Genome-wide scan for bovine twinning rate QTL using linkage disequilibrium

Twinning is a complex trait with negative impacts on health and reproduction, which cause economic loss in dairy production. Several twinning rate quantitative trait loci (QTL) have been detected in previous studies, but confidence intervals for QTL location are broad and many QTL are unreplicated. To identify genomic regions or genes associated with twinning rate, QTL analysis based on linkage combined with linkage disequilibrium (LLD) and individual marker associations was conducted across the genome using high-throughput single nucleotide polymorphism (SNP) genotypes. A total of 9919 SNP markers were genotyped with 200 sires and sons in 19 half-sib North American Holstein dairy cattle families. After SNPs were genotyped, informative markers were selected for genome-wide association tests and QTL searches. Evidence for twinning rate QTL was found throughout the genome. Thirteen markers significantly associated with twinning rate were detected on chromosomes 2, 5 and 14 ( P  < 2.3 × 10⁻⁵). Twenty-six regions on fourteen chromosomes were identified by LLD analysis at P  < 0.0007. Seven previously reported ovulation or twinning rate QTL were supported by results of single marker association or LLD analyses. Single marker association analysis and LLD mapping were complementary tools for the identification of putative QTL in this genome scan.     

金针菇单孢菌株菌丝生长速度QTL定位分析

本研究以已经完成基因组测序的单核菌株“6-3”与“6-21”为出发菌株,配对后获得有锁状联合的异核菌株并进行出菇,收集担孢子,单孢分离获得90个菌株构成作图群体,对作图群体的每个菌株进行二代测序并测定菌丝在PDA培养基的生长速度。分析“6-3”与“6-21”两单核菌株的SNP,获得68 914个高质量SNP标记用于遗传连锁群分析,构建了14个遗传连锁群,总长度744.32cM,平均长度为53.17cM,标记间平均遗传距离为1.88cM。QTL分析获得一个控制菌丝生长速度的基因座qMGRP1-LG7,该基因座包含134个基因,富集了与物质代谢有关的通路和基因。     

Analysis of population differentiation in North Eurasian cattle (Bos taurus) using single nucleotide polymorphisms in three genes associated with production traits

Single nucleotide polymorphisms (SNPs) in growth hormone 1 (GH1), insulin-like growth factor 1 (IGF1) and leptin (LEP), all candidates for production traits in cattle, were characterized in North Eurasian cattle breeds. Allele frequencies of IGF1 exhibited significant (P < 0.05) deviation from neutral expectation and therefore, might be associated with divergence in North Eurasian cattle because of genetic selection. Allele frequencies and lower heterozygosity of LEP may indicate a recent introduction of an alternative allele in this geographic region. Locus F(ST) estimates were highest for IGF1 (0.151, sigma = 0.042) and lowest for GH (0.062, sigma = 0.020). Our results suggest a slightly higher population differentiation across the candidate genes (FST = 0.108) than across microsatellites (FST = 0.095), possibly because of selection and stochastic effects.     

Single nucleotide polymorphisms for pig identification and parentage exclusion

Single nucleotide polymorphisms (SNPs) have become an important type of marker for commercial diagnostic and parentage genotyping applications as automated genotyping systems have been developed that yield accurate genotypes. Unfortunately, allele frequencies for public SNP markers in commercial pig populations have not been available. To fulfil this need, SNP markers previously mapped in the USMARC swine reference population were tested in a panel of 155 boars that were representative of US purebred Duroc, Hampshire, Landrace and Yorkshire populations. Multiplex assay groups of 5-7 SNP assays/group were designed and genotypes were determined using Sequenom's massarray system. Of 80 SNPs that were evaluated, 60 SNPs with minor allele frequencies >0.15 were selected for the final panel of markers. Overall identity power across breeds was 4.6 x 10(-23), but within-breed values ranged from 4.3 x 10(-14) (Hampshire) to 2.6 x 10(-22) (Yorkshire). Parentage exclusion probability with only one sampled parent was 0.9974 (all data) and ranged from 0.9594 (Hampshire) to 0.9963 (Yorkshire) within breeds. Sire exclusion probability when the dam's genotype was known was 0.99998 (all data) and ranged from 0.99868 (Hampshire) to 0.99997 (Yorkshire) within breeds. Power of exclusion was compared between the 60 SNP and 10 microsatellite markers. The parental exclusion probabilities for SNP and microsatellite marker panels were similar, but the SNP panel was much more sensitive for individual identification. This panel of SNP markers is theoretically sufficient for individual identification of any pig in the world and is publicly available.     

