Effect of genetic variants of the heart fatty acid-binding protein gene on intramuscular fat and performance traits in pigs.

In order to find genetic markers to improve the meat quality of pigs by breeding we studied the relationship between variation in the heart fatty acid-binding protein (H-FABP) gene (FABP3) and intramuscular fat (IMF) content. To estimate the effect of H-FABP, pigs from two Duroc populations were selectively mated in such a way that at least two genotypes were present in each litter. In total, data from 983 pigs and pedigree information from three preceding generations were analyzed. Offspring were tested for IMF content as well as backfat thickness (BFT), BW, and drip loss of the meat (DRIP). All pigs were assigned to H-FABP RFLP genotype classes either by the assessed genotype (75%) or based on a probability score determined according to genotypic information of their relatives (25%). Contrasts were detected between homozygous H-FABP RFLP genotype classes for IMF content (.4%, P < .05), BFT (.6 mm, P < .01), and BW (2.4 kg, P < .10). No significant contrasts were detected for DRIP. Results for IMF content, BFT, and BW were confirmed when only genotyped animals were analyzed. Variation in BFT partially explained the effect on IMF content. Although other closely linked genes on porcine chromosome 6 might be responsible for the observed effect, interference of the halothane gene was excluded because all parental animals were noncarriers. In conclusion, H-FABP RFLP can be used as markers to select for increased IMF content and growth in breeding programs.     

巨型玫瑰冠鸡H-FABP、A-FABP基因表达的发育性变化及其肌内脂肪含量研究

为探讨心脏型脂肪酸结合蛋白（heart-type fatty acid-binding protein，H-FABP）和脂肪型脂肪酸结合蛋白（adipocyte fatty acid-binding protein，A-FABP）基因与巨型玫瑰冠鸡生长发育及肌内脂肪含量（IMF）的关系，研究H-FABP、A-FABP基因对巨型玫瑰冠鸡IMF含量和腹脂沉积的作用机制，本试验采集了巨型玫瑰冠鸡与良凤花鸡在不同周龄（2、4、6、8、10、12周龄）的腹脂、心肌、胸肌、腿肌组织样品共480份，采用实时荧光定量PCR对巨型玫瑰冠鸡与良凤花鸡不同生长阶段组织中H-FABP、A-FABP基因mRNA表达量进行了检测，并采用索氏浸提法测定了两种鸡12周龄的胸肌与腿肌的IMF含量。结果表明，巨型玫瑰冠鸡与良凤花鸡的H-FABP、A-FABP基因mRNA在腹脂、心肌、胸肌和腿肌组织中均有不同程度的表达，且两种鸡H-FABP基因mRNA在心肌组织中高度表达，在脂肪组织中表达量较低，在胸肌、腿肌组织中中度表达，而A-FABP基因相反，推测H-FABP基因主要在肌肉组织中表达，而A-FABP基因主要在脂肪组织中表达。良凤花鸡生长速度高于巨型玫瑰冠鸡；巨型玫瑰冠鸡的腹脂率均低于同性别的良凤花鸡，但胸肌、腿肌的IMF均高于同性别的良凤花鸡，表明巨型玫瑰冠鸡的肉品质优于良凤花鸡。本试验结果为巨型玫瑰冠鸡H-FABP、A-FABP基因分子选育奠定了基础。     

Investigation of two candidate genes for meat quality traits in a quantitative trait locus region on SSC6: the porcine short heterodimer partner and heart fatty acid binding protein genes

A highly significant quantitative trait locus (QTL) on pig chromosome 6, affecting intramuscular fat (IMF), has previously been detected by our group and others. Two genes of positional and biological interest, the small heterodimer partner (SHP; NR0B2) and the heart fatty acid binding protein (FABP3; H‐FABP), were investigated for meat quality traits and IMF respectively. SHP was partially sequenced (GenBank: DQ002896 and DQ002897 ) and mapped to the QTL region on porcine chromosome 6, affecting IMF. The map shows no recombination between SHP and FABP3, which was previously mapped to the same QTL region. Twelve single nucleotide polymorphisms were detected in the sequenced region of SHP gene. Haplotype information was used to investigate association between genetic variation and different meat quality traits. SHP haplotype combinations were found to have significant effect on connective tissue. However, further studies are needed to evaluate this possible association more effectively. The FABP3 is involved in fatty acid transport and has been studied as a candidate gene for IMF by several research groups. In our study, FABP3 genotypes were confirmed to be significantly associated with IMF in pigs. The average content of IMF in our population was 1.6%, which may indicate that the FABP3 polymorphism explains as much as 30–35% of the variation in IMF in our pig cross‐population.     

