landrace pigs genotyped with PorcineSNP50 BeadChip. Two different single-trait methods, single SNP linear model GWAS (LM-GWAS) and single-step GWAS (ssGWAS), were implemented. Our results showed that the two methods showed high consistency with respect to SNP identification. A total of 32 common significant SNPs associated with the four FE related traits were identified. Bioinformatics analysis revealed eight common QTL regions, of which three QTL regions related to ADFI and RFI traits were overlapped. Gene ontology analysis revealed six common candidate genes (PRELID2, GPER1, PDX1, TEX2, PLCL2, ICAM2) relevant for the four FE related traits. These genes are involved in the processes of fat synthesis and decomposition, lipid transport process, insulin metabolism, among others. Our results provide, new insights into the genetic mechanisms and candidate function genes of FE related traits in pigs. However, further investigations to validate these results are warranted.

A Transcriptome Analysis Reveals that Hepatic Glycolysis and Lipid Synthesis Are Negatively Associated with Feed Efficiency in DLY Pigs

Feed efficiency (FE) is an important trait in the porcine industry. Therefore, understanding the molecular mechanisms of FE is vital for the improvement of this trait. In this study, 6 extreme high-FE and 6 low-FE pigs were selected from 225 Duroc × (Landrace × Yorkshire) (DLY) pigs for transcriptomic analysis. RNA-seq analysis was performed to determine differentially expressed genes (DEGs) in the liver tissues of the 12 individuals, and 507 DEGs were identified between high-FE pigs (HE- group) and low-FE pigs (LE- group). A gene ontology (GO) enrichment and pathway enrichment analysis were performed and revealed that glycolytic metabolism and lipid synthesis-related pathways were significantly enriched within DEGs; all of these DEGs were downregulated in the HE- group. Moreover, Weighted gene co-expression analysis (WGCNA) revealed that oxidative phosphorylation, thermogenesis, and energy metabolism-related pathways were negatively related to HE- group, which might result in lower energy consumption in higher efficiency pigs. These results implied that the higher FE in the HE- group may be attributed to a lower glycolytic, energy consumption and lipid synthesizing potential in the liver. Furthermore, our findings suggested that the inhibition of lipid synthesis and glucose metabolic activity in the liver may be strategies for improving the FE of DLY pigs.

Genome-Wide Epistatic Interaction Networks Affecting Feed Efficiency in Duroc and Landrace Pigs

Interactions among genomic loci have often been overlooked in genome-wide association studies, revealing the combinatorial effects of variants on phenotype or disease manifestation. Unexplained genetic variance, interactions among causal genes of small effects, and biological pathways could be identified using a network biology approach. The main objective of this study was to determine the genome-wide epistatic variants affecting feed efficiency traits [feed conversion ratio (FCR) and residual feed intake (RFI)] based on weighted interaction SNP hub (WISH-R) method. Herein, we detected highly interconnected epistatic SNP modules, pathways, and potential biomarkers for the FCR and RFI in Duroc and Landrace purebreds considering the whole population, and separately for low and high feed efficient groups. Highly interacting SNP modules in Duroc (1,247 SNPs) and Landrace (1,215 SNPs) across the population and for low feed efficient (Duroc-80 SNPs, Landrace-146 SNPs) and high feed efficient group (Duroc-198 SNPs, Landrace-232 SNPs) for FCR and RFI were identified. Gene and pathway analyses identified ABL1, MAP3K4, MAP3K5, SEMA6A, KITLG, and KAT2B from chromosomes 1, 2, 5, and 13 underlying ErbB, Ras, Rap1, thyroid hormone, axon guidance pathways in Duroc. GABBR2, GNA12, and PRKCG genes from chromosomes 1, 3, and 6 pointed towards thyroid hormone, cGMP-PKG and cAMP pathways in Landrace. From Duroc low feed efficient group, the TPK1 gene was found involved with thiamine metabolism, whereas PARD6G, DLG2, CRB1 were involved with the hippo signaling pathway in high feed efficient group. PLOD1 and SETD7 genes were involved with lysine degradation in low feed efficient group in Landrace, while high feed efficient group pointed to genes underpinning valine, leucine, isoleucine degradation, and fatty acid elongation. Some SNPs and genes identified are known for their association with feed efficiency, others are novel and potentially provide new avenues for further research. Further validation of epistatic SNPs and genes identified here in a larger cohort would help to establish a framework for modelling epistatic variance in future methods of genomic prediction, increasing the accuracy of estimated genetic merit for FE and helping the pig breeding industry.

