The effect of adipocyte and heart fatty acid-binding protein genes on intramuscular fat and backfat content in Meishan crossbred pigs

Effects of genetic variation in porcine adipocyte and heart fatty acid-binding protein genes, A-FABP and H-FABP, respectively, on intramuscular fat (IMF) content and backfat thickness (BFT) were examined in F2 crossbreds of Meishan and Western pigs. The involvement of each FABP gene in IMF accretion was studied to confirm previous results for Duroc pigs. The F2 crossbred pigs were genotyped for various markers including microsatellite sequences situated within both FABP genes. Linkage analysis assigned the A-FABP and H-FABP genes to marker intervals S0001-S0217 (20 cM) on SSC4 and Sw316-S0003 (16.6 cM) on SSC6, respectively, refining previous chromosomal assignments. Next, the role of both chromosome regions/genes on genetic variation in IMF content and BFT was studied by 1) screening SSC4 and SSC6 for QTL affecting both traits by performing a line-cross analysis and 2) estimation of the effect of individual A-FABP and H-FABP alleles on both traits. In the first analysis, suggestive and chromosome-wise significant evidence for a QTL affecting IMF was detected on SSC6. The H-FABP gene is a candidate gene for this effect because it resides within the large region containing this putative QTL. The second analysis showed a considerable but nonsignificant effect of H-FABP microsatellite alleles on IMF content. Suggestive evidence for a QTL affecting BFT was found on SSC6, but H-FABP was excluded as a candidate gene. In conclusion, present and previous results support involvement of H-FABP gene polymorphisms in IMF accretion independently from BFT in pigs. Therefore, implementation of these polymorphisms in marker-assisted selection to control IMF content independently from BFT may be considered. In contrast to previous findings for Duroc pigs, no evidence was found for an effect of the A-FABP gene on IMF or BFT in this population.     

Single nucleotide polymorphisms in several porcine cathepsin genes are associated with growth, carcass, and production traits in Italian Large White pigs

To identify DNA markers associated with performance, carcass, and meat production traits including muscle postmortem cathepsin activity, several porcine genes encoding for lysosomal proteinases (cathepsin B, CTSB; cathepsin D, CTSD; cathepsin F, CTSF; cathepsin H, CTSH; cathepsin L, CTSL; and cathepsin Z, CTSZ) and for a cathepsin inhibitor (cystatin B) were investigated. Single nucleotide polymorphisms were identified in CTSD, CTSH, CTSL, and CTSZ genes with a combination of in silico expressed sequence tag database mining and single-strand conformation polymorphism analysis. Sequencing and PCR-RFLP protocols were used to validate the identified polymorphisms. Allele frequencies at these loci were investigated in Italian Large White, Landrace, Duroc, Piétrain, Belgian Landrace, Hampshire, and Meishan breeds. Genotyping CTSD and CTSH markers made it possible to genetically map these genes to SSC 2 and 7, respectively. Markers in CTSD, CTSH, CTSL, and CTSZ genes, together with mutations we previously reported in cystatin B, CTSB, and CTSF genes, were genotyped in an Italian Large White sib-tested population (272 or 482 animals). For these animals, meat quality traits (cathepsin B activity, pH measured at 2 h postmortem, pH measured at 24 h postmortem, glycogen, lactate, and glycolytic potential of semimembranosus muscle) and EBV for ADG, lean cuts (LC), backfat thickness (BFT), ham weight (HW), and feed:gain ratio (FGR) were determined. Analyzed markers did not show any association with muscle cathepsin B activity. Thus, it could be possible that different genes, other than these investigated candidates, affect this trait, which is correlated with the excessive softness defect of dry-cured hams. The results of association analysis confirmed the effects we already reported in another study for CTSF on ADG (P = 0.008), LC (P = 0.001), and BFT (P = 0.02). Moreover, CTSD was associated with ADG, LC (P < 0.0001), BFT, HW, and FGR (P < 0.001); CTSH was associated with FGR (P = 0.026); and CTSZ was associated with ADG (P = 0.006), LC (P = 0.01), HW (P = 0.024), and FGR (P = 0.029). The biochemical and physiological functions of the lysosomal proteinases, together with the results obtained in our investigation, suggest that the cathepsin gene family might play important roles affecting economic traits in pigs.     

