Estimation of genetic parameters for bull conception rate and its genetic correlations with semen production traits in Japanese Black bulls

The P of achieving pregnancy is an important trait of bull fertility in beef cattle and is defined as the bull conception rate (BCR). This study aimed to clarify and better understand the genetic architecture of the BCR calculated using artificial insemination and pregnancy diagnosis records from a progeny testing program in Japanese Black bulls. In this study, we estimated the genetic parameters of the BCR and their correlation with semen production traits. In addition, we assessed the correlated responses in BCR by considering the selection of semen production traits. Nine hundred and sixteen Japanese Black bulls were selected based on fertility, with 28 869 pregnancy diagnostic records from the progeny testing program. Our results showed that the heritability estimate was 0.04 in the BCR at the first service and 0.14 in BCR for the three services, and an increase in the inbreeding coefficient led to a significant decrease in BCR. The phenotypic trend of BCR remained almost constant over the years, whereas the genetic trend increased. In addition, the changes in the progeny testing year effect showed a similar tendency to the phenotypic trends, suggesting that the phenotypic trends could be mainly due to non-genetic effects, including progeny testing year effects. The estimated genetic correlation of BCR with sperm motility traits was favorably moderate to high (ranging from 0.49 to 0.97), and those with sperm quantity traits such as semen volume were favorably low to moderate (ranging from 0.23 to 0.51). In addition, the correlated responses in BCR at the first service by selection for sperm motility traits resulted in a higher genetic gain than direct selection. This study provides new insights into the genetic factors affecting BCR and the possibility of implementing genetic selection to improve BCR by selecting sperm motility traits in Japanese Black bulls.

A potent allele marker related to low bull conception rate in Japanese Black bulls

Over the years, there has been considerable variation in the bull conception rate (BCR) of Japanese Black cattle; moreover, several Japanese Black bulls with a low BCR of ≤10% have been identified. However, the alleles responsible for the low BCR are not determined yet. Therefore, in this study, we aimed to identify single-nucleotide polymorphisms (SNPs) for predicting low BCR. To this end, the genome of Japanese Black bulls was comprehensively examined by a genome-wide association study with whole-exome sequencing (WES), and the effect of the identified marker regions on BCR was determined. The WES analysis of six sub-fertile bulls with a BCR of ≤10% and 73 normal bulls with a BCR of ≥40% identified a homozygous genotype for low BCR in Bos taurus autosome 5 in the region between 116.2 and 117.9 Mb. The g.116408653G > A SNP in this region had the most significant effect on the BCR (P-value = 1.0 × 10^-23), and the GG (55.4 ± 11.2%) and AG (54.4 ± 9.4%) genotypes in the SNP had a higher phenotype than the AA (9.5 ± 6.1%) genotype for the BCR. The mixed model analysis revealed that g.116408653G > A was related to approximately 43% of the total genetic variance. In conclusion, the AA genotype of g.116408653G > A is a useful index for identifying sub-fertile Japanese Black bulls. Some positive and negative effects of SNP on the BCR were presumed to identify the causative mutations, which can help evaluate bull fertility.

Genome-wide detection of non-additive quantitative trait loci for semen production traits in beef and dairy bulls

Semen production traits are important aspects of bull fertility, because semen quantity leads to direct profits for artificial insemination centres, and semen quality is associated with the probability of achieving a pregnancy. Most genome-wide association studies (GWASs) for semen production traits have assumed that each quantitative trait locus (QTL) has an additive effect. However, GWASs that account for non-additive effects are also important in fitness traits, such as bull fertility. Here, we performed a GWAS using models that accounted for additive and non-additive effects to evaluate the importance of non-additive effects on five semen production traits in beef and dairy bulls. A total of 65 463 records for 615 Japanese Black bulls (JB) and 50 734 records for 873 Holstein bulls (HOL), which were previously genotyped using the Illumina BovineSNP50 BeadChip, were used to estimate genetic parameters and perform GWAS. The heritability estimates were low (ranged from 0.11 to 0.23), and the repeatability estimates were low to moderate (ranged from 0.28 to 0.45) in both breeds. The estimated repeatability was approximately twice as high as the estimated heritability for all traits. In this study, only one significant region with an additive effect was detected in each breed, but multiple significant regions with non-additive effects were detected for each breed. In particular, the region at approximately 64 Mbp on Bos taurus autosome 17 had the highest significant non-additive effect on four semen production traits in HOL. The rs41843851 single nucleotide polymorphism (SNP) in the region had a much lower P-value for the non-additive effect (P-value = 1.1 × 10^-31) than for the additive effect (P-value = 1.1 × 10^-8) in sperm motility. The AA and AB genotypes on the SNP had a higher phenotype than the BB genotype in HOL, and there was no bull with the BB genotype in JB. Our results showed that non-additive QTLs affect semen production traits, and a novel QTL accounting for non-additive effects could be detected by GWAS. This study provides new insights into non-additive QTLs that affect fitness traits, such as semen production traits in beef and dairy bulls.

