A genome scan for quantitative trait loci affecting three ear traits in a White Duroc × Chinese Erhualian resource population

Genome-wide association study reveals that the IBSP locus affects ear size in cattle

Ear size is a classical model for hot climate adaptation following the evolution, but the genetic basis of the traits associated with ear size remains to be elucidated. Here, we performed a genome-wide association study on 158 cattle to explain the genetic mechanism of ear size. One region on BTA6 between 36.79 and 38.80 Mb included 50 suggestive SNPs and 4 significant SNPs that were significantly associated with ear size. The most significant locus (P = 1.30 × 10-8) was a missense mutation (T250I) on the seventh exon of integrin-binding sialoprotein (IBSP), which had an allele substitution effect of 23.46 cm2 for ear size. Furthermore, this mutation will cause changes in the three-dimensional structure of the protein. To further identify genes underlying this typical feature, we performed a genome scan among nine cattle breeds with different ear sizes by using SweeD. Results suggested that IBSP was under positive selection among four breeds with relatively large ear sizes. The expression levels of IBSP in ear tissues of large- and small-ear cattle were significantly different. A haplotype diversity survey of this missense mutation in worldwide cattle breeds strongly implied that the origin of this missense mutation event was Bos taurus. These findings have important theoretical importance for the exploration of major genes associated with ear size and provide important molecular markers for the identification of cattle germplasm resources.

Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states

In this study, we identified copy number variants (CNVs) in 19 European autochthonous pig breeds and in two commercial breeds (Italian Large White and Italian Duroc) that represent important genetic resources for this species. The genome of 725 pigs was sequenced using a breed-specific DNA pooling approach (30-35 animals per pool) obtaining an average depth per pool of 42×. This approach maximised CNV discovery as well as the related copy number states characterising, on average, the analysed breeds. By mining more than 17.5 billion reads, we identified a total of 9592 CNVs (~683 CNVs per breed) and 3710 CNV regions (CNVRs; 1.15% of the reference pig genome), with an average of 77 CNVRs per breed that were considered as private. A few CNVRs were analysed in more detail, together with other information derived from sequencing data. For example, the CNVR encompassing the KIT gene was associated with coat colour phenotypes in the analysed breeds, confirming the role of the multiple copies in determining breed-specific coat colours. The CNVR covering the MSRB3 gene was associated with ear size in most breeds. The CNVRs affecting the ELOVL6 and ZNF622 genes were private features observed in the Lithuanian Indigenous Wattle and in the Turopolje pig breeds respectively. Overall, the genome variability unravelled here can explain part of the genetic diversity among breeds and might contribute to explain their origin, history and adaptation to a variety of production systems.

Whole genome SNPs discovery in Nero Siciliano pig

Autochthonous pig breeds represent an important genetic reserve to be utilized mainly for the production of typical products. To explore its genetic variability, here we present for the first time whole genome sequencing data and SNPs discovered in a male domestic Nero Siciliano pig compared to the last pig reference genome Sus scrofa11.1.A total of 346.8 million paired reads were generated by sequencing. After quality control, 99.03% of the reads were mapped to the reference genome, and over 11 million variants were detected.Additionally, we evaluated sequence diversity in 21 fitness-related loci selected based on their biological function and/or their proximity to relevant QTLs. We focused on genes that have been related to environmental adaptation and reproductive traits in previous studies regarding local breeds. A total of 6,747 variants were identified resulting in a rate of 1 variant every ~276 bases. Among these variants 1,132 were novel to the dbSNP151 database. This study represents a first step in the genetic characterization of Nero Siciliano pig and also provides a platform for future comparative studies between this and other swine breeds.

