Genome-wide association studies for osteochondrosis in French Trotter horses

A genome-wide association study for osteochondrosis (OC) in French Trotter horses was carried out to detect QTL using genotype data from the Illumina EquineSNP50 BeadChip assay. Analysis data came from 161 sire families of French Trotter horses with 525 progeny and family sizes ranging from 1 to 20. Genotypes were available for progeny (n = 525) and sires with at least 2 progeny (n = 98). Radiographic data were obtained from progeny using at least 10 views to reveal OC. All radiographic findings were described by at least 2 veterinary experts in equine orthopedics, and severity indices (scores) were assigned based on the size and location of the lesion. Traits used were a global score, the sum of all severity scores lesions (GM, quantitative measurement), and the presence or absence of OC on the fetlock (FM), hock (HM), and other sites (other). Data were analyzed using 2 mixed models including fixed effects, polygenic effects, and SNP or haplotype cluster effects. By combining results with both methods at moderate evidence of association threshold P < 5 × 10(-5), this genome-wide association study displayed 1 region for GM on the Equus caballus chromosome (ECA) 13, 2 for HM on ECA 3 and 14, and 1 for other on ECA 15. One region on ECA 3 for HM represented the most significant hit (P = 3 × 10(-6)). By comparing QTL between traits at a decreased threshold (P < 5 × 10(-4)), the 4 QTL detected for GM were associated to a QTL detected for FM or HM but never both. Another interesting result was that no QTL were found in common between HM and FM.     

Review of genetic aspects of radiological alterations in the navicular bone of the horse

Navicular disease or podotrochlosis has long been known to cause forelimb lameness in horses. It had been proposed that the development of podotrochlosis has similarities to the human osteoarthritis (OA) complex. Alterations of the navicular bone can be made visible early in life only on the basis of radiographs. Reports on the prevalences of navicular disease indicate that radiological alterations in the navicular bone are present in different warmblood populations at frequencies of between 14.9% and 87.6%. Genetic factors play an important role in the development of the radiological signs. Estimates of heritability using animal threshold models range from h2 = 0.09 to h2 = 0.40. Estimated additive genetic correlations between radiological changes in the navicular bone and other orthopaedic health traits indicated that they mostly develop genetically independently of each other. There was a negative genetic correlation between radiological changes in the navicular bone and the number of tournament entries and placings. It has also been shown that reduction of radiological changes of navicular bones and improvement of breeding values for performance of riding horses can be achieved if selection is based on breeding values for these traits simultaneously. An optimised markerset was developed to detect quantitative trait loci (QTL) for pathologic changes in the navicular bone of Hanoverian warmblood horses. The horse genome was scanned using 214 highly polymorphic microsatellites chromosome-wide significant QTL were located on equine chromosomes (ECA) 2, 3, 4, 10, and 26. Genome-wide significant QTL were on ECA2 and on ECA10. Unravelling QTL associated with navicular disease will enhance selection progress for a healthy limb constitution in horses.     

Polymorphism identification, RH mapping, and association analysis with the anxiety trait of the equine serotonin transporter (SLC6A4) gene

Equine anxiety trait is considered an important temperament in various situations, including riding, training, and daily care. This study examined the polymorphism of the equine serotonin transporter (SLC6A4) gene as a candidate genetic element influencing equine anxiety trait. The sequence of the coding region of this gene was highly homologous with those of other mammals, and four single nucleotide polymorphisms were found by comparing the sequences of ten genetically unrelated thoroughbred horses. Radiation hybrid mapping revealed that this gene was located 26.92 cR from neurofibromin 1 on ECA 11. Using two-year-old thoroughbred horses (n=67), the association of these polymorphisms with the anxiety trait was examined, but no significant association was identified between each haplotype of the serotonin transporter gene and the anxiety score.     