Estimation of genetic parameter for feed efficiency and resilience traits in three pig breeds

Recently, automatic feeders have become popular for collecting daily feed intake data in the pig industry, making it possible to evaluate genetic effects on feed efficiency and resilience traits, expressed as day-to-day fluctuations in feeding records. This study aimed to understand the influence of genetic factors on feed efficiency traits, including residual intake and BW gain (RIG), and resilience traits, as well as to compare the differences in genetic parameter estimates among three purebred pig breeds. A total of 6 103 pigs from three breeds (Large White: 1 193 pigs, Landrace: 3 010 pigs, and Duroc: 1 900 pigs) were raised in a specific pathogen-free environment. The growth and feed intake records during the testing period were obtained using automatic feeders, and the average daily gain (ADG) and average feed intake (AFI) were calculated. Feed conversion ratio (FCR), residual feed intake (RFI), residual gain, and RIG were calculated as feed efficiency traits, and the log-transformed variance of deviation for the daily feed intake (LnVar_FI), daily occupation time (LnVar_OC), and the daily number of visits to the feeder (LnVar_VT) was calculated as resilience traits. After estimating the genetic parameters for each breed, a meta-analysis was performed to obtain the weighted mean of heritability estimates (h_m²) and genetic correlation estimates (GC_m) for the three breeds. The h_m² were moderate and ranged from 0.31 to 0.39 for feed efficiency traits and 0.31 to 0.40 for resilience traits, and there were no significant differences in heritability estimates among the three breeds except for AFI, RFI, and RIG. For feed efficiency traits, the FCR and RIG showed favourably moderate GC_m with AFI (0.29 and -0.33, respectively) and ADG (-0.39 and 0.31, respectively). For resilience traits, the LnVar_FI and LnVar_VT showed favourably low to moderate GC_m with FCR (0.33 and 0.28, respectively) and RIG (-0.37 and 0.28, respectively), and there were no genetic relationships of LnVar_OC with FCR and RIG (the absolute value of GC_m was 0.01). There was no significant difference in the genetic correlation estimates among the three breeds for feed efficiency and resilience traits. Our results suggest that feed efficiency and resilience traits were heritable, and resilience traits showed favourable or no genetic correlation with feed efficiency traits. In addition, the influence of genetic factors on feed efficiency and resilience traits could be the same among breeds.

Abstract P2-08-37: The prognostic impact of synaptojanin 2 expression in estrogen receptor α-positive breast cancer patients

Background: Synaptojanin 2 (SYNJ2) was reported to be a druggable mediator of metastasis. It is overexpressed and amplified in breast cancer, particularly estrogen receptor α (ERα)-positive breast cancer. SYNJ2 was also shown to promote cell migration and invasion in breast cancer xenograft cultures and lung metastasis in mice. Here, we investigated SYNJ2 mRNA expression in breast cancer patients during long-term follow-up.

Materials and methods: A total of 434 invasive breast cancer tissues were analyzed for SYNJ2mRNA expression using TaqMan PCR, and the correlation of this expression with patient clinicopathological factors was determined. We also examined the expression of markers associated with tumor-initiating capacity, such as SNAI1, SNAI2, and VIM. Survival curves were analyzed using the Kaplan–Meier method. Cox proportional hazards regression analysis was used for univariate and multivariate analyses of prognostic values.

