Mapping QTL for porcine muscle fibre traits in a White Duroc × Erhualian F2 resource population

Muscle fibre traits are related with meat quality in meat animals. In this study, a whole‐genome scan with 183 microsatellite markers covering the pig genome was performed to identify quantitative trait loci (QTL) for cross‐sectional area, numerical percentage and relative area of type I, IIA and IIB myofibres, fibre number per square centimetre and total fibre number in the longissimus muscle by using 120 F₂ animals in a White Duroc × Erhualian intercross. In total, 20 QTL were mapped on pig chromosomes (SSC) 1, 2, 7, 8, 9, 11, 15, 16 and X, of which eight reached genome‐wide significance levels and explained large proportions (6.53–34.63%) of phenotypic variance. Five QTL detected in this study confirmed the previous QTL reports and the others were detected for the first time. Chinese Erhualian alleles are generally associated with muscle fibre traits favourable for meat quality.     

A genome scan for quantitative trait loci affecting male reproductive traits in a White Duroc x Chinese Erhualian resource population

Chinese Erhualian boars have dramatically smaller testes, greater concentrations of circulating androgens, and fewer Sertoli cells than Western commercial breeds. To identify QTL for boar reproductive traits, testicular weight, epididymal weight, seminiferous tubular diameter at 90 and 300 d, and serum testosterone concentration at 300 d were measured in 347 F(2) boars from a White Duroc x Chinese Erhualian cross. A whole genome scan was performed with 183 microsatellites covering 19 porcine chromosomes. A total of 16 QTL were identified on 9 chromosomes, including 1% genome-wide significant QTL for testicular weight at 90 and 300 d and seminiferous tubular diameter at 90 d on SSCX, and for epididymal weight and testosterone concentration at 300 d on SSC7. Two 5% genome-wide significant QTL were detected for testicular weight at 300 d on SSC1 and seminiferous tubular diameter at 300 d on SSC16. Nine suggestive QTL were found on SSC1, 2, 3, 5, 7, 13, and 14. Chinese Erhualian alleles were not systematically favorable for greater reproductive performance. This study confirmed the previous significant QTL for testicular weight on SSCX and for epididymal weight on SSC7, and reported QTL for seminiferous tubular diameter and testosterone concentration at the first time. The observed different QTL for the same trait at different ages reflect the involvement of distinct genes in the development of male reproductive traits.     

利用大规模F_2及F_3群体研究猪小肠长度及其生长发育性状的相关性

小肠是猪的主要消化吸收器官,对个体的生长发育非常重要,但到目前为止,国内外对猪小肠的研究还很少。为探讨其长度与生长发育性状之间的关系,本试验测定了白色杜洛克×二花脸资源家系F2和F3群体共计1 508头个体的240日龄小肠长度、出生重、21日龄体重、46日龄体重、0~46日龄平均日增重、46~240日龄平均日增重、240日龄平均日增重、240日龄宰前活重及屠宰后胴体直长、胴体斜长等10项生长性状指标,并对其与小肠长度的相关性进行了分析。结果显示猪240日龄小肠长度与这些生长性状都存在极显著相关(P0.001),表明小肠可能通过影响个体对营养成分的消化吸收而影响个体的生长发育。据我们所知,本试验是首次在大规模样本群体中研究猪小肠长度与生长发育性状的相关性,其结果为小肠和个体发育研究提供了重要参考。     

Power of a genome scan to detect and locate quantitative trait loci in cattle using dense single nucleotide polymorphisms

There is increasing use of dense single nucleotide polymorphisms (SNPs) for whole‐genome association studies (WGAS) in livestock to map and identify quantitative trait loci (QTL). These studies rely on linkage disequilibrium (LD) to detect an association between SNP genotypes and phenotypes. The power and precision of these WGAS are unknown, and will depend on the extent of LD in the experimental population. One complication for WGAS in livestock populations is that they typically consist of many paternal half‐sib families, and in some cases full‐sib families; unless this subtle population stratification is accounted for, many spurious associations may be reported. Our aim was to investigate the power, precision and false discovery rates of WGAS for QTL discovery, with a commercial SNP array, given existing patterns of LD in cattle. We also tested the efficiency of selective genotyping animals. A total of 365 cattle were genotyped for 9232 SNPs. We simulated a QTL effect as well as polygenic and environmental effects for all animals. One QTL was simulated on a randomly chosen SNP and accounted for 5%, 10% or 18% of the total variance. The power to detect a moderate‐sized additive QTL (5% of the phenotypic variance) with 365 animals genotyped was 37% (p < 0.001). Most importantly, if pedigree structure was not accounted for, the number of false positives significantly increased above those expected by chance alone. Selective genotyping also resulted in a significant increase in false positives, even when pedigree structure was accounted for.     

