Genome-wide identification of quantitative trait loci for carcass composition and meat quality in a large-scale White Duroc × Chinese Erhualian resource population

Carcass and meat quality traits are economically important in pigs. In this study, 17 carcass composition traits and 23 meat quality traits were recorded in 1028 F₂ animals from a White Duroc × Erhualian resource population. All pigs in this experimental population were genotyped for 194 informative markers covering the entire porcine genome. Seventy-seven genome-wide significant quantitative trait loci (QTL) for carcass traits and 68 for meat quality were mapped to 34 genomic regions. These results not only confirmed many previously reported QTL but also revealed novel regions associated with the measured traits. For carcass traits, the most prominent QTL was identified for carcass length and head weight at 57 cM on SSC7, which explained up to 50% of the phenotypic variance and had a 95% confidence interval of only 3 cM. Moreover, QTL for kidney and spleen weight and lengths of cervical vertebrae were reported for the first time in pigs. For meat quality traits, two significant QTL on SSC5 and X were identified for both intramuscular fat content and marbling score in the longissimus muscle, while three significant QTL on SSC1 and SSC9 were found exclusively for IMF. Both LM and the semimembranous muscle showed common QTL for colour score on SSC4, 5, 7, 8, 13 and X and discordant QTL on other chromosomes. White Duroc alleles at a majority of QTL detected were favourable for carcass composition, while favourable QTL alleles for meat quality originated from both White Duroc and Erhualian.     

Genome wide QTL mapping to identify candidate genes for carcass traits in Hanwoo (Korean Cattle)

Meat quality traits are the most economically important traits affecting the beef industry in Korea. We performed a whole genome quantitative trait locus (QTL) mapping study of carcass data in Hanwoo Korean cattle. Two hundred sixty-six Hanwoo steers from 65 sires were genotyped using a 10K Affymetrix SNP chip. The average SNP interval across the bovine genome was 1.5Mb. Associations between each individual SNP and four carcass traits [carcass weight (CWT), eye muscle area (EMA), back fat thickness (BFT), and marbling (MAR)] were assessed using a linear mixed model of each trait. Combined linkage and linkage disequilibrium analysis (LDLA) detected six potential QTL on BTA04, 06, 13, 16, 17, and 23 at the chromosome-wise level (P<0.05). Two MAR QTL were detected at 52.2 cM of BTA06 and 46.04 cM of BTA17. We identified three genes (ARAP2, LOC539460, and LOC511424) in the QTL region of BTA06 and seven genes (RPS14, SCARB1, LOC782103, BRI3BP, AACS, DHX37, and UBC) in the QTL region of BTA17. One significant QTL for CWT was detected at 100 cM on BTA04 and the corresponding QTL region spanned 1.7 cM from 99.7 to 101.4 cM. For EMA QTL, one significant QTL was detected at 3.9 cM of BTA23 and the most likely QTL interval was 1.4 cM, placing 15 candidate genes in the marker bracket. Finally, two QTL for BFT were identified at 68 cM on BTA13 and 24 cM on BTA16. The LPIN3 gene, which is functionally associated with lipodystrophy in humans, is located in the BFT QTL on BTA13. Thus, two potential candidate genes, acetoacetyl-CoA synthetase (AACS) and lipin (LPIN), were detected in QTL regions on BTA17 for MAR and BTA13 for BFT, respectively. In conclusion, LDLA analysis can be used to detect chromosome regions harboring QTL and candidate genes with a low density SNP panel, yielding relatively narrow confidence intervals regarding location.     

