Genome-wide association study identifies candidate genes for piglet splay leg syndrome in different populations

Elucidation of population stratifying markers and selective sweeps in crossbred Landlly pig population using genome-wide SNP data

The present study was aimed at the identification of population stratifying markers from the commercial porcine SNP 60K array and elucidate the genome-wide selective sweeps in the crossbred Landlly pig population. Original genotyping data, generated on Landlly pigs, was merged in various combinations with global suid breeds that were grouped as exotic (global pig breeds excluding Indian and Chinese), Chinese (Chinese pig breeds only), and outgroup pig populations. Post quality control, the genome-wide SNPs were ranked for their stratifying power within each dataset in TRES (using three different criteria) and FIFS programs and top-ranked SNPs (0.5K, 1K, 2K, 3K, and 4K densities) were selected. PCA plots were used to assess the stratification power of low-density panels. Selective sweeps were elucidated in the Landlly population using intra- and inter-population haplotype statistics. Additionally, Tajima's D-statistics were calculated to determine the status of balancing selection in the Landlly population. PCA plots showed 0.5K marker density to effectively stratify Landlly from other pig populations. The A-score in DAPC program revealed the Delta statistic of marker selection to outperform other methods (informativeness and FST methods) and that 3000-marker density was suitable for stratification of Landlly animals from exotic pig populations. The results from selective sweep analysis revealed the Landlly population to be under selection for mammary (NAV2), reproductive efficiency (JMY, SERGEF, and MAP3K20), body conformation (FHIT, WNT2, ASRB, DMGDH, and BHMT), feed efficiency (CSRNP1 and ADRA1A), and immunity (U6, MYO3B, RBMS3, and FAM78B) traits. More than two methods suggested sweeps for immunity and feed efficiency traits, thus giving a strong indication for selection in this direction. The study is the first of its kind in Indian pig breeds with a comparison against global breeds. In conclusion, 500 markers were able to effectively stratify the breeds. Different traits under selective sweeps (natural or artificial selection) can be exploited for further improvement.

Mapping and functional characterization of structural variation in 1060 pig genomes

BACKGROUND

Structural variations (SVs) have significant impacts on complex phenotypes by rearranging large amounts of DNA sequence.

RESULTS

We present a comprehensive SV catalog based on the whole-genome sequence of 1060 pigs (Sus scrofa) representing 101 breeds, covering 9.6% of the pig genome. This catalog includes 42,487 deletions, 37,913 mobile element insertions, 3308 duplications, 1664 inversions, and 45,184 break ends. Estimates of breed ancestry and hybridization using genotyped SVs align well with those from single nucleotide polymorphisms. Geographically stratified deletions are observed, along with known duplications of the KIT gene, responsible for white coat color in European pigs. Additionally, we identify a recent SINE element insertion in MYO5A transcripts of European pigs, potentially influencing alternative splicing patterns and coat color alterations. Furthermore, a Yorkshire-specific copy number gain within ABCG2 is found, impacting chromatin interactions and gene expression across multiple tissues over a stretch of genomic region of ~200 kb. Preliminary investigations into SV's impact on gene expression and traits using the Pig Genotype-Tissue Expression (PigGTEx) data reveal SV associations with regulatory variants and gene-trait pairs. For instance, a 51-bp deletion is linked to the lead eQTL of the lipid metabolism regulating gene FADS3, whose expression in embryo may affect loin muscle area, as revealed by our transcriptome-wide association studies.

CONCLUSIONS

This SV catalog serves as a valuable resource for studying diversity, evolutionary history, and functional shaping of the pig genome by processes like domestication, trait-based breeding, and adaptive evolution.