Genome-wide identification of quantitative trait loci for pork temperature, pH decline, and glycolytic potential in a large-scale White Duroc x Chinese Erhualian resource population

The pH values and temperatures at 45 min, and 3, 9, 15, and 24 h postmortem in the LM and semimembranosus muscle (SM) and glycolytic potential in LM were measured in 1,030 F(2) animals from a White Duroc x Erhualian resource population. A whole genome scan was performed with 183 microsatellites covering 19 porcine chromosomes to detect QTL for traits measured. A total of 73 QTL have been identified, including 1% genome-wise significant QTL for 24-h pH in LM and SM on SSC 15, and for glycolytic potential, total glycogen, and residual glycogen on SSC3, 6, and 7. Six 5% genome-wise significant QTL were detected for 9-h pH in SM on SSC3, pH decline from 3/9 h to 24 h in SM on SSC7, glycolytic potential on SSC1, and total glycogen on SSC1 and 6. This study confirmed QTL previously identified for pH except those on SSC1, 11, 12, and X, and found 11 new 5% genome-wise significant QTL for glycogen-related traits. This is the first time to report QTL for pH development during post-slaughter and for glycolytic potential at 5% genome-wise significance level. In addition, the observed different QTL for pH and pH decline at different times show that causal genes for pH postmortem play distinct roles at specific stages, in specific muscles, or both. These results provide a starting point for fine mapping of QTL for the traits measured and improve the understanding of the genetic basis of pH metabolism after slaughter.     

Evaluations of Boar Gonad Development,Spermatogenesis with regard to Semen Characteristics,Libido and Serum Testosterone Levels based on large White Duroc × Chinese Erhualian Crossbred Boars

Chinese Erhualian pigs are known for prolificacy with distinct reproductive traits compared with Western commercial breeds. In this study, a four‐generation intercross resource population was constructed using White Duroc boars and Chinese Erhualian sows as founder animals, and a total of 14 male reproductive traits were recorded in 411 F₂/F₃ boars including the testis and epididymis weights, the seminiferous tubular diameter and spermatogenesis at 60, 90 and 300 days of age, semen characteristics, serum testosterone concentration and libido level at 300 days of age. The White Duroc–Erhualian boars showed remarkable segregations in the traits measured except for the seminiferous tubular diameter and had high ratio (13.9%) of the abnormality of spermatogenesis, providing a good experimental population for detecting quantitative trait loci affecting these male reproductive traits. Furthermore, the correlations among nine male reproductive traits at 300 days of age indicated that the testis weight and the body weight were strongly correlated with the sperm production, supporting the two traits as important parameters for boar selection to increase sperm production and ultimately improve boar fertility. The libido level in the White Duroc–Erhualian boars that was evaluated by a new and easily recorded scoring system showed a significant correlation with serum testosterone concentration. Yet, both libido and serum testosterone concentration were not correlated with the sperm production. Results of this study provided new information on the male reproductive physiology and genetics in Chinese Erhualian and White Duroc boars.     

A genome‐wide SNP scan in a porcine Large White × Minzhu intercross population reveals a locus influencing muscle mass on chromosome 2

A high‐density single nucleotide polymorphism (SNP) array containing 62 163 markers was employed for a genome‐wide association study (GWAS) to identify variants associated with lean meat in ham (LMH, %) and lean meat percentage (LMP, %) within a porcine Large White × Minzhu intercross population. For each individual, LMH and LMP were measured after slaughter at the age of 240 ± 7 days. A total of 557 F2 animals were genotyped. The GWAS revealed that 21 SNPs showed significant genome‐wide or chromosome‐wide associations with LMH and LMP by the Genome‐wide Rapid Association using Mixed Model and Regression‐Genomic Control approach. Nineteen significant genome‐wide SNPs were mapped to the distal end of Sus Scrofa Chromosome (SSC) 2, where a major known gene responsible for muscle mass, IGF2 is located. A conditioned analysis, in which the genotype of the strongest associated SNP is included as a fixed effect in the model, showed that those significant SNPs on SSC2 were derived from a single quantitative trait locus. The two chromosome‐wide association SNPs on SSC1 disappeared after conditioned analysis suggested the association signal is a false association derived from using a F2 population. The present result is expected to lead to novel insights into muscle mass in different pig breeds and lays a preliminary foundation for follow‐up studies for identification of causal mutations for subsequent application in marker‐assisted selection programs for improving muscle mass in pigs.     