Results: The median follow-up period was 10.7 years. We found positive correlations between high expression of SYNJ2 mRNA and shorter disease-free survival in breast cancer patients (P=0.049), which was limited to ERα-positive patients (P=0.020) and not seen in ERα-negative patients (P=0.863). High SYNJ2 mRNA levels were positively correlated with high tumor grade, ERα negativity, and node positivity. Multivariate analysis indicated that high SYNJ2 mRNA expression was an independent factor for poor disease-free survival in breast cancer patients.

Multivariate analysis of poor disease-free survival   DFS    Mutivariate   All patientsp valueHR (95%CI)Tumor size2cm and fewer1540.43151 (Reference) more than 2cm280 1.19 (0.78-1.85)Lymph node metastasisNegative2190.0001 and fewer1 (Reference) Positive184 5.61 (3.59-9.05) Unknown31 2.40 (0.89-5.48)Grade1,22330.38471 (Reference) 3195 1.20 (0.79-1.81) Unknown6 0.17 (1.78-3.49)ER statusPositive3370.02621 (Reference) Negative97 2.06 (1.87-4.07)PgR statusPositive2930.39511 (Reference) Negative141 1.30 (0.70-2.28)SYNJ2 mRNA expressionlow2170.02251 (Reference) high217 1.57 (1.07-2.34)

Conclusion:High SYNJ2 expression was shown to be an independent predictive factor of poor prognosis in ERα-positive breast cancer patients. SYNJ2 could therefore be used as a candidate biomarker and therapeutic target in breast cancer.

Citation Format: Nishikawa S, Kondo N, Wanifuchi-Endo Y, Hisada T, Uemoto Y, Katagiri Y, Dong Y, Kato H, Takahashi S, Toyama T. The prognostic impact of synaptojanin 2 expression in estrogen receptor α-positive breast cancer patients [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P2-08-37.

Abstract P3-03-34: Sentinel lymph node biopsy is unnecessary in ductal carcinoma in situ patients diagnosed by biopsy

Background: Japanese Breast Cancer Society Clinical Practice Guidelines for Breast Cancer 2018 state that sentinel lymph node (SN) biopsy is unnecessary for patients treated with breast-conserving therapy (BCT) and with an expected final pathological diagnosis of ductal carcinoma in situ (DCIS). Regardless of whether they were diagnosed with DCIS by biopsy before surgery, 78% of patients currently undergo axial procedures in Japan because invasive lesions may be detected in surgical specimens. This study examined whether SN biopsy can be omitted in DCIS patients diagnosed by biopsy and which factors are associated with invasion.

Methods: Patients who underwent definitive surgery for DCIS diagnosed by preoperative biopsy at our institution from May 2004 to January 2018 were investigated retrospectively. The factors associated with upstaging to invasive cancer from DCIS were examined with Fisher's exact test and the t-test. (Age, Tumor size, Operation (Mastectomy or BCT), Biopsy method (Core Needle Biopsy or Vaccume-Assisted Biopsy), Mammography (ditected or not-detected), Ultrasound (ditected or not-detected, mass or non-mass), Comedo, ER, PgR, HER2)

Results: A total of 311 patients were enrolled in this study, of whom 277 (89.1%) underwent SN; six of these (2.2%) had SN metastasis. All six cases were upstaging to invasive cancer: five (1.8%) had micrometastasis and one had macrometastasis (0.4%). From a surgical viewpoint, SN metastasis were detected in 3/161 (1.9%) cases treated with mastectomy and 3/150 (2.4%) cases treated with BCT. Although all three cases treated with BCT had micrometastasis, one case treated with mastectomy had macrometastasis (the other two cases had micrometatastasis). A total of 80/311 cases (25.7%) upstaged to invasive cancer and the only predictor of invasion was tumor size on images (p=0.0002). We could not determine the effective cut-off for tumor size because the area under the receiver operating characteristic curve was 0.63<0.70.

Tabule 1.Tumor size on images was the only predictor of invasion. Upstaging (N=80)DCIS (N=231)P valueTumor size: mm (95% Confidence Interval)47.5 (41.9-53.2)33.9 (30.5-37.3)0.0002

Conclusion: Tumor size was found to be the only predictor of invasion. Only 2.2% of DCIS patients had SN metastasis despite the fact that 25.7% patients were upstaged to invasive cancer. We conclude that SN biopsy is not necessary for DCIS patients diagnosed by biopsy.