Single nucleotide polymorphism association study for backfat and intramuscular fat content in the region between SW2098 and SW1881 on pig chromosome 6

This study was carried out to identify SNP associated with fatness traits on pig chromosome 6. In total, 11,067 putative genomic variations were detected in 125 complete bacterial artificial chromosome sequences corresponding to the region between SW2098 and SW1881, which harbors multiple QTL affecting intramuscular fat content (IMF) and backfat thickness (BFT). Among 173 putative SNP validated by MassArray, 120 SNP were used in an association study on 541 offspring produced by a cross of Korean native pig and Landrace breeds. The significance level of each SNP was determined using single marker regression analysis. Further, significant threshold values were determined using a false discovery rate. Nine out of 120 SNP showed significant effects on BFT or IMF or both. Of the 9 significant SNP, 4 were significantly associated with IMF, 7 were significantly related to BFT, and 2 SNP (Kps8172 and Kps6413) showed significant effects on both traits. Moreover, multiple regression analysis considering all significant SNP was used to correct spurious false positives due to linkage disequilibrium. Consequently, only 1 SNP (Kps6413) was significant for IMF, whereas 4 SNP including Kps6413 showed significant effects on BFT. The significant SNP had generally additive effects and on average explained 1.72% of the genetic variation for IMF and 3.92% for BFT, respectively. These markers can potentially be applied in pig breeding programs for improving IMF and BFT traits after validation in other populations.     

Identification of quantitative trait loci for carcass composition and pork quality traits in a commercial finishing cross

A QTL study for carcass composition and meat quality traits was conducted on finisher pigs of a cross between a synthetic Piétrain/Large White boar line and a commercial sow cross. The mapping population comprised 715 individuals evaluated for a total of 30 traits related to growth and fatness (4 traits), carcass composition (11 traits), and meat quality (15 traits). Offspring of 8 sires (n = 715) were used for linkage analysis and genotyped for 73 microsatellite markers covering 14 chromosomal regions representing approximately 50% of the pig genome. The regions examined were selected based on previous studies suggesting the presence of QTL affecting carcass composition or meat quality traits. Thirty-two QTL exceeding the 5% chromosome-wise significance level were identified. Among these, 5 QTL affecting 5 different traits were significant at the 1% chromosome-wise level. The greatest significance levels were found for a QTL affecting loin weight on SSC11 and a QTL with an effect on the Japanese color scale score of the loin on SSC4. About one-third of the identified QTL were in agreement with QTL previously reported. Results showed that QTL affecting carcass composition and meat quality traits segregated within commercial lines. Use of these results for marker-assisted selection offers opportunities for improving pork quality by within-line selection.     

The identification of common haplotypes on bovine chromosome 5 within commercial lines of Bos taurus and their associations with growth traits

The cosegregation between a genetic marker and the QTL in a well-designed mapping population is the basis for successful QTL mapping. Linkage disequilibria are, however, also expected among individuals that descended from the same breeding line, and some common haplotypes should carry on and segregate among individuals of the line. These identical by descent haplotypes make it possible to identify and locate the QTL segregating in the line. We report the identification of common haplotypes within commercial lines of Bos taurus and their associations with growth traits. One hundred and seventy six male calves and their 12 sires (9 to 30 male calves of each sire) of the Beefbooster, Inc., M1 line selected for maternal traits over 30 yr were genotyped using 16 microsatellite markers chosen from bovine chromosome 5 for the initial haplotype and growth association analysis. In order to verify the results from the M1 line, another 170 male calves and their 14 sires from the Beefbooster M3 line were genotyped using nine microsatellite markers chosen from bovine chromosome 5. The alleles of each male calf contributed by the sire and by the dam were identified, and haplotypes in the M1 line were established along 93% of bovine chromosome 5. The haplotypes in the M3 line were established along the chosen regions of bovine chromosome 5. Regression analysis detected 10 haplotypes in three chromosomal regions (0 to 30 cM, 55 to 70 cM, and 70 to 80 cM) that showed significant associations with birth weight, preweaning average daily gain, and average daily gain on feed in M1 line and 9 haplotypes associated with the growth traits in the same chromosomal regions in the M3 line at the comparisonwise threshold level. On average, the 19 haplotypes have an effect of 0.68 SD on the growth traits, ranging from 0.41 SD to 1.02 SD The results provide a useful reference for further positional candidate gene research and marker-assisted selection.     