Genetic risk factors for osteochondrosis in various horse breeds

Osteochondrosis (OC) is an injury to cartilage canals with a following necrosis in the growth cartilage, from there it can develop to osteochondrosis dissecans (OCD). Due to its high impact in the equine industry, new insights into predisposing factors and potential high‐risk genetic variants are warranted. This article reviews advancements in quantitative and molecular genetics in refining estimation of genetic parameters and identifying predisposing genetic loci. Heritabilities were highest for hock OC with estimates at 0.29–0.46 in Hanoverian warmblood and Norwegian trotters, whereas in Thoroughbreds only very low genetic variation seemed to be present in hock OC lesions. Whole genome scans using the Illumina Equine SNP50 or SNP70 Beadchip were performed in Thoroughbred, Standardbred, French and Norwegian trotter, Hanoverian and Dutch warmblood. Validation studies in Spanish Purebred and Hanoverian warmblood horses corroborated OC risk loci on ECA 3, 14, 27 and 29. Particularly, a strong association with hock‐OCD was found for a single nucleotide polymorphism (SNP) on horse chromosome (ECA) 3 upstream to the LCORL gene. Gene expression and microRNA analyses may be helpful to understand pathophysiological processes in equine OC and to connect OCD‐associated genomic regions with potential candidate genes. Furthermore progress in elucidating the underlying genetic variants and pathophysiological changes in OC may be expected from whole genome DNA and RNA next‐generation sequencing studies.     

A Genome-Wide Association Analysis in Noriker Horses Identifies a SNP Associated With Roan Coat Color

The roan coat color in horses is characterized by dispersed white hair and dark points. This phenotype segregates in a broad range of horse breeds, while the underlying genetic background is still unknown. Previous studies mapped the roan locus to the KIT gene on equine chromosome 3 (ECA3). However, this association could not be validated across different horse breeds. Performing a genome-wide association analysis (GWAS) in Noriker horses, we identified a single nucleotide polymorphism (SNP) (ECA3:g.79,543.439 A > G) in the intron 17 of the KIT gene. The G -allele of the top associated SNP was present in other roan horses, namely Quarter Horse, Murgese, Slovenian, and Belgian draught horse, while it was absent in a panel of 15 breeds, including 657 non-roan horses. In further 379 gray Lipizzan horses, eight animals exhibited a heterozygous genotype (A/G). Comparative whole-genome sequence analysis of the KIT region revealed two deletions in the downstream region (ECA3:79,533,217_79,533,224delTCGTCTTC; ECA3:79,533,282_79,533,285delTTCT) and a 3 bp deletion combined with 17 bp insertion in intron 20 of KIT (ECA3:79,588,128_79,588,130delinsTTATCTCTATAGTAGTT). Within the Noriker sample, these loci were in complete linkage disequilibrium (LD) with the identified top SNP. Based upon pedigree information and historical records, we were able to trace back the genetic origin of roan coat color to a baroque gene pool. Furthermore, our data suggest allelic heterogeneity and the existence of additional roan alleles in ponies and breeds related to the English Thoroughbred. In order to study the roan phenotype segregating in those breeds, further association and verification studies are required.     

A whole genome scan to map QTL for milk production traits and somatic cell score in Canadian Holstein bulls

The detection and mapping of genetic markers linked to quantitative trait loci (QTL) can be utilized to enhance genetic improvement of livestock populations. With the completion of the bovine genome sequence assembly, single nucleotide polymorphisms (SNP) assays spanning the whole bovine genome and research work on large scale identification, validation and analysis of genotypic variation in cattle has become possible. The objective of the present study was to perform a whole genome scan to identify and map QTL affecting milk production traits and somatic cell scores using linkage disequilibrium (LD) regression and 1536 SNP markers. Three and 18 SNP were found to be associated with only milk yield (MY) at a genome and chromosome wise significance (p < 0.05) level respectively. Among the 21 significant SNP, 16 were in a region reported to have QTL for MY in other dairy cattle populations and while the rest five were new QTL finding. Four SNP out of 21 are significant for the milk production traits (MY, fat yield, protein yield (PY), and milk contents) in the present study. Six and nine SNP were associated with PY at a genome and chromosome wise significant (p < 0.05) level respectively. Three and 17 SNP were found to be associated with FY at a genome and chromosome wise significant (p < 0.05) level. Five and seven SNP were mapped with somatic cell score at a genome and chromosome wise significant (p < 0.05) level respectively. The results of this study have revealed QTL for MY, PY, protein percentage, FY, fat percentage, somatic cell score and persistency of milk in the Canadian dairy cattle population. The chromosome regions identified in this study should be further investigated to potentially identify the causative mutations underlying the QTL.     