SNPs in the porcine GOT1 gene improve a QTL for serum aspartate aminotransferase activity on SSC14

Clinical–chemical traits are essential parameters to quantify the health status of individuals and herds, but the knowledge about their genetic architecture is sparse, especially in swine. We have recently described three QTL for serum aspartate aminotransferase activity (sAST), and one of these maps to a region on SSC14 where the aspartate aminotransferase coding gene GOT1 is located. This QTL was only apparent under the acute burden of a model disease. The aim of the present study was to characterize GOT1 as a candidate gene and to test the effects of different GOT1 SNPs as potential quantitative trait nucleotides (QTNs) for sAST. Nine SNPs within GOT1 were identified, and SNP c.‐793C>G significantly increased the QTL effects and narrowed the confidence interval from 90 to 15 cM. Additionally, we found a significant association of SNP c.‐793C>G in a commercial outbred line, but with reversed phase. We conclude that GOT1 is a putative candidate gene for the sAST QTL on SSC14, and that SNP c.‐793C>G is close to the responsible QTN.     

Genome-wide association analysis for feed efficiency in Angus cattle

Estimated breeding values for average daily feed intake (AFI; kg/day), residual feed intake (RFI; kg/day) and average daily gain (ADG; kg/day) were generated using a mixed linear model incorporating genomic relationships for 698 Angus steers genotyped with the Illumina BovineSNP50 assay. Association analyses of estimated breeding values (EBVs) were performed for 41,028 single nucleotide polymorphisms (SNPs), and permutation analysis was used to empirically establish the genome-wide significance threshold (P < 0.05) for each trait. SNPs significantly associated with each trait were used in a forward selection algorithm to identify genomic regions putatively harbouring genes with effects on each trait. A total of 53, 66 and 68 SNPs explained 54.12% (24.10%), 62.69% (29.85%) and 55.13% (26.54%) of the additive genetic variation (when accounting for the genomic relationships) in steer breeding values for AFI, RFI and ADG, respectively, within this population. Evaluation by pathway analysis revealed that many of these SNPs are in genomic regions that harbour genes with metabolic functions. The presence of genetic correlations between traits resulted in 13.2% of SNPs selected for AFI and 4.5% of SNPs selected for RFI also being selected for ADG in the analysis of breeding values. While our study identifies panels of SNPs significant for efficiency traits in our population, validation of all SNPs in independent populations will be necessary before commercialization.     

