Single-step genomic BLUP (ssGBLUP) effectively models small cattle populations: lessons from the Israeli-Holstein Herdbook.

Background: Routine genomic-estimated breeding values (gEBVs) are computed for the Israeli dairy cattle population by a two-step methodology in combination with the much larger Dutch population. Only sire genotypes are included. This work evaluated the contribution of cow genotypes obtained from the Israeli Holstein population to enhance gEBVs predictions via single-step genomic best-linear unbiased prediction (ssGBLUP).

Genetic analysis of rumination time based on an analysis of 77,697 Israeli dairy cows.

Reduction of methane emission may become necessary for sustainable milk production. Several studies indicate a relationship between rumination time and the level of methane emission. The objectives of the current study were to estimate environmental factors affecting daily rumination time in high-yielding dairy cattle, genetic parameters for rumination time across parities, and environmental and genetic correlations between rumination time and economic traits, and to predict the consequence of inclusion of this trait in the Israeli breeding index.

Estimating the Effect of the Kappa Casein Genotype on Milk Coagulation Properties in Israeli Holstein Cows.

In Israel, about 26% of produced milk is used to produce hard cheeses and 29% for soft cheeses. Milk with preferred coagulation properties requires a shorter coagulation time and yields a higher curd firmness than milk with inferior coagulation properties. Studies have shown that milk from cows with the B allele of kappa casein (κ-CN) produces more cheese than milk from those with A and E alleles.

Genetic and Genomic Analysis of Cow Mortality in the Israeli Holstein Population.

"Livability" was defined as the inverse of the probability of death. The objectives of this study were to estimate the heritability, genetic and phenotypic trends for the livability of Israeli Holstein cows; estimate the genetic and environmental correlations between livability and the nine traits included in the Israeli breeding index; estimate the effect of the inclusion of livability in the Israeli breeding index on expected genetic gains; and compute a genome-wide association study (GWAS) for livability. Seven data sets were analyzed.

Breeding Dairy Cattle for Female Fertility and Production in the Age of Genomics.

Phenotypic and genetic changes for female fertility and production traits in the Israeli Holstein population over the last three decades were studied in order to determine if long term selection has resulted in reduced heritability and negative genetic correlations. Annual means for conception status, defined as the inverse of the number of inseminations to conception in percent, decreased from 55.6 for cows born in 1983 to 46.

Genomic Prediction of Complex Traits in Animal Breeding with Long Breeding History, the Dairy Cattle Case.

In accordance with the infinitesimal model for quantitative traits, a very large number of genes affect nearly all economic traits. In only two cases has the causative polymorphism been determined for genes affecting economic traits in dairy cattle. Most current methods for genomic evaluation are based on the "two-step" method.

Genetic and genomic analysis of age at first insemination in Israeli dairy cattle.

We performed a genetic analysis of age at first insemination, including estimation of the heritability and genetic correlations with other economic traits, and the consequences of including this trait in the Israeli selection index. The genetic factors affecting age at first insemination were determined via GWAS. Five data sets were analyzed.

Broad phenotypic impact of the effects of transgenerational heat stress in dairy cattle: a study of four consecutive generations.

Background: Global warming has increased the frequency of heat stress in livestock. Although heat stress directly leads to negative effects on production and reproduction traits in dairy cattle, the transgenerational transition of these changes is poorly understood. We hypothesized that heat stress in pregnant cows might induce epigenetic modifications in the developing embryo germ cells, which, in turn, might lead to phenotypic effects in the offspring.

Genetic and Genome-Wide Association Analysis of Yearling Weight Gain in Israel Holstein Dairy Calves.

Yearling weight gain in male and female Israeli Holstein calves, defined as 365 × ((weight - 35)/age at weight) + 35, was analyzed from 814,729 records on 368,255 animals from 740 herds recorded between 1994 and 2021. The variance components were calculated based on valid records from 2008 through 2017 for each sex separately and both sexes jointly by a single-trait individual animal model analysis, which accounted for repeat records on animals. The analysis model also included the square root, linear, and quadratic effects of age at weight.