猪部分内脏器官性状和乳头数的QTL检测

对内脏器官重量性状的QTL定位研究,所见报道不多;对于猪的繁殖性状,尚需做进一步的探讨。本研究在总共214头(180头F2个体)组成的资源家系中,在猪的SSC4、SSC6、SSC7、SSC8 和 SSC13上共选取39个微卫星标记,检测了8种内脏器官的重量性状:心重 (HW)、肺重 (LW)、肝 胆重 (LGW)、脾重 (SPW)、胃重 (STW)、小肠重(SIW)、大肠重(LIW) 和肾重(KW);其他一些胴体性状:胴体长性状1(自第一颈椎,CL1)、胴体长性状2(自第一胸椎,CL2)、肋骨数(RNS)和繁殖性状乳头数(TNS)的QTL定位。结果表明,检测到3个染色体极显著水平的QTL(P≤0.01),它们是HW QTL定位在SSC6上30 cM处,RNS QTL定位在SSC7上115 cM处和TNS QTL定位在SSC7上 110 cM处;另外6个染色体显著水平的QTL(P≤0.05)是:LW(SSC13上119 cM处)、LGW(SSC6上94 cM处)、SPW(SSC8上106 cM处)、SIW(SSC 4上0 cM处)、LIW(SSC 4上170 cM 处)和TNS(SSC 6上95 cM处)。上述QTL解释的表型变异从 0.04% 到 14.06%,有些位点的 QTL 可以解释表型变异的 10%以上,如 HW 的 QTL 解释表型变异的9.52%、SIW的QTL解释表型变异的13.47%、定位在SSC6上的TNS QTL解释表型变异的14.06%,而定位在 SSC7上的TNS QTL解释表型变异的11.30%。多数内脏器官重量性状的QTL定位结果未见报道。胴体长未见显著水平的QTL,而在SSC7上定位染色体极显著水平的肋骨数QTL。     

Quantitative trait loci segregating in crosses between New Hampshire and White Leghorn chicken lines: II. Muscle weight and carcass composition

In order to identify genetic factors influencing muscle weight and carcass composition in chicken, a linkage analysis was performed with 278 F₂ males of reciprocal crosses between the extremely different inbred lines New Hampshire (NHI) and White Leghorn (WL77). The NHI line had been selected for high meat yield and the WL77 for low egg weight before inbreeding. Highly significant quantitative trait loci (QTL) controlling body weight and the weights of carcass, breast muscle, drumsticks–thighs and wings were identified on GGA4 between 151.5 and 160.5 cM and on GGA27 between 4 and 52 cM. These genomic regions explained 13.7–40.2% and 5.3–13.8% of the phenotypic F₂ variances of the corresponding traits respectively. Additional genome‐wide highly significant QTL for the weight of drumsticks–thighs were mapped on GGA1, 5 and 7. Moreover, significant QTL controlling body weight were found on GGA2 and 11. The data obtained in this study can be used for increasing the mapping resolution and subsequent gene targeting on GGA4 and 27 by combining data with other crosses where the same QTL were found.     

Results of a whole-genome quantitative trait locus scan for growth, carcass composition and meat quality in a porcine four-way cross

A whole-genome quantitative trait locus (QTL) scan for 31 phenotypes related to growth, carcass composition and meat quality was conducted using 1187 progeny of a commercial four-way cross. Animals were genotyped for 198 microsatellite markers that spanned the entire porcine genome. QTL analysis was conducted to extract information from paternal and maternal meioses separately using a rank-based nonparametric approach for half-sib designs. Nine QTL exceeded genome-wide significance: one QTL affecting growth (average daily gain on SSC1), two QTL influencing carcass composition (fatness on SSC3 and muscle mass on SSC15) and six QTL influencing meat quality (tenderness on SSC4 and SSC14; colour on SSC5, SSC6 and SSCX; and conductivity on SSC16). All but one of these coincided with previously reported QTL. In addition, we present evidence for 78 suggestive QTL with a combined false discovery rate of 40%.     