Maternal effects on traits measured during postweaning performance test of swine from four breeds

The objective of this study was to investigate the importance of maternal genetic effects on postweaning performance traits of Yorkshire, Landrace, Duroc, and Hampshire breeds of swine. Data consisted of performance test records collected in a commercial swine operation from 1992 to 1999. Boars from 60% of the litters were culled at weaning based on a combination of maternal and performance indexes that differed by breed. Remaining boars and all females were grown to 100 d of age. At this time all pigs were weighed (WT100) and selected for testing using recalculated breed-specific indexes (n = 15,594, 55,497, 12,267, and 9,782 for Landrace, Yorkshire, Duroc, and Hampshire, respectively). All pigs were weighed at the end of the 77-d test, and backfat (BF) and loin eye area (LEA) were measured over the 12th rib by ultrasound. Average daily feed intake was calculated for boars, and ADG was calculated for all animals. Genetic parameters were estimated for each breed and trait using multiple-trait DFREML procedures. Fixed effects were contemporary groups and either initial or final test age as a covariate. Four models were examined. Model 1 included only the additive genetic effect of the animal. Model 2 added the common litter environmental effect; Model 3 added the maternal genetic value assumed to be uncorrelated with additive genetic effects. Model 4 was the same as Model 3 with additive and maternal genetic effects assumed to be correlated. All models were two-trait models with WT100 as the second trait. Ratios of likelihoods were used to compare models. Maternal effects were important (P < 0.05) for WT100, ADG, ADFI, LEA, and BF in Landrace; for WT100, ADG, LEA, and BF in Yorkshire; for WT100 and ADG in Duroc, and for WT100 in Hampshire. Estimates of heritabilities for direct additive effects using the appropriate model for ADG, ADFI, LEA, and BF were 0.28, 0.34, 0.48, and 0.63 for Landrace; 0.26, 0.31, 0.39, and 0.65 for Yorkshire; 0.14, 0.20, 0.26, and 0.35 for Duroc; and 0.17, 0.23, 0.25, and 0.31 for Hampshire, respectively. Heritability estimates for maternal genetic effects for ADG, ADFI, LEA, and BF were 0.02, 0.05, 0.06, and 0.07 for Landrace and 0.02, 0, 0.04, and 0.06 for Yorkshire, respectively. They were zero for all traits except ADG (0.03) in Duroc and for all traits in Hampshire. Maternal effects may need to be considered in genetic evaluation of performance traits in some breeds of swine.     

杜洛克猪专门化品系选育研究

杜洛克猪专门化品系是以丹系杜洛克为育种素材,采用不完全闭锁的群体继代选育法,运用最佳线性无偏估计(BLUP)法、综合选择指数和分子标记辅助选择(MAS)等育种新方法,主选日增重和活体背膘厚等性状。经5个世代选育,产仔数达10.48头,产活仔数9.85头;肥育期日增重831g,料重比2.55:1,活体背膘厚11.83mm;瘦肉率69.5%,肌内脂肪为2.95%,主选性状全面达到或超过育种目标,成功培育了一个高性能的专门化父本新品系(ZFD系)。     

Genetic parameters and trends for production traits and their relationship with litter traits in Landrace and Yorkshire pigs

Genetic parameters and trends in the average daily gain (ADG), backfat thickness (BF), loin muscle area (LMA), lean percentage (LP), and age at 90 kg (D90) were estimated for populations of Landrace and Yorkshire pigs. Additionally, the correlations between these production traits and litter traits were estimated. Litter traits included total born (TB) and number born alive (NBA). The data used for this study were obtained from eight farms during 1999 to 2016. Analyses were carried out with a multivariate animal model to estimate genetic parameters for production traits while bivariate analyses were performed to estimate the correlations between production and litter traits. The heritability estimates were 0.52 and 0.43 for ADG; 0.54 and 0.45 for BF; 0.25 and 0.26 for LMA; 0.54 and 0.48 for LP; and 0.56 and 0.46 for D90 in the Landrace and Yorkshire breeds, respectively. The ADG and D90 showed low genetic correlation with BF and LP. The LMA had ?0.40, ?0.32, 0.49, and 0.39 genetic correlations with ADG, BF, LP, and D90, respectively. Genetic correlations between production and litter traits were generally low, except for the correlations between LMA and TB (?0.23) in Landrace and ADG and TB (?0.16), ADG and NBA (?0.18), D90 and TB (0.19), and D90 and NBA (0.20) in Yorkshire. Genetic trends in production traits were all favorable except for LMA.     

