Single nucleotide polymorphisms of the KIT and KITLG genes in pigs

Population structure of 3907 worldwide pigs and the introgression of Chinese indigenous pigs by European pigs

With the improvement in sequencing technology and the decrease in sequencing cost, increasing amounts of genomic data for pigs have been uploaded to public databases. However, no researchers have to date integrated all currently available data to uncover the global genetic status of pigs. Meanwhile, little is known about the introgression from European to Chinese pigs and its underlying influences. Therefore, we integrated the effective genotype data of 3907 pigs from 193 populations worldwide using population genetic analysis, gene flow analysis and a sharing-IBD study. These findings illustrate not only the population structure of 59 Chinese native breeds and others but also the amounts of gene flow and introgression that have occurred between Western and Chinese pigs. In addition, we demonstrate the presence of introgressed European haplotypes in Chinese indigenous breeds and identify relevant introgressed regions that contain genes associated with growth and feed efficiency. Moreover, we compare the introgression patterns of Western and Chinese pigs and further discuss possible explanations for why the level of introgression differs between Chinese pig breeds and Western modern breeds. Collectively, this study provides a fine global population structure analysis of pigs and presents evidence of European pigs being interbred with local breeds in China.

Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features

Background

A large number of pig breeds are distributed around the world, their features and characteristics vary among breeds, and they are valuable resources. Understanding the underlying genetic mechanisms that explain across-breed variation can help breeders develop improved pig breeds.

Results

In this study, we performed GWAS using a standard mixed linear model with three types of genome variants (SNP, InDel, and CNV) that were identified from public, whole-genome, sequencing data sets. We used 469 pigs of 57 breeds, and we identified and analyzed approximately 19 million SNPs, 1.8 million InDels, and 18,016 CNVs. We defined six biological phenotypes by the characteristics of breed features to identify the associated genome variants and candidate genes, which included coat color, ear shape, gradient zone, body weight, body length, and body height. A total of 37 candidate genes was identified, which included 27 that were reported previously (e.g., PLAG1 for body weight), but the other 10 were newly detected candidate genes (e.g., ADAMTS9 for coat color).

Conclusion

Our study indicated that using GWAS across a modest number of breeds with high density genome variants provided efficient mapping of complex traits.

Supplementary Information

Supplementary information accompanies this paper at 10.1186/s40104-020-00520-8.

Polymorphisms of four candidate genes and their correlations with growth traits in blue fox (Alopex lagopus)

To improve the accuracy and genetic progress of blue fox breeding, the relationships between genetic polymorphisms and growth and reproductive traits of the blue fox were investigated. MC4R, MC3R, INHA and INHBA were selected as candidate genes for molecular evolution and statistical analyses. Single-factor variance analyses showed that the MC4R (g.267C > T, g.423C > T, and g.731C > A) and MC3R (g.677C > T) genotypes had significant impacts on body weight, chest circumference, abdominal perimeter and body mass index (BMI) (P < 0.05) in blue fox. The MC4R and MC3R combined genotypes had significant effects on the body weight and abdominal circumference. The different genotypes of INHA g.75G > A had significant effects on female fecundity, whereas the different genotypes of INHBA g.404G > T and g.467G > T and the INHA and INHBA combined genotypes had significant effects on male fecundity. The proteins encoded by the open reading frames (ORFs) of different polymorphic loci were predicted and analysed. The aims of this study were to identify genetic markers related to growth and reproduction in the blue fox and to provide an efficient, economical and accurate theoretical approach for auxiliary fox breeding.

