Partial short-read sequencing of a highly inbred Iberian pig and genomics inference thereof

Despite dramatic reduction in sequencing costs with the advent of next generation sequencing technologies, obtaining a complete mammalian genome sequence at sufficient depth is still costly. An alternative is partial sequencing. Here, we have sequenced a reduced representation library of an Iberian sow from the Guadyerbas strain, a highly inbred strain that has been used in numerous QTL studies because of its extreme phenotypic characteristics. Using the Illumina Genome Analyzer II (San Diego, CA, USA), we resequenced ～ 1% of the genome with average 4 × depth, identifying 68,778 polymorphisms. Of these, 55,457 were putative fixed differences with respect to the assembly, based on the genome of a Duroc pig, and 13,321 were heterozygous positions within Guadyerbas. Despite being highly inbred, the estimate of heterozygosity within Guadyerbas was ～ 0.78 kb(-1) in autosomes, after correcting for low depth. Nucleotide variability was consistently higher at the telomeric regions than on the rest of the chromosome, likely a result of increased recombination rates. Further, variability was 50% lower in the X-chromosome than in autosomes, which may be explained by a recent bottleneck or by selection. We divided the whole genome in 500 kb windows and we analyzed overrepresented gene ontology terms in regions of low and high variability. Multi organism process, pigmentation and cell killing were overrepresented in high variability regions and metabolic process ontology, within low variability regions. Further, a genome wide Hudson-Kreitman-Aguadé test was carried out per window; overall, variability was in agreement with neutral expectations.     

Copy number variations identified in the chicken using a 60K SNP BeadChip

Copy number variation (CNV) is considered an important genetic variation, contributing to many economically important traits in the chicken. Although CNVs can be detected using a comparative genomic hybridization array, the high‐density SNP array has provided an alternative way to identify CNVs in the chicken. In the current study, a chicken 60K SNP BeadChip was used to identify CNVs in two distinct chicken genetic lines (White Leghorn and dwarf) using the penncnv program. A total of 209 CNV regions were identified, distributing on chromosomes 1–22 and 24–28 and encompassing 13.55 Mb (1.42%) of chicken autosomal genome area. Three of seven selected CNVs (73.2% individuals) were completely validated by quantitative PCR. To our knowledge, this is the first report in the chicken identifying CNVs using a SNP array. Identification of 190 new identified CNVs illustrates the feasibility of the chicken 60K SNP BeadChip to detect CNVs in the chicken, which lays a solid foundation for future analyses of associations of CNVs with economically important phenotypes in chickens.     

Segmental duplications are hot spots of copy number variants affecting barley gene content

Copy number variants (CNVs) are pervasive in several animal and plant genomes and contribute to shaping genetic diversity. In barley, there is evidence that changes in gene copy number underlie important agronomic traits. The recently released reference sequence of barley represents a valuable genomic resource for unveiling the incidence of CNVs that affect gene content and for identifying sequence features associated with CNV formation. Using exome sequencing and read count data, we detected 16 605 deletions and duplications that affect barley gene content by surveying a diverse panel of 172 cultivars, 171 landraces, 22 wild relatives and other 32 uncategorized domesticated accessions. The quest for segmental duplications (SDs) in the reference sequence revealed many low‐copy repeats, most of which overlap predicted coding sequences. Statistical analyses revealed that the incidence of CNVs increases significantly in SD‐rich regions, indicating that these sequence elements act as hot spots for the formation of CNVs. The present study delivers a comprehensive genome‐wide study of CNVs affecting barley gene content and implicates SDs in the molecular mechanisms that lead to the formation of this class of CNVs.     

Characterization of OCA2 cDNA in different porcine breeds and analysis of its potential effect on skin pigmentation in a red Iberian strain

Although the function of the OCA2 gene product has not been totally clarified, variation in OCA2 has been associated with skin and hair pigmentation in human and mouse. However, its contribution to skin colour in domestic species has not been reported. In this study, cDNA and intron 9 sequences of the porcine OCA2 gene have been characterized in several pig populations. The cDNA sequence alignment of 20 animals from eight porcine populations allowed the identification of 10 single nucleotide polymorphisms (SNPs); five of the 10 SNPs were non-synonymous. The intron 9 sequence alignment of 12 animals belonging to four pig populations revealed four additional SNPs. Skin colour variation was analysed in a red strain of Iberian pigs with segregation of three SNPs forming two OCA2 intragenic haplotypes. Results from this study provide evidence of a suggestive dominant effect of haplotypes on colour intensity and indicate an important contribution of additive polygenic effects (h2 = 0.56 +/- 0.21) to the variance of this trait.     