An imputation‐based genome‐wide association study on traits related to male reproduction in a White Duroc × Erhualian F2 population

Boar reproductive traits are economically important for the pig industry. Here we conducted a genome‐wide association study (GWAS) for 13 reproductive traits measured on 205 F₂ boars at day 300 using 60 K single nucleotide polymorphism (SNP) data imputed from a reference panel of 1200 pigs in a White Duroc × Erhualian F₂ intercross population. We identified 10 significant loci for seven traits on eight pig chromosomes (SSC). Two loci surpassed the genome‐wide significance level, including one for epididymal weight around 60.25 Mb on SSC7 and one for semen temperature around 43.69 Mb on SSC4. Four of the 10 significant loci that we identified were consistent with previously reported quantitative trait loci for boar reproduction traits. We highlighted several interesting candidate genes at these loci, including APN, TEP1, PARP2, SPINK1 and PDE1C. To evaluate the imputation accuracy, we further genotyped nine GWAS top SNPs using PCR restriction fragment length polymorphism or Sanger sequencing. We found an average of 91.44% of genotype concordance, 95.36% of allelic concordance and 0.85 of r² correlation between imputed and real genotype data. This indicates that our GWAS mapping results based on imputed SNP data are reliable, providing insights into the genetic basis of boar reproductive traits.     

Mapping the quantitative trait loci (QTL) for body shape and conformation measurements on BTA1 in Japanese Black cattle

The detection and mapping of segregating quantitative trait loci (QTL) that influence withers height, hip height, hip width, body length, chest width, chest depth, shoulder width, lumbar width, thurl width, pin bone width, rump length, cannon circumference, chest girth, abdominal width and abdominal girth at weaning was conducted on chromosomal regions of bovine chromosome one. The QTL analysis was performed by genotyping half‐sib progeny of five Japanese Black sires using microsatellite DNA markers. Probability coefficients of inheriting allele 1 or 2 from the sire at specific chromosomal locations were computed. The phenotypic data of progeny were regressed on these probability coefficients in a within‐common‐parent regression analysis using a linear model that included fixed effects of sex, parity and season of birth, as well as age as a covariate. F‐statistics were calculated every 1 cM on a linkage map. Permutation tests of 10 000 iterations were conducted to obtain chromosome‐wide significance thresholds. A significant QTL for chest width was detected at 91 cM in family 3. The detection of this QTL boosts the prospects of implementing marker‐assisted selection for body conformation traits in Japanese Black beef cattle.     

An association study using imputed whole‐genome sequence data identifies novel significant loci for growth‐related traits in a Duroc × Erhualian F2 population

The average daily gain (ADG) and body weight (BW) are very important traits for breeding programs and for the meat production industry, which have attracted many researchers to delineate the genetic architecture behind these traits. In the present study, single‐ and multi‐trait genome‐wide association studies (GWAS) were performed between imputed whole‐genome sequence data and the traits of the ADG and BW at different stages in a large‐scale White Duroc × Erhualian F₂ population. A bioinformatics annotation analysis was used to assist in the identification of candidate genes that are associated with these traits. Five and seven genome‐wide significant quantitative trait loci (QTLs) were identified by single‐ and multi‐trait GWAS, respectively. Furthermore, more than 40 genome‐wide suggestive loci were detected. On the basis of the whole‐genome sequence association study and the bioinformatics analysis, NDUFAF6, TNS1 and HMGA1 stood out as the strongest candidate genes. The presented single‐ and multi‐trait GWAS analysis using imputed whole‐genome sequence data identified several novel QTLs for pig growth‐related traits. Integrating the GWAS with bioinformatics analysis can facilitate the more accurate identification of candidate genes. Higher imputation accuracy, time‐saving algorithms, improved models and comprehensive databases will accelerate the identification of causal genes or mutations, which will contribute to genomic selection and pig breeding in the future.