Selective Sweeps in the Austrian Turopolje and Other Commercial Pig Populations

The goal of our study was to identify signatures of selection in the Turopolje pigs and other commercial pig breeds. We conducted a comprehensive analysis of five datasets, including one local pig breed (Turopolje) and four commercial pig breeds (Large White, Landrace, Pietrain, and Duroc), using strict quality control measures. Our final dataset consisted of 485 individuals and 54,075 single nucleotide polymorphisms (SNPs). To detect selection signatures within these pig breeds, we utilized the XP-EHH and XP-nSL methodologies, which allowed us to identify candidate genes that have been subject to positive selection. Our analysis consistently highlighted the PTBP2 and DPYD genes as commonly targeted by selection in the Turopolje breed. DPYD is associated with muscular development in pigs and other species and PTBP2 emerges as one of the potential genes linked to seminal characteristics. Furthermore, in the Large White breed, a number of genes were detected with the two methods, such as ATP1A1, CASQ2, CD2, IGSF3, MAB21L3, NHLH2, SLC22A15, VANGL1. In the Duroc breed, a different set of genes was detected, such as ARSB, BHMT, BHMT2, DMGDH, JMY. The function of these genes was related to body weight, production efficiency and meat quality, average daily gain, and other similar traits. Overall, our results have identified a number of genomic regions that are under selective pressure between local and commercial pig breeds. This information can help to improve our understanding of the mechanisms underlying pig breeding, and ultimately contribute to the development of more efficient and sustainable pig production practices. Our study highlights the power of using multiple genomic methodologies to detect genetic signatures of selection, and provides important insights into the genetic diversity of pig breeds.

Homer 1 genotype AA variant relates to congenital splay leg syndrome in piglets by repressing Pax7 in myogenic progenitors

Introduction

Porcine congenital splay leg syndrome (PCS) is a major birth defect in piglets, resulting in lameness and high mortality rates. The multifactorial pathogenesis of PSC is not well understood but includes a polygenic inheritance.

Methods

Here, in addition to morphological investigations, we characterized the expression of myogenic genes and functional (proliferation and differentiation) properties of myogenic precursor/satellite cells (SATCs) in 1 day-old PCS piglets, non-affected littermates (LCs), and piglets from PCS-free healthy litters (HCs). In addition, PCS phenotypes were related to the SNP Homer1_rs325197091 within the Homer1 locus, which has been identified as a potential hereditary cause of PCS.

Results and discussion

Samples from musculus semitendinosus (ST) of PCS piglets had a higher proportion of type II fibers, reflecting myofiber immaturity. In addition, myofiber atrophy, a lower number of myonuclei per fiber (ST), and a higher apoptotic activity (in ST and longissimus dorsi muscle; LD) were found in the PCS group. A higher proportion of cycling committed myoblasts (Pax7+/Ki67+ cells) occurred in samples from PCS-affected piglets, and on the other hand, the mRNA expression of genes involved in differentiation (muscle differentiation 1; MyoD, myogenin; MyoG) was repressed compared with HCs. Cultured SATCs from PCS-affected animals showed a temporal shift in peak expression of Pax7, MyoD, and MyoG toward days 3 and 4 of their 7 days differentiation regime. In vitro experiments with isolated SATCs confirmed the lower differentiation potential and the delayed progression of the myogenic processes in cells from piglets with PCS phenotype. In addition, Pax7 and desmin were differently expressed in Homer1_rs325197091 genotype variants (GG, GA, and AA). Both genes showed the lowest expression in the homozygous AA-variant, which was most frequently found in PCS-affected animals. The homozygous AA-variant was also associated with lower expression of the truncated Homer1-subtype 205. Thus, we hypothesize that in PCS, the balance between Homer1 proteins and its signaling functions is changed in a way detrimental to the myogenic differentiation program. Our results demonstrated direct negative effects of the Homer1 AA genotype on Pax7 expression, but the exact mode of action still needs to be elucidated.

A questionnaire-based investigation of the swimming puppy syndrome: 115 dogs

Swimming Puppy Syndrome (SPS) is a benign reversible condition of unknown etiology in multiple dog breeds. Affected dogs show laterally abducted limbs and are unable to stand and walk on their own. The current knowledge of this condition derives from few case reports or small case series. Therefore, the aim of this study was to collect data on the clinical course from a large cohort of dogs with SPS with an online questionnaire supported by video footage. Potential risk factors were compared between 110 litters with SPS and 103 unaffected litters. SPS was reported in 115 dogs from 48 different breeds comprising a wide range of small, middle, and large breeds. Litters with SPS were significantly smaller than unaffected litters. Cesarean sections were reported more frequently in affected litters, but the overall rate of reported birth complications did not differ significantly from unaffected litters. Most puppies were able to stand and walk at a median age of 4.5 weeks (up to 12 weeks) and clinical signs resolved at a median age of six weeks (up to 12 weeks). Puppies from large breeds showed faster recovery than puppies from medium and small breeds. Occasionally, residual deficits were reported and only three dogs failed to recover. A clustering of SPS occurred in closely related litters in four kennels of four different dog breeds (Greater Swiss Mountain Dog, Golden Retriever, Miniature Bull Terrier, Norwich Terrier). The study shows the benign clinical course of SPS in a large cohort of puppies from multiple dog breeds. Potential risk factors including reports on birth complications, size and muscle mass compared to littermates and diet of the dam during pregnany were evaluated and no influence on the occurrence of SPS was identified.