Prediction of performance of progeny from test station boars.

Data were obtained from 1,954 Duroc and 2,252 Yorkshire purebred and crossbred progeny sired by 34 Duroc and 32 Yorkshire boars, respectively. Boars were purchased from the North Carolina Swine Evaluation Station during August 1983 to December 1988. Boars were selected to represent high and low indexes at the test station. Progeny were raised and tested under conditions similar to commercial pig production at the Tidewater Research Station. For each breed of boar (Duroc and Yorkshire), breed type (purebred and crossbred), and sex (castrates and gilts) of progeny, regression coefficients of progeny traits on each sire trait were computed. Progeny traits were ADG, days to 104.3 kg BW (DAYS), backfat thickness (BF), and feed conversion ratio (FC). Sire traits were ADG, DAYS, BF, FC, and INDEX. Effects of boar test group and progeny test group were included in the models. Averaged over breed type and sex, a 25-unit (1 SD) increase in sire INDEX resulted in 14.5 g more ADG, 3.2 fewer DAYS, .57 mm more BF, and .017 lower FC in Durocs and 5.6 g more ADG, .01 more DAYS, .81 mm less BF, and .083 lower FC in Yorkshires. The low magnitude and variable signs of some regression coefficients suggested that predictions of progeny performance from performance of individual sires at the North Carolina Swine Evaluation Station were not very reliable. Differences between regressions for purebreds and crossbreds implied small correlations between the two breed types. Differences between Durocs and Yorkshires indicated that genetic parameters might not be the same for the two breeds.     

Identification of Markers Significantly Associated with Litter Size Traits and Uniformity of the Piglet's Birth Weight on Porcine Chromosome 3

This study was aimed to find the molecular markers significantly associated with litter size traits and uniformity of the piglet's birth weight,and provided a basis for genetic improvement of reproductive traits in pigs.This study was based on the genome-wide selective sweep analysis of pig conducted by the research group in the previous studies,two SNPs (rs338309012 and rs335824784) on porcine chromosome 3 were selected,and the genotyping-in-thousand by sequencing was used,the relationship between two SNPs and litter size traits (including total number born,total number born alive,number of stillborn pigs and number of mummified pigs,etc.) and the uniformity of the piglet's birth weight was association analyzed in Danish Yorkshire and American Yorkshire pigs.The results showed that rs338309012 were significantly associated with the total number born and the number of mummified pigs (P<0.05),and the total number born and the number of mummified pigs of AC genotype sows was significantly higher than CC genotype (P<0.05).rs335824784 was significantly associated with the effective number of born alive and the number of mummified pigs (P<0.05),and was also extremely significantly associated with the total number born alive and the number of stillborn pigs (P<0.01).The effect of different genotypes on the total number born alive and effective number of born alive were GG > CG > CC.On the contrary,the effect of different genotypes on the coefficient of variation of the birth weight of piglets,the number of dead and mummified fetuses were GG < CG < CC.Thus,the GG genotype sows with rs335824784 not only had more total number born alive,but also had regular piglet's birth weight and lower number of stillborn and mummified pigs,which could be used as a molecular marker to improve the litter size traits and uniformity of the piglet's birth weight.     