Citation Format: Uemoto Y, Kondo N, Wanifuchi-Endo Y, Hisada T, Nishikawa S, Katagiri Y, Kato H, Takahashi S, Toyama T. Sentinel lymph node biopsy is unnecessary in ductal carcinoma in situ patients diagnosed by biopsy [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-03-34.

Accuracy of high-density genotype imputation in Japanese Black cattle

Genotype imputation facilitates the identification of missing genotypes on a high-density array using low-density arrays and has great potential for reducing genotyping costs for cattle populations. However, the imputation quality varies across breeds, which have different effective population sizes. Therefore, the accuracy of genotype imputation must be evaluated in each breed. The Japanese Black cattle population has a unique genetic background, and this study aimed to investigate different factors affecting imputation quality in this population. A total of 1368 animals were genotyped using the Illumina BovineHD BeadChip, and the accuracy of imputation was evaluated using information from four lower density arrays. The extent of linkage disequilibrium for this population was relatively higher than that in other beef breeds but lower than that in dairy breeds. The accuracy of arrays with more than 20 000 single nucleotide polymorphisms (SNPs) was similar to or higher than that of lower density arrays. In addition, the minor allele frequency of SNPs in the reference population affected the accuracy. The accuracy increased as the size of the reference population increased, up to 400 animals, beyond which there was little increase. A higher genetic relationship between the reference and test populations increased imputation accuracy. These results indicate that high imputation accuracy can be achieved using high-density arrays, having enough reference animals and including relatives in the reference population.

Whole-genome association study for fatty acid composition of oleic acid in Japanese Black cattle

Fatty acid composition, especially oleic acid (C18:1), plays an important role in the eating quality of meat in Japanese Black cattle. Therefore, the objective of this study was to identify loci associated with C18:1 in the intramuscular fat of the trapezius muscles in Japanese Black cattle using the Illumina BovineSNP50 BeadChip whole genome single nucleotide polymorphism (SNP) assay. We also evaluated the relationship between C18:1 and three fatty acid synthesis genes, fatty acid synthase (FASN), stearoyl-CoA desaturase and sterol regulatory element-binding protein-1. In this experiment, we applied a mixed model and Genomic Control approach using selective genotyping to perform a genome-wide association study. A total of 160 animals (80 animals with higher values and 80 animals with lower values), selected from 3356 animals based on corrected phenotype, were genotyped using the Illumina BovineSNP50 BeadChip and three fatty acid synthesis genes, and the quality of these SNPs was assessed. In this study, a total of 38 955 SNPs, which included SNPs in the three fatty acid synthesis genes, were used, and the estimated inflation factor was 1.06. In the studied population, a total of 32 SNPs, including the FASN gene, had significant effects, and in particular 30 SNPs of all significant SNPs were located between 49 and 55 Mbp on chromosome 19. This study is one of the first genome-wide association studies for fatty acid composition in a cattle population using the recently released Illumina BovineSNP50 BeadChip.

Evaluation of quantitative trait loci affecting intramuscular fat and reproductive traits in pigs using marker-assisted introgression

We investigated the effects of previously identified quantitative trait loci (QTL) in an experimental backcross (BC) between Chinese Meishan pigs and commercial Duroc pigs. We performed marker-assisted introgression of two QTL for intramuscular fat (IMF) content (IMF population) and three QTL for reproductive traits (reproduction population) from a donor Meishan pig into a recipient Duroc pig. At the fourth BC generation of the IMF population and third BC generation of the reproduction population, carrier animals were selected for the production of animals homozygous for the QTL. Our previous studies have shown that the presence of a Meishan allele on the IMF QTL is associated with low IMF values, and the Meishan allele on the reproductive QTL is associated with large litters. In this study, the presence of a Duroc allele at the IMF QTL on SSC9 resulted in a 0.27% increase in IMF (additive effect = 0.27 ± 0.08), whereas the presence of a Meishan allele at the IMF QTL on SSC7 resulted in a 0.34% increase in IMF (additive effect = -0.34 ± 0.09). The presence of the Meishan allele at the IMF QTL on SSC7 thus had the opposite effect to our previous studies, that is, increased IMF. In the reproduction population, we observed no differences between the genotypes of the three QTL in regard to number of corpora lutea or litter size. Marker-assisted introgression at these QTL is thus unlikely to result in an associated increase in litter size. These results show that it is possible to introgress alleles from other breeds into a selection population using molecular markers; any unexpected results might be associated with the genetic background.

