Genome‐wide genetic variation discovery in Chinese Taihu pig breeds using next generation sequencing

The Chinese Taihu pig breeds are an invaluable component of the world's pig genetic resources, and they are the most prolific breeds of swine in the world. In this study, the genomes of 252 pigs of the six indigenous breeds in the Taihu Lake region were sequenced using the genotyping by genome reducing and sequencing approach. A total of 950 million good reads were obtained using an Illumina Hiseq2000 at an average depth of 13× (for SNP calling) and an average coverage of 2.3%. In total, 122 632 indels, 31 444 insertions, 44 056 deletions and 455 CNVs (copy number variants) were identified in the genomes of the pigs. Approximately 2.3% of these genetic markers were mapped to gene exon regions, and 25% were in QTL regions related to economically important traits. The KEGG pathway or GO enrichment analyses revealed that genetic variants assumed to be large‐effect mutations were significantly overrepresented in 22 SNP, 56 indel, 26 insertion, 28 deletion and three CNV gene sets. A total of 343 breed‐specific SNPs were also identified in the six Chinese indigenous pigs. The findings from this study can contribute to future investigations of the genetic diversity, population structure, positive selection signals and molecular evolutionary history of these pigs at the genome level and can serve as a valuable reference for improving the breeding and cultivation of these pigs.     

The Fat Mass and Obesity-Associated (FTO) Gene is Associated with Intramuscular Fat Content and Growth Rate in the Pig

The association of the FTO gene with obesity has been implicated in various human populations. The FTO gene is also most likely involved in the regulation of energy balance and feed intake. Here, the FTO gene was studied as a candidate gene for fatness and growth rate traits in pigs. The amino acid sequence of the FTO gene showed high conservation among human, pig, and other important domestic animals. Twelve variants including ten SNPs and two indels were detected, and then five SNPs within different genomic regions were genotyped in the ISU Berkshire × Yorkshire pig resource family. The linkage disequilibrium analyses revealed that most of these FTO variants were not in strong LD with each other. The SNPs c.46–139A > T within intron 1 and a synonymous mutation c.594C > G (Ala198Ala) within exon 3 had significant (P < 0.01) associations with average daily gain on test and total lipid percentage in muscle, respectively. Five major haplotypes were identified and the subsequent association analyses suggested that haplotype 2 (-CTTGG-) was the most favorable for increased growth rate, while haplotype 1 (-CTACG-) was unfavorably associated with intramuscular fatness traits.     

Detailed characterization of the porcine MC4R gene in relation to fatness and growth

In contrast to the human MC4R gene, where multiple variants have been described, several of which are associated with appetite and obesity, few MC4R variants have been reported in the pig. The most interesting polymorphism reported to date in the pig is p.Asp298Asn, which is significantly associated with variation in growth and fatness traits in most breeds and crosses. However, some reports have seemingly failed to confirm this association. The discrepancy of p.Asp298Asn associations in some pig populations suggested that further discovery of SNPs in MC4R would be useful. Utilizing the recently released pig genome sequence information, we obtained the whole MC4R genome sequence and detected five additional SNPs, a variable (CA) _n repeat and a C indel in the ISU Berkshire × Yorkshire pig resource family. Linkage disequilibrium (LD) analysis revealed that the additional five SNPs were not in strong LD with p.Asp298Asn, but single marker association analysis indicated that they were significantly ( P  <   0.05) associated with fatness measures and very highly significantly ( P  <   0.0001) associated with average daily gain on test (ADGTEST). Three major haplotypes were identified and the subsequent association analyses suggested that the two non-synonymous SNPs had different effects, e.g. p.Arg236His influenced back fat and growth on test while p.Asp298Asn was primarily associated with variation in growth rate in this population. An interaction effect between these two SNPs was found for ADGTEST, which may partly explain some of the previous discrepancies reported for MC4R in different pig populations . Examination of the p.Arg236His polymorphism in populations where the effect of p.Asp298Asn is limited is warranted.     

A comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves

The domestic dog serves as an excellent model to investigate the genetic basis of disease. More than 400 heritable traits analogous to human diseases have been described in dogs. To further canine medical genetics research, we established the Dog Biomedical Variant Database Consortium (DBVDC) and present a comprehensive list of functionally annotated genome variants that were identified with whole genome sequencing of 582 dogs from 126 breeds and eight wolves. The genomes used in the study have a minimum coverage of 10× and an average coverage of ~24×. In total, we identified 23 133 692 single‐nucleotide variants (SNVs) and 10 048 038 short indels, including 93% undescribed variants. On average, each individual dog genome carried ～4.1 million single‐nucleotide and ~1.4 million short‐indel variants with respect to the reference genome assembly. About 2% of the variants were located in coding regions of annotated genes and loci. Variant effect classification showed 247 141 SNVs and 99 562 short indels having moderate or high impact on 11 267 protein‐coding genes. On average, each genome contained heterozygous loss‐of‐function variants in 30 potentially embryonic lethal genes and 97 genes associated with developmental disorders. More than 50 inherited disorders and traits have been unravelled using the DBVDC variant catalogue, enabling genetic testing for breeding and diagnostics. This resource of annotated variants and their corresponding genotype frequencies constitutes a highly useful tool for the identification of potential variants causative for rare inherited disorders in dogs.     

Association mapping of morphological traits in wild and captive zebra finches: reliable within,but not between populations

Identifying causal genetic variants underlying heritable phenotypic variation is a long‐standing goal in evolutionary genetics. We previously identified several quantitative trait loci (QTL) for five morphological traits in a captive population of zebra finches (Taeniopygia guttata) by whole‐genome linkage mapping. We here follow up on these studies with the aim to narrow down on the quantitative trait variants (QTN) in one wild and three captive populations. First, we performed an association study using 672 single nucleotide polymorphisms (SNPs) within candidate genes located in the previously identified QTL regions in a sample of 939 wild‐caught zebra finches. Then, we validated the most promising SNP–phenotype associations (n = 25 SNPs) in 5228 birds from four populations. Genotype–phenotype associations were generally weak in the wild population, where linkage disequilibrium (LD) spans only short genomic distances. In contrast, in captive populations, where LD blocks are large, apparent SNP effects on morphological traits (i.e. associations) were highly repeatable with independent data from the same population. Most of those SNPs also showed significant associations with the same trait in other captive populations, but the direction and magnitude of these effects varied among populations. This suggests that the tested SNPs are not the causal QTN but rather physically linked to them, and that LD between SNPs and causal variants differs between populations due to founder effects. While the identification of QTN remains challenging in nonmodel organisms, we illustrate that it is indeed possible to confirm the location and magnitude of QTL in a population with stable linkage between markers and causal variants.     

Genomic variation in Pekin duck populations developed in three different countries as revealed by whole‐genome data

It is well known that both British and American Pekin ducks originated from China. However, the populations differ substantially in production performance, but the genetic changes involved are still poorly understood. Herein, we sequenced 24 individual Pekin ducks (eight from each population) with an average sequencing depth of more than 45× for each population (mean coverage of 6.29 per individual). Among these populations from three different countries, we identified a large number of SNPs and indels as well as many unique population variants, which can be used as population‐specific molecular markers. Genomic comparisons among the three duck populations revealed many candidate genes as well as pathways and Gene Ontology categories that are putatively associated with meat yield in the British population, growth in the American population and brain development in all three populations. These findings will enable a better understanding of the artificial selection history of Pekin ducks and provide a valuable resource for future research on the breeding of this species.     

The South Asian Genome

The genetic sequence variation of people from the Indian subcontinent who comprise one-quarter of the world''s population, is not well described. We carried out whole genome sequencing of 168 South Asians, along with whole-exome sequencing of 147 South Asians to provide deeper characterisation of coding regions. We identify 12,962,155 autosomal sequence variants, including 2,946,861 new SNPs and 312,738 novel indels. This catalogue of SNPs and indels amongst South Asians provides the first comprehensive map of genetic variation in this major human population, and reveals evidence for selective pressures on genes involved in skin biology, metabolism, infection and immunity. Our results will accelerate the search for the genetic variants underlying susceptibility to disorders such as type-2 diabetes and cardiovascular disease which are highly prevalent amongst South Asians.     

SNP discovery and genotyping using restriction‐site‐associated DNA sequencing in chickens

Single nucleotide polymorphisms (SNPs) are essential to the understanding of population genetic variation and diversity. Here, we performed restriction‐site‐associated DNA sequencing (RAD‐seq) on 72 individuals from 13 Chinese indigenous and three introduced chicken breeds. A total of 620 million reads were obtained using an Illumina Hiseq2000 sequencer. An average of 75 587 SNPs were identified from each individual. Further filtering strictly validated 28 895 SNPs candidates for all populations. When compared with the NCBI dbSNP (chicken_9031), 15 404 SNPs were new discoveries. In this study, RAD‐seq was performed for the first time on chickens, implicating the remarkable effectiveness and potential applications on genetic analysis and breeding technique for whole‐genome selection in chicken and other agricultural animals.     