Primary genome scan to identify putative quantitative trait loci for feedlot growth rate, feed intake, and feed efficiency of beef cattle

Feed intake and feed efficiency of beef cattle are economically relevant traits. The study was conducted to identify QTL for feed intake and feed efficiency of beef cattle by using genotype information from 100 microsatellite markers and 355 SNP genotyped across 400 progeny of 20 Angus, Charolais, or Alberta Hybrid bulls. Traits analyzed include feedlot ADG, daily DMI, feed-to-gain ratio [F:G, which is the reciprocal of the efficiency of gain (G:F)], and residual feed intake (RFI). A mixed model with sire as random and QTL effects as fixed was used to generate an F-statistic profile across and within families for each trait along each chromosome, followed by empirical permutation tests to determine significance thresholds for QTL detection. Putative QTL for ADG (chromosome-wise P < 0.05) were detected across families on chromosomes 5 (130 cM), 6 (42 cM), 7 (84 cM), 11 (20 cM), 14 (74 cM), 16 (22 cM), 17 (9 cM), 18 (46 cM), 19 (53 cM), and 28 (23 cM). For DMI, putative QTL that exceeded the chromosome-wise P < 0.05 threshold were detected on chromosomes 1 (93 cM), 3 (123 cM), 15 (31 cM), 17 (81 cM), 18 (49 cM), 20 (56 cM), and 26 (69 cM) in the across-family analyses. Putative across-family QTL influencing F:G that exceeded the chromosome-wise P < 0.05 threshold were detected on chromosomes 3 (62 cM), 5 (129 cM), 7 (27 cM), 11 (16 cM), 16 (30 cM), 17 (81 cM), 22 (72 cM), 24 (55 cM), and 28 (24 cM). Putative QTL influencing RFI that exceeded the chromosome-wise P < 0.05 threshold were detected on chromosomes 1 (90 cM), 5 (129 cM), 7 (22 cM), 8 (80 cM), 12 (89 cM), 16 (41 cM), 17 (19 cM), and 26 (48 cM) in the across-family analyses. In addition, a total of 4, 6, 1, and 8 chromosomes showed suggestive evidence (chromosome-wise, P < 0.10) for putative ADG, DMI, F:G, and RFI QTL, respectively. Most of the QTL detected across families were also detected within families, although the locations across families were not necessarily the locations within families, which is likely because of differences among families in marker informativeness for the different linkage groups. The locations and direction of some of the QTL effects reported in this study suggest potentially favorable pleiotropic effects for the underlying genes. Further studies will be required to confirm these QTL in other populations so that they can be fine-mapped for potential applications in marker-assisted selection and management of beef cattle.     