Molecular cloning of WIF1 and HMGA2 reveals ear-preferential expression while uncovering a missense mutation associated with porcine ear size in WIF1

Considerable diversity exists in porcine ear size, which is an important morphological feature of pig breeds. Previously, we localized four crucial candidate genes-high mobility group AT-hook 2 (HMGA2), LEM domain-containing 3 (LEMD3), methionine sulfoxide reductase B3 (MSRB3) and Wnt inhibitory factor 1 (WIF1)-on Sus Scrofa chromosome 5 affecting porcine ear size, then cloned LEMD3 and MSBR3. In this study, we performed rapid amplification of cDNA ends to obtain full-length cDNA sequences of 2338-bp WIF1 and 2998-bp HMGA2. Using quantitative real-time PCR, we revealed that WIF1 expression was highest in ear cartilage of 60-day-old pigs and that this is therefore a better candidate gene for ear size than HMGA2. We further screened coding sequence variants in both genes and identified only one missense mutation (WIF1:c.1167C>G) in a conserved epidermal growth factor-like domain from the mammalian WIF1 protein. The protein-altering mutation was significantly associated with ear size across the Large White × Minzhu hybrid and Beijing Black pig populations. When WIF1:c.1167C>G was included as fixed effect in the model to re-run a genome-wide association study in the Large White × Minzhu intercross population the P-value of the peak SNP on SSC5 from re-running the genome-wide association study dropped from 2.45E-12 to 7.33E-05. Taken together, the WIF1:c.1167C>G could be an important mutation associated with ear size. Our findings provide helpful information for further studies of the molecular mechanisms controlling porcine ear size.

Copy number variation in the MSRB3 gene enlarges porcine ear size through a mechanism involving miR-584-5p

Background

The size and type of ears are important conformation characteristics that distinguish pig breeds. A significant quantitative trait locus (QTL) for ear size has been identified on SSC5 (SSC for Sus scrofa chromosome) but the underlying causative gene and mutation remain unknown. Thus, our aim was to identify the gene responsible for enlarged ears in pig.

Results

First, we narrowed down the QTL region on SSC5 to a 137.85-kb interval that harbors only the methionine sulfoxide reductase B3 (MSRB3) gene. Then, we identified a 38.7-kb copy number variation (CNV) that affects the last two exons of MSRB3 and could be the candidate causative mutation for this QTL. This CNV showed complete concordance with genotype at the QTL of the founder animals in a white Duroc × Erhualian F₂ intercross and was found only in pigs from six Chinese indigenous breeds with large ears and from the Landrace breed with half-floppy ears. Moreover, it accounted for the significant association with ear size on SSC5 across the five pig populations tested. eQTL mapping revealed that this CNV was significantly associated with the expression of the microRNA (miRNA) miR-584-5p, which interacts with MSRB3, one of its target genes. In vivo and in vitro experiments confirmed that miR-584-5p inhibits the translation of MSRB3 mRNA. Taken together, these results led us to conclude that presence of the 38.7-kb CNV in the genome of some pig breeds affects ear size by altering the expression of miR-584-5p, which consequently hinders the expression of one of its target genes (e.g. MSRB3).

Conclusions

Our findings shed insight into the underlying mechanism of development of external ears in mammals and contribute to a better understanding of how the presence of CNV can regulate gene expression.

Electronic supplementary material

The online version of this article (10.1186/s12711-018-0442-6) contains supplementary material, which is available to authorized users.

Whole-genome resequencing reveals candidate mutations for pig prolificacy

Changes in pig fertility have occurred as a result of domestication, but are not understood at the level of genetic variation. To identify variations potentially responsible for prolificacy, we sequenced the genomes of the highly prolific Taihu pig breed and four control breeds. Genes involved in embryogenesis and morphogenesis were targeted in the Taihu pig, consistent with the morphological differences observed between the Taihu pig and others during pregnancy. Additionally, excessive functional non-coding mutations have been specifically fixed or nearly fixed in the Taihu pig. We focused attention on an oestrogen response element (ERE) within the first intron of the bone morphogenetic protein receptor type-1B gene (BMPR1B) that overlaps with a known quantitative trait locus (QTL) for pig fecundity. Using 242 pigs from 30 different breeds, we confirmed that the genotype of the ERE was nearly fixed in the Taihu pig. ERE function was assessed by luciferase assays, examination of histological sections, chromatin immunoprecipitation, quantitative polymerase chain reactions, and western blots. The results suggest that the ERE may control pig prolificacy via the cis-regulation of BMPR1B expression. This study provides new insight into changes in reproductive performance and highlights the role of non-coding mutations in generating phenotypic diversity between breeds.