猪3号染色体上与产仔性状和窝内仔猪初生重整齐度显著关联的标记鉴定

试验旨在寻找与猪产仔性状和窝内仔猪初生重整齐度显著关联的分子标记,为猪繁殖性状的遗传改良提供依据。在课题组前期进行的猪全基因组清扫分析的基础上,选定猪3号染色体上的2个SNPs位点（rs338309012和rs335824784）,利用目标序列捕获测序分型技术,在丹系大白猪和美系大白猪群中对这2个SNPs位点与猪产仔性状（包括总产仔数、产活仔数、死胎及木乃伊胎数等）及窝内仔猪初生重整齐度进行关联分析。结果显示,rs338309012位点与总产仔数、木乃伊胎数显著关联（P<0.05）,AC基因型母猪的总产仔数、木乃伊胎数均显著高于CC基因型（P<0.05）;rs335824784位点与有效活仔数、木乃伊胎数显著关联（P<0.05）,与产活仔数和死胎数极显著关联（P<0.01）,不同基因型对产活仔数和有效活仔数的影响为GG > CG > CC,与之相反,对窝内仔猪初生重的变异系数、死胎及木乃伊胎数的影响为GG < CG < CC。因此,rs335824784位点GG基因型猪不仅产活仔数多,而且窝内仔猪初生重整齐,死胎和木乃伊胎数低,可以作为提高猪产仔性状和窝内仔猪初生重整齐度的分子标记。     

Fine-mapping of quantitative trait loci for body weight and bone traits and positional cloning of the RB1 gene in chicken

Previously, a quantitative trait locus (QTL) that affects body weight (BW) at 4-12 weeks of age and carcass weight at 12 weeks of age had been mapped on chicken chromosome 1. After including more markers and individuals, the confidence interval was narrowed down to approximately 5.5 Mbps and located this QTL near a microsatellite marker (ADL328). This QTL is the same as the QTL for 12 bone traits, including metatarsus length and metatarsus circumference at 4, 6, 8, 10 and 12 weeks of age and keel length and metatarsus claw weight at 12 weeks of age, that was identified using the same population. In the current study, 1010 individuals from the Northeast Agricultural University F(2) resource population were used and 14 single-nucleotide polymorphism (SNPs) around ADL328 were developed to construct haplotypes, and an association analysis was performed to fine-map the QTL. The haplotypes were constructed on the basis of a sliding 'window', with three SNP markers included in each 'window'. The association analysis results indicated that the haplotypes in 'windows' 6-12 were significantly associated with BW and bone traits and suggested that the QTL for BW and bone traits was located between SNP8 and SNP14 or was in linkage disequilibrium with this region. The interval from SNP8 to SNP14 was approximately 400 kbps. This region contained five RefSeq genes (RB1, P2RY5, FNDC3A, MLNR and CAB39L) on the University of California Santa Cruz website. The RB1 gene was selected as a candidate gene and five SNPs were identified in the gene. The association results indicated that the RB1 gene was a major gene for BW and bone traits. The SNPs g.39692 G>A and g.77260 A>G in RB1 gene might be two quantitative trait nucleotides for BW and bone traits.     

Evaluation of effects of multiple candidate genes (LEP,LEPR, MC4R,PIK3C3, and VRTN) on production traits in Duroc pigs

We evaluated multiple effects of genetic variations of five candidate loci (LEP, LEPR, MC4R, PIK3C3 and VRTN) on four production traits (average daily weight gain (ADG); backfat thickness (BFT); loin eye muscle area (EMA); and intramuscular fat content (IMF)) in a closed nucleus herd of pure Duroc pigs. Polymorphisms in LEPR, MC4R and PIK3C3 had significant single gene effects on ADG and BFT. The additive genetic variance in ADG and BFT (16.99% and 22.51%, respectively) was explained by genetic effects of these three loci. No correlations were observed between the LEP genotype and production traits in this study. Although we detected marginally epistatic interactions between LEPR and PIK3C3 on the eye muscle area, there were no significant epistatic effects on any traits among all loci pairs. These results suggest that LEPR, MC4R, PIK3C3 and VRTN may independently influence growth rate and fat deposition. Furthermore, the statistical models for predicting the breeding values of each trait had the lowest Akaike's information criterion values when considering the effect of the MC4R, LEPR, PIK3C3 and VRTN genotype simultaneously. These results suggest that LEPR, MC4R, PIK3C3 and VRTN are useful markers for accurately predicting breeding values in Duroc pigs.     