Artificial selection on introduced Asian haplotypes shaped the genetic architecture in European commercial pigs

Early pig farmers in Europe imported Asian pigs to cross with their local breeds in order to improve traits of commercial interest. Current genomics techniques enabled genome-wide identification of these Asian introgressed haplotypes in modern European pig breeds. We propose that the Asian variants are still present because they affect phenotypes that were important for ancient traditional, as well as recent, commercial pig breeding. Genome-wide introgression levels were only weakly correlated with gene content and recombination frequency. However, regions with an excess or absence of Asian haplotypes (AS) contained genes that were previously identified as phenotypically important such as FASN, ME1, and KIT. Therefore, the Asian alleles are thought to have an effect on phenotypes that were historically under selection. We aimed to estimate the effect of AS in introgressed regions in Large White pigs on the traits of backfat (BF) and litter size. The majority of regions we tested that retained Asian deoxyribonucleic acid (DNA) showed significantly increased BF from the Asian alleles. Our results suggest that the introgression in Large White pigs has been strongly determined by the selective pressure acting upon the introgressed AS. We therefore conclude that human-driven hybridization and selection contributed to the genomic architecture of these commercial pigs.

Two mutations in the 5'-flanking region of the KITLG gene are associated with litter size of dairy goats

In this study, Xinong Saanen (SN) and Guanzhong (GZ) dairy goat breeds were used to detect single nucleotide polymorphisms (SNPs) in the 5'-flanking region of the KITLG gene by DNA sequencing and primer-introduced restriction analysis-polymerase chain reaction. Two novel SNPs (g.13090G>T and g.13664C>A) were identified (GenBank Accession no. KM658964). Furthermore, g.13090G>T and g.13664C>A loci were closely linked in SN and GZ breeds (r(2) > 0.33). Association analysis results showed that g.13090G>T and g.13664C>A SNPs significantly affected litter size (P < 0.05). The litter size of individuals with the combined genotype GG/CC from both dairy goat breeds was greater than that of individuals with TT/AA in average parity (P < 0.05). Known biochemical and physiological functions, along with our results, indicated that GG/CC could be used in marker-assisted selection to choose individuals with greater litter size from both breeds. These results extend the spectrum of genetic variation in the caprine KITLG gene and may contribute to genetic resources and breeding of goats.

Association analysis between variants in KITLG gene and litter size in goats

Xinong Saanen (SN) and Guanzhong (GZ) goat breeds were used to detect single nucleotide polymorphisms (SNPs) in the coding regions with their intron-exon boundaries and the proximal flanking regions of KITLG gene by DNA sequencing and genotyped by PCR-restriction fragment (PCR-RFLP). Four novel SNPs (g.12654G>A, g.12772G>A, g.12829T>C and g.23683C>T) were identified (GenBank accession No. KM609289). It was shown that Xinong Saanen and Guanzhong goat breeds were in Hardy-Weinberg disequilibrium at g.12654G>A, g.12772G>A and g.12829T>C loci (P<0.05). The g.12654G>A, g.12772G>A and g.12829T>C loci were closely linked in both goat breeds (r(2)>0.33). Results of an association analysis indicated that SNPs g.12654G>A, g.12772G>A and g.12829T>C had significant effects on litter size (P<0.05). The combined genotypes of four SNP loci also affected litter size with the C7(GG/GG/CC/CC) genotype in the SN goat breed and C1(AA/GG/CC/CC) and C7(GG/GG/CC/CC) genotypes in the GZ goat breed having the highest litter size. The biochemical and physiological functions, together with the results obtained in our investigation, suggest that C7(GG/GG/CC/CC) could be used in marker-assisted selection to select the individuals with higher litter size in both goat breeds. The results extend the spectrum of genetic variation of the caprine KITLG gene, which might contribute to goat genetic resources and breeding.