Genetic and environmental analysis of female calf survival in the Israel Holstein cattle population.

The objectives were to estimate the effects of various environmental factors on female calf survival of Israeli Holsteins, to estimate the economic value of calf survival under Israeli conditions, to estimate the genetic and environmental variance components for calf and cow survival using the individual animal model, to perform GWAS analyses of survival to first calving and herd life after first calving, to estimate the genetic and environmental trends for calf survival since 1985, to estimate genetic correlations of calf survival with the traits included in the current Israeli breeding index, and to estimate the consequences of inclusion of calf survival in the national selection index. Mean calf survival rate of Israeli Holsteins from 2001 through 2008 was 0.85, and the mean economic value of survival to first calving was $526.

Preferential Mapping of Sex-Biased Differentially-Expressed Genes of Larvae to the Sex-Determining Region of Flathead Grey Mullet ().

Flathead gray mullet () is a cosmopolitan mugilid species popular in fishery and aquaculture with an economic preference for all-female population. However, it displays neither sexual dimorphisms nor heteromorphic sex chromosomes. We have previously presented a microsatellite-based linkage map for this species locating a single sex determination region (SDR) on linkage group 9 (LG9) with evidence for XX/XY sex determination (SD) mechanism.

Genetic and genomic analysis of long insemination interval in Israeli dairy cattle as an indicator of early abortions.

One of the causes of observed low fertility is embryo loss after fertilization. Previous findings suggested that more than half of fertilizations result in embryo loss before pregnancy is detected. We proposed reinsemination between 49 and 100 d after the first insemination as an indicator trait for early abortion (EA) in dairy cattle based on the mean estrus interval of 21 d.

Mapping of the Sex Determining Region on Linkage Group 12 of Guppy ().

is one of the most popular ornamental fish species with a higher demand for males due to their large colorful fins. The objectives of this study were mapping of the sex-determining (SD) region on linkage group 12 of guppy, and identification of a sex specific marker. We generated eight polymorphic microsatellite markers distributed along the distal 5.

Genetic and environmental analysis of diseases with major economic impact in Israeli Holsteins.

Incidences of ketosis, metritis, mastitis, and retained placenta were studied in Israeli Holstein cows calving between 2008 and 2017. These diseases were selected based on their economic impact. Ketosis, metritis, and retained placenta were scored dichotomously.

Short communication: Selection for persistency by changing the shape of lactation curves with geometric morphometrics.

The objective was to simulate the response to selection by modifying the shape of the lactation curve to improve persistency in Israeli first-parity Holstein cattle using geometric morphometrics and multivariate quantitative genetics. The 2-dimensional Cartesian coordinates representing the shape of the lactation curve were characterized using geometric morphometrics. Genetic parameters of daily milk yield were estimated for the individual animal model using REML.

Using geometric morphometrics for the genetics analysis of shape and size of lactation curves in Israeli first-parity Holstein cattle.

Our objective was to combine the methods of geometric morphometrics and multivariate quantitative genetics to genetic evaluation of the size and shape of lactation curves of milk of 3,492 Israeli first-parity Holstein cattle. Lactation records were treated as morphological data, for which 2 different lactation shape functions were evaluated, one depicted by a line graph and the other by an orbital graph. The lactation curves from both shape functions were represented by 2-dimensional Cartesian landmark coordinates.

Quantitative trait loci on LGs 9 and 14 affect the reproductive interaction between two Oreochromis species, O. niloticus and O. aureus.

Effective farming of tilapia requires all-male culture, characterized by uniformity and high growth rate. Males of O. aureus (Oa) and females of O.

Identification of male-specific amh duplication, sexually differentially expressed genes and microRNAs at early embryonic development of Nile tilapia (Oreochromis niloticus).