Polymorphism of the prion protein gene (<Emphasis Type="Italic">PRNP</Emphasis>) in Polish cattle affected by classical bovine spongiform encephalopathy

Recent attempts to discover genetic factors affecting cattle resistance/susceptibility to bovine spongiform encephalopathy (BSE) have led to the identification of two insertion/deletion (indel) polymorphisms, located within the promoter and intron 1 of the prion protein gene PRNP, showing a significant association with the occurrence of classical form of the disease. Because the effect of the polymorphisms was studied only in few populations, in this study we investigated whether previously described association of PRNP indel polymorphisms with BSE susceptibility in cattle is also present in Polish cattle population. We found a significant relation between the investigated PRNP indel polymorphisms (23 and 12 bp indels), and susceptibility of Polish Holstein-Friesian cattle to classical BSE (P < 0.05). The deletion variants of both polymorphisms were related to increased susceptibility, whereas insertion variants were protective against BSE.     

Comprehensive Characterization of Human Genome Variation by High Coverage Whole-Genome Sequencing of Forty Four Caucasians

Whole genome sequencing studies are essential to obtain a comprehensive understanding of the vast pattern of human genomic variations. Here we report the results of a high-coverage whole genome sequencing study for 44 unrelated healthy Caucasian adults, each sequenced to over 50-fold coverage (averaging 65.8×). We identified approximately 11 million single nucleotide polymorphisms (SNPs), 2.8 million short insertions and deletions, and over 500,000 block substitutions. We showed that, although previous studies, including the 1000 Genomes Project Phase 1 study, have catalogued the vast majority of common SNPs, many of the low-frequency and rare variants remain undiscovered. For instance, approximately 1.4 million SNPs and 1.3 million short indels that we found were novel to both the dbSNP and the 1000 Genomes Project Phase 1 data sets, and the majority of which (∼96%) have a minor allele frequency less than 5%. On average, each individual genome carried ∼3.3 million SNPs and ∼492,000 indels/block substitutions, including approximately 179 variants that were predicted to cause loss of function of the gene products. Moreover, each individual genome carried an average of 44 such loss-of-function variants in a homozygous state, which would completely “knock out” the corresponding genes. Across all the 44 genomes, a total of 182 genes were “knocked-out” in at least one individual genome, among which 46 genes were “knocked out” in over 30% of our samples, suggesting that a number of genes are commonly “knocked-out” in general populations. Gene ontology analysis suggested that these commonly “knocked-out” genes are enriched in biological process related to antigen processing and immune response. Our results contribute towards a comprehensive characterization of human genomic variation, especially for less-common and rare variants, and provide an invaluable resource for future genetic studies of human variation and diseases.     

Genetic diversity of Toll-like receptor 5 among pig populations

The Toll-like receptor 5 (TLR5) recognizes flagellin of Gram-positive and -negative bacteria and plays an important role in the host defense system. Here, we surveyed single nucleotide polymorphisms (SNPs) in the coding sequence of the porcine TLR5 gene in 83 individuals from five pig breeds, these including Chinese local populations and Western commercial pig breeds. A total of 19 medium polymorphic SNPs (0.25 < PIC < 0.5) were identified, three of which were missense mutations that clustered within the extracellular domain of TLR5. One of the non-synonymous SNPs fell within a 228-amino acid region which has been shown to be important for flagellin recognition. Four SNPs were only found with high frequencies in Oriental pig breeds. The 19 SNPs were found in 30 haplotypes, one of which segregated at high frequency in all samples. Compared with Western pig breeds, Chinese local populations had higher genetic diversity and more haplotypes. Tajima’s test showed no evidence for deviation from neutrality. The data provide useful information for future genetic marker characterization by means of disease association analysis and/or stimulating the mutation carrier with relevant ligands.     

Exome analysis and functional classification of identified variants in racing Quarter Horses

The main objectives of this study were to identify and functionally classify SNPs and indels by exome sequencing of animals of the racing line of Quarter Horses. Based on the individual genomic estimated breeding values (GEBVs) for maximum speed index (SImax) obtained for 349 animals, two groups of 20 extreme animals were formed. Of these individuals, 20 animals with high GEBVs for SImax and 19 with low GEBVs for SImax had their exons and 5′ and 3′ UTRs sequenced. Considering SNPs and indels, 105 182 variants were identified in the expressed regions of the Quarter Horse genome. Of these, 72 166 variants were already known and 33 016 are new variants and were deposited in a database. The analysis of the set of gene variants significantly related (P_adjusted < 0.05) to extreme animals in conjunction with the predicted impact of the changes and the physiological role of protein product pointed to two candidate genes potentially related to racing performance: SLC3A1 on ECA15 and CCN6 on ECA10.     