Microsatellite mapping of quantitative trait loci affecting meat quality, stress hormones and production traits in Duroc × Large White F2 pigs

An F2 cross between Duroc and Large White pigs was carried out in order to detect quantitative trait loci (QTL) for 11 meat quality traits (L*, a* and b* Minolta coordinates and water-holding capacity (WHC) of two ham muscles, ultimate pH of two ham and one loin muscles), 13 production traits (birth weight, average daily gain during post-weaning and fattening periods, carcass fat depths at three locations, estimated lean meat content, carcass length and weights of five carcass cuts) and three stress hormone-level traits (cortisol, adrenaline and noradrenaline). Animals from the three generations of the experimental design (including 456 F2 pigs) were genotyped for 91 microsatellite markers covering all the autosomes. A total of 56 QTL were detected: 49 reached the chromosome-wide level (suggestive QTL with a maximal probability of 0.05) and seven were significant at the genome-wide level (with a probability varying from 6 × 10(-4) to 3 × 10(-3)). Twenty suggestive QTL were identified for ultimate pH, colour measurements and WHC on chromosome (SSC) 5, 6, 7, 8, 9, 11, 13, 14, 15 and 17. For production traits, 33 QTL were detected on all autosomes except SSC6, 8 and 9. Seven of these QTL, located on SSC2, 3, 10, 13, 16 and 17, exceeded the genome-wide significance threshold. Finally, three QTL were identified for levels of stress hormones: a QTL for cortisol level on SSC7 in the cortisol-binding globulin gene region, a QTL for adrenaline level on SSC10 and a QTL for noradrenaline level on SSC13. Among all the detected QTL, seven are described for the first time: a QTL for ultimate pH measurement on SSC5, two QTL affecting birth weight on SSC2 and 10, two QTL for growth rate on SSC15 (during fattening) and 17 (during post-weaning) and two QTL affecting the adrenaline and noradrenaline levels. For each QTL, only one to five of the six F1 sires were found to be heterozygous. It means that all QTL are segregating in at least one of the founder populations used in this study. These results suggest that both meat quality and production traits can be improved in purebred Duroc and Large White pigs through marker-assisted selection. It is of particular interest for meat quality traits, which are difficult to include in classical selection programmes.     

QTL mapping for growth and carcass traits in an Iberian by Landrace pig intercross: additive,dominant and epistatic effects

Results from a QTL experiment on growth and carcass traits in an experimental F2 cross between Iberian and Landrace pigs are reported. Phenotypic data for growth, length of carcass and muscle mass, fat deposition and carcass composition traits from 321 individuals corresponding to 58 families were recorded. Animals were genotyped for 92 markers covering the 18 porcine autosomes (SSC). The results from the genomic scan show genomewide significant QTL in SSC2 (longissimus muscle area and backfat thickness), SSC4 (length of carcass, backfat thickness, loin, shoulder and belly bacon weights) and SSC6 (longissimus muscle area, backfat thickness, loin, shoulder and belly bacon weights). Suggestive QTL were also found on SSC1, SSC5, SSC7, SSC8, SSC9, SSC13, SCC14, SSC16 and SSC17. A bidimensional genomic scan every 10 cM was performed to detect interaction between QTL. The joint action of two suggestive QTL in SSC2 and SSC17 led to a genome-wide significant effect in live weight. The results of the bidimensional genomic scan showed that the genetic architecture was mainly additive or the experimental set-up did not have enough power to detect epistatic interactions.     

Genomic regions affecting backfat thickness and cannon bone circumference identified by genome‐wide association study in a Duroc pig population

We performed a genome‐wide association study using the porcine 60K SNP array to detect QTL regions for nine traits in a three‐generational Duroc samples (n = 651), viz. generations 1, 2 and 3 from a population selected over five generations using a closed nucleus breeding scheme. We applied a linear mixed model for association mapping to detect SNP effects, adjusting for fixed effects (sex and season) and random polygenic effects (reflecting genetic relatedness), and derived a likelihood ratio statistic for each SNP using the efficient mixed‐model association method. We detected a region on SSC6 for backfat thickness (BFT) and on SSC7 for cannon bone circumference (CANNON), with a genome‐wide significance of P < 0.01 after Bonferroni correction. These regions had been detected previously in other pig populations. Six genes are located in the BFT‐associated region, while the CANNON‐associated region includes 66 genes. In the future, significantly associated SNPs, derived by sequencing the coding regions of the six genes in the BFT region, can be used in marker‐assisted selection of BFT, whereas haplotypes constructed from the SSC7 region with strong LD can be used to select for the CANNON trait in our resource family.     