Identifying Signatures of Selection Related to Comb Development

The aim of this study was to identify genes involved in comb development to provide insights into the molecular mechanism of chickens'' comb formation. Fixation index (F_ST) and average number of base differences (π) of males with large and small combs were calculated based on whole-genome resequencing data. Chromosome regions with larger F_ST values and smaller π were considered candidate selection regions. Through further annotation of gene functions and pathways, we sought to screen possible selected genes associated with comb development. By screening whole genome resequencing data, F_ST and π were calculated using a 40 Kb sliding window strategy and eight regions were identified. Quantitative trait loci (QTL; FOX1 gene) related to comb length were found on chromosome 1. QTL (GLP1R, BTBD9, MIR6633, and MDGA1 genes) related to comb weight were found on chromosome 3. QTL (ALDH1A1, TMC1, and ANXA1 genes) associated with comb area were found on the Z chromosome. Nineteen genes, Wnt signaling pathway and neuroactive ligand-receptor interaction signaling pathway directly or indirectly related to comb growth and development were found through functional annotation and GO analysis. Among the selected genes LYN, GLP1R, FOX1, TBK1, STRAP, ST6GALNAC, and Wnt signaling pathways were related to immunity. MDGA1, BTBD9, MTSS1, SrGAPs, and neuroactive ligand receptor interaction signaling pathways related to neural function were screened. ALDH1A1, ANXAl, THBS, HIF-1α, and ACTN1 genes were related to heat dissipation. Among the selected genes FOX1, MDGAl, and ANXAl associated with immunity, neurological function, and heat dissipation function coincided with genes affecting the length, weight, and area of the comb. Comprehensive analysis suggested that comb development was due to multiple genes and signaling pathways.     

Sequence variations in equine candidate genes For XX and XY inherited disorders of sexual development

Inherited disorders of sexual development (DSD) cause sterility and infertility in horses. Mutations causing such disorders have been identified in other mammals, but there is little information on the molecular causes in horses. While the equine genome sequence has made it possible to identify candidate genes, additional tools are needed to routinely screen them for causative mutations. In this study, we designed a screening panel of polymerase chain reaction primer pairs for 15 equine genes. These are the candidate genes for testicular or ovotesticular XX DSD and XY DSD, the latter of which includes gonadal dysgenesis, androgen insensitivity syndrome (AIS), persistent Mullerian duct syndrome and isolated cryptorchidism. Six horses with testicular or ovotesticular XX DSD and controls were screened. In addition, candidate genes for androgen insensitivity syndrome, persistent Mullerian duct syndrome and isolated cryptorchidism were screened in normal horses. While no sequence variants were uniquely associated with XX DSD, the 38 sequence variants identified can serve as intragenic markers in genome-wide association studies or linkage studies to hasten mutation identification in equine XX DSD and XY DSD.     

Clinical relevance of monocyte procoagulant activity in horses with colic

Endotoxin-activated monocytes express a thromboplastin-like procoagulant activity on the cell surface that may serve as a focal point for formation of microvascular thrombi. Because coagulopathy is a common sequela to endotoxemia in the equine species, we investigated the ability of monocytes, isolated from horses with colic, to express procoagulant activity. On the day of admission, and on the third and fifth day of hospitalization, monocytes were isolated from 30 adult horses with colic. A coagulation profile, including prothrombin time, activated partial thromboplastin time, thrombin time, and plasma fibrinogen and serum fibrin degradation products concentrations, was determined at each sample collection. The concentration of endotoxin in the plasma was quantitated at the time of admission. Ten clinically normal adult horses served as controls. The procoagulant activity of monocytes isolated from horses with colic was significantly (P less than 0.05) greater than that of the monocytes isolated from clinically normal horses. On the first and third day of hospitalization, the mean prothrombin time was significantly (P less than 0.05) longer in horses with colic, compared with clinically normal horses, and was the most common abnormality in the coagulation profile on the day of admission (25/30; 83%). Mean fibrin degradation products concentration was significantly (P less than 0.05) greater in horses with colic on the day of admission and was the second most common abnormality in the coagulation profile on day 1 (23/30; 77%). In horses with colic, the mean prothrombin and activated partial thromboplastin times were significantly (P less than 0.05) longer in horses that did not survive, compared with horses that survived.(ABSTRACT TRUNCATED AT 250 WORDS)     

Detection of QTL for greasy fleece weight in sheep using a 50 K single nucleotide polymorphism chip