Balanced polymorphism fuels rapid selection in an invasive crab despite high gene flow and low genetic diversity

Adaptation across environmental gradients has been demonstrated in numerous systems with extensive dispersal, despite high gene flow and consequently low genetic structure. The speed and mechanisms by which such adaptation occurs remain poorly resolved, but are critical to understanding species spread and persistence in a changing world. Here, we investigate these mechanisms in the European green crab Carcinus maenas, a globally distributed invader. We focus on a northwestern Pacific population that spread across >12 degrees of latitude in 10 years from a single source, following its introduction <35 years ago. Using six locations spanning >1500 km, we examine genetic structure using 9376 single nucleotide polymorphisms (SNPs). We find high connectivity among five locations, with significant structure between these locations and an enclosed lagoon with limited connectivity to the coast. Among the five highly connected locations, the only structure observed was a cline driven by a handful of SNPs strongly associated with latitude and winter temperature. These SNPs are almost exclusively found in a large cluster of genes in strong linkage disequilibrium that was previously identified as a candidate for cold tolerance adaptation in this species. This region may represent a balanced polymorphism that evolved to promote rapid adaptation in variable environments despite high gene flow, and which now contributes to successful invasion and spread in a novel environment. This research suggests an answer to the paradox of genetically depauperate yet successful invaders: populations may be able to adapt via a few variants of large effect despite low overall diversity.     

Implication of genetic variants near TMEM18, BCDIN3D/FAIM2, and MC4R with coronary artery disease and obesity in Chinese: a angiography-based study

Coronary artery disease (CAD) is multifactorial disease which occurs as a result of the interaction of genetic and environmental factors. Obesity is an independent risk factor for cardiovascular disease. Recent genome-wide association studies have identified several genes associated with obesity in Europeans. We wondered whether these genetic variants were associated with CAD. Three single nucleotide polymorphisms (SNPs) rs7561317 near TMEM18, rs7138803 near BCDIN3D/FAIM2 and rs12970134 near MC4R were examined in 930 Han Chinese subjects based on coronary angiography, using polymerase chain reaction (PCR) followed by restriction fragment length polymorphism (RFLP) analysis. There were no significant differences in genotypes and allele distributions of three SNPs between CAD and CAD-free groups. The AA genotype of SNP rs12970134 near MC4R was associated to obesity both in CAD group and CAD-free group in Han Chinese population (P < 0.001, OR = 2.96, 95% CI 2.01–3.73; and P = 0.003, OR = 2.59, 95% CI 1.86–3.19, respectively). Our observations suggest that the polymorphism rs12970134 near MC4R may be associated to the risk of obesity in Han Chinese population.     

Ethnic and Geographical Aspects of the Prevalence of the Polymorphic Variants of Genes Associated with Tuberculosis

Specificity of the structure of gene pools of different ethno-territorial groups of the human population can underlie the epidemiological features of the spread of tuberculosis (TB) and the structure of the genetic component of the susceptibility to the disease. The variability of 62 genetic variants potentially associated with the risk of the development of TB in the Russian population of the city of Tomsk has been studied and the differentiation of various ethno-territorial groups of the world by these markers has been assessed. The studied sample comprised 445 Russian residents of the city of Tomsk without bronchopulmonary pathology. For comparison, the data on the variability of the genetic markers of interest in 26 populations from the 1000 Genomes Project was involved. In the Tomsk population, only the ancestral allele was found for seven of the 58 SNPs studied; the allele frequencies for 36 markers were within the limits of the values seen in other European populations; for 12 SNPs, the observed frequencies were closer to populations with a significant Mongoloid component. By the total of the SNPs, the Tomsk population, despite the geographical distance from the rest of the European populations, did not differ from them (in genetic distances and G_st statistics), although it had some features of the gene pool. Intergroup differentiation of the world populations by these SNPs reflects mainly interracial differences. The greatest differences in the genetic structure between the studied populations were seen for the markers localized in intergenic regions. Statistically significant differences were found when comparing the levels of the average expected heterozygosity between groups of “L4 carrier populations” of mycobacteria and “non-L4” populations, which indicates the impact of the prevalence of different pathogenic lineages of M. tuberculosis on the formation of population specificity of the allelic frequencies.