Single nucleotide polymorphisms for DNA typing in the domestic horse

Genetic markers are important resources for individual identification and parentage assessment. Although short tandem repeats (STRs) have been the traditional DNA marker, technological advances have led to single nucleotide polymorphisms (SNPs) becoming an attractive alternative. SNPs can be highly multiplexed and automatically scored, which allows for easier standardization and sharing among laboratories. Equine parentage is currently assessed using STRs. We obtained a publicly available SNP dataset of 729 horses representing 32 diverse breeds. A proposed set of 101 SNPs was analyzed for DNA typing suitability. The overall minor allele frequency of the panel was 0.376 (range 0.304–0.419), with per breed probability of identities ranging from 5.6 × 10^?35 to 1.86 × 10^?42. When one parent was available, exclusion probabilities ranged from 0.9998 to 0.999996, although when both parents were available, all breeds had exclusion probabilities greater than 0.9999999. A set of 388 horses from 35 breeds was genotyped to evaluate marker performance on known families. The set included 107 parent–offspring pairs and 101 full trios. No horses shared identical genotypes across all markers, indicating that the selected set was sufficient for individual identification. All pairwise comparisons were classified using ISAG rules, with one or two excluding markers considered an accepted parent–offspring pair, two or three excluding markers considered doubtful and four or more excluding markers rejecting parentage. The panel had an overall accuracy of 99.9% for identifying true parent–offspring pairs. Our developed marker set is both present on current generation SNP chips and can be highly multiplexed in standalone panels and thus is a promising resource for SNP‐based DNA typing.     

Genome-wide association study of birth weight in sheep

Birth weight is the earliest available growth trait with considerable impacts on lamb survivability and growth performance traits. This study was conducted to perform a genome-wide association study of birth weight in a meat-type sheep. A total of 132 Lori-Bakhtiari sheep were selected based on estimated of breeding values (EBVs) for BW analyses. The selected animals were genotyped using Illumina Ovine SNP50 Bead Chip. After quality control, a total of 41 323 single-nucleotide polymorphisms (SNPs) and 130 sheep were used for subsequent analyses. Plink 1.90 beta software was used for the analyses. Seven SNPs on chromosomes 1, 16, 19 and 22 were detected based on genome-wide unadjusted P-values (P <10⁻⁶), which jointly accounted for 1.2% of total genetic variation. However, based on Bonferroni-adjusted P-values, only three SNPs on chromosome 1 had significant associations with EBVs for birth weight (P <0.05), which jointly explained 0.8% of total genetic variation. A total of seven genes were found in 50 kb intervals from the three significant SNPs on chromosome 1, but only three genes, including RAB6B (a member of RAS oncogene family), Tf serotransferrin and GIGYF2 (a GRB10 interacting GYF protein 2), could be considered as candidate genes for birth weight in future studies. The results of this study may facilitate potential use of the genes involving in growth and production traits for genetic improvement of productivity in sheep.     

Single nucleotide polymorphisms in the imprinted bovine insulin-like growth factor 2 receptor gene (IGF2R) are associated with body size traits in Irish Holstein-Friesian cattle

The regulation of the bioavailability of insulin‐like growth factors (IGFs) is critical for normal mammalian growth and development. The imprinted insulin‐like growth factor 2 receptor gene (IGF2R) encodes a transmembrane protein receptor that acts to sequester and degrade excess circulating insulin‐like growth factor 2 (IGF‐II) – a potent foetal mitogen – and is considered an important inhibitor of growth. Consequently, IGF2R may serve as a candidate gene underlying important growth‐ and body‐related quantitative traits in domestic mammalian livestock. In this study, we have quantified genotype–phenotype associations between three previously validated intronic bovine IGF2R single nucleotide polymorphisms (SNPs) (IGF2R:g.64614T>C, IGF2R:g.65037T>C and IGF2R:g.86262C>T) and a range of performance traits in 848 progeny‐tested Irish Holstein‐Friesian artificial insemination sires. Notably, all three polymorphisms analysed were associated (P ≤ 0.05) with at least one of a number of performance traits related to animal body size: angularity, body depth, chest width, rump width, and animal stature. In addition, the C‐to‐T transition at the IGF2R:g.65037T>C polymorphism was positively associated with cow carcass weight and angularity. Correction for multiple testing resulted in the retention of two genotype–phenotype associations (animal stature and rump width). None of the SNPs analysed were associated with any of the milk traits examined. Analysis of pairwise r² measures of linkage disequilibrium between all three assayed SNPs ranged between 0.41 and 0.79, suggesting that some of the observed SNP associations with performance may be independent. To our knowledge, this is one of the first studies demonstrating associations between IGF2R polymorphisms and growth‐ and body‐related traits in cattle. These results also support the increasing body of evidence that imprinted genes harbour polymorphisms that contribute to heritable variation in phenotypic traits in domestic livestock species.     

