Polymorphisms in ten candidate genes are associated with conformational and locomotive traits in Spanish Purebred horses

The Spanish Purebred horses, also known as Andalusian horses, compete to the highest standards in international dressage events. Gait and conformation could be used as early selection criteria to detect young horses with promising dressage ability. Although the genetic background of equine size variation has been recently uncovered, the genetic basis of horse conformational and locomotive traits is not known, hampered by the complex genetic architecture underlying quantitative traits and the lack of phenotypic data. The aim of this study was to validate the loci associated with size in 144 Spanish Purebred horses, and to seek novel associations between loci previously associated with the development of osteochondrosis (OC) lesions and 20 conformational and locomotive traits. Ten loci were associated with different conformational and locomotive traits (LCORL/NCAPG, HMGA2, USP31, MECR, COL24A1, MGP, FAM184B, PTH1R, KLF3 and SGK1), and the LCORL/NCAPG association with size in the Spanish Purebred horse was validated. Except for HMGA2, all polymorphisms seem to influence both the prevalence of OC lesions and morphological characters, supporting the link between conformation and OC. Also, the implication of most genes in either immune and inflammatory responses and cellular growth, or ossification processes, reinforces the role that these mechanisms have in the aetiology of OC, as well as their reflection on the general conformation of the individual. These polymorphisms could be used in marker-assisted selection (MAS) programmes to improve desirable conformational traits, but taking into account their possible detrimental effect on OC prevalence.     

Genomewide association study for economic traits in the large yellow croaker with different numbers of extreme phenotypes

A traditional genomewide association study (GWAS) detects genotype–phenotype associations by the vast number of genotyped individuals. This method requires large-scale samples and considerable sequencing costs. Extreme phenotypic sampling proposes make GWAS more cost-efficient and are applied more widely. With extreme phenotypic sampling, we performed a GWAS for n-3 highly unsaturated fatty acids (HUFA) and eviscerated weight (EW) traits in the large yellow croaker population. Of the 32,249 and 29,748 detected SNPs for the two traits, three candidate regions were found in each trait. Three candidate regions associated with HUFA were known near genes on chromosomes 4 and 11, and three candidate regions were on chromosome 6, and 15 for the EW trait. By combing through our GWAS results and the biological functional analysis of the genes, we suggest that the FABP, DGAT, ATP8B1, FAF2 and CERS2 genes,  as well as the IGF2, BORA, CYP1A1, GRTP1 and HOX genes are promising candidate genes for n-3 HUFA and EW, respectively, in the large yellow croaker. Moreover, compared with the different numbers of the extreme phenotypic sampling, we conclude that 60% of the extreme phenotypic subsample can obtain a similar result as GWAS with whole phenotypes. Thus, extreme phenotypic sampling could save 40% of the cost for genotyping and DNA extraction without loss of the candidate regions and functional genes. Our study may provide a basis for further genomic breeding and a reference for others who want to perform GWAS with extreme phenotypes.     

SNP markers associated with body size and pelt length in American mink (<Emphasis Type="Italic">Neovison vison</Emphasis>)

Background

Identification of genes underlying production traits is a key aim of the mink research community. Recent availability of genomic tools have opened the possibility for faster genetic progress in mink breeding. Availability of mink genome assembly allows genome-wide association studies in mink.

Results

In this study, we used genotyping-by-sequencing to obtain single nucleotide polymorphism (SNP) genotypes of 2496 mink. After multiple rounds of filtering, we retained 28,336 high quality SNPs and 2352 individuals for a genome-wide association study (GWAS). We performed the first GWAS for body weight, behavior, along with 10 traits related to fur quality in mink.

Conclusions

Combining association results with existing functional information of genes and mammalian phenotype databases, we proposed WWC3, MAP2K4, SLC7A1 and USP22 as candidate genes for body weight and pelt length in mink.

     

Genome-wide association study of <Emphasis Type="Italic">Mycobacterium avium</Emphasis> subspecies <Emphasis Type="Italic">Paratuberculosis</Emphasis> infection in Chinese Holstein

Background

Paratuberculosis is a contagious, chronic and enteric disease in ruminants, which is caused by Mycobacterium avium subspecies paratuberculosis (MAP) infection, resulting in enormous economic losses worldwide. There is currently no effective cure for MAP infection or a vaccine, it is thus important to explore the genetic variants that contribute to host susceptibility to infection by MAP, which may provide a better understanding of the mechanisms of paratuberculosis and benefit animal genetic improvement. Herein we performed a genome-wide association study (GWAS) to identify genomic regions and candidate genes associated with susceptibility to MAP infection in dairy cattle.