Genome-wide association studies (GWAS) have introduced an influential tool in the search for quantitative trait loci (QTL) influencing economically important traits in sheep. To identify QTL associated with greasy fleece weight, a GWAS with 50 K single nucleotide polymorphisms (SNPs) was performed in a Baluchi sheep population. Association with greasy fleece weights was tested using the software Plink. The results of our GWAS provided three novel SNP markers and candidate genes associated with greasy fleece weight. A total of three chromosome-wide significant associations were detected for SNP on chromosomes 17 and 20 affecting greasy fleece weight across the four shearing. One of the significant SNP markers was located within ovine known genes namely FAM101A. Further investigation of these identified regions in validation studies will facilitate the identification of strong candidate genes for wool production in sheep.     

Need for sharp phenotypes in QTL detection for calving traits in dairy cattle

The aim of the study was to investigate whether parity‐specific phenotypes provide a clearer picture of quantitative trait loci (QTL) affecting calving traits in German Holsteins than breeding values estimated across parities. In experiment I, approximate daughter yield deviations were calculated by applying a univariate sire model assuming unrelated sires used as phenotypes in a QTL mapping study. These results were compared with those obtained using deregressed estimated breeding values obtained from the routine German sire evaluation (experiment II). In experiment I, 17 chromosome‐wise significant QTL were found for the first parity, but only 12 for the second parity. Only three QTL for maternal stillbirth, located on BTA7, 15 and 23, showed an experiment‐wise significance. Experiment II revealed 15 chromosome‐wise significant QTL. The results differed markedly between first and second parity within experiment I, as well as between experiment I and II. The present study showed that parity‐specific daughter yield deviations are beneficial for mapping QTL for calving traits. Furthermore, it is expected that the use of sharper phenotypes will also be advantageous for QTL fine mapping and the identification of candidate genes.     

拷贝数变异全基因组关联分析及数量性状基因座定位联合鉴定猪体高性状候选基因

旨在利用全基因组拷贝数变异区域（copy number variation regions,CNVRs）关联分析以及全基因组数量性状基因座（quantitative trait locus,QTLs）定位联合筛选出影响猪体高性状的候选基因。本研究利用快速检测基因组拷贝数变异软件CNVcaller对本实验室构建的大白×民猪F2代资源群体的重测序数据进行拷贝数变异检测。利用混合线性模型（mixed-linear model,MLM）将性别和胎次作为固定效应对体高性状进行拷贝数变异全基因组关联分析（CNVR-GWAS）。采用软件R/qtl进行QTL分析,并使用置换检验（permutation test,PT）进行检验。将CNVR-GWAS与QTL结果进行联合注释,结合GO富集和KEGG通路分析,对影响猪体高的位点和基因进行挖掘。利用实时荧光定量PCR（qPCR）方法验证候选基因。结果表明,本群体在全基因组范围内共有3 099个CNVRs,其中有两个CNVRs与体高性状在全基因组范围内显著相关,分别位于7号染色体的25 358 001~26 696 400 bp处（CNVR1）和54 087 201~54 090 000 bp处（CNVR2）。在混合线性模型分析的结果中发现,CNVR1拷贝数增加（P<0.01）和CNVR2拷贝数缺失（P<0.01）对猪的体高性状具有显著影响。基因组显著水平可找到2个显著影响猪体高的QTLs,分别为BH-1和BH-2,其中BH-2对体高性状的影响较大。CNVR1和BH-2重叠区存在1个嗅觉受体基因OR12D3和18个未被注释的基因。qPCR验证OR12D3的拷贝数变异与利用混合线性模型统计推断出的结果一致。初步推测,OR12D3基因的拷贝数变异可能与猪体高性状相关。     

A retrospective study of cutaneous equine sarcoidosis and its potential infectious aetiological agents