QTL and QTL x environment effects on agronomic and nitrogen acquisition traits in rice

Agricultural environments deteriorate due to excess nitrogen application.Breeding for low nitrogen responsive genotypes can reduce soil nitrogen input.Rice genotypes respond variably to soil available nitrogen.The present study attempted quantification of genotype x nitrogen level interaction and mapping of quantitative trait loci (QTLs) associated with nitrogen use efficiency (NUE) and other associated agronomic traits.Twelve parameters were observed across a set of 82 double haploid (DH) lines derived from IR64/Azucena.Three nitrogen regimes namely,native (0 kg/ha; no nitrogen applied),optimum (100 kg/ha) and high (200 kg/ha) replicated thrice were the environments.The parents and DH lines were significantly varying for all traits under different nitrogen regimes.All traits except plant height recorded significant genotype x environment interaction.Individual plant yield was positively correlated with nitrogen use efficiency and nitrogen uptake.Sixteen QTLs were detected by composite interval mapping.Eleven QTLs showed significant QTL x environment interactions.On chromosome 3,seven QTLs were detected associated with nitrogen use,plant yield and associated traits.A QTL region between markers RZ678,RZ574 and RZ284 was associated with nitrogen use and yield.This chromosomal region was enriched with expressed gene sequences of known key nitrogen assimilation genes.     

SNP detection and genetic mapping of porcine genes encoding enzymes in hepatic metabolic pathways and evaluation of linkage with carcass traits

We have previously identified and mapped porcine expressed sequence tags (ESTs) derived from genes that are preferentially expressed in liver. The aim of the present study was to identify single nucleotide polymorphisms (SNPs) in porcine genes encoding enzymes in hepatic metabolic pathways and use the SNPs for mapping. Furthermore, these genes, which are involved in utilization and partitioning of nutrients, were examined for their effects on carcass and meat quality traits by linkage analyses. In total, 100 ESTs were screened for SNPs by single strand conformation polymorphism analyses across a diverse panel of animals with a 36% success rate. Twelve of 36 polymorphic loci segregated in a three-generation Duroc x Berlin Miniature Pig (F2) resource population, the DUMI resource population, and were genetically mapped. Interval mapping of the corresponding chromosomes was performed to verify mapping of the genes within quantitative trait loci (QTL) regions detected in this resource population. QTL with genome-wide significance were detected in the vicinity of GNMT, ESTL147 and HGD. These loci therefore are positional candidate genes.     

Characterization of 12 single nucleotide polymorphisms in weathervane scallop

We describe 27 single nucleotide polymorphisms (SNPs) in a commercially important bivalve, the weathervane scallop (Patinopecten caurinus), identified using a targeted‐gene approach. We further characterize 12 of these using 5′‐nuclease and allele‐specific PCR assays. Polymorphisms were identified in both mitochondrial and nuclear genes. These are the first SNPs developed for delineating population structure in the weathervane scallop and will provide a useful complement to currently available genetic markers.     

Mapping of homoeologous chromosome exchanges influencing quantitative trait variation in Brassica napus

Genomic rearrangements arising during polyploidization are an important source of genetic and phenotypic variation in the recent allopolyploid crop Brassica napus. Exchanges among homoeologous chromosomes, due to interhomoeologue pairing, and deletions without compensating homoeologous duplications are observed in both natural B. napus and synthetic B. napus. Rearrangements of large or small chromosome segments induce gene copy number variation (CNV) and can potentially cause phenotypic changes. Unfortunately, complex genome restructuring is difficult to deal with in linkage mapping studies. Here, we demonstrate how high‐density genetic mapping with codominant, physically anchored SNP markers can detect segmental homoeologous exchanges (HE) as well as deletions and accurately link these to QTL. We validated rearrangements detected in genetic mapping data by whole‐genome resequencing of parental lines along with cytogenetic analysis using fluorescence in situ hybridization with bacterial artificial chromosome probes (BAC‐FISH) coupled with PCR using primers specific to the rearranged region. Using a well‐known QTL region influencing seed quality traits as an example, we confirmed that HE underlies the trait variation in a DH population involving a synthetic B. napus trait donor, and succeeded in narrowing the QTL to a small defined interval that enables delineation of key candidate genes.     