Runs of Homozygosity Uncover Potential Functional-Altering Mutation Associated With Body Weight and Length in Two Duroc Pig Lines

Runs of homozygosity (ROH) are widely used to investigate genetic diversity, demographic history, and positive selection signatures of livestock. Commercial breeds provide excellent materials to reveal the landscape of ROH shaped during the intense selection process. Here, we used the GeneSeek Porcine 50K single-nucleotide polymorphism (SNP) Chip data of 3,770 American Duroc (AD) and 2,096 Canadian Duroc (CD) pigs to analyze the genome-wide ROH. First, we showed that AD had a moderate genetic differentiation with CD pigs, and AD had more abundant genetic diversity and significantly lower level of inbreeding than CD pigs. In addition, sows had larger levels of homozygosity than boars in AD pigs. These differences may be caused by differences in the selective intensity. Next, ROH hotspots revealed that many candidate genes are putatively under selection for growth, sperm, and muscle development in two lines. Population-specific ROHs inferred that AD pigs may have a special selection for female reproduction, while CD pigs may have a special selection for immunity. Moreover, in the overlapping ROH hotspots of two Duroc populations, we observed a missense mutation (rs81216249) located in the growth and fat deposition-related supergene (ARSB-DMGDH-BHMT) region. The derived allele of this variant originated from European pigs and was nearly fixed in Duroc pigs. Further selective sweep and association analyses indicated that this supergene was subjected to strong selection and probably contributed to the improvement of body weight and length in Duroc pigs. These findings will enhance our understanding of ROH patterns in different Duroc lines and provide promising trait-related genes and a functional-altering marker that can be used for genetic improvement of pigs.

Genome-wide association study identifies SNPs for growth performance and serum indicators in Valgus-varus deformity broilers (Gallus gallus) using ddGBS sequencing

Background

Valgus-varus deformity (VVD) is a lateral or middle deviation of the tibiotarsus or tarsometatarsus, which is associated with compromised growth, worse bone quality and abnormal changes in serum indicators in broilers. To investigate the genetic basis of VVD, a genome wide association study (GWAS) was performed to identify candidate genes and pathways that are responsible for VVD leg disease, serum indicators and growth performance in broilers.

Results

In total, VVD phenotype, seven serum indicators and three growth traits were measured for 126 VVD broilers (case group) and 122 sound broilers (control group) based on a high throughput genome wide genotyping-by-sequencing (GBS) method. After quality control 233 samples (113 sound broilers and 120 VVD birds) and 256,599 single nucleotide polymorphisms (SNPs) markers were used for further analysis. As a result, a total of 5 SNPs were detected suggestively significantly associated with VVD and 70 candidate genes were identified that included or adjacent to these significant SNPs. In addition, 43 SNPs located on Chr24 (0.22 Mb - 1.79 Mb) were genome-wide significantly associated with serum alkaline phosphatase (ALP) and 38 candidate genes were identified. Functional enrichment analysis showed that these genes are involved in two Gene Ontology (GO) terms related to bone development (cartilage development and cartilage condensation) and two pathways related to skeletal development (Toll−like receptor signaling pathway and p53 signaling pathway). BARX2 (BARX homeobox 2) and Panx3 (Pannexin 3) related to skeleton diseases and bone quality were obtained according to functional analysis. According to the integration of GWAS with transcriptome analysis, HYLS1 (HYLS1 centriolar and ciliogenesis associated) was an important susceptibility gene.