Loss of secreted hemolysin activity in the mutant strain Hsb. 1 is due to a lesion in a plasmid copy number locus

Further studies have been carried out on mutation hsb which was previously suggested to block hemolysin secretion (Mu?oa et al., 1988, FEMS Microbiol. Lett. 56: 167-172). We show that the reported reduction in the extracellular hemolytic activity of mutant Hsb. 1 is due to lower hemolysin synthesis and that this is itself a consequence of a decrease in plasmid copy number. We suggest that the hsb is identical to the pcnB lesion located at minute 3.6 of the chromosome.     

Copy number variation in Fayoumi and Leghorn chickens analyzed using array comparative genomic hybridization

Copy number variation refers to regions along chromosomes that harbor a type of structural variation, such as duplications or deletions. Copy number variants (CNVs) play a role in many important traits as well as in genetic diversity. Previous analyses of chickens using array comparative genomic hybridizations or single‐nucleotide polymorphism chip assays have been performed on various breeds and genetic lines to discover CNVs. In this study, we assessed individuals from two highly inbred (inbreeding coefficiency > 99.99%) lines, Leghorn G‐B2 and Fayoumi M15.2, to discover novel CNVs in chickens. These lines have been previously studied for disease resistance, and to our knowledge, this represents the first global assessment of CNVs in the Fayoumi breed. Genomic DNA from individuals was examined using the Agilent chicken 244 K comparative genomic hybridization array and quantitative PCR. We identified a total of 273 CNVs overall, with 112 CNVs being novel and not previously reported. Quantitative PCR using the standard curve method validated a subset of our array data. Through enrichment analysis of genes within CNV regions, we observed multiple chromosomes, terms and pathways that were significantly enriched, largely dealing with the major histocompatibility complex and immune responsiveness. Using an additional round of computational and statistical analysis with a different bioinformatic pipeline, we identified 43 CNVs among these as high‐confidence regions, 14 of which were found to be novel. We further compared and contrasted individuals of the two inbred lines to discover regions that have a significant difference in copy number between lines. A total of 40 regions had significant deletions or duplications between the lines. Gene Ontology analysis of genomic regions containing CNVs between lines also was performed. This between‐line candidate CNV list will be useful in studies with these two unique genetic lines, which may harbor variations that underlie quantitative trait loci for disease resistance and other important traits. Through the global discovery of novel CNVs in chicken, these data also provide resources for further genetic and functional genomics studies.     

Copy number variants in Italian Large White pigs detected using high‐density single nucleotide polymorphisms and their association with back fat thickness

The aim of this study was to identify copy number variants (CNVs) in Italian Large White pigs and test them for association with back fat thickness (BFT). Within a population of 12 000 performance‐tested pigs, two groups of animals with extreme and divergent BFT estimated breeding values (EBVs; 147 with negative and 150 with positive EBVs) were genotyped with the Illumina Porcine SNP60 BeadChip. CNVs were detected with penncnv software. We identified a total of 4146 CNV events in 170 copy number variation regions (CNVRs) located on 15 porcine autosomes. Validation of detected CNVRs was carried out (i) by comparing CNVRs already detected by other studies and (ii) by semiquantitative fluorescent multiplex (SQFM) PCR of a few CNVRs. Most of CNVRs detected in Italian Large White pigs (71.2%) were already reported in other pig breeds/populations, and 82.1% of the CNV events detected by penncnv were confirmed by SQFM PCR. For each CNVR, we compared the occurrence of CNV events between the pigs of the high and low BFT EBV tails. Sixteen regions showed significance at P < 0.10, and seven were significant at P < 0.05 but were not significant after Bonferroni correction (Fisher's exact test). These results indicated that CNVs could explain a limited fraction of the genetic variability of fat deposition in Italian Large White pigs. However, it was interesting to note that one of these CNVRs encompassed the ZPLD1 gene. In humans, a rare CNV event including this gene is associated with obesity. Studies identifying CNVs in pigs could assist in elucidating the genetic mechanisms underlying human obesity.     

Mapping of the porcine oestrogen receptor 2 gene and association study with litter size in Iberian pigs

Genes encoding the oestrogen receptors (ESR) are considered candidate genes for prolificacy traits due to the key role these molecules play in the regulation of reproductive physiology. In this paper, we report the assignment of the pig ESR2 gene to porcine chromosome 1 by radiation hybrid mapping. Most of the ESR2 cDNA was sequenced from Iberian pig ovarian RNA samples and one A/G single nucleotide polymorphism (SNP) was found at exon 5, being associated with a Met/Val substitution at position 949. This SNP was genotyped using a PCR-RFLP (Hsp92II) protocol and its potential effect on litter size was evaluated in two Iberian pig populations. However, no statistically significant association between the ESR2 polymorphism and litter size was found.     