鸡H-FABP和A-FABP基因表达与肌内脂肪含量相关研究

选用H-FABP和A-FABP基因作为影响鸡肌内脂肪沉积的候选基因,以北京油鸡、矮脚鸡、白莱航鸡和AA肉鸡为研究群体,利用RT-PCR和实时荧光定量PCR技术,分别对56、90、120日龄H-FABP和A-FABP基因mRNA进行定量分析,结合IMF含量及屠体性状测定,分析H-FABP及A-FABP基因表达水平对IMF含量等的影响.结果表明：H-FABP基因mRNA随日龄的增长表达量显著降低,而A-FABP基因mRNA随日龄的增长表达量显著升高,并表现出显著的品种效应（P＜0.01）,性别因素对A-FABP基因表达影响显著.北京油鸡、白莱航鸡和AA鸡群体的H-FABP基因mRNA表达水平与IMF含量及屠体重呈现显著的负相关,而A-FABP基因mRNA表达水平与屠体重显著相关,与IMF含量没有显著的相关性.矮脚鸡A-FABP基因mRNA水平与IMF含量呈现显著的负相关,其H-FABP基因mRNA水平对屠体重影响显著,表现出显著的品种差异.     

辽宁种猪H-FABP和A-FABP基因位点多态性研究

目的:检测辽宁种猪H-FABP和A-FABP基因位点多态性。方法:采用PCR-RFLP技术。结果:4个猪种H-FABP基因HinfI和HaeⅢ点酶切位点上都显示多态性,优势基因型分别为HH和dd型,荷包猪H-FABP基因5′上游区和第二内含子多态性分析的结果显示H和d基因的频率较高;4个猪种A-FABP基因内含子IBsmI位点进行PCR-RFLP均检测到3种基因型,在地方猪种东北荷包猪中,等位基因A为优势基因,在国外引进猪种大白,长白,杜洛克猪中,等位基因B为优势基因。结论:荷包猪具有高肌内脂肪含量,我国地方猪种肉质优于引入品种。     

Quantitative trait loci analysis for growth and carcass traits in a Meishan x Duroc F2 resource population

We constructed a pig F2 resource population by crossing a Meishan sow and a Duroc boar to locate economically important trait loci. The F2 generation was composed of 865 animals (450 males and 415 females) from four F1 males and 24 F1 females and was genotyped for 180 informative microsatellite markers spanning 2,263.6 cM of the whole pig genome. Results of the genome scan showed evidence for significant quantitative trait loci (<1% genomewise error rate) affecting weight at 30 d and average daily gain on Sus scrofa chromosome (SSC) 6, carcass yield on SSC 7, backfat thickness on SSC 7 and SSC X, vertebra number on SSC 1 and SSC 7, loin muscle area on SSC 1 and SSC 7, moisture on SSC 13, intramuscular fat content on SSC 7, and testicular weight on SSC 3 and SSC X. Moreover, 5% genomewise significant QTL were found for birth weight on SSC 7, average daily gain on SSC 4, carcass length on SSC 6, SSC 7, and SSC X and lightness (L value) on SSC 3. We identified 38 QTL for 28 traits at the 5% genomewise level. Of the 38 QTL, 24 QTL for 17 traits were significant at the 1% genomewise level. Analysis of marker genotypes supported the breed of origin results and provided further evidence that a suggestive QTL for circumference of cannon bone also was segregating within the Meishan parent. We identified genomic regions related with growth and meat quality traits. Fine mapping will be required for their application in introgression programs and gene cloning.     

Intramuscular fat content and genetic variants at fatty acid-binding protein loci in Austrian pigs.

