Construction of a circRNA- lincRNA-lncRNA-miRNA-mRNA ceRNA regulatory network identifies genes and pathways linked to goat fertility.

There is growing interest in the genetic improvement of fertility traits in female goats. With high-throughput genotyping, single-cell RNA sequencing (scRNA-seq) is a powerful tool for measuring gene expression profiles. The primary objective was to investigate comparative transcriptome profiling of granulosa cells (GCs) of high- and low-fertility goats, using scRNA-seq.

A comprehensive study on size and definition of the core group in the proven and young algorithm for single-step GBLUP.

Background: The algorithm for proven and young (APY) has been suggested as a solution for recursively computing a sparse representation for the inverse of a large genomic relationship matrix (G). In APY, a subset of genotyped individuals is used as the core and the remaining genotyped individuals are used as noncore. Size and definition of the core are relevant research subjects for the application of APY, especially given the ever-increasing number of genotyped individuals.

Dissecting genetic trends to understand breeding practices in livestock: a maternal pig line example.

Background: Understanding whether genomic selection has been effective in livestock and when the results of genomic selection became visible are essential questions which we have addressed in this paper. Three criteria were used to identify practices of breeding programs over time: (1) the point of divergence of estimated genetic trends based on pedigree-based best linear unbiased prediction (BLUP) versus single-step genomic BLUP (ssGBLUP), (2) the point of divergence of realized Mendelian sampling (RMS) trends based on BLUP and ssGBLUP, and (3