Linked and pleiotropic QTLs influencing carcass composition traits detected on porcine chromosome 7

A multivariate QTL detection was carried out on fatness and carcass composition traits on porcine chromosome 7 (SSC7). Single-trait QTLs have already been detected in the SLA region, and multivariate approaches have been used to exploit the correlations between the traits to obtain more information on their pattern: almost 500 measurements were recorded for backfat thickness (BFT1, BFT2), backfat weight (BFW) and leaf fat weight (LFW) but only about half that number for intramuscular fat content (IMF), affecting the detection. First, groups of traits were selected using a backward selection procedure: traits were selected based on their contribution to the linear combination of traits discriminating the putative QTL haplotypes. Three groups of traits could be distinguished based on successive discriminant analyses: external fat (BFT1, BFT2), internal fat (LFW, IMF) and BFW. At least four regions were distinguished, preferentially affecting one or the other group, with the SLA region always influencing all the traits. Meishan alleles decreased all trait values except IMF, confirming an opportunity for marker-assisted selection to improve meat quality with maintenance of carcass composition based on Meishan alleles.     

A genome‐wide association analysis for carcass traits in a commercial Duroc pig population

We performed a genome‐wide association study to map the genetic determinants of carcass traits in 350 Duroc pigs typed with the Porcine SNP60 BeadChip. Association analyses were carried out using the gemma software. The proportion of phenotypic variance explained by the SNPs ranged between negligible to moderate (= 0.01–0.30) depending on the trait under consideration. At the genome‐wide level, we detected one significant association between backfat thickness between the 3^rd and 4^th ribs and six SNPs mapping to SSC12 (37–40 Mb). We also identified several chromosome‐wide significant associations for ham weight (SSC11: 51–53 Mb, three SNPs; 67–68 Mb, two SNPs), carcass weight (SSC11: 66–68 Mb, two SNPs), backfat thickness between the 3^rd and 4^th ribs (SSC12: 21 Mb, one SNP; 33–40 Mb, 17 SNPs; 51–58 Mb, two SNPs), backfat thickness in the last rib (SSC12: 37 Mb, one SNP; 40–41 Mb, nine SNPs) and lean meat content (SSC13: 34 Mb, three SNPs and SSC16: 45.1 Mb, one SNP; 62–63 Mb, 10 SNPs; 71–75 Mb, nine SNPs). The ham weight trait‐associated region on SSC11 contains two genes (UCHL3 and LMO7) related to muscle development. In addition, the ACACA gene, which encodes an enzyme for the catalysis of fatty acid synthesis, maps to the SSC12 (37–41 Mb) region harbouring trait‐associated regions for backfat thickness traits. Sequencing of these candidate genes may help to uncover the causal mutations responsible for the associations found in the present study.     

Mapping quantitative trait loci affecting some carcass and meat traits in duck (Anas platyrhynchos)

Contrary to chicken and livestock mammals, duck genome has not been explored much. Nowadays a relatively small number of reports on molecular variability and mapping of loci in Peking ducks has been published. Therefore, the objective of this study was to detect single loci affecting body weight, carcass and meat traits in Peking ducks (Anas platyrhynchos). The study was based on an F2 cross between two parental lines A-55 and GL-30. Phenotypes of 387 birds from generation F2 including carcass and meat quality traits were collected. Linkage map, of the linkage group CAU1, consisting of 29 microsatellite markers was constructed. One highly significant (p?p?相似文献   

A genome scan reveals QTL for growth, fatness, leanness and meat quality in a Duroc-Pietrain resource population