Conclusions

The results provide some reference for understanding the relationship between metabolic mechanism of ALP and pathogenesis of VVD, which will provide a theoretical basis for disease-resistant breeding of chicken leg soundness.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08236-3.

Detection of genomic regions associated malformations in newborn piglets: a machine-learning approach

Background

A significant proportion of perinatal losses in pigs occurs due to congenital malformations. The purpose of this study is the identification of genomic loci associated with fetal malformations in piglets.

Methods

The malformations were divided into two groups: associated with limb defects (piglet splay leg) and associated with other congenital anomalies found in newborn piglets. 148 Landrace and 170 Large White piglets were selected for the study. A genome-wide association study based on the gradient boosting machine algorithm was performed to identify markers associated with congenital anomalies and piglet splay leg.

Results

Forty-nine SNPs (23 SNPs in Landrace pigs and 26 SNPs in Large White) were associated with congenital anomalies, 22 of which were localized in genes. A total of 156 SNPs (28 SNPs in Landrace; 128 in Large White) were identified for piglet splay leg, of which 79 SNPs were localized in genes. We have demonstrated that the gradient boosting machine algorithm can identify SNPs and their combinations associated with significant selection indicators of studied malformations and productive characteristics.

Data availability

Genotyping and phenotyping data are available at http://www.compubioverne.group/data-and-software/.

Single-Step Genome Wide Association Study Identifies QTL Signals for Untrimmed and Trimmed Thigh Weight in Italian Crossbred Pigs for Dry-Cured Ham Production

Simple Summary

Along with the traditional traits, swine breeding programs for Italian dry-cured ham production have recently aimed to include novel phenotypes. The identification of the genomic regions underlying such new traits helps to untangle their genetic architecture and may provide useful information to be integrated in genetic selection. With this aim, we estimated genetic parameters and conducted a single step genome wide association studies (GWAS) on untrimmed and trimmed thigh weight considering two pig crossbred lines approved for Italian Protected Designation of Origin ham production. Quantitative trait loci (QTLs) were characterized based on the variance of 10-SNP sliding windows genomic estimated breeding values. In particular, we identified interesting QTL signals on several chromosomes, notably on chromosome 4, 6, 7 and 15. A high heritability and genetic correlation were observed for the two traits under investigation and although independent studies including other pig populations are required to disentangle the possible effects of specific linkage disequilibrium in our population, our findings suggest that such QTL could be investigated in future pig breeding programs to improve the reliability of genomic estimated breeding values for the dry-cured ham production.

Abstract

Protected Designation of Origin (PDO) dry-cured ham is the most important product in the Italian pig breeding industry, mainly oriented to produce heavy pig carcasses to obtain hams of the right weight and maturity. Recently, along with the traditional traits swine breeding programs have aimed to include novel carcass traits. The identification at the genome level of quantitative trait loci (QTLs) affecting such new traits helps to reveal their genetic determinism and may provide information to be integrated in prediction models in order to improve prediction accuracy as well as to identify candidate genes underlying such traits. This study aimed to estimate genetic parameters and perform a single step genome wide association studies (ssGWAS) on novel carcass traits such as untrimmed (UTW) and trimmed thigh weight (TTW) in two pig crossbred lines approved for the ham production of the Italian PDO. With this purpose, phenotypes were collected from ~1800 animals and 240 pigs were genotyped with Illumina PorcineSNP60 Beadchip. The single-step genomic BLUP procedure was used for the heritability estimation and to implement the ssGWAS. QTL were characterized based on the variance of 10-SNP sliding window genomic estimated breeding values. Moderate heritabilities were detected and QTL signals were identified on chromosome 1, 4, 6, 7, 11 and 15 for both traits. As expected, the genetic correlation among the two traits was very high (~0.99). The QTL regions encompassed a total of 249 unique candidate genes, some of which were already reported in association with growth, carcass or ham weight traits in pigs. Although independent studies are required to further verify our findings and disentangle the possible effects of specific linkage disequilibrium in our population, our results support the potential use of such new QTL information in future breeding programs to improve the reliability of genomic prediction.