Quantitative trait loci analysis on Sus scrofa chromosome 7 for meat production, meat quality, and carcass traits within a Duroc purebred population

Many QTL analyses related to meat production and meat quality traits have been carried out using an F(2) resource population produced by crossing 2 genetically different breeds. This experiment was intended to investigate whether these QTL were segregating in a purebred Duroc population that had been selected for meat production and meat quality traits during 7 generations. Sus scrofa chromosome 7, for which significant QTL of intramuscular fat and many other traits have already been reported, was studied. The polymorphism of 10 microsatellite markers that were arranged at about 20-cM intervals was investigated on 1,004 pigs. In the selected population, 954 progeny were produced from mating of 99 sires and 286 dams. The QTL analysis for a full-sib family population was examined with the multigeneration pedigree structure of the population. Variance component analysis was used to detect QTL in this population and was examined for the multigeneration pedigree population. In this study, multigenerational pedigree estimated identical by descent coefficients among sibs were produced using Markov chain Monte Carlo methods. The maximum likelihood of odds score was found at the 70-cM position for the LM area, at the 0-cM position for the pork color standard, and at the 120-cM position for the number of thoracic vertebra, but no significant QTL for intramuscular fat were detected on SSC 7. These results indicate that QTL analysis via a variance component method within a purebred population was effective to determine that QTL were segregating in a population of purebred Durocs.     

A directed search in the region of GDF8 for quantitative trait loci affecting carcass traits in Texel sheep

A directed search for QTL affecting carcass traits was carried out in the region of growth differentiation factor 8 (GDF8, also known as myostatin) on ovine chromosome 2 in seven Texel-sired half-sib families totaling 927 progeny. Weights were recorded at birth, weaning, ultrasound scanning, and slaughter. Ultrasonic measures of LM cross-sectional dimensions and s.c. fat above the LM were made, with the same measurements made on the LM after slaughter. Following slaughter, linear measurements of carcass length and width were made on all carcasses, and legs and loins from 540 lambs were dissected. Genotyping was carried out using eight microsatellite markers from FCB128 to RM356 on OAR 2 and analyzed using Haley-Knott regression. There was no evidence for QTL for growth rates or linear carcass traits. There was some evidence for QTL affecting LM dimensions segregating in some sire families, although it was not consistent between ultrasound and carcass measures of the same traits. There was strong and consistent evidence for a QTL affecting muscle and fat traits in the leg that mapped between markers BM81124 and BULGE20 for the four sires that were heterozygous in this region, but not for the three sires that were homozygous. The size of the effect varied across the four sires, ranging from 0.5 to 0.9 of an adjusted SD for weight-adjusted leg muscle traits, and ranging from 0.6 to 1.2 of an adjusted SD for weight-adjusted leg fat traits. The clearest effect shown was for multivariate analysis combining all leg muscle and fat traits analyzed across sires, where the -log(10) probability was 14. Animals carrying the favorable haplotype had 3.3% more muscle and 9.9% less fat in the leg relative to animals carrying other haplotypes. There was evidence for a second peak in the region of marker TEXAN2 for one sire group. It seems that a QTL affecting muscle and fat traits exists within the New Zealand Texel population, and it maps to the region of GDF8 on OAR2.     

Genome-wide mapping and identification of new quantitative trait loci affecting meat production, meat quality, and carcass traits within a Duroc purebred population

Most QTL detection studies in pigs have been carried out in experimental F(2) populations. However, segregation of a QTL must be confirmed within a purebred population for successful implementation of marker-assisted selection. Previously, QTL for meat quality and carcass traits were detected on SSC 7 in a Duroc purebred population. The objectives of the present study were to carry out a whole-genome QTL analysis (except for SSC 7) for meat production, meat quality, and carcass traits and to confirm the presence of segregating QTL in a Duroc purebred population. One thousand and four Duroc pigs were studied from base to seventh generation; the pigs comprised 1 closed population of a complex multigenerational pedigree such that all individuals were related. The pigs were evaluated for 6 growth traits, 7 body size traits, 8 carcass traits, 2 physiological traits, and 11 meat quality traits, and the number of pigs with phenotypes ranged from 421 to 953. A total of 119 markers were genotyped and then used for QTL analysis. We utilized a pedigree-based, multipoint variance components approach to test for linkage between QTL and the phenotypic values using a maximum likelihood method; the logarithm of odds score and QTL genotypic heritability were estimated. A total of 42 QTL with suggestive linkages and 3 QTL with significant linkages for 26 traits were detected. These included selection traits such as daily BW gain, backfat thickness, loin eye muscle area, and intramuscular fat content as well as correlated traits such as body size and meat quality traits. The present study disclosed QTL affecting growth, body size, and carcass, physiological, and meat quality traits in a Duroc purebred population.     