Genomic analysis reveals selection for Asian genes in European pigs following human-mediated introgression

The independent domestication of local wild boar populations in Asia and Europe about 10,000 years ago led to distinct European and Asian pig breeds, each with very different phenotypic characteristics. During the Industrial Revolution, Chinese breeds were imported to Europe to improve commercial traits in European breeds. Here we demonstrate the presence of introgressed Asian haplotypes in European domestic pigs and selection signatures on some loci in these regions, using whole genome sequence data. The introgression signatures are widespread and the Asian haplotypes are rarely fixed. The Asian introgressed haplotypes are associated with regions harbouring genes involved in meat quality, development and fertility. We identify Asian-derived non-synonymous mutations in the AHR gene that associate with increased litter size in multiple European commercial lines. These findings demonstrate that increased fertility was an important breeding goal for early nineteenth century pig farmers, and that Asian variants of genes related to this trait were preferentially selected during the development of modern European pig breeds.

Signatures of diversifying selection in European pig breeds

Following domestication, livestock breeds have experienced intense selection pressures for the development of desirable traits. This has resulted in a large diversity of breeds that display variation in many phenotypic traits, such as coat colour, muscle composition, early maturity, growth rate, body size, reproduction, and behaviour. To better understand the relationship between genomic composition and phenotypic diversity arising from breed development, the genomes of 13 traditional and commercial European pig breeds were scanned for signatures of diversifying selection using the Porcine60K SNP chip, applying a between-population (differentiation) approach. Signatures of diversifying selection between breeds were found in genomic regions associated with traits related to breed standard criteria, such as coat colour and ear morphology. Amino acid differences in the EDNRB gene appear to be associated with one of these signatures, and variation in the KITLG gene may be associated with another. Other selection signals were found in genomic regions including QTLs and genes associated with production traits such as reproduction, growth, and fat deposition. Some selection signatures were associated with regions showing evidence of introgression from Asian breeds. When the European breeds were compared with wild boar, genomic regions with high levels of differentiation harboured genes related to bone formation, growth, and fat deposition.

The domestic pig, an important source of protein worldwide, was domesticated from the ancestral wild boar in multiple locations throughout the world. In Europe, local types were developed following domestication, but phenotypically distinct breeds only arose in the eighteenth century with the advent of systematic breeding. Recently developed molecular tools for pigs (as well as other livestock species) now allow a genetic characterisation of breed histories, including identification of regions of the genome that have been under selection in the establishment of breeds. We have applied these tools to identify genomic regions associated with breed development in a set of commercial and traditional pig breeds. We found strong evidence of genetic differentiation between breeds near genes associated with traits that are used to define breed standards, such as ear morphology and coat colour, as well as in regions of the genome that are associated with pork production traits. It is well documented that crosses with Asian pigs have been used to modify European breeds. We have found evidence of genetic influence from Asian pigs in European breeds, again in regions of the genome associated with breed standard characteristics, including ear shape and coat colour, as well as production traits.

Porcine single nucleotide polymorphism (SNP) development and population structure of pigs assessed by validated SNPs

In this study, we identified porcine single nucleotide polymorphisms (SNPs) by aligning eight sequences generated with two approaches: amplification of 665 intronic regions using one sample from each of eight breeds, including three East Asian pigs, and amplification of 289 3'-UTR regions using two samples from each of four major commercial breeds. The 1,760 and 599 SNPs were validated using two 384-sample DNA panels by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The phylogenetic tree and Structure analyses classified the pigs into two large clusters: Euro-American and East Asian populations. The membership proportions, however, differed between inferred clusters for K = 2 generated by the two approaches. With intronic SNPs, Euro-American breeds constituted about 100% of the Euro-American cluster, but with 3'-UTR SNPs, about 17% of the East Asian cluster comprised five Euro-American breeds. The differences in the SNP discovery panels may affect population structure found in study panels of large samples.