Congenital Splay Leg Syndrome in Piglets-Current Knowledge and a New Approach to Etiology

The porcine congenital splay leg syndrome (PCS), even though being of transient nature, is still one of the most important causes for piglet losses due to its high incidence and mortality. Although, described decades ago, the pathogenetic mechanism is still elusive. Numerous, mostly descriptive studies characterized the syndrome at clinical, histological and cellular levels but resulted in a highly diverse picture of the syndrome. Broad variability in phenotypical expression and, in case of proper care, the rapid recovery of affected animals complicated a systematical analysis of the underlying pathogenesis. Although, several environmental factors were discussed as potential causes of PCS, most of the evidence points to a hereditary basis of PCS. Nevertheless, only few of the suggested candidate genes from transcriptome and mapping analyses, like F-box protein 32 (FBXO32), could be confirmed so far. Only recently, a genome wide association study revealed genomic regions on five porcine chromosomes and named a number of potential candidate genes, among them homer scaffold protein 1 (HOMER1). This new candidate-a cellular scaffold protein-plays a role in a plethora of cellular signaling cascades, and is not only involved in skeletal muscle differentiation but also critical for muscular function. In this review, we critically elucidate the current state of knowledge in the field and evaluate current achievements in the identification of the pathogenetic mechanism for the syndrome.

Genome-Wide Detection of Selection Signatures in Duroc Revealed Candidate Genes Relating to Growth and Meat Quality

With the development of high-throughput genotyping techniques, selection signatures in the genome of domestic pigs have been extensively interrogated in the last decade. The Duroc, a major commercial pig breed famous for its fast growth rate and high lean ratio, has not been extensively studied focusing on footprints of intensively artificial selection in their genomes by a lot of re-sequencing data. The goal of this study was to investigate genomic regions under artificial selection and their contribution to the unique phenotypic traits of the Duroc using whole-genome resequencing data from 97 pigs. Three complementary methods (d_i, CLR, and iHH12) were implemented for selection signature detection. In Total, 464 significant candidate regions were identified, which covered 46.4 Mb of the pig genome. Within the identified regions, 709 genes were annotated, including 600 candidate protein-coding genes (486 functionally annotated genes) and 109 lncRNA genes. Genes undergoing selective pressure were significantly enriched in the insulin resistance signaling pathway, which may partly explain the difference between the Duroc and other breeds in terms of growth rate. The selection signatures identified in the Duroc population demonstrated positive pressures on a set of important genes with potential functions that are involved in many biological processes. The results provide new insights into the genetic mechanisms of fast growth rate and high lean mass, and further facilitate follow-up studies on functional genes that contribute to the Duroc's excellent phenotypic traits.

Significance testing and genomic inflation factor using high-density genotypes or whole-genome sequence data

Significance testing for genome‐wide association study (GWAS) with increasing SNP density up to whole‐genome sequence data (WGS) is not straightforward, because of strong LD between SNP and population stratification. Therefore, the objective of this study was to investigate genomic control and different significance testing procedures using data from a commercial pig breeding scheme. A GWAS was performed in GCTA with data of 4,964 Large White pigs using medium density, high density or imputed whole‐genome sequence data, fitting a genomic relationship matrix based on a leave‐one–chromosome‐out approach to account for population structure. Subsequently, genomic inflation factors were assessed on whole‐genome level and the chromosome level. To establish a significance threshold, permutation testing, Bonferroni corrections using either the total number of SNPs or the number of independent chromosome fragments, and false discovery rates (FDR) using either the Benjamini–Hochberg procedure or the Benjamini and Yekutieli procedure were evaluated. We found that genomic inflation factors did not differ between different density genotypes but do differ between chromosomes. Also, the leave‐one‐chromosome‐out approach for GWAS or using the pedigree relationships did not account appropriately for population stratification and gave strong genomic inflation. Regarding different procedures for significance testing, when the aim is to find QTL regions that are associated with a trait of interest, we recommend applying the FDR following the Benjamini and Yekutieli approach to establish a significance threshold that is adjusted for multiple testing. When the aim is to pinpoint a specific mutation, the more conservative Bonferroni correction based on the total number of SNPs is more appropriate, till an appropriate method is established to adjust for the number of independent tests.