Investigations in the character of QTL affecting negatively correlated milk traits

The primary aim of this study was to investigate the quantitative trait loci (QTL) on BTA6 that affect negatively correlated milk traits, using bivariate covariance component analysis of milk yield and fat (or protein) content, protein yield and fat content, and fat yield and protein content. A set of five different genetic models was adapted to differentiate trait‐specific QTL in close linkage from pleiotropy. Using a grand‐daughter design consisting of five half‐sib families from the German Holstein population and 298 sons genotyped for 16 microsatellite markers on BTA6, we found significant trait‐specific QTL for fat content and protein yield, 24 cM apart. Markers BM1329 and FBN12 bracketed the QTL for fat content, and the region between TGLA37 and FBN13 most likely harbours a QTL for protein yield. The analysis based on the close linkage model fully confirmed this result. Despite the pure QTL findings confirming results from the literature, distinguishing pleiotropic and closely linked QTL for competitive traits is a new aspect. Our multivariate analysis results did not suggest a pleiotropic QTL for the investigated negatively correlated traits. The QTL‐based trait correlations were discussed as an important aspect of modelling that needs to be considered in the future.     

A genome scan for quantitative trait loci and imprinted regions affecting reproduction in pigs

Quantitative trait loci for reproductive traits in a three-generation resource population of a cross between low-indexing pigs from a control line and high-indexing pigs from a line selected 10 generations for increased index of ovulation rate and embryonic survival are reported. Phenotypic data were collected in F2 females for birth weight (BWT, n = 428), weaning weight (WWT, n = 405), age at puberty (AP, n = 295), ovulation rate (OR, n = 423), number of fully formed pigs (FF, n = 370), number of pigs born alive (NBA, n = 370), number of mummified pigs (MUM, n = 370), and number of stillborn pigs (NSB, n = 370). Grandparent, F1, and F2 animals were genotyped for 151 microsatellite markers. Sixteen putative QTL (P < 0.10) for reproductive traits were identified in previous analyses of these data with single QTL line-cross models. Data were reanalyzed with multiple QTL models, including imprinting effects. Data also were analyzed with half-sib models. Permutation was used to establish genome-wide significance levels ( = 0.01, 0.05, and 0.10). Thirty-one putative QTL for reproductive traits and two QTL for birth weight were identified (P < 0.10). One Mendelian QTL for FF (P < 0.05), one for NBA (P < 0.05), three for NSB (P < 0.05), three for NN (P < 0.05), seven for AP (P < 0.10), five for MUM (P < 0.10), and one for BWT (P < 0.10) were found. Partial imprinting of QTL affecting OR (P < 0.01), BWT (P < 0.05), and MUM (P < 0.05) was detected. There were four paternally expressed QTL for NN (P < 0.10) and one each for AP (P < 0.05) and MUM (P < 0.10). Maternally expressed QTL affecting NSB (P < 0.10), NN (P < 0.10), and MUM (P < 0.10) were detected. No QTL were detected with half-sib analyses. Multiple QTL models with imprinting effects are more appropriate for analyzing F2 data than single Mendelian QTL line-cross models.     

Detection and fine mapping of quantitative trait loci for bone traits on chicken chromosome one

In broiler chickens, bone problems are an important welfare issue that has been linked to genetic selection for rapid growth. The objectives of this study were to identify and fine map quantitative trait loci (QTL) associated with bone traits. The Northeast Agricultural University resource population (NEAURP) being an F(2) population was used in this study, and a total of 17 bone traits were measured. In primary genome scan, the linkage map was constructed with 23 microsatellite markers across the entire chicken chromosome 1. Seventeen QTLs for bone traits were identified and 12 of these were found between LEI0079 and ROS0025 (50.8 cM apart). To fine map the QTLs located between LEI0079 and ROS0025, more markers and more individuals were used and a new partial linkage map was constructed. The confidence intervals for QTLs were sharply narrowed down from 24.5～52.6 to 2.7～17.0 Mb. This study identified chromosome regions harbouring significant QTLs affecting bone traits and showed that the use of more markers and individuals could decrease the confidence interval of QTL effectively. The results provide a useful reference for further candidate gene research and MAS for bone traits.