Fine mapping of the chicken congenital loco locus on chromosome 12

Congenital loco in chicks is characterized by an apparent lack of control of the muscles of the neck. This disorder is inherited as a simple Mendelian recessive disease, caused by an autosomal recessive gene, lo. To date, there are no reports on the localization of this gene. The objective of this study was therefore to identify the genomic region of the lo locus. The experimental congenital loco population used here were selected from a Rhode Island Red (RIR) line and consisted of six generations, resulting in 124 chickens. A total of 113 DNA samples from offspring of four generations (G3, G4, G5, and G6) were used for genotyping. At first, genome-wide linkage mapping was performed using 122 microsatellite markers on 22 autosomal chromosomes, and the lo locus was mapped to chromosome 12. We then performed fine mapping in two steps on chromosome 12. First, the lo locus was mapped to the interval between GGA12_5 and GGA12_11 using 13 new polymorphic markers. In the second step, fine mapping was performed by adding new families and 11 additional new polymorphic markers. Linkage mapping and haplotype information enabled the localization of the lo locus to a 1.1-Mb region between GGA12_28 and GGA12_30. Genetic markers between GGA12_28 and GGA12_30 may be used to remove the carriers of congenital loco through this RIR line.

A genome-wide scan for quantitative trait loci affecting respiratory disease and immune capacity in Landrace pigs

Respiratory disease is the most important health concern for the swine industry. Genetic improvement for disease resistance is challenging because of the difficulty in obtaining good phenotypes related with disease resistance; however, identification of genes or markers associated with disease resistance can help in the genetic improvement of pig health. The purpose of our study was to investigate whether quantitative trait loci (QTL) associated with disease resistance were segregated in a purebred population of Landrace pigs that had been selected for meat production traits and mycoplasmal pneumonia of swine (MPS) scores over five generations. We analysed 1395 pigs from the base to the fifth generation of this population. Two respiratory disease traits [MPS scores and atrophic rhinitis (AR) scores] and 11 immune-capacity traits were measured in 630-1332 animals at 7 weeks of age and when the animal's body weight reached 105 kg. Each of the pigs, except sires in the base population, was genotyped using 109 microsatellite markers, and then, QTL analysis of the full-sib family population with a multi-generational pedigree structure was performed. Variance component analysis was used to detect QTL associated with MPS or AR scores, and the logarithm of odds (LOD) score and genotypic heritability of the QTL were estimated. Five significant (LOD > 2.51) and 18 suggestive (LOD > 1.35) QTL for respiratory disease traits and immune-capacity traits were detected. The significant QTL for Log-MPS score, located on S. scrofa chromosome 2, could explain 87% of the genetic variance of this score in this analysis. This is the first report of QTL associated with respiratory disease lesions.

Sequence analysis of a pea comb locus on chicken chromosome 1

To facilitate gene identification, this study aimed to narrow the scope of the genome region affecting chicken comb type by using two bird populations. First, an F2 resource population was generated by crossing Japanese game fowl (Shamo; pea comb, P/p and P/P) with White Plymouth Rock (single comb, p/p). Comb types of the 240 F2 offspring produced by an F1 intercross between eight males and 57 females were segregated at a ratio of 3:1 (pea:single). The pea comb locus was mapped to a chromosomal region on Gallus gallus chromosome 1 that was flanked by microsatellite markers MCW0112, MCW0019 and ABR521. The second population (five-generation, n=1300 animals) was derived from a cross between Shamo and Rhode Island Red (single comb, p/p) that had been genotyped for additional polymorphic single nucleotide polymorphisms and microsatellite markers within this region through development of chicken draft sequences. To close some gaps in these draft sequences, we constructed a bacterial artificial chromosome contig and sequenced it using the shotgun sequencing technique. Chickens selected from pedigrees in these populations were grouped by inheritance of a P or p haplotype at the locus constructed by the additional markers. Finally, this locus was fine-mapped to roughly 60 kb based on the association of haplotypes and comb types. Chicken genome sequences suggest that the most likely polymorphism responsible for the pea comb locus is a duplicated sequence and that the sex determining region Y-box 5 gene, one predicted gene and one expressed sequence tag in a critical region may be associated with the duplicated sequence.