Results

Using Illumina Bovine 50?K (54,609 SNPs) and GeneSeek HD (138,893 SNPs) chips, two analytical approaches were performed, GRAMMAR-GC and ROADTRIPS in 937 Chinese Holstein cows, among which individuals genotyped by the 50?K chip were imputed to HD SNPs with Beagle software. Consequently, 15 and 11 significant SNPs (P?<?5?×?10^??5) were identified with GRAMMAR-GC and ROADTDRIPS, respectively. A total of 10 functional genes were in proximity to (i.e., within 1?Mb) these SNPs, including IL4, IL5, IL13, IRF1, MyD88, PACSIN1, DEF6, TDP2, ZAP70 and CSF2. Functional enrichment analysis showed that these genes were involved in immune related pathways, such as interleukin, T cell receptor signaling pathways and inflammatory bowel disease (IBD), implying their potential associations with susceptibility to MAP infection. In addition, by examining the publicly available cattle QTLdb, a previous QTL for MAP was found to be overlapped with one of regions detected currently at 32.5?Mb on BTA23, where the TDP2 gene was anchored.

Conclusions

In conclusion, we identified 26 SNPs located on 15 chromosomes in the Chinese Holstein population using two GWAS strategies with high density SNPs. Integrated analysis of GWAS, biological functions and the reported QTL information helps to detect positional candidate genes and the identification of regions associated with susceptibility to MAP traits in dairy cattle.

     

Association of SNPs in dopamine and serotonin pathway genes and their interacting genes with temperament traits in Charolais cows

Cattle temperament is a complex trait, and molecular studies aimed at defining this trait are scarce. We used an interaction networks approach to identify new genes (interacting genes) and to estimate their effects and those of 19 dopamine- and serotonin-related genes on the temperament traits of Charolais cattle. The genes proopiomelanocortin (POMC), neuropeptide Y (NPY), solute carrier family 18, member 2 (SLC18A2) and FBJ murine osteosarcoma viral oncogene homologue (FOSFBJ) were identified as new candidates. Their potential to be associated with temperament was estimated according to their reported biological activities, which included interactions with neural activity, receptor function, targeting or synthesis of neurotransmitters and association with behaviour. Pen score (PS) and exit velocity (EV) measures were determined from 412 Charolais cows to calculate their temperament score (TS). Based on the TS, calm (n?=?55; TS, 1.09?±?0.33) and temperamental (n?=?58; TS, 2.27?±?0.639) cows were selected and genotyped using a 248 single-nucleotide variation (SNV) panel. Of the 248 variations in the panel, only 151 were confirmed to be polymorphic (single-nucleotide polymorphisms; SNPs) in the tested population. Single-marker association analyses between genotypes and temperament measures (EV, PS and/or TS) indicated significant associations of six SNPs from four candidate genes. The markers rs109576799 and rs43696138, located in the DRD3 and HTR2A genes, respectively, were significantly associated with both EV and TS traits. Four markers, rs110365063 and rs137756569 from the POMC gene and rs110365063 and rs135155082 located in SLC18A2 and DRD2, respectively, were associated with PS. The variant rs110365063 located in bovine SLC18A2 causes a change in the amino acid sequence from Ala to Thr. Further studies are needed to confirm the association of genetic profile with cattle temperament; however, our study represents important progress in understanding the regulation of cattle temperament by different genes with divergent functions.     