Weighted Transmission Disequilibrium Test for Family Trio Association Design

BACKGROUND

Family-based design is one of the most popular designs in genetic studies. Transmission disequilibrium test (TDT) for family trio design is optimal only under the additive trait model and may lose power under the other trait models. The TDT-type tests are powerful only when the underlying trait model is correctly specified. Usually, the true trait model is unknown, and the selection of the TDT-type test is problematic. Several methods, which are robust against the mis-specification of the trait model, have been proposed. In this paper, we propose a new efficiency robust procedure for family trio design, namely, the weighted TDT (WTDT) test.

METHODS

We combine information of the largest two TDT-type tests by using weights related to the three TDT-type tests and take the weighted sum as the test statistic.

RESULTS

Simulation results demonstrate that WTDT has power close to, but much more robust than, the optimal TDT-type test based on a single trait model. WTDT also outperforms other efficiency robust methods in terms of power. Applications to real and simulated data from Genetic Analysis Workshop (GAW15) illustrate the practical application of the WTDT method.

CONCLUSION

WTDT is not only efficiency robust to model mis-specifications but also efficiency robust against mis-specifications of risk allele.

Treatment With Probiotic Bacteria Does Not Diminish the Impact of a Cystoisospora suis Challenge in Suckling Piglets

Colonization of newborn piglets with beneficial and ubiquitous microorganisms in combination with colostral passive immunity is the prerequisite for development of immunity and gut maturation. In this study living strains of Clostridium perfringens type A (CpA) and non-pathogenic Escherichia (E.) coli strains harvested from healthy piglets were administered to piglets prior to first colostrum intake in order to prevent disease caused by pathogenic variants of the same bacterial species by competitive exclusion. In addition, it was investigated whether these potential beneficial colonizers were able to prevent harmful effects of infection with Cystoisospora (C.) suis as a primary invasive pathogen. In a first trial, half of the piglets from four litters were treated with a bacterial cocktail consisting of two E. coli and four CpA strains immediately after birth on two consecutive days, while the other half of the litters served as control group. In a second trial, piglets were treated following the protocol of the first trial, and additionally all piglets were infected 4 h after the end of littering with ~1,000 sporulated oocysts of a C. suis laboratory strain. General health, body weight development, fecal consistency and, in the second trial, oocyst excretion were monitored from birth until weaning. No adverse effects of the cocktail on the health status were observed. Treated piglets of the first trial showed a higher average daily weight gain until weaning. In the second trial, no significant differences were found with respect to average daily weight gain, fecal consistency, amount, and duration of oocyst excretion assessed in daily samples. In treatment group 51.1% and in the control group 38.5% of the fecal samples were positive for oocysts in autofluorescence. The average duration of oocyst excretion was longer in treatment group (7.7 days) than in control group (5.6 days). Application of bacterial cocktail could not effectively minimize disease symptoms caused by C. suis. There was a trend toward an increase in severity of disease symptoms in treated pigs, suggesting that the synergism between CpA and C. suis was independent of the bacterial strains, but is exclusively dominated by the pathogenic effect of C. suis.

Polymorphisms of HOMER1 gene are associated with piglet splay leg syndrome and one significant SNP can affect its intronic promoter activity in vitro

BACKGROUND

In our previous genome-wide association study (GWAS) on the piglet splay leg (PSL) syndrome, the homer scaffolding protein 1 (HOMER1) was detected as a candidate gene. The aim of this work was to further verify the candidate gene by sequencing the gene and find the significantly associated mutation. Then we preliminarily analyzed the effect of the significant SNP on intronic promoter activity. This research provided a reference for further investigation of the pathogenesis of PSL.

RESULT

We investigated the 19 SNPs on HOMER1 and found 12 SNPs significant associated with PSL, including 8 SNPs resided in the potential intronic promoter region in intron 4. The - 663~ - 276 bp upstream the exon 5 had promoter activity and it could be an intronic promoter that regulated the transcription of HOMER1-205 transcript. The promoter activity of the - 663~ - 276 bp containing the rs339135425 and rs325197091 mutant alleles was significantly higher than of the wild type (P < 0.05). The G allele of rs325197091 (A > G) may create a new binding site of transcription factor aryl hydrocarbon receptor nuclear translocator (ARNT) and could enhance HOMER1 intronic promoter activity.

CONCLUSIONS

HOMER1 gene was associated with the PSL, and the rs325197091 could influence HOMER1 intronic promoter activity in vitro.