Intramuscular fat is an important meat quality trait in pig production. Previously, genetic variants of the heart fatty acid-binding protein (H-FABP) gene and the adipocyte fatty acid-binding protein (A-FABP) gene were suggested to be associated with intramuscular fat content. The objective of this investigation was to study these associations in the three most important Austrian breeding populations (Piétrain, Large White, and Landrace). Restriction fragment length polymorphism analysis of the H-FABP gene revealed a new MspI polymorphic site and genetic variation in all three breeds. Microsatellite analysis of the A-FABP locus showed up to nine different microsatellite alleles segregating. In Austrian breeds, no significant influence of the A-FABP and H-FABP gene polymorphisms on intramuscular fat could be detected. We also evaluated possible associations between the genetic variations at the H-FABP and A-FABP loci and other growth and carcass traits (average daily gain, feed conversion ratio, lean meat content, pH values, meat color, and drip loss). With regard to the extent of the effects, these genetic markers cannot be recommended for selection on growth and carcass traits in Austrian breeding populations.     

Evaluation of approaches to detect quantitative trait loci for growth, carcass, and meat quality on swine chromosomes 2, 6, 13, and 18. I. Univariate outbred F2 and sib-pair analyses

Results from univariate outbred F2 interval mapping and sib-pair analyses of 12 growth and 28 carcass traits to identify QTL on SSC 2, 6, 13, and 18 were compared. Phenotypic and genetic data were recorded on a three-generation resource population including 832 F2 pigs from a cross between three Berkshire sires and 18 Duroc dams. Thirty markers with an average spacing of approximately 16 cM were genotyped across the four chromosomes. The outbred F2 mixed model included the effects of sex, birth month, and year, one-QTL additive, dominance and imprinting coefficients calculated every 1 cM using interval mapping, and a random family effect. The general sib-pair model used to describe the phenotypic differences between sib-pairs included the same systematic and random effects and a one-QTL additive coefficient calculated every 1 cM. The outbred F2 analysis found significant evidence of QTL on SSC 2 associated with 105-d weight, backfat thicknesses, LM area, fat percent, shear force, juiciness, marbling, and tenderness. In addition, QTL were identified on SSC 6 relating to 42-d weight and LM area, and on SSC 18 for fat and moisture percents. In most instances, the outbred F2 approach offered greater power to detect QTL; however, the sib-pair analysis offered greater power in several instances. The trait-specific superiority could be due to the relative advantage of each model within a trait data set. The two approaches provided complementary evidence for QTL segregating between the Berkshire and Duroc breeds used in the study that may be used to aid marker-assisted introgression and selection and candidate gene studies to improve swine growth and meat quality characteristics.     

Use of microsatellite markers to detect quantitative trait loci in Yorkshire pigs

To identify genetic markers associated with economic traits in pigs, 157 microsatellite markers were examined in Yorkshire pigs. Thirty eight female Yorkshire pigs were initially examined and six of them were selected as progenitors; half were more than 1.5 standard deviations (SD) above the mean for average daily gain (ADG) and backfat thickness (BFT), and the remaining half were more than 1.5 SD below the mean. These pigs were then mated to male Duroc pigs, and 200 F2 pig offspring were examined for the association of specific alleles with ADG and BFT. To confirm the specific markers identified in the initial analysis, associations of significant markers with economic traits were further examined in 228 additional performance-tested purebred pigs. Twenty-five microsatellite markers were significantly associated with either ADG or BFT, and among these, 17 were associated with both traits. The markers with the highest association to ADG were also associated with BFT. Our study reveals that specific markers could be used to predict economic significance, and confirms several quantitative trait loci (QTL) identified in previous studies. However, further analysis with more closely-spaced microsatellite markers is required to refine predictive values for economic traits and positions of QTL that are reliable for actual phenotypic prediction.     

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.     

An evaluation of four candidate genes for use in selection programmes aimed at increased intramuscular fat in Duroc swine

Summary A sufficient level of intramuscular fat (IMF) is needed to enhance consumer acceptance of pork products, and is currently receiving greater attention within swine genetic improvement programmes. An examination of previously described and novel genetic variants within candidate genes for IMF deposition was performed to evaluate potential use of genetic markers in marker-assisted selection (MAS). Biological candidate genes implicated to play a role in adipogenesis were investigated within two different lines of purebred Duroc pigs. These included MC4R , FABP3 , DLK1 , and TCF7L2 . Significant variation in IMF within the control line was described by the MC4R genotype and a novel Bsr fI single nucleotide polymorphism within the FABP3 gene. Genetic markers for DLK1 and TCF7L2 evaluated in this population are not currently recommended for selection in Duroc swine. Existence of MC4R and FABP3 mutations may be useful markers in MAS aimed at IMF improvement, provided that gene effects are segregating and the presence of an association is detected within the population. However, additional work to confirm the use of the investigated genetic markers in selection programmes is needed.     