Porcine methionine sulfoxide reductase B3: molecular cloning, tissue-specific expression profiles, and polymorphisms associated with ear size in Sus scrofa

Background

In Sus scrofa, methionine sulfoxide reductase B3 (MSRB3) is a crucial candidate gene for ear size, and an important conformational trait of pig breeds. However, challenges in MSRB3 cDNA amplification have prevented further identification of MSRB3 allelic variants influencing pig ear size.

Results

We cloned a full-length cDNA sequence of porcine MSRB3 by rapid-amplification of cDNA ends. The 3,765-bp gene contained a 5’-untranslated region (UTR) (190 bp), a coding region (552 bp), and a 3’-UTR (3,016 bp) and shared 84 %, 84 %, 87 %, 86 %, and 70 % sequence identities with human, orangutan, mouse, chicken, and zebrafish, respectively. The gene encoded a 183-amino acid protein, which shared 88 %, 91 %, 89 %, 86 %, and 67 % identities with human, orangutan, mouse, chicken, and zebrafish, respectively. Tissue expression analysis using qRT-PCR revealed that MSRB3 was expressed in the heart, liver, lung, kidney, spleen, ear, muscle, fat, lymph, skeletal, and hypothalamic tissues. Three single nucleotide polymorphisms (SNPs) were identified in MSRB3: c.-735C > T in the 5’ flanking region, c.2571 T > C in the 3’-UTR, and a synonymous mutation of c.484 T > C in the coding region. The SNPs c.-735C > T and c.2571 T > C were significantly associated with ear size in a Large White × Minzhu F2 population other than in Beijing Black pigs. Subsequently, at SNP c.-735C > T, the mRNA of MSRB3 was significantly higher expressed in ears of individuals with the TT genotype (Minzhu) than those with CC (Large White).

Conclusions

The porcine MSRB3 owned a 3,765-bp full-length cDNA sequence and was detected to express in ear tissue. Two SNPs of this gene were shown to be significantly associated with ear size in a Large White × Minzhu intercross population instead of Beijing Black pig population. What’s more, the individuals with higher mRNA expression of MSRB3 have larger ear sizes. These results provide useful information for further functional analyses of MSRB3 influencing ear size in pigs.

Electronic supplementary material

The online version of this article (doi:10.1186/s40104-015-0060-x) contains supplementary material, which is available to authorized users.

Whole-genome sequence analysis reveals differences in population management and selection of European low-input pig breeds

BACKGROUND

A major concern in conservation genetics is to maintain the genetic diversity of populations. Genetic variation in livestock species is threatened by the progressive marginalisation of local breeds in benefit of high-output pigs worldwide. We used high-density SNP and re-sequencing data to assess genetic diversity of local pig breeds from Europe. In addition, we re-sequenced pigs from commercial breeds to identify potential candidate mutations responsible for phenotypic divergence among these groups of breeds.

RESULTS

Our results point out some local breeds with low genetic diversity, whose genome shows a high proportion of regions of homozygosis (>50%) and that harbour a large number of potentially damaging mutations. We also observed a high correlation between genetic diversity estimates using high-density SNP data and Next Generation Sequencing data (r = 0.96 at individual level). The study of non-synonymous SNPs that were fixed in commercial breeds and also in any local breed, but with different allele, revealed 99 non-synonymous SNPs affecting 65 genes. Candidate mutations that may underlie differences in the adaptation to the environment were exemplified by the genes AZGP1 and TAS2R40. We also observed that highly productive breeds may have lost advantageous genotypes within genes involve in immune response--e.g. IL12RB2 and STAB1-, probably as a result of strong artificial in the intensive production systems in pig.

CONCLUSIONS

The high correlation between genetic diversity computed with the 60K SNP and whole genome re-sequence data indicates that the Porcine 60K SNP Beadchip provides reliable estimates of genomic diversity in European pig populations despite the expected bias. Moreover, this analysis gave insights for strategies to the genetic characterization of local breeds. The comparison between re-sequenced local pigs and re-sequenced commercial pigs made it possible to report candidate mutations to be responsible for phenotypic divergence among those groups of breeds. This study highlights the importance of low input breeds as a valuable genetic reservoir for the pig production industry. However, the high levels of ROHs, inbreeding and potentially damaging mutations emphasize the importance of the genetic characterization of local breeds to preserve their genomic variability.