Impact of variants on type-2 diabetes risk genes identified through genomewide association studies in polycystic ovary syndrome: a case–control study

Polycystic ovary syndrome (PCOS) is a common endocrine disorder in females, and is associated with altered metabolic processes in particular insulin resistance and diabetes mellitus. PCOS shares with type-2 diabetes (T2D) a number of features, including beta cell dysfunction, impaired glucose tolerance and dyslipidaemia. Recently, genomewide association studies (GWAS) have reported a number of genes with reproducible associations and susceptibilities to T2D. To address this, we examined the association between the T2D GWAS candidate genes (CDKAL1, CDKN2B, COL8A1, HHEX, IGF2BP2, KCNJ1, KCNQ1 and SLC30A8) and PCOS in Saudi women. A case–control study, includes 162 cases and 162 controls was enrolled. Genotyping was carried out by the allelic discrimination method. Our results showed that the variants including rs792837 of COL8A1, rs61873498 of KCNQ1 and rs13266634 of SLC30A8 genes to be significantly more frequent in PCOS patients than in controls. Our results suggest that COL8A1, KCNQ1 and SLC30A8, which are previously identified through GWAS as T2D-associated genes, are associated with PCOS.     

Evaluation of European Schizophrenia GWAS Loci in Asian Populations via Comprehensive Meta-Analyses

Schizophrenia is a severe and highly heritable neuropsychiatric disorder. Recent genetic analyses including genome-wide association studies (GWAS) have implicated multiple genome-wide significant variants for schizophrenia among European populations. However, many of these risk variants were not largely validated in other populations of different ancestry such as Asians. To validate whether these European GWAS significant loci are associated with schizophrenia in Asian populations, we conducted a systematic literature search and meta-analyses on 19 single nucleotide polymorphisms (SNPs) in Asian populations by combining all available case-control and family-based samples, including up to 30,000 individuals. We employed classical fixed (or random) effects inverse variance weighted methods to calculate summary odds ratios (ORs) and 95 % confidence intervals (CIs). Among the 19 GWAS loci, we replicated the risk associations of nine markers (e.g., SNPs at VRK2, ITIH3/4, NDST3, NOTCH4) surpassing significance level (two-tailed P?<?0.05), and three additional SNPs in MIR137 and ZNF804A also showed trend associations (one-tailed P?<?0.05). These risk associations are in the same directions of allelic effects between Asian replication samples and initial European GWAS findings, and the successful replications of these GWAS loci in a different ethnic group provide stronger evidence for their clinical associations with schizophrenia. Further studies, focusing on the molecular mechanisms of these GWAS significant loci, will become increasingly important for understanding of the pathogenesis to schizophrenia.     

Analysis of the association of interleukin 4 and interleukin 10 gene variants with basic personality traits

There is growing evidence that serum levels of various inflammation markers are associated with personality traits. However, only few studies investigated the link between genetic variants of cytokine encoding genes and psychological characteristics. In this study, we examined genotypes in 297 individuals to assess the association between common variants of interleukin 4 (IL-4) and interleukin 10 (IL-10) genes and basic personality traits of extraversion and neuroticism, measured using the Eysenck Personality Questionnaire (EPQ). We found that, in homozygous female carriers of high expression alleles Т (IL-4 C-589T) and G (IL-10 G-1082A), neuroticism scores were higher (p = 0.045 and p = 0.08, respectively). In turn, extraversion scores were significantly higher in both male and female carriers of heterozygous variants CT and GA (p = 0.01). Our results are in accordance with the behavioral immune system hypothesis, and the general paradigm on the role of personality traits in health and longevity.     

Genome-wide association study on chicken carcass traits using sequence data imputed from SNP array

Chicken carcass traits are economically important for the chicken industry. Detecting which genes affect chicken carcass traits is of great benefit to the genetic improvement of this important agricultural species. To investigate the genetic mechanism of carcass traits in chickens, we carried out a genome-wide association study (GWAS). A total of 435 Chinese indigenous chickens were phenotyped for carcass weight (CW), eviscerated weight with giblets (EWG), and eviscerated weight (EW) after slaughter at 91 days and were genotyped using a 600-K single nucleotide polymorphism (SNP) genotyping array. Twenty-four birds were selected for sequencing, and the 600 K SNP panel data were imputed to sequence data with the 24 birds as the reference. Univariate GWASs were performed with GEMMA software using the whole genome sequence data imputed from SNP chip data. Finally, 3, 25, and 63 suggestively significant SNPs were identified to be associated with carcass weight (CW), eviscerated weight with giblets (EWG), and eviscerated weight (EW), respectively. Six candidate genes, RNF219, SCEL, MYCBP2, ETS1, APLP2, and PRDM10 were detected. SCEL and MYCBP2 were potentially associated with these three traits, RNF219 and APLP2 were potentially associated with EWG and EW, and ETS1 and PRDM10 were only potentially associated with EWG and EW, respectively. Compared with forefathers’ research, 10 reported QTLs associated with CW were located within a 5-Mb distance near the SNPs with P value lower than 1×10^?5. This study enriched the knowledge of the genetic mechanisms of chicken carcass traits.     