转基因猪中外源基因拷贝数和整合位点的研究

主要采用了绝对定量PCR和热不均一交错PCR(thermal asymmetric interlaced PCR,TAIL-PCR),检测了体细胞核移植技术生产的绿色荧光蛋白转基因猪中外源基因拷贝数和整合位点,并利用旁侧PCR(Junction PCR)对整合位点进行确定,同时进一步分析了整合位点的纯合性．结果表明,绝对定量PCR可以准确有效地检测外源基因拷贝数,标准曲线为：log₂N (拷贝数) =-0.935 4ΔCt + 3.411 6 (R²=0.997 4,P < 0.001),两只转基因猪中外源基因拷贝数分别为30.85 ± 1.77和18.87 ± 1.34;TAIL-PCR能成功地克隆转基因猪中外源基因整合位点,得到25条特异性条带,经BLAST比对,共获得TgInS1 (1 440 bp)、TgInS2 (1 263 bp)和TgInS3 (1 861 bp) 3个整合位点．以整合位点侧翼序列特异性引物与外源基因特异性引物的组合引发Junction PCR,得到预计大小的特异性片段,确定了整合位点上、下游侧翼序列的准确性．采用整合位点5′上游和3′下游侧翼序列特异性引物与外源基因特异性引物的组合,进行Junction PCR,在两只转基因猪中都得到与野生型猪一致的侧翼序列特异性引物扩增片段,表明我们获得的转基因猪都为整合位点杂合子．初步建立了绝对定量PCR和TAIL-PCR对外源基因拷贝数和整合位点检测的体系,为今后研究外源基因在转基因猪中遗传和表达的稳定性打下了基础．     

基因组拷贝数变异及其突变机理与人类疾病

拷贝数变异(Copy number variation,CNV)是由基因组发生重排而导致的,一般指长度为1 kb以上的基因组大片段的拷贝数增加或者减少,主要表现为亚显微水平的缺失和重复。CNV是基因组结构变异(Structural variation,SV)的重要组成部分。CNV位点的突变率远高于SNP(Single nucleotide polymorphism),是人类疾病的重要致病因素之一。目前,用来进行全基因组范围的CNV研究的方法有:基于芯片的比较基因组杂交技术(array-based comparative genomic hybridization,aCGH)、SNP分型芯片技术和新一代测序技术。CNV的形成机制有多种,并可分为DNA重组和DNA错误复制两大类。CNV可以导致呈孟德尔遗传的单基因病与罕见疾病,同时与复杂疾病也相关。其致病的可能机制有基因剂量效应、基因断裂、基因融合和位置效应等。对CNV的深入研究,可以使我们对人类基因组的构成、个体间的遗传差异、以及遗传致病因素有新的认识。     

Haplotype structure and copy number polymorphism of the beta‐defensin 7 genes in diverse chicken breeds

Beta‐defensins is a family of avian peptides related to the innate immune system. Copy number variation was recently reported for the avian beta‐defensin 7 gene (AvBD7) between the highly inbred Leghorn and Fayoumi lines. Here, we examined copy number variants in 35 different chicken breeds and found that 31 of them have at least the same representation of the duplicated AvBD7 allele. We also found haplotypes upstream of the AvBD6 regions that are strongly linked to the AvBD7 duplication. We observed a strong linkage disequilibrium spanning of the upstream region of the AvBD6 gene, with two SNPs being flanking markers to detect duplication of the AvBD7.     

Copy number variations of HLA-DRB5 is associated with systemic lupus erythematosus risk in Chinese Han population

Systemic lupus erythematosus （SLE） is a polygenic, systemic, autoimmune disease. Copy number variants （CNVS） have been discovered to be associated with a number of complex disorders. We undertook the current study to explore the potential associations between genomic CNVS and SLE in Chinese Han population. In the discovery stage, seven SLE patients were examined with the high-density comparative genomic hybridization microarrays in the screening test for SLE associated CNVS. Then, in the validation stage, 135 SLE patients and 219 matched healthy subjects were investigated for the CNVS of gene HLA-DRB5 by AccuCopyTM technol- ogy. Quantitative polymerase chain reaction was carried out to determine the copy number （CN） and mRNA level of HLA- DRB5 in SLE patients. Although the mRNA level of HLA- DRB5 between the CN deletion group and the CN normal group in SLE patients was not statistically positive （P = 0.46）, our results still showed more CN of HLA-DRB5 in SLE patients than in healthy controls （P = 3.98×10^-6）. Odds ratio for CN deletion was 0.38 （95% confidence interval （C1）, 0.23-0.61, P = 7.79×10^-5） and for CN duplication was 1.89 （95% CI, 0.56-7.66, P = 0.37）, respectively. These findings indicated that CNVS of HLA-DRB5 was associated with the risk of SLE, and CN deletion appeared to be protective for SLE.     