Background: The probable influence of genes and the environment on sex determination in Nile tilapia suggests that it should be regarded as a complex trait. Detection of sex determination genes in tilapia has both scientific and commercial importance. The main objective was to detect genes and microRNAs that were differentially expressed by gender in early embryonic development.

Fine Mapping of a QTL for Fertility on BTA7 and Its Association With a CNV in the Israeli Holsteins.

A quantitative trait locus (QTL) affecting female fertility, scored as the inverse of the number of inseminations to conception, on Bos taurus chromosome 7 was detected by a daughter design analysis of the Israeli Holstein population (P < 0.0003). Sires of five of the 10 families analyzed were heterozygous for the QTL.

Analysis of copy loss and gain variations in Holstein cattle autosomes using BeadChip SNPs.

Background: Copy number variation (CNV) has been recently identified in human and other mammalian genomes, and there is a growing awareness of CNV's potential as a major source for heritable variation in complex traits. Genomic selection is a newly developed tool based on the estimation of breeding values for quantitative traits through the use of genome-wide genotyping of SNPs. Over 30,000 Holstein bulls have been genotyped with the Illumina BovineSNP50 BeadChip, which includes 54,001 SNPs (~SNP/50,000 bp), some of which fall within CNV regions.

Combining mouse mammary gland gene expression and comparative mapping for the identification of candidate genes for QTL of milk production traits in cattle.

Background: Many studies have found segregating quantitative trait loci (QTL) for milk production traits in different dairy cattle populations. However, even for relatively large effects with a saturated marker map the confidence interval for QTL location by linkage analysis spans tens of map units, or hundreds of genes. Combining mapping and arraying has been suggested as an approach to identify candidate genes.

Current and future developments in patents for quantitative trait loci in dairy cattle.

Many studies have proposed that rates of genetic gain in dairy cattle can be increased by direct selection on the individual quantitative loci responsible for the genetic variation in these traits, or selection on linked genetic markers. The development of DNA-level genetic markers has made detection of QTL nearly routine in all major livestock species. The studies that attempted to detect genes affecting quantitative traits can be divided into two categories: analysis of candidate genes, and genome scans based on within-family genetic linkage.

Accelerated expansion of group IID-like phospholipase A2 genes in Bos taurus.

Low-molecular-weight, calcium-dependent phospholipase A2 genes (PLA2s) that belong to the secreted type of PLA2s are clustered within a syntenic group on human 1p35-p36 and mouse 4qD3. We reassembled trace files available from the Whole Genome Sequencing (WGS) Project, obtaining an 86-kb contig with three tandem PLA2G2D duplications in the Hereford strain. We used mate-pair data to monitor the assembly and to exclude chimeric clones, demonstrating that the current WGS data may be assembled even in a highly repetitive region with a coverage exceeding fivefold.

Natural compounds derived from foods modulate nitric oxide production and oxidative status in epithelial lung cells.

The effects of natural antioxidants on nitric oxide (NO) modulation and oxidative status were determined in rat epithelial lung cells (L-2). Cells were stimulated with cytokines and treated with one of the following: resveratrol, soybean saponin group B (SSB), quercetin, genistein, olive leaf polyphenol concentrate (OLPC), or N-acetyl-L-cystein (NAC). NAC had no effect on NO levels, whereas resveratrol and OLPC were found to be effective in reducing nitrite levels, modifying iNOS mRNA, and decreasing free radical production.

Efficient inference of haplotypes from genotypes on a large animal pedigree.

We present a simple algorithm for reconstruction of haplotypes from a sample of multilocus genotypes. The algorithm is aimed specifically for analysis of very large pedigrees for small chromosomal segments, where recombination frequency within the chromosomal segment can be assumed to be zero. The algorithm was tested both on simulated pedigrees of 155 individuals in a family structure of three generations and on real data of 1149 animals from the Israeli Holstein dairy cattle population, including 406 bulls with genotypes, but no females with genotypes.