Identification of quantitative trait loci affecting corpora lutea and number of teats in a Meishan x Duroc F2 resource population

Understanding of the genetic control of female reproductive performance in pigs would offer the opportunity to utilize natural variation and improve selective breeding programs through marker-assisted selection. The Chinese Meishan is one of the most prolific pig breeds known, farrowing 3 to 5 more viable piglets per litter than Western breeds. This difference in prolificacy is attributed to the Meishan's superior prenatal survival. Our study utilized a 3-generation resource population, in which the founder grandparental animals were purebred Meishan and Duroc pigs, in a genome scan for QTL. Grandparent, F1, and F2 animals were genotyped for 180 microsatellite markers. Reproductive traits, including number of corpora lutea (number of animals = 234), number of fetuses per animal (n = 226), number of teats (n = 801), and total number born (n = 288), were recorded for F2 females. Genome-wide significance level thresholds of 1, 5, and 10% were calculated using a permutation approach. We identified 9 QTL for 3 traits at a 10% genome-wise significance level. Parametric interval mapping analysis indicated evidence of a 1% genome-wise significant QTL for corpora lutea on SSC 3. Nonparametric interval mapping for number of teats found 4 significant QTL on chromosomes SSC3 (P < 0.01), SSC7 (P < 0.01), SSC8 (P < 0.01), and SSC12 (P < 0.05). Partial imprinting of a QTL affecting teat number (P < 0.10) was detected on SSC8. Using the likelihood-ratio test for a categorical trait, 2 QTL for pin nipples were detected on SSC2 and SSC16 (P < 0.01). Fine mapping of the QTL regions will be required for their application to introgression programs and gene cloning.     

宗地花猪H-FABP基因mRNA的表达与肉质性状的相关研究

为研究不同饲养条件对地方猪种宗地花猪心脏型脂肪酸结合蛋白(heart fatty acid binding protein,H-FABP)基因表达及肌内脂肪(intramuscular fat,IMF)含量的影响,试验利用实时荧光定量PCR技术,分别测定放养型和圈养型宗地花猪背最长肌中H-FABP基因的表达水平,并测定背最长肌的IMF、大理石纹、嫩度.结果发现,圈养型宗地花猪的IMF、大理石纹、嫩度均高于放养型宗地花猪(P >0.05),pH、肉色极显著高于放养型宗地花猪(P <0.01);放养型宗地花猪背最长肌中H-FABP mRNA 水平显著高于圈养型宗地花猪(P <0.05);放养型、圈养型宗地花猪H-FABP基因表达与IMF均无显著相关性(P >0.05).以上结果表明,不同饲养条件影响H-FABP基因表达并在一定程度上影响IMF,但影响不显著.     

Multiple QTL on chromosome six in dairy cattle affecting yield and content traits

A granddaughter design containing five half-sib families from German Holstein–Friesian cattle was subjected to QTL analysis starting from the hypothesis of the existence of more than one QTL on chromosome BTA 6 affecting milk yield, fat yield, protein yield and content of fat and protein. The marker map consisted of 16 microsatellite markers with marker heterozygosity varying from 0.44 to 0.94. Two statistical methods were used: least squares (LS) and residual maximum likelihood (REML) allowing for two QTL simultaneously. The test statistics were calculated in steps of one cM along the chromosome. Significant QTL at the chromosome-wise 5% level according to the permutation test critical value were detected mainly in single families. The results were in conformance with the findings of several previous studies with approximate positions of putative QTL at 49 cM for milk yield, at 70 cM for fat and protein yield, and at 46 cM for protein content. Further QTL positions were suggested mostly for yield traits and protein content in the area of the casein gene cluster at 90…95 cM. The results of the two-QTL model analyses when using LS led to family specific inferences of a second QTL for fat yield and content of protein and fat, partly supported by the epistasis model.     