A genomic map of climate adaptation in Mediterranean cattle breeds

Domestic species such as cattle (Bos taurus taurus and B. t. indicus) represent attractive biological models to characterize the genetic basis of short-term evolutionary response to climate pressure induced by their post-domestication history. Here, using newly generated dense SNP genotyping data, we assessed the structuring of genetic diversity of 21 autochtonous cattle breeds from the whole Mediterranean basin and performed genome-wide association analyses with covariables discriminating the different Mediterranean climate subtypes. This provided insights into both the demographic and adaptive histories of Mediterranean cattle. In particular, a detailed functional annotation of genes surrounding variants associated with climate variations highlighted several biological functions involved in Mediterranean climate adaptation such as thermotolerance, UV protection, pathogen resistance or metabolism with strong candidate genes identified (e.g., NDUFB3, FBN1, METTL3, LEF1, ANTXR2 and TCF7). Accordingly, our results suggest that main selective pressures affecting cattle in Mediterranean area may have been related to variation in heat and UV exposure, in food resources availability and in exposure to pathogens, such as anthrax bacteria (Bacillus anthracis). Furthermore, the observed contribution of the three main bovine ancestries (indicine, European and African taurine) in these different populations suggested that adaptation to local climate conditions may have either relied on standing genomic variation of taurine origin, or adaptive introgression from indicine origin, depending on the local breed origins. Taken together, our results highlight the genetic uniqueness of local Mediterranean cattle breeds and strongly support conservation of these populations.

A Transcriptome Analysis Identifies Biological Pathways and Candidate Genes for Feed Efficiency in DLY Pigs

Feed cost accounts for approximately 65–75% of overall commercial pork production costs. Therefore, improving the feed efficiency of pig production is important. In this study, 12 individuals with either extremely high (HE) or low (LE) feed efficiency were selected from 225 Duroc × (Landrace × Yorkshire) (DLY) pigs. After the pigs were slaughtered, we collected small intestine mucosal tissue. Next, RNA sequencing (RNA-seq) analysis was used to reveal the presence and quantity of genes expressed between these extremely HE- and LE-groups. We found 433 significantly differentially expressed genes (DEGs) between the HE- and LE-groups. Of these, 389 and 44 DEGs were upregulated and downregulated in the HE-group, respectively. An enrichment analysis showed that the DEGs were mainly enriched in functions related to apical plasma membrane composition, transporter activity, transport process and hormone regulation of digestion and absorption. Protein network interaction and gene function analyses revealed that SLC2A2 was an important candidate gene for FE in pigs, which may give us a deeper understanding of the mechanism of feed efficiency. Furthermore, some significant DEGs identified in the current study could be incorporated into artificial selection programs for increased feeding efficiency in pigs.

Effects of genetic variations within goat PITX2 gene on growth traits and mRNA expression

Paired-like homeodomain 2 (PITX2), a key gene in hypothalamic-pituitary-adrena axis, influences animal growth and development. The objective of this study was to identify the association of the functional genetic variations within goat PITX2 gene with growth traits and mRNA expression levels. According to the reported single nucleotide polymorphisms (SNPs) information in Guanzhong dairy goat (GZDG), we identified genotypes of the known SNPs in Hainan black goat (HNBG). Association analysis uncovered that the SNPs of AC_000163: g.18117T > C, g.18161C > G and g.18353T > C loci were significantly associated with several growth traits (e.g., body height and body length) in HNBG and GZDG breeds. According to the quantitative real-time PCR assay, β-Actin and ribosomal protein L19 (RPL19) were the most stable expressed housekeeping genes in heart and skeletal muscle, respectively; meanwhile, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was the most stable expressed housekeeping gene in the other tissues. Based on the best housekeeping gene of varied tissues, we found the different genotypes of above loci were significantly associated with PITX2 mRNA expression in heart, muscle and small intestine. Briefly, the genetic variants of goat PITX2 associating with mRNA expression affected growth traits significantly, which would benefit for goat breeding in the future.

Neuronal Signal Transduction-Involved Genes in Pig Hypothalamus Affect Feed Efficiency as Revealed by Transcriptome Analysis

Feed efficiency (FE) is an important trait affecting costs in swine industry. Investigation on FE-related genes in different tissues is valuable for molecular breeding. Hypothalamus is a convergent and integrated centre for multiple nutrient-related signals. The present study identified 363 differentially expressed (DE) genes and 14 DE lincRNAs in the hypothalamus of high- and low-FE Yorkshire pigs. Furthermore, 983 significantly correlated DE gene-lincRNA pairs were identified through weighted correlation network analysis (WGCNA) and Pearson correlation analysis. These DE genes were primarily enriched in the neuronal signal transduction process containing the upregulated genes of VIPR1, CCR1, CCR5, LEPR, INSR, ADRA1A, CCKAR, and ADORA3 and the downregulated genes of GRM1, GRM4, GRM5, and VIPR2, which were located in the cell membrane. These signal receptors were mainly connected to downstream Jak-STAT signaling that involved the increased genes (JAK2, STAT3, and POMC) and mTOR signaling pathway, including the decreased genes (CAMKK2, AMPK, and MTOR). STAT3 and AMPK genes also played a role in two major hypothalamic neurons of POMC and NPY/AGRP. A total of eight DE lincRNAs also participated in the potential network. In conclusion, neuronal signaling transduction-involved genes and lincRNAs were related to FE variation in pig hypothalamus.