Nine horses from ages 5 to 21 years were diagnosed with cutaneous equine sarcoidosis (ES) over an 18-year period. In addition to skin, the lungs were frequently involved, with other organ systems affected less commonly. A predisposition for thoroughbreds and geldings was noted. Cutaneous lesions and signs included crusts, scales, alopecia and pruritus. These were found at various sites, particularly the legs/thighs/elbows, thorax, neck, face and ventral abdomen. Three horses were euthanized shortly after hospitalization; others survived as long as 12 years. Histopathologic stains, immunohistochemistry and polymerase chain reaction assays on paraffin-embedded cutaneous specimens from eight horses for Mycobacterium spp., Coccidioides immitis, Cryptococcus neoformans, Corynebacterium pseudotuberculosis, and Borrelia burgdorferi were all negative. The aetiology of ES is unlikely microbial and continues to be a diagnosis of exclusion. ES, when limited to the skin, is associated with a good prognosis, with either partial or complete response to glucocorticoid therapy in all the surviving horses.     

Assessment of positional candidate genes myf5 and igf1 for growth on bovine chromosome 5 in commercial lines of Bos taurus

Quantitative trait loci for growth traits in beef cattle have been previously reported and fine-mapped in three chromosomal regions of 0 to 30 cM, 55 to 70 cM, and 70 to 80 cM of bovine chromosome 5. In this study, we further examined the association between gene-specific single nucleotide polymorphisms (SNP) of two positional candidate genes, bovine myogenic factor 5 (myf5) and insulin-like growth factor-1 (igf1), in the QTL regions and the birth weight (BWT), preweaning average daily gain (PWADG), and average daily gain on feed (ADGF) in commercial lines of Bos taurus. The QTL regions for the growth traits identified using a haplotype association analysis, which included the gene-specific SNP markers for both genes in this study, were in agreement with previous studies. The gene-specific SNP marker association analysis indicated that the SNP in myf5 had a significant additive effect on PWADG in the M1 line of Beefbooster Inc. (P < 0.10), and a significant additive effect (P < 0.05) and a significant dominance effect (P < 0.10) on ADGF in the M3 line of Beefbooster Inc. When the data from the two commercial lines were pooled, the SNP in myf5 showed a significant association with PWADG (P < 0.10) and with ADGF (P < 0.05). The association between the SNP and BWT, however, did not reach a significance level in the M1 line, the M3 line, or across the lines. For igf1, no significant association between the SNP and the growth traits was detected in either the M1 line or the M3 line, whereas there was only a significant dominance effect (P < 0.10) on BWT detected for the SNP in igfl when the data from the two commercial lines were pooled. These results suggest that myf5 is a strong candidate gene that influences PWADG and ADGF in beef cattle. The SNP of igf1 may not be a causative or close to the causative mutation that affects the three growth traits in the populations of beef cattle examined in this study. Other SNP of igf1 and myf5 or other genes in their respective chromosomal regions, however, should also be studied.     

基于SNP芯片的海南猪全基因组选择信号分析

旨在通过检测海南猪全基因组上的选择信号,以挖掘与海南猪重要经济性状相关的候选基因,并解析讨论海南猪在进化驯化历史中的受选择情况.本研究利用68头海南猪的GeneSeek Genomic Profiler Procine SNP 80K芯片数据,使用整合单倍型分数(integrated haplotype score,i...     

Lack of Detectable Equine Herpesviruses 1 and 2 in Paraffin-Embedded Specimens of Equine Sarcoidosis