Genome-wide scan reveals LEMD3 and WIF1 on SSC5 as the candidates for porcine ear size

The quantitative trait loci (QTL) for porcine ear size was previously reported to mainly focus on SSC5 and SSC7. Recently, a missense mutation, G32E, in PPARD in the QTL interval on SSC7 was identified as the causative mutation for ear size. However, on account of the large interval of QTL, the responsible gene on SSC5 has not been identified. In this study, an intercross population was constructed from the large-eared Minzhu, an indigenous Chinese pig breed, and the Western commercial Large White pig to examine the genetic basis of ear size diversity. A GWAS was performed to detect SNPs significantly associated with ear size. Thirty-five significant SNPs defined a 10.78-Mb (30.14–40.92 Mb) region on SSC5. Further, combining linkage disequilibrium and haplotype sharing analysis, a reduced region of 3.07-Mb was obtained. Finally, by using a selective sweep analysis, a critical region of about 450-kb interval containing two annotated genes LEMD3 and WIF1 was refined in this work. Functional analysis indicated that both represent biological candidates for porcine ear size, with potential application in breeding programs. The two genes could also be used as novel references for further study of the mechanism underlying human microtia.

Genome-wide scans to detect positive selection in Large White and Tongcheng pigs

Due to the direction, intensity, duration and consistency of genetic selection, especially recent artificial selection, the production performance of domestic pigs has been greatly changed. Therefore, we reasoned that there must be footprints or selection signatures that had been left during domestication. In this study, with porcine 60K BeadChip genotyping data from both commercial Large White and local Chinese Tongcheng pigs, we calculated the extended haplotype homozygosity values of the two breeds using the long-range haplotype method to detect selection signatures. We found 34 candidate regions, including 61 known genes, from Large White pigs and 25 regions comprising 57 known genes from Tongcheng pigs. Many selection signatures were found on SSC1, SSC4, SSC7 and SSC14 regions in both populations. According to quantitative trait loci and network pathway analyses, most of the regions and genes were linked to growth, reproduction and immune responses. In addition, the average genetic differentiation coefficient FST was 0.254, which means that there had already been a significant differentiation between the breeds. The findings from this study can contribute to further research on molecular mechanisms of pig evolution and domestication and also provide valuable references for improvement of their breeding and cultivation.

Fine mapping of a QTL for ear size on porcine chromosome 5 and identification of high mobility group AT-hook 2 (HMGA2) as a positional candidate gene

Background

Ear size and shape are distinct conformation characteristics of pig breeds. Previously, we identified a significant quantitative trait locus (QTL) influencing ear surface on pig chromosome 5 in a White Duroc × Erhualian F₂ resource population. This QTL explained more than 17% of the phenotypic variance.

Methods

Four new markers on pig chromosome 5 were genotyped across this F₂ population. RT-PCR was performed to obtain expression profiles of different candidate genes in ear tissue. Standard association test, marker-assisted association test and F-drop test were applied to determine the effects of single nucleotide polymorphisms (SNP) on ear size. Three synthetic commercial lines were also used for the association test.

Results

We refined the QTL to an 8.7-cM interval and identified three positional candidate genes i.e. HMGA2, SOX5 and PTHLH that are expressed in ear tissue. Seven SNP within these three candidate genes were selected and genotyped in the F₂ population. Of the seven SNP, HMGA2 SNP (JF748727: g.2836 A > G) showed the strongest association with ear size in the standard association test and marker-assisted association test. With the F-drop test, F value decreased by more than 97% only when the genotypes of HMGA2 g.2836 A > G were included as a fixed effect. Furthermore, the significant association between g.2836 A > G and ear size was also demonstrated in the synthetic commercial Sutai pig line. The haplotype-based association test showed that the phenotypic variance explained by HMGA2 was similar to that explained by the QTL and at a much higher level than by SOX5. More interestingly, HMGA2 is also located within the dog orthologous chromosome region, which has been shown to be associated with ear type and size.