QTL mapping for teat number in an Iberian-by-Meishan pig intercross

The aim of this study was to investigate chromosomal regions affecting the number of teats in pigs and possible epistatic interactions between the identified quantitative trait loci (QTL). An experimental F2 cross between Iberian and Chinese Meishan lines was used for this purpose. A genomic scan was conducted with 117 markers covering the 18 porcine autosomes. Linkage analyses were performed by interval mapping using an animal model to estimate QTL and additive polygenic effects. Complementary analyses with models fitting two QTL were also carried out. The results showed three genomewide significant QTL mapping on chromosomes 5, 10 and 12, whose joint action control up to 30% of the phenotypic variance of the trait. Meishan alleles had a positive additive effect on teat number, and a positive-additive x additive-epistatic interaction was detected between QTL on chromosomes 10 and 12.     

Copy number variation profile-based genomic typing of premenstrual dysphoric disorder in Chinese

Premenstrual dysphoric disorder (PMDD) affects nearly 5% of women of reproductive age. Symptomatic heterogeneity, together with largely unknown genetics, has greatly hindered its effective treatment. In the present study, analysis of genomic sequencing-based copy number variations (CNVs) called from 100 kb white blood cell DNA sequence windows by means of semisupervized clustering led to the segregation of patient genomes into the D and V groups, which correlated with the depression and invasion clinical types, respectively, with 89.0% consistency. Application of diagnostic CNV features selected using the correlation-based machine learning method enabled the classification of the CNVs obtained into the D group, V group, total patient group, and control group with an average accuracy of 83.0%. The power of the diagnostic CNV features was 0.98 on average, suggesting that these CNV features could be used for the molecular diagnosis of the major clinical types of PMDD. This demonstrated concordance between the CNV profiles and clinical types of PMDD supported the validity of symptom-based diagnosis of PMDD for differentiating between its two major clinical types, as well as the predominantly genetic nature of PMDD with a host of overlaps between multiple susceptibility genes/pathways and the diagnostic CNV features as indicators of involvement in PMDD etiology.     

Enzyme markers in inbred rat strains: Genetics of new markers and strain profiles

Twenty-six inbred strains of the laboratory rat (Rattus norvegicus) were examined for electrophoretic variation at an estimated 97 genetic loci. In addition to previously documented markers, variation was observed for the enzymes aconitase, aldehyde dehydrogenase, and alkaline phosphatase. The genetic basis of these markers (Acon-1, Ahd-2, and Akp-1) was confirmed. Linkage analysis between 35 pairwise comparisons revealed that the markers Fh-1 and Pep-3 are linked. The strain profiles of the 25 inbred strains at 11 electrophoretic markers are given.     

Characterization of a porcine variable number tandem repeat sequence specific for the glucosephosphate isomerase locus

A variable number of tandem repeat from a porcine glucosephosphate isomerase intron has been isolated and sequenced. The repeat has a unit size of 39 bp, is highly conserved and is present in at least 14 copies. Flanking sequences show a sequence periodicity of 53-54 bp and some sequence homology to the 39 bp repeat. A considerable part of the genomic DNA has been lost during subcloning and is considered to be deletion prone or refractory to propagation in E. coli. The tandem repeat is locus specific and detects at least six alleles in BamHI digested porcine DNA. No homology to other tandem repeat sequences has been found.     

Copy number variation associates with mortality in long‐lived individuals: a genome‐wide assessment

Copy number variants (CNVs) represent a significant source of genetic variation in the human genome and have been implicated in numerous diseases and complex traits. To date, only a few studies have investigated the role of CNVs in human lifespan. To investigate the impact of CNVs on prospective mortality at the extreme end of life, where the genetic component of lifespan appears most profound, we analyzed genomewide CNV data in 603 Danish nonagenarians and centenarians (mean age 96.9 years, range 90.0–102.5 years). Replication was performed in 500 long‐lived individuals from the Leiden Longevity Study (mean age 93.2 years, range 88.9–103.4 years). First, we assessed the association between the CNV burden of each individual (the number of CNVs, the average CNV length, and the total CNV length) and mortality and found a significant increase in mortality per 10 kb increase in the average CNV length, both for all CNVs (hazard ratio (HR) = 1.024, P = 0.002) and for duplications (HR = 1.011, P = 0.005), as well as per 100 kb increase in the total length of deletions (HR = 1.009, P = 0.0005). Next, we assessed the relation between specific deletions and duplications and mortality. Although no genome–wide significant associations were discovered, we identified six deletions and one duplication that showed consistent association with mortality in both or either of the sexes across both study populations. These results indicate that the genome–wide CNV burden, specifically the average CNV length and the total CNV length, associates with higher mortality in long‐lived individuals.