Background: Equine sarcoidosis is a rare, multisystemic, noncaseating, granulomatous and lymphoplasmacytic disease of unknown etiology. A recent report described a horse with granulomatous skin disease displaying histologic, electron microscopic, and polymerase chain reaction (PCR) findings consistent with equine herpesvirus 2 (EHV-2).
Objective: To investigate the presence of EHV-2 and equine herpesvirus 1 (EHV-1) in 8 horses with sarcoidosis.
Animals: Eight horses with sarcoidosis, reported previously.
Methods: Retrospective study. PCR assays of the tissues were performed to detect DNA associated with EHV-1 and EHV-2. For both herpesviruses the target was their respective glycoprotein B gene. Positive controls consisted of DNA from viral cultures of culturettes from naturally occurring respiratory infections of EHV-1 and EHV-2.
Results: The PCR analyses for both equine herpesviruses' DNA were negative in all 8 horses.
Conclusion: The failure to detect DNA from EHV-1 and EHV-2 in paraffin-embedded skin of these 8 horses does not discount EHV-1 or EHV-2 as causing some cases of ES, but lends support to the presumably multifactorial etiologic nature of the disease.     

Detection of quantitative trait loci for growth and carcass composition in cattle

The objective of the present study was to detect quantitative trait loci for economically important traits in a family from a Bos indicus x Bos taurus sire. A Brahman x Hereford sire was used to develop a half-sib family (n = 547). The sire was mated to Bos taurus cows. Traits analyzed were birth (kg) and weaning weights (kg); hot carcass weight (kg); marbling score; longissimus area (cm2); USDA yield grade; estimated kidney, pelvic, and heart fat (%); fat thickness (cm); fat yield (%); and retail product yield (%). Meat tenderness was measured as Warner-Bratzler shear force (kg) at 3 and 14 d postmortem. Two hundred and thirty-eight markers were genotyped in 185 offspring. One hundred and thirty markers were used to genotype the remaining 362 offspring. A total of 312 markers were used in the final analysis. Seventy-four markers were common to both groups. Significant QTL (expected number of false-positives < 0.05) were observed for birth weight and longissimus area on chromosome 5, for longissimus area on chromosome 6, for retail product yield on chromosome 9, for birth weight on chromosome 21, and for marbling score on chromosome 23. Evidence suggesting (expected number of false-positives < 1) the presence of QTL was detected for several traits. Putative QTL for birth weight were detected on chromosomes 1, 2, and 3, and for weaning weight on chromosome 29. For hot carcass weight, QTL were detected on chromosomes 10, 18, and 29. Four QTL for yield grade were identified on chromosomes 2, 11, 14, and 19. Three QTL for fat thickness were detected on chromosomes 2, 3, 7, and 14. For marbling score, QTL were identified on chromosomes 3, 10, 14, and 27. Four QTL were identified for retail product yield on chromosomes 12, 18, 19, and 29. A QTL for estimated kidney, pelvic, and heart fat was detected on chromosome 15, and a QTL for meat tenderness measured as Warner-Bratzler shear force at 3 d postmortem was identified on chromosome 20. Two QTL were detected for meat tenderness measured as Warner-Bratzler shear force at 14 d postmortem on chromosomes 20 and 29. These results present a complete scan in all available progeny in this family. Regions underlying QTL need to be assessed in other populations.     

Genomic regions associated with ventro-cranial chronic pleuritis in pig

Ventro‐cranial chronic pleuritis can be a result of pleuropneumonia and enzootic pneumonia. These diseases cause severe losses in intensive pig production worldwide, but host resistance is difficult to breed for. It could be beneficial to use marker‐assisted selection, and a step towards this is to identify genomic regions associated with the trait. For this purpose, 7304 pigs from 11 boar families were analysed for associations between single nucleotide polymorphisms and ventro‐cranial chronic pleuritis. The pigs were genotyped by the use of the iSelect Custom 7 K porcine SNP Chip. Quantitative trait loci (QTL), significant at the chromosome‐wide level, were identified on Sus scrofa chromosomes (SSC) 2, 4, 11, 12 and 13 in four different boar families. The QTL on SSC 4 in family G was also significant at the genome‐wide threshold according to Bonferroni correction. We have identified a number of candidate genes, but the causative mutations still need to be identified. Markers closely associated with the resistance traits have a strong potential for use in breeding towards animals with improved characteristics concerning ventro‐cranial chronic pleuritis.