Fine mapping of porcine SSC14 QTL and SCD gene effects on fatty acid composition and melting point of fat in a Duroc purebred population

The stearoyl-CoA desaturase (delta-9-desaturase; SCD) gene is a candidate gene for fatty acid composition. It is located on pig SSC14 in a region where quantitative trait loci (QTL) for fatty acid composition were previously detected in a Duroc purebred population. The objective of the present study was to fine map the QTL, to identify polymorphisms of the pig SCD gene and to examine the effects of SCD polymorphisms on fatty acid composition and melting point of fat in the population. The pigs were examined for fatty acid composition and melting point of inner and outer subcutaneous fat and inter- and intramuscular fat; the number of pigs examined was 479-521. Two SNPs (g.-353C>T and g.-233T>C) were identified in the promoter region of the SCD gene and were completely linked in the pigs from the base generation. In all pigs, 19 microsatellite markers and SCD haplotypes were then genotyped. Different statistical models were applied to evaluate the effects of QTL and the possible causality of the SCD gene variants with respect to the QTL. The results show that all significant QTL for C14:0, C18:0, C18:1 and melting point of fat were detected in the same region, located near the SCD gene. The results also show a significant association between SCD haplotypes and fatty acid composition and fat melting point in this population. These results indicate that the haplotype of the SCD gene has a strong effect on fatty acid composition and melting point of fat.

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.

Polymorphism of the ovocalyxin-32 gene and its association with egg production traits in the chicken

We performed candidate gene analysis to identify SNP in the chicken ovocalyxin-32 (OCX-32) gene in the F(2) resource population, to develop a PCR-RFLP method for genotyping and to evaluate the associations of the gene polymorphism with egg production traits. The F(2) resource population-comprising 272 chickens-was obtained by crossing White Leghorn (WL) males and Rhode Island Red (RIR) females. They were measured for egg production traits and used for candidate gene analysis. Among parental individuals of the F(2) population, 2 novel nonsynonymous polymorphisms (c.267T>G and c.494A>C) and 1 known nonsynonymous polymorphism (c.381G>C) in the coding sequences of the chicken OCX-32 gene were detected. The PCR-RFLP method was used for screening the chickens of the F(2) population. In parental populations, genotype c.267T>G and c.494A>C were segregated within WL and RIR breeds, respectively, but genotype c.381G>C was breed-specific SNP between WL and RIR breeds. A total of 4 haplotypes were constructed based on the 3 SNP in parental populations, and there was no recombination between c.267T>G and c.494A>C. There was a significant association (P < 0.05) between the OCX-32 gene SNP and egg production traits, but there was no significant association between the haplotypes of the OCX-32 gene and egg production traits in the F(2) population. In the present study, there was the most significant association between c.381G>C of the OCX-32 gene and rate of egg production. The current study is the first step to confirm the relationship between OCX-32 gene polymorphisms and egg production traits.

Genetic mapping of quantitative trait loci affecting growth and carcass traits in F2 intercross chickens

We constructed a chicken F(2) resource population to facilitate the genetic improvement of economically important traits, particularly growth and carcass traits. An F(2) population comprising 240 chickens obtained by crossing a Shamo (lean, lightweight Japanese native breed) male and White Plymouth Rock breed (fat, heavyweight broiler) females was measured for BW, carcass weight (CW), abdominal fat weight (AFW), breast muscle weight (BMW), and thigh muscle weight (TMW) and was used for genome-wide linkage and QTL analysis, using a total of 240 microsatellite markers. A total of 14 QTL were detected at a 5% chromosome-wide level, and 7 QTL were significant at a 5% experiment-wide level for the traits evaluated in the F(2) population. For growth traits, significant and suggestive QTL affecting BW (measured at 6 and 9 wk) and average daily gain were identified on similar regions of chromosomes 1 and 3. For carcass traits, the QTL effects on CW were detected on chromosomes 1 and 3, with the greatest F-ratio of 15.0 being obtained for CW on chromosome 3. Quantitative trait loci positions affecting BMW and TMW were not detected at the same loci as those detected for BMW percentage of CW and TMW percentage of CW. For AFW, QTL positions were detected at the same loci as those detected for AFW percentage of CW. The present study identified significant QTL affecting BW, CW, and AFW.

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.