Discovery,validation and characterization of 1039 cattle single nucleotide polymorphisms

We identified ～13 000 putative single nucleotide polymorphisms (SNPs) by comparison of repeat‐masked BAC‐end sequences from the cattle RPCI‐42 BAC library with whole‐genome shotgun contigs of cattle genome assembly Btau 1.0. Genotyping of a subset of these SNPs was performed on a panel containing 186 DNA samples from 18 cattle breeds including 43 trios. Of 1039 SNPs confirmed as polymorphic in the panel, 998 had minor allele frequency ≥0.25 among unrelated individuals of at least one breed. When Btau 4.0 became available, 974 of these validated SNPs were assigned in silico to known cattle chromosomes, while 41 SNPs were mapped to unassigned sequence scaffolds, yielding one SNP every ～3 Mbp on average. Twenty‐four SNPs identified in Btau 1.0 were not mapped to Btau 4.0. Of the 1015 SNPs mapped to Btau 4.0, 959 SNPs had nucleotide bases identical in Btau 4.0 and Btau 1.0 contigs, whereas 56 bases were changed, resulting in the loss of the in silico SNP in Btau 4.0. Because these 1039 SNPs were all directly confirmed by genotyping on the multi‐breed panel, it is likely that the original polymorphisms were correctly identified. The 1039 validated SNPs identified in this study represent a new and useful resource for genome‐wide association studies and applications in animal breeding.     

Association analysis of adiponectin and somatostatin polymorphisms on BTA1 with growth and carcass traits in Angus cattle

This study tested positional candidate genes adiponectin (ADIPOQ) and somatostatin (SST) for effects on carcass traits in a commercially relevant cattle population. Both genes are located within a region of BTA1 previously reported to harbour quantitative trait loci (QTL) that affect marbling, quality grade, yield grade, ribeye area and weaning weight in Bos taurus x Bos indicus crosses. Except for the first intron of ADIPOQ, both genes, including over 2 kb upstream of the promoters, were sequenced in five registered Angus sires to identify polymorphisms. A variable copy duplication and three single nucleotide polymorphisms (SNPs) in ADIPOQ and one SNP in SST were genotyped and tested for association with 19 traits in a 14-generation pedigree of 1697 registered Angus artificial insemination sires representing all the major USA lineages of the breed. Linear models that parameterized predicted genetic merits in terms of allele substitution effects were fit by weighted least squares, and goodness-of-fit tests were employed to differentiate causal mutations or polymorphisms in strong linkage disequilibrium (LD) with causal mutations from markers in weak LD with QTL. We confirmed the presence of QTL affecting marbling, ribeye muscle area and fat thickness in the vicinity of SST and ADIPOQ on BTA1 in Angus; excluded SST as underlying the ribeye muscle area QTL; and excluded ADIPOQ as underlying the marbling score QTL. However, association analysis provides very limited information about QTL location and has little intrinsic value when performed in the absence of linkage or LD analysis using flanking marker data to localize the QTL effect relative to positional candidate genes.     