Conclusions

HMGA2 was the closest gene with a potential functional effect to the QTL or marker for ear size on chromosome 5. This study will contribute to identify the causative gene and mutation underlying this QTL.

A missense mutation in PPARD causes a major QTL effect on ear size in pigs

Chinese Erhualian is the most prolific pig breed in the world. The breed exhibits exceptionally large and floppy ears. To identify genes underlying this typical feature, we previously performed a genome scan in a large scale White Duroc × Erhualian cross and mapped a major QTL for ear size to a 2-cM region on chromosome 7. We herein performed an identical-by-descent analysis that defined the QTL within a 750-kb region. Historically, the large-ear feature has been selected for the ancient sacrificial culture in Erhualian pigs. By using a selective sweep analysis, we then refined the critical region to a 630-kb interval containing 9 annotated genes. Four of the 9 genes are expressed in ear tissues of piglets. Of the 4 genes, PPARD stood out as the strongest candidate gene for its established role in skin homeostasis, cartilage development, and fat metabolism. No differential expression of PPARD was found in ear tissues at different growth stages between large-eared Erhualian and small-eared Duroc pigs. We further screened coding sequence variants in the PPARD gene and identified only one missense mutation (G32E) in a conserved functionally important domain. The protein-altering mutation showed perfect concordance (100%) with the QTL genotypes of all 19 founder animals segregating in the White Duroc × Erhualian cross and occurred at high frequencies exclusively in Chinese large-eared breeds. Moreover, the mutation is of functional significance; it mediates down-regulation of β-catenin and its target gene expression that is crucial for fat deposition in skin. Furthermore, the mutation was significantly associated with ear size across the experimental cross and diverse outbred populations. A worldwide survey of haplotype diversity revealed that the mutation event is of Chinese origin, likely after domestication. Taken together, we provide evidence that PPARD G32E is the variation underlying this major QTL.

A central but challenging objective in current biology is to dissect the genetic basis of quantitative traits. Numerous quantitative trait loci (QTL) have been uncovered in model and farm animals, providing unexpected insights into the biology of complex traits. However, only a few causal variants underlying the QTL have been explicitly identified. By using a battery of genetic and functional assays, we herein show that a major QTL effect on pig ear size is most likely caused by a single base substitution in an evolutionary conserved region of the PPARD gene. The protein-altered mutation is of functional significance and explains a proportion of variation in ear size across diverse pig breeds. A worldwide survey showed that the mutant allele for increased ear size was derived from a common ancestor in Chinese pigs, likely after domestication. These findings establish, for the first time, an essential role of PPARD in ear development and highlight the great potential of naturally occurring mutations in farm animals to gain insights into mammalian biology. Moreover, the knowledge of the PPARD causal mutation adds to the limited list of quantitative trait genes and quantitative trait nucleotides characterized in domesticated animals.

High throughput analyses of epistasis for swine body dimensions and organ weights

High throughput analyses were performed to detect epistatic QTL in 17 body dimension and organ weight traits from a large F(2) pig population derived from a White Duroc and Erhualian intercross. The analyses used a nested test framework to handle multiple tests and a combined search algorithm to map epistatic QTL with empirical genome-wide thresholds derived via prior permutation. Alternative statistical models (e.g. including vs. excluding carcass weight as a covariate) were tested to develop an in-depth understanding of the role of epistasis in these kinds of traits. Epistasis signals were detected in only two or three traits under each statistical model studied. The interaction component of each pair of epistatic QTL explained a small proportion (0.7 to 2.1%) of the phenotypic variance in general. About half of the detected epistatic QTL pairs involved one of the two major QTL on porcine chromosomes 7 and 4. In those traits, the Erhualian allele consistently increased the phenotypes for the chromosome 7 QTL but decreased them for the chromosome 4 QTL. Models including carcass weight as covariate detected epistasis in body dimension traits whereas those excluding carcass weight found epistasis in organ weight traits. In addition, the epistasis results suggested that a QTL on chromosome 14 could be important for a number of organ weight traits. Using the high-throughput analysis tool to examine different statistical models was essential for the generation of a complete picture of epistasis in a whole category of traits.