Genetic variants and haplotype combination in the bovine CRTC3 affected conformation traits in two Chinese native cattle breeds (Bos Taurus)

CREB-regulated transcription coactivator 3 (CRTC3) plays an extensive role in glucose and lipid metabolism. This study investigated the genetic variation and haplotype combination in CRTC3 and verified their contribution to bovine growth traits. Firstly, investigated the mRNA expression of CRTC3 in adult Qinchuan cattle and evaluated the effects that genetic variation of CRTC3 had on conformation and carcass traits in two Chinese cattle breeds (Qinchuan and Jiaxian). Four SNPs (single nucleotide polymorphisms) were identified including two in introns (SNP1: g.62652 A > G and SNP4: g.91297C > T) and two in exons (SNP2 g.62730C > T and SNP3: g.66478G > C). The association and haplotype combination results showed that there was an association with some growth and carcass traits(P < 0.05). Individuals with haplotype combination H1H1 (-AACCCCTT-) were associated with a conformation of a larger framed animal and an animal that produced a larger loin area. Variations in the CRTC3 genes and the haplotype combination H1H1 may be considered as molecular markers for carcass traits that are associated with more lean meat yield for use in cattle breeding programs in China.

Genomic Analysis To Identify Signatures of Artificial Selection and Loci Associated with Important Economic Traits in Duroc Pigs

Identifying genetic basis of domestication and improvement in livestock contributes to our understanding of the role of artificial selection in shaping the genome. Here we used whole-genome sequencing and the genotyping by sequencing approach to detect artificial selection signatures and identify the associated SNPs of two economic traits in Duroc pigs. A total of 38 candidate selection regions were detected by combining the fixation index and the Composite Likelihood Ratio methods. Further genome-wide association study revealed seven associated SNPs that were related with intramuscular fat content and feed conversion ratio traits, respectively. Enrichment analysis suggested that the artificial selection regions harbored genes, such as MSTN, SOD2, MC5R and CD83, which are responsible for economic traits including lean muscle mass, fertility and immunization. Overall, this study found a series of candidate genes putatively associated with the breeding improvement of Duroc pigs and the polygenic basis of adaptive evolution, which can provide important references and fundamental information for future breeding programs.

Genome-Wide Association Study Identifies Candidate Genes Related to Seed Oil Composition and Protein Content in Gossypium hirsutum L

Cotton (Gossypium spp.) is a leading natural fiber crop and an important source of vegetable protein and oil for humans and livestock. To investigate the genetic architecture of seed nutrients in upland cotton, a genome-wide association study (GWAS) was conducted in a panel of 196 germplasm resources under three environments using a CottonSNP80K chip of 77,774 loci. Relatively high genetic diversity (average gene diversity being 0.331) and phenotypic variation (coefficient of variation, CV, exceeding 3.9%) were detected in this panel. Correlation analysis revealed that the well-documented negative association between seed protein (PR) and oil may be to some extent attributable to the negative correlation between oleic acid (OA) and PR. Linkage disequilibrium (LD) was unevenly distributed among chromosomes and subgenomes. It ranged from 0.10-0.20 Mb (Chr19) to 5.65-5.75 Mb (Chr25) among the chromosomes and the range of Dt-subgenomes LD decay distances was smaller than At-subgenomes. This panel was divided into two subpopulations based on the information of 41,815 polymorphic single-nucleotide polymorphism (SNP) markers. The mixed linear model considering both Q-matrix and K-matrix [MLM(Q+K)] was employed to estimate the association between the SNP markers and the seed nutrients, considering the false positives caused by population structure and the kinship. A total of 47 SNP markers and 28 candidate quantitative trait loci (QTLs) regions were found to be significantly associated with seven cottonseed nutrients, including protein, total fatty acid, and five main fatty acid compositions. In addition, the candidate genes in these regions were analyzed, which included three genes, Gh_D12G1161, Gh_D12G1162, and Gh_D12G1165 that were most likely involved in the control of cottonseed protein concentration. These results improved our understanding of the genetic control of cottonseed nutrients and provided potential molecular tools to develop cultivars with high protein and improved fatty acid compositions in cotton breeding programs through marker-assisted selection.