We performed a genome-wide QTL scan for production traits in a line cross between Duroc and Pietrain breeds of pigs, which included 585 F(2) progeny produced from 31 full-sib families genotyped with 106 informative microsatellites. A linkage map covering all 18 autosomes and spanning 1987 Kosambi cM was constructed. Thirty-five phenotypic traits including body weight, growth, carcass composition and meat quality traits were analysed using least square regression interval mapping. Twenty-four QTL exceeded the genome-wide significance threshold, while 47 QTL reached the suggestive threshold. These QTL were located at 28 genomic regions on 16 autosomal chromosomes and QTL in 11 regions were significant at the genome-wide level. A QTL affecting pH value in loin was detected on SSC1 between marker-interval S0312-S0113 with strong statistical support (P < 3.0 x 10(-14)); this QTL was also associated with meat colour and conductivity. QTL for carcass composition and average daily gain was also found on SSC1, suggesting multiple QTL. Seventeen genomic segments had only a single QTL that reached at least suggestive significance. Forty QTL exhibited additive inheritance whereas 31 QTL showed (over-) dominance effects. Two QTL for trait backfat thickness were detected on SSC2; a significant paternal effect was found for a QTL in the IGF2 region while another QTL in the middle of SSC2 showed Mendelian expression.     

A genome‐wide association study for a proxy of intermuscular fat level in the Italian Large White breed identifies genomic regions affecting an important quality parameter for dry‐cured hams

Intermuscular fat content in protected designations of origin dry‐cured hams is a very important meat quality trait that affects the acceptability of the product by the consumers. An excess in intermuscular fat (defined as the level of fat deposition between leg muscles) is a defect that depreciates the final product. In this study we carried out a genome‐wide association study for visible intermuscular fat (VIF) of hams in the Italian Large White pig breed. This trait was evaluated on the exposed muscles of green legs in 1122 performance‐tested gilts by trained personnel, according to a classification scale useful for routine and cheap evaluation. All animals were genotyped with the Illumina PorcineSNP60 BeadChip. The genome‐wide association study identified three QTL regions on porcine chromosome 1 (SSC1; accounting for ~79% of the SNPs below the 5.0E?04 threshold) and SSC2, two on SSC7 and one each on SSC3, SSC6, SSC9, SSC11, SSC13, SSC15, SSC16 and SSC17. The most significant SNP (ALGA0004143 on SSC1 at 77.3 Mb; P_FDR < 0.05), included in the largest QTL region which spanned about 6.8 Mb on SSC1, is located within the glutamate ionotropic receptor kainate type subunit 2 (GRIK2) gene. Functional annotation of all genes included in QTL regions for VIF suggested that intermuscular fat in the Italian Large White breed is a complex trait apparently influenced by complex biological mechanisms also involving obesity‐related processes. These QTL target mainly chromosome regions different from those affecting subcutaneous and intramuscular fat deposition.     

QTL analysis of body weight and carcass body length traits in an F2 intercross between Landrace and Korean native pigs

Growth traits, such as body weight and carcass body length, directly affect productivity and economic efficiency in the livestock industry. We performed a genome‐wide linkage analysis to detect the quantitative trait loci (QTL) that affect body weight, growth curve parameters and carcass body length in an F₂ intercross between Landrace and Korean native pigs. Eight phenotypes related to growth were measured in approximately 1000 F₂ progeny. All experimental animals were subjected to genotypic analysis using 173 microsatellite markers located throughout the pig genome. The least squares regression approach was used to conduct the QTL analysis. For body weight traits, we mapped 16 genome‐wide significant QTL on SSC1, 3, 5, 6, 8, 9 and 12 as well as 22 suggestive QTL on SSC2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16 and 17. On SSC12, we identified a major QTL affecting body weight at 140 days of age that accounted for 4.3% of the phenotypic variance, which was the highest test statistic (F‐ratio = 45.6 under the additive model, nominal P = 2.4 × 10^?11) observed in this study. We also showed that there were significant QTL on SSC2, 5, 7, 8, 9 and 12 affecting carcass body length and growth curve parameters. Interestingly, the QTL on SSC2, 3, 5, 6, 8, 9, 10, 12 and 17 influencing the growth‐related traits showed an obvious trend for co‐localization. In conclusion, the identified QTL may play an important role in investigating the genetic structure underlying the phenotypic variation of growth in pigs.     