A genome-wide association study identifies genomic loci associated with backfat thickness,carcass weight,and body weight in two commercial pig populations

Growth and fatness traits are economically important in the pig industry. To dissect the genetic architecture of these traits in commercial pigs, we conducted a genome-wide association study (GWAS) for carcass weight, backfat thickness, and body weight in two commercial populations: Duroc × (Landrace × Yorkshire) (DLY) and Duroc populations. To enhance the detection power, three GWAS approaches including single-trait GWAS, multi-trait GWAS and meta-analysis were used in this study. A total of 13 suggestive loci were identified on nine chromosomes. The most significant locus was detected at 272.05 Mb on SSC1, and it was associated with backfat thickness at the first rib in the DLY population. Three genes at the identified loci (TBC1D1, BAAT and PHLPP1) were highlighted as functionally plausible candidate genes for pig growth and fatness traits. Genome-wide significant locus was not evidenced in this study, indicating that large populations are required to identify QTL with minor effects on growth and fatness traits in commercial pig populations, in which intensively artificial selections have been imposed on these traits and small genetical variances usually retain in these traits.     

Genome-wide analyses of the Jeju,Thoroughbred, and Jeju crossbred horse populations using the high density SNP array

The Jeju horse is an indigenous Korean horse breed that is currently registered with the Food and Agriculture Organization of the United Nations. However, there is severe lack of genomic studies on Jeju horse. This study was conducted to investigate genetic characteristics of horses including Jeju horse, Thoroughbred and Jeju crossbred (Jeju?×?Thoroughbred) populations. We compared the genomes of three horse populations using the Equine SNP70 Beadchip array. Short-range Linkage disequilibrium was the highest in Thoroughbred, whereas r² values were lowest in Jeju horse. Expected heterozygosity was the highest in Jeju crossbred (0.351), followed by the Thoroughbred (0.337) and Jeju horse (0.311). The level of inbreeding was slightly higher in Thoroughbred (??0.009) than in Jeju crossbred (??0.035) and Jeju horse (??0.038). F_ST value was the highest between Jeju horse and Thoroughbred (0.113), whereas Jeju crossbred and Thoroughbred showed the lowest value (0.031). The genetic relationship was further assessed by principal component analysis, suggesting that Jeju crossbred is more genetically similar to Thoroughbred than Jeju horse population. Additionally, we detected potential selection signatures, for example, in loci located on LCORL/NCAPG and PROP1 genes that are known to influence body. Genome-wide analyses of the three horse populations showed that all the breeds had somewhat a low level of inbreeding within each population. In the population structure analysis, we found that Jeju crossbred was genetically closer to Thoroughbred than Jeju horse. Furthermore, we identified several signatures of selection which might be associated with traits of interest. To our current knowledge, this study is the first genomic research, analyzing genetic relationships of Jeju horse, Thoroughbred and Jeju crossbred.     

Targeted imputation of sequence variants and gene expression profiling identifies twelve candidate genes associated with lactation volume,composition and calving interval in dairy cattle

Dairy cattle are an interesting model for gaining insights into the genes responsible for the large variation between and within mammalian species in the protein and fat content of their milk and their milk volume. Large numbers of phenotypes for these traits are available, as well as full genome sequence of key founders of modern dairy cattle populations. In twenty target QTL regions affecting milk production traits, we imputed full genome sequence variant genotypes into a population of 16,721 Holstein and Jersey cattle with excellent phenotypes. Association testing was used to identify variants within each target region, and gene expression data were used to identify possible gene candidates. There was statistical support for imputed sequence variants in or close to BTRC, MGST1, SLC37A1, STAT5A, STAT5B, PAEP, VDR, CSF2RB, MUC1, NCF4, and GHDC associated with milk production, and EPGN for calving interval. Of these candidates, analysis of RNA-Seq data demonstrated that PAEP, VDR, SLC37A1, GHDC, MUC1, CSF2RB, and STAT5A were highly differentially expressed in mammary gland compared to 15 other tissues. For nine of the other target regions, the most significant variants were in non-coding DNA. Genomic predictions in a third dairy breed (Australian Reds) using sequence variants in only these candidate genes were for some traits more accurate than genomic predictions from 632,003 common SNP on the Bovine HD array. The genes identified in this study are interesting candidates for improving milk production in cattle and could be investigated for novel biological mechanisms driving lactation traits in other mammals.     