Analysis of public single nucleotide polymorphisms in commercial pig populations

More than 5500 pig single nucleotide polymorphisms (SNPs) were recently identified and deposited in the public domain. To test the usefulness of these public SNPs, 109 SNPs were analysed for polymorphism within six commercial pig populations. A functional polymerase chain reaction (PCR) assay was obtained for 103 SNPs and it was possible to validate c. 59% by PCR-restriction fragment length polymorphism. Furthermore, polymorphism was found using a relatively limited number of genomic DNA samples, indicating that these polymorphisms are segregating at a useful frequency in these populations. The high percentage of validated markers demonstrates the utility of these public pig SNPs to identify loci responsible for economically important traits in commercial pig populations.     

SNP markers‐based map construction and genome‐wide linkage analysis in Brassica napus

An Illumina Infinium array comprising 5306 single nucleotide polymorphism (SNP) markers was used to genotype 175 individuals of a doubled haploid population derived from a cross between Skipton and Ag‐Spectrum, two Australian cultivars of rapeseed (Brassica napus L.). A genetic linkage map based on 613 SNP and 228 non‐SNP (DArT, SSR, SRAP and candidate gene markers) covering 2514.8 cM was constructed and further utilized to identify loci associated with flowering time and resistance to blackleg, a disease caused by the fungus Leptosphaeria maculans. Comparison between genetic map positions of SNP markers and the sequenced Brassica rapa (A) and Brassica oleracea (C) genome scaffolds showed several genomic rearrangements in the B. napus genome. A major locus controlling resistance to L. maculans was identified at both seedling and adult plant stages on chromosome A07. QTL analyses revealed that up to 40.2% of genetic variation for flowering time was accounted for by loci having quantitative effects. Comparative mapping showed Arabidopsis and Brassica flowering genes such as Phytochrome A/D, Flowering Locus C and agamous‐Like MADS box gene AGL1 map within marker intervals associated with flowering time in a DH population from Skipton/Ag‐Spectrum. Genomic regions associated with flowering time and resistance to L. maculans had several SNP markers mapped within 10 cM. Our results suggest that SNP markers will be suitable for various applications such as trait introgression, comparative mapping and high‐resolution mapping of loci in B. napus.     

犬髋关节发育不良数量性状位点及致病基因研究进展

犬髋关节发育不良(canine hip dysplasia,CHD)是一种以髋关节松弛为主要特征的先天遗传性疾病,受环境和基因共同作用,发病率较高,但其发病机制尚未完全明了。近年来,在CHD基因组学研究方面取得了重要进展,譬如,发现数量性状位点(quantitative trait locus,QTL)与CHD中髋关节Norberg角、背外侧半脱位评分及分离指数存在联系,FBN2、LRR1、COL6A3与FN1等基因也与CHD的发生相关。为进一步明确CHD的发病机制,本文就CHD相关的QTL及相关候选致病基因的研究进展,尤其对相关QTL在染色体中的位置与功能以及候选致病基因的功能进行综述。     

Integration of QTL and bioinformatic tools to identify candidate genes for triglycerides in mice

To identify genetic loci influencing lipid levels, we performed quantitative trait loci (QTL) analysis between inbred mouse strains MRL/MpJ and SM/J, measuring triglyceride levels at 8 weeks of age in F2 mice fed a chow diet. We identified one significant QTL on chromosome (Chr) 15 and three suggestive QTL on Chrs 2, 7, and 17. We also carried out microarray analysis on the livers of parental strains of 282 F2 mice and used these data to find cis-regulated expression QTL. We then narrowed the list of candidate genes under significant QTL using a "toolbox" of bioinformatic resources, including haplotype analysis; parental strain comparison for gene expression differences and nonsynonymous coding single nucleotide polymorphisms (SNP); cis-regulated eQTL in livers of F2 mice; correlation between gene expression and phenotype; and conditioning of expression on the phenotype. We suggest Slc25a7 as a candidate gene for the Chr 7 QTL and, based on expression differences, five genes (Polr3 h, Cyp2d22, Cyp2d26, Tspo, and Ttll12) as candidate genes for Chr 15 QTL. This study shows how bioinformatics can be used effectively to reduce candidate gene lists for QTL related to complex traits.