Investigation of LDHA and COPB1 as candidate genes for muscle development in the MYOD1 region of pig chromosome 2

Porcine MYOD1 gene has been mapped to swine chromosome (SSC) 2p14-p17, which is involved in the regulation of the proliferation and differentiation of skeletal muscle cells. The LDHA (lactate dehydrogenase A) and COPB1 (coatomer protein complex, subunit beta 1) genes, which map close to MYOD1, are involved in energy metabolism and protein transport processes. Both genes might play important roles in muscle development. However, little is known about the porcine LDHA and COPB1 genes. In the present study, the full-length cDNA of these two genes were cloned. The mapping results demonstrated that porcine LDHA and COPB1 were all mapped to SSC 2p14-p17. In this region, there are several QTL for growth and carcass traits, including average backfat thickness, lean and fat percentage. The RT-PCR results revealed that both LDHA and COPB1 were highly expressed in porcine skeletal muscle tissues, implying their potential regulatory function of muscle development. LDHA and COPB1 were then mapped to the region and multipoint analyses generated a best sex-averaged map order of each gene between linked markers: MYOD1_75.2 cM _LDHA_79 cM _CSRP3_83.8 cM _TEF-1_86.5 cM _COPB1_90 cM. Association analyses revealed that the substitution of c.423A>G had a significant effect on average daily gain on test, average backfat thickness (BFT), loin muscle area, lumbar BFT, marbling score, tenth rib BFT, average drip loss and fiber type II ratio. The substitution of c.3096C>T had a significant effect on average BFT, lumbar BFT, tenth rib BFT, carcass weight and last rib BFT. Interestingly, both SNPs were all associated with average BFT, lumbar BFT and tenth rib BFT.     

Three novel quantitative trait loci for skin thickness in swine identified by linkage and genome‐wide association studies

Skin is the largest organ in the pig body and plays a key role in protecting the body against pathogens and excessive water loss. Deciphering the genetic basis of swine skin thickness would enrich our knowledge about the skin. To identify the loci for porcine skin thickness, we first performed a genome scan with 194 microsatellite markers in a White Duroc × Erhualian F₂ intercross. We identified three genome‐wide significant QTL on pig chromosomes (SSC) 4, 7 and 15 using linkage analysis. The most significant QTL was found on SSC7 with a small confidence interval of ~5 cM, explaining 23.9 percent of phenotypic variance. Further, we conducted a genome‐wide association study (GWAS) using Illumina PorcineSNP60 Beadchips for the F₂ pedigree and a population of Chinese Sutai pigs. We confirmed significant QTL in the F₂ pedigree and replicated QTL on SSC15 in Chinese Sutai pigs. A meta‐analysis of GWASs on both populations detected a genomic region associated with skin thickness on SSC4. GWAS results were generally consistent with QTL mapping. Identical‐by‐descent analysis defined QTL on SSC7 in a 683‐kb region harboring an interesting candidate gene: HMGA1. On SSC15, the linkage disequilibrium analysis showed a haplotype block of 2.20 Mb that likely harbors the gene responsible for skin thickness. Our findings provide novel insights into the genetic basis of swine skin thickness, which would benefit further understanding of porcine skin function.     