A GWA study reveals genetic loci for body conformation traits in Chinese Laiwu pigs and its implications for human BMI

Pigs share numerous physiological and phenotypic similarities with human and thus have been considered as a good model in nonrodent mammals for the study of genetic basis of human obesity. Researches on candidate genes for obesity traits have successfully identified some common genes between humans and pigs. However, few studies have assessed how many similarities exist between the genetic architecture of obesity in pigs and humans by large-scale comparative genomics. Here, we performed a genome-wide association study (GWAS) using the porcine 60 K SNP Beadchip for BMI and other four conformation traits at three different ages in a Chinese Laiwu pig population, which shows a large variability in fat deposition. In total, 35 SNPs were found to be significant at Bonferroni-corrected 5 % chromosome-wise level (P = 2.13 × 10^?5) and 88 SNPs had suggestive (P < 10^?4) association with the conformation traits. Some SNPs showed age-dependent association. Intriguingly, out of 32 regions associated with BMI in pigs, 18 were homologous with the loci for BMI in humans. Furthermore, five closest genes to GWAS peaks including HIF1AN, SMYD3, COX10, SLMAP, and GBE1 have been already associated with BMI in humans, which makes them very promising candidates for these QTLs. The result of GO analysis provided strong support to the fact that mitochondria and synapse play important roles in obesity susceptibility, which is consistent with previous findings on human obesity, and it also implicated new gene sets related to chromatin modification and Ig-like C2-type 5 domain. Therefore, these results not only provide new insights into the genetic architecture of BMI in pigs but also highlight that humans and pigs share the significant overlap of obesity-related genes.     

Natural variation and genetic make-up of leaf blade area in spring barley

Key message

GWAS analysis for leaf blade area (LA) revealed intriguing genomic regions associated with putatively novel QTL and known plant stature-related phytohormone and sugar-related genes.

Abstract

Despite long-standing studies in the morpho-physiological characters of leaf blade area (LA) in cereal crops, advanced genetic studies to explore its natural variation are lacking. The importance of modifying LA in improving cereal grain yield and the genes controlling leaf traits have been well studied in rice but not in temperate cereals. To better understand the natural genetic variation of LA at four developmental stages, main culm LA was measured from 215 worldwide spring barleys including 92 photoperiod-sensitive accessions [PHOTOPERIOD RESPONSE LOCUS 1 (Ppd-H1)] and 123 accessions with reduced photoperiod sensitivity (ppd-H1) locus under controlled greenhouse conditions (long-day; 16/8 h; ~ 20/~ 16 °C day/night). The LA of Ppd-H1-carrying accessions was always smaller than in ppd-H1-carrying accessions. We found that nine SNPs from the Ppd-H1 gene were present in the collection of which marker 9 (M9; G/T in the CCT-domain) showed the most significant and consistent effect on LA at all studied developmental stages. Genome-wide association scans (GWAS) showed that the accessions carrying the ppd-H1 allele T/M9 (late heading) possessed more genetic variation in LA than the Ppd-H1 group carrying G/M9 (early heading). Several QTL with major effects on LA variation were found close to plant stature-related heading time, phytohormone- and sugar-related genes. The results provide evidence that natural variation of LA is an important source for improving grain yield, adaptation and canopy architecture of temperate cereals.

     

Identification of loci controlling forage yield and nutritive value in diploid alfalfa using GBS-GWAS

Key message

We attempted to identify genomic regions controlling forage yield and nutritive value in alfalfa. Several candidate genes and associated genetic markers were identified that could potentially be useful for alfalfa breeding to more efficiently develop improved cultivars.