Exploring polymorphisms and their effects on reproductive traits of the INHA and INHβA genes in three goat breeds

In this study, we report the analysis of INHA and INHβA gene polymorphisms in 786 goats of three breeds: Xinong Saanen (SN), Guanzhong (GZ) and Boer (BG). We identified three new allelic variants: P1-C80G and/126G (GenBank accession no. HQ202573) in the three goat breeds and P2-C936T (GenBank accession no. HQ202572) in SN and GZ goat breeds. At P1 locus, AA, AB and BB genotypes were found in the three goat breeds. At P2 locus, CC and CT genotypes were found in SN and GZ goat breeds. After comparing genotype distribution within the three goat breeds, BG had conspicuous differences from SN and GZ (P < 0.001) at P2 locus. The SNP locus was in Hardy-Weinberg disequilibrium at P1 locus in the three goat breeds (P < 0.05). At P2 locus, the SNP locus was in Hardy-Weinberg disequilibrium in SN and GZ goat breeds (P < 0.05). Association of polymorphisms with litter size was done at P1 locus in the three goat breeds. The result showed that AA genotype had remarkable litter size at P1 locus in the three goat breeds (P < 0.05). Therefore, these results suggest that INHA gene is a strong candidate gene that affects litter size in goats.

Polymorphism identification in the goat KITLG gene and association analysis with litter size

This study reported the analysis of KIT ligand (KITLG) gene polymorphisms in 681 goats of three breeds: Xinong Saanen (SN), Guanzhong (GZ), and Boer (BG). In addition, the study identified three allelic variants: g.769T>C and g.817G>T in SN and GZ breeds, and g.9760G>C in the three goat breeds. The g.769T>C and g.817G>T loci were closely linked (r(2)  > 0.33). All the single nucleotide polymorphism loci were in Hardy-Weinberg disequilibrium (P < 0.05). Significant associations were found for litter size with all three loci. Therefore, these results suggest that the KITLG gene is a strong candidate gene affecting litter size in goats.

Genotypes of chicken major histocompatibility complex B locus associated with regression of Rous sarcoma virus J-strain tumors

The chicken MHC-B locus affects the response to several strains of Rous sarcoma virus (RSV). We evaluated the association between haplotypes of the MHC-B locus and responses to the J strain of RSV by using an F(2) experimental resource family constructed with tumor-regressive (White Leghorn) and tumor-progressive (Rhode Island Red) chickens. The MHC-B haplotypes were determined by genotyping of the microsatellite marker LEI0258 and MHC-B locus class I alpha chain 2 (BF2). Two haplotypes in the resource family, one associated with tumor regression and one with progression, were defined by these 2 markers. To discriminate more precisely the regressive haplotype in this family, we further developed 35 SNP markers at the MHC-B locus. Information on the haplotypes revealed here should be useful for identifying chickens with regression and progression phenotypes of J-strain RSV-induced tumors.

Differences in distribution of single nucleotide polymorphisms among intracellular pattern recognition receptors in pigs

Pathogens localized extracellularly or incorporated into endosomes are recognized mainly by Toll-like receptors, whereas pathogens and pathogen-derived molecules that invade into the cytoplasm of host cells typically are recognized by intracellular pattern recognition receptors (PRRs), such as retinoic acid-inducible gene (RIG)-like helicases (RLHs) and nucleotide-binding oligmerization domain (NOD)-like receptors (NLRs). RIG-I and melanoma differentiation-associated gene 5 (MDA5), which belong to the RLH family, recognize viral genomic RNA, whereas NOD2, a member of the NLR family, responds to microbial peptidoglycans. These receptors may play an important role in pig opportunistic infectious diseases, such as pneumonia and diarrhea, which markedly impair livestock productivity, such that polymorphisms of these receptor genes are potential targets of pig breeding to increase disease resistance. Here, we report single nucleotide polymorphisms (SNPs) in porcine DDX58, IFIH1, and NOD2, which encode RIG-I, MDA5, and NOD2, respectively. Interestingly, compared with DDX58 and IFIH1, NOD2 abounded in nonsynonymous SNPs both throughout the coding sequence and in sequences encoding domains important for ligand recognition, such as helicase domains for RIG-I and MDA5 and leucine-rich repeats in NOD2. These differences in the distribution of SNPs in intracellular PRRs may parallel the diversity of their ligands, which include nucleic acids and peptidoglycans.