Quantitative trait loci associated with AutoFOM grading characteristics, carcass cuts and chemical body composition during growth of Sus scrofa

A three-generation full-sib resource family was constructed by crossing two commercial pig lines. Genotypes for 37 molecular markers covering chromosomes SSC1, SSC6, SSC7 and SSC13 were obtained for 315 F2 animals of 49 families and their parents and grandparents. Phenotypic records of traits including carcass characteristics measured by the AutoFOM grading system, dissected carcass cuts and meat quality characteristics were recorded at 140 kg slaughter weight. Furthermore, phenotypic records on live animals were obtained for chemical composition of the empty body, protein and lipid accretion (determined by the deuterium dilution technique), daily gain and feed intake during the course of growth from 30 to 140 kg body weight. Quantitative trait loci (QTL) detection was conducted using least-squares regression interval mapping. Highest significance at the 0.1% chromosome-wise level was obtained for five QTL: AutoFOM belly weight on SSC1; ham lean-meat weight, percentage of fat of primal cuts and daily feed intake between 60 and 90 kg live weight on SSC6; and loin lean-meat weight on SSC13. QTL affecting daily gain and protein accretion were found on SSC1 in the same region. QTL for protein and lipid content of empty body at 60 kg liveweight were located close to the ryanodine receptor 1 (RYR1) locus on SSC6. On SSC13, significant QTL for protein accretion and feed conversion ratio were detected during growth from 60 to 90 kg. In general, additive genetic effects of alleles originating from the Piétrain line were associated with lower fatness and larger muscularity as well as lower daily gain and lower protein accretion rates. Most of the QTL for carcass characteristics were found on SSC6 and were estimated after adjustment for the RYR1 gene. QTL for carcass traits, fatness and growth on SSC7 reported in the literature, mainly detected in crosses of commercial lines x obese breeds, were not obtained in the present study using crosses of only commercial lines, suggesting that these QTL are not segregating in the analysed commercial lines.     

Genetic mapping of quantitative trait loci for meat quality and muscle metabolic traits in cattle

A whole‐genome scan was carried out in New Zealand and Australia to detect quantitative trait loci (QTL) for live animal and carcass composition traits and meat quality attributes in cattle. Backcross calves (385 heifers and 398 steers) were generated, with Jersey and Limousin backgrounds. The New Zealand cattle were reared and finished on pasture, whilst Australian cattle were reared on grass and finished on grain for at least 180 days. This paper reports on meat quality traits (tenderness measured as shear force at 4–5 ages on two muscles as well as associated traits of meat colour, pH and cooking loss) and a number of metabolic traits. For meat quality traits, 18 significant QTL (P < 0.05), located in nine linkage groups, were detected on a genome‐wise basis, in combined‐sire (seven QTL) or within‐sire analyses (11 QTL). For metabolic traits, 11 significant QTL (P < 0.05), located in eight linkage groups, were detected on a genome‐wise basis, in combined‐sire (five QTL) or within‐sire analyses (six QTL). BTA2 and BTA3 had QTL for both metabolic traits and meat quality traits. Six significant QTL for meat quality and metabolic traits were found at the proximal end of chromosome 2. BTA2 and BTA29 were the most common chromosomes harbouring QTL for meat quality traits; QTL for improved tenderness were associated with Limousin‐derived and Jersey‐derived alleles on these two chromosomes, respectively.     

A Genome-Wide Association Study to Detect QTL for Commercially Important Traits in Swiss Large White Boars

The improvement of meat quality and production traits has high priority in the pork industry. Many of these traits show a low to moderate heritability and are difficult and expensive to measure. Their improvement by targeted breeding programs is challenging and requires knowledge of the genetic and molecular background. For this study we genotyped 192 artificial insemination boars of a commercial line derived from the Swiss Large White breed using the PorcineSNP60 BeadChip with 62,163 evenly spaced SNPs across the pig genome. We obtained 26 estimated breeding values (EBVs) for various traits including exterior, meat quality, reproduction, and production. The subsequent genome-wide association analysis allowed us to identify four QTL with suggestive significance for three of these traits (p-values ranging from 4.99×10⁻⁶ to 2.73×10⁻⁵). Single QTL for the EBVs pH one hour post mortem (pH1) and carcass length were on pig chromosome (SSC) 14 and SSC 2, respectively. Two QTL for the EBV rear view hind legs were on SSC 10 and SSC 16.