Abstract

Alfalfa is one of the most widely cultivated forage legumes worldwide and improving alfalfa forage yield and nutritive value is a major global breeding goal. Genotyping-by-sequencing (GBS) provides cost-effective molecular marker genotyping for genome-wide association studies (GWAS). Using more than 15,000 genome-wide single nucleotide polymorphisms (SNP) identified from GBS, we conducted a GWAS to investigate forage yield and nutritive value-related traits. We have detected a number of associations for all the traits evaluated and a number of associations detected were located on the Medicago truncatula genome. The SNP in a coding region of a cell wall biosynthesis gene was associated with several cell wall-related traits, and we suggest that it may be the causative polymorphism. Two other SNPs residing in meristematic development and early growth genes were found to associate with the total biomass yield. None of the SNPs associated with regrowth after harvest or with spring regrowth were mapped to the M. truncatula genome, possibly reflecting the fact that M. truncatula is an annual species related to alfalfa that typically has limited ability to regrow. The alleles we identify with the major impact on forage yield and nutritive value can be rapidly incorporated into our breeding program.

     

Genome-wide association study identified genetic variations and candidate genes for plant architecture component traits in Chinese upland cotton

Key message

Thirty significant associations between 22 SNPs and five plant architecture component traits in Chinese upland cotton were identified via GWAS. Four peak SNP loci located on chromosome D03 were simultaneously associated with more plant architecture component traits. A candidate gene, Gh_D03G0922, might be responsible for plant height in upland cotton.

Abstract

A compact plant architecture is increasingly required for mechanized harvesting processes in China. Therefore, cotton plant architecture is an important trait, and its components, such as plant height, fruit branch length and fruit branch angle, affect the suitability of a cultivar for mechanized harvesting. To determine the genetic basis of cotton plant architecture, a genome-wide association study (GWAS) was performed using a panel composed of 355 accessions and 93,250 single nucleotide polymorphisms (SNPs) identified using the specific-locus amplified fragment sequencing method. Thirty significant associations between 22 SNPs and five plant architecture component traits were identified via GWAS. Most importantly, four peak SNP loci located on chromosome D03 were simultaneously associated with more plant architecture component traits, and these SNPs were harbored in one linkage disequilibrium block. Furthermore, 21 candidate genes for plant architecture were predicted in a 0.95-Mb region including the four peak SNPs. One of these genes (Gh_D03G0922) was near the significant SNP D03_31584163 (8.40 kb), and its Arabidopsis homologs contain MADS-box domains that might be involved in plant growth and development. qRT-PCR showed that the expression of Gh_D03G0922 was upregulated in the apical buds and young leaves of the short and compact cotton varieties, and virus-induced gene silencing (VIGS) proved that the silenced plants exhibited increased PH. These results indicate that Gh_D03G0922 is likely the candidate gene for PH in cotton. The genetic variations and candidate genes identified in this study lay a foundation for cultivating moderately short and compact varieties in future Chinese cotton-breeding programs.

     

Detection of Insertions/Deletions Within <Emphasis Type="Italic">SIRT1</Emphasis>, <Emphasis Type="Italic">SIRT2</Emphasis> and <Emphasis Type="Italic">SIRT3</Emphasis> Genes and Their Associations with Body Measurement Traits in Cattle

Growth traits are complex quantitative traits controlled by numerous candidate genes, and they can be well-evaluated using body measurement traits. As the members of the nicotinamide adenine dinucleotide-dependent family of histone deacetylases, class I sirtuin genes (including SIRT1, SIRT2 and SIRT3) play crucial roles in regulating lipid metabolism, cellular growth and metabolism, suggesting that they are potential candidate genes affecting body measurement traits in animals. Hence, the objective of this work aimed to detect novel insertions/deletions (indels) of SIRT1, SIRT2 and SIRT3 genes in 955 cattle belonging to five breeds, as well as to evaluate their effects on body measurement traits. Herein, the novel 12-bp indel of SIRT1 gene, the 7-bp indel of SIRT2 gene and the 26-bp indel of SIRT3 gene were firstly reported, respectively. The association analysis indicated that the indels within SIRT1 and SIRT2 genes were significantly associated with body measurement traits such as body weight, chest circumference, height at hip cross, hip width, body height, etc. (P?<?0.05 or P?<?0.01). Therefore, based on these findings, the two novel indel variants within bovine SIRT1 and SIRT2 genes could be considered as potential molecular markers for growth traits in cattle selection practices and breeding.