Transcriptome Analysis of Adipose Tissue Indicates That the cAMP Signaling Pathway Affects the Feed Efficiency of Pigs

Feed efficiency (FE) is one of the main factors that determine the production costs in the pig industry. In this study, RNA Sequencing (RNA-seq) was applied to identify genes and long intergenic non-coding RNAs (lincRNAs) that are differentially expressed (DE) in the adipose tissues of Yorkshire pigs with extremely high and low FE. In total, 147 annotated genes and 18 lincRNAs were identified as DE between high- and low-FE pigs. Seventeen DE lincRNAs were significantly correlated with 112 DE annotated genes at the transcriptional level. Gene ontology (GO) analysis revealed that DE genes were significantly associated with cyclic adenosine monophosphate (cAMP) metabolic process and Ca²⁺ binding. cAMP, a second messenger has an important role in lipolysis, and its expression is influenced by Ca²⁺ levels. In high-FE pigs, nine DE genes with Ca²⁺ binding function, were down-regulated, whereas S100G, which encodes calbindin D9K that serve as a Ca²⁺ bumper, was up-regulated. Furthermore, ATP2B2, ATP1A4, and VIPR2, which participate in the cAMP signaling pathway, were down-regulated in the upstream of lipolysis pathways. In high-FE pigs, the key genes involved in the lipid biosynthetic process (ELOVL7 and B4GALT6), fatty acid oxidation (ABCD2 and NR4A3), and lipid homeostasis (C1QTNF3 and ABCB4) were down-regulated. These results suggested that cAMP was involved in the regulation on FE of pigs by affecting lipid metabolism in adipose tissues.

Genetic Architecture of Feeding Behavior and Feed Efficiency in a Duroc Pig Population

Increasing feed efficiency is a major goal of breeders as it can reduce production cost and energy consumption. However, the genetic architecture of feeding behavior and feed efficiency traits remains elusive. To investigate the genetic architecture of feed efficiency in pigs, three feeding behavior traits (daily feed intake, number of daily visits to feeder, and duration of each visit) and two feed efficiency traits (feed conversion ratio and residual feed intake) were considered. We performed genome-wide association studies (GWASs) of the five traits using a population of 1,008 Duroc pigs genotyped with an Illumina Porcine SNP50K BeadChip. A total of 9 genome-wide (P < 1.54E-06) and 35 suggestive (P < 3.08E-05) single nucleotide polymorphisms (SNPs) were detected. Two pleiotropic quantitative trait loci (QTLs) on SSC 1 and SSC 7 were found to affect more than one trait. Markers WU_10.2_7_18377044 and DRGA0001676 are two key SNPs for these two pleiotropic QTLs. Marker WU_10.2_7_18377044 on SSC 7 contributed 2.16 and 2.37% of the observed phenotypic variance for DFI and RFI, respectively. The other SNP DRGA0001676 on SSC 1 explained 3.22 and 5.46% of the observed phenotypic variance for FCR and RFI, respectively. Finally, functions of candidate genes and gene set enrichment analysis indicate that most of the significant pathways are associated with hormonal and digestive gland secretion during feeding. This study advances our understanding of the genetic mechanisms of feeding behavior and feed efficiency traits and provide an opportunity for increasing feeding efficiency using marker-assisted selection or genomic selection in pigs.

Genome-wide association study reveals genetic loci and candidate genes for average daily gain in Duroc pigs

Objective

Average daily gain (ADG) is an important target trait of pig breeding programs. We aimed to identify single nucleotide polymorphisms (SNPs) and genomic regions that are associated with ADG in the Duroc pig population.

Methods

We performed a genome-wide association study involving 390 Duroc boars and by using the PorcineSNP60K Beadchip and two linear models.

Results

After quality control, we detected 3,5971 SNPs, which included seven SNPs that are significantly associated with the ADG of pigs. We identified six quantitative trait loci (QTL) regions for ADG. These QTLs included four previously reported QTLs on Sus scrofa chromosome (SSC) 1, SSC5, SSC9, and SSC13, as well as two novel QTLs on SSC6 and SSC16. In addition, we selected six candidate genes (general transcription factor 3C polypeptide 5, high mobility group AT-hook 2, nicotinamide phosphoribosyltransferase, oligodendrocyte transcription factor 1, pleckstrin homology and RhoGEF domain containing G4B, and ENSSSCG00000031548) associated with ADG on the basis of their physiological roles and positional information. These candidate genes are involved in skeletal muscle cell differentiation, diet-induced obesity, and nervous system development.

Conclusion

This study contributes to the identification of the casual mutation that underlies QTLs associated with ADG and to future pig breeding programs based on marker-assisted selection. Further studies are needed to elucidate the role of the identified candidate genes in the physiological processes involved in ADG regulation.