鸡肌内脂肪双向选择对脂肪性状及相关基因mRNA表达的影响

本试验旨在研究鸡肌内脂肪（IMF）双向选择对脂肪性状及相关基因mRNA表达的影响。试验采用北京油鸡肌内脂肪双向选育系和对照系雏鸡,饲养至56和120 d时,每个系分别屠宰30只母鸡,测定胸肌和腿肌IMF含量、腹脂重、腹脂率及LPL、H-FABP和A-FABP基因mRNA表达量,比较双选系各性状差异,分析IMF遗传选择效果。结果表明,上选系肌肉IMF含量和肉色亮度值（L^＊）显著大于下选系（P〈0.05）,胸肉终pH（pHu）显著低于下选系（P〈0.05）。LPL基因在120日龄上选系腹脂中的mRNA表达量显著高于下选系（P〈0.05）,下选系胸肌中H-FABP基因mRNA的表达显著高于上选系（P〈0.05）。结果表明IMF的双向选择是有效的,该双选系可以作为未来基因定位和基因互作效应研究的宝贵资源群体。     

莱芜猪ACSL4和H-FABP基因的多态性及育种应用

选取了106头莱芜猪核心群及部分后备猪,用PCR-RFLP的方法分别检测了酰基辅酶A合成酶长链4（Acly-CoA synthetase long chain family 4,ACSL4）基因的SNP G2645A位点和心脏型脂肪酸结合蛋白（Heart fatty acid-binding protein,H-FABP）基因的HinfⅠ及MspⅠ位点的多态性。结果显示,在ACSL4的SNP G2645A位点共检测到AG和GG 2种基因型,没有检测到AA基因型;G等位基因是优势等位基因;莱芜猪该位点呈高度多态。在H-FABP的HinfⅠ位点共检测到HH、Hh和hh 3种基因型,莱芜猪在该位点呈中度多态。莱芜猪在上述2个位点均处于Hardy-Weinberg平衡状态。经测序验证,莱芜猪H-FABP基因HinfⅠ位点的多态性是1 324位点T的插入、缺失所造成的。莱芜猪在H-FABP的MspⅠ位点没有多态性。在莱芜猪本品种选育中,可以顺序选择ACSL4G2645A位点GG基因型纯合个体和H-FABP HinfⅠ位点HH基因型纯合个体,提高莱芜猪IMF性状的均一性,将进一步促进莱芜猪种质的保护和利用。     

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.     

Exclusion of the swine leukocyte antigens as candidate region and reduction of the position interval for the Sus scrofa chromosome 7 QTL affecting growth and fatness

Pig chromosome 7 (SSC 7) has been shown to be rich in QTL affecting performance and quality traits. Most studies mapped the QTL close to the swine leukocyte antigens (SLA), which has a large effect on adaptability and natural selection. Previous comparative mapping studies suggested that the 15-cM region limited by markers LRA1 (mapped at 55 cM) and S0102 (mapped at 70 cM) contains hundreds of genes. To decrease the number of candidate genes, we improved the mapping resolution with a genetic chromosome dissection through a backcross recombinant progeny test program between Meishan (MS) and European (EU; i.e., Large White or Landrace) breeds. Three first-generation backcross--(EU x MS) x EU--and two second-generation backcross--([EU x MS] x EU) x EU--sires carrying a recombination in the QTL mapping interval were progeny-tested (i.e., measured for a total of 44 growth, fatness, carcass and meat quality traits). Progeny family size varied from 29 to 119 pigs. Animals were genotyped for markers covering the region of interest. Progeny-test results allowed the QTL interval to be decreased from 15 to 20 cM down to 10 cM, and even less than 6 cM if we assumed that the EU pigs used in this study share only one QTL allele. Except for a putative QTL affecting some carcass composition traits, the SLA is excluded as a candidate region, suggesting that it might be possible to apply a marker-assisted selection strategy for this QTL, while controlling SLA allele diversity. The strong QTL effects remaining in animals with only 12.5% (issued from first-generation backcross boars) and 6.25% (issued from second-generation back-cross boars) Meishan genetic background shows that epistatic interactions are likely to be limited. Finally, the QTL does not have strong effects on meat quality traits.