Abstract Intensive use of a few elite sires has increased the risk of the manifestation of deleterious recessive traits in cattle. Substantial genotyping data gathered using single-nucleotide polymorphism (SNP) arrays have identified the haplotypes with homozygous deficiency, which may compromise survival. We developed Japanese Black cattle haplotypes (JBHs) using SNP array data (4843 individuals) and identified deleterious recessive haplotypes using exome sequencing of 517 sires. We identified seven JBHs with homozygous deficiency. JBH_10 and JBH_17 were associated with the resuming of estrus after artificial insemination, indicating that these haplotypes carried deleterious mutations affecting embryonic survival. The exome data of 517 Japanese Black sires revealed that AC_000165.1:g.85341291C>G of IARS in JBH_8_2, AC_000174.1:g.74743512G>T of CDC45 in JBH_17, and a copy variation region (CNVR_27) of CLDN16 in JBH_1_1 and JBH_1_2 were the candidate mutations. A novel variant AC_000174.1:g.74743512G>T of CDC45 in JBH_17 was located in a splicing donor site at a distance of 5 bp, affecting pre-mRNA splicing. Mating between heterozygotes of JBH_17 indicated that homozygotes carrying the risk allele died around the blastocyst stage. Analysis of frequency of the CDC45 risk allele revealed that its carriers were widespread throughout the tested Japanese Black cattle population. Our approach can effectively manage the inheritance of recessive risk alleles in a breeding population.
On the Cover: Isolated fibrocytes produce a second wave of connective tissue growth factor (CTGF) in AngII-induced myocardial fibrosis.Purified fibrocytes isolated from the myocardium of AngII-exposed mice demonstrate immunofluorescent staining for the mesenchymal marker COL1 (green) and the hematopoietic marker CD45 (red), with nuclei counterstained with Hoescht stain (blue).
The low heritability and moderate repeatability of semen production traits in beef and dairy bulls suggest that nonadditive genetic effects, such as dominance and epistatic effects, play an important role in semen production and should therefore be considered in genetic improvement programs. In this study, the repeatability of semen production traits in Japanese Black bulls (JB) as beef bulls and Holstein bulls (HOL) as dairy bulls was evaluated by considering additive and nonadditive genetic effects using the Illumina BovineSNP50 BeadChip. We also evaluated the advantage of using more complete models that include nonadditive genetic effects by comparing the rank of genotyped animals and the phenotype prediction ability of each model. In total, 65,463 records for 615 genotyped JB and 48,653 records for 845 genotyped HOL were used to estimate additive and nonadditive (dominance and epistatic) variance components for semen volume (VOL), sperm concentration (CON), sperm motility (MOT), MOT after freeze-thawing (aMOT), and sperm number (NUM). In the model including both additive and nonadditive genetic effects, the broad-sense heritability (0.17 to 0.43) was more than twice as high as the narrow-sense heritability (0.04 to 0.11) for all traits and breeds, and the differences between the broad-sense heritability and repeatability were very small for VOL, NUM, and CON in both breeds. A large proportion of permanent environmental variance was explained by epistatic variance. The epistatic variance as a proportion of total phenotypic variance was 0.07 to 0.33 for all traits and breeds. In addition, heterozygosity showed significant positive relationships with NUM, MOT, and aMOT in JB and NUM in HOL, when the heterozygosity rate was included as a covariate. In a comparison of models, the inclusion of nonadditive genetic effects resulted in a re-ranking of the top genotyped bulls for the additive effects. Adjusting for nonadditive genetic effects could be expected to produce a more accurate breeding value, even if the models have similar fitting. However, including nonadditive genetic effects did not improve the ability of any model to predict phenotypic values for any trait or breed compared with the predictive ability of a model that includes only additive effects. Consequently, although nonadditive genetic effects, especially epistatic effects, play an important role in semen production traits, they do not improve prediction accuracy in beef and dairy bulls.Improving reproductive efficiency is a key objective in the beef and dairy cattle industries, and bull fertility is an important determinant of the reproductive performance of cows. The heritability of semen production traits is generally low; however, their repeatability is moderate. This difference between repeatability and heritability suggests that nonadditive genetic effects, such as dominance and epistatic genetic effects, could have an important role in semen production traits in bulls. Here, we estimated repeatability for semen production traits in beef and dairy bulls by considering additive and nonadditive genetic effects. Our results suggest that the contribution of nonadditive genetic effects to differences between repeatability and heritability was very high. Nonadditive genetic effects, especially epistatic effects, played important roles in semen production traits in beef and dairy bulls. However, we found that the inclusion of nonadditive genetic effects in a predictive model does not improve phenotypic prediction accuracy; further studies are needed to improve the predictive ability when using nonadditive genetic effects.
The main goal of our current study was to improve the growth curve of meat animals by decreasing the birth weight while achieving a finishing weight that is the same as that before selection but at younger age.
A dwarfing gene (allele) sd1-d has been intensively utilized to develop short-culm indica varieties in southeast Asia up to now. Before the first sd1-d-carrying variety IR8 was released, rice researchers had recognized the general tendency that culm length is higher in indica varieties than in temperate-japonica ones. Inter-subspecific difference of the tall (wild-type) allele SD1 at the sd1 locus was examined on the common genetic background, using five isogenic lines developed by substituting sd1-d of the recurrent parent IR36 by SD1s of two indica varieties, two temperate-japonica varieties and one tropical-japonica variety. The two indica -donor isogenic lines had longer culms than the three japonica-donor isogenic lines consistently in two different environmental conditions. Moreover, nonsynonymous single-nucleotide polymorphism between the two subspecies was detected at two sites in Exon 1 and Exon 3 of the sd1 locus. It is demonstrated that the inter-subspecific differentiation of SD1 contributes height difference between indica and japonica. The indica-originating and japonica-originating alleles at the sd1 locus were designated as SD1-in(t) and SD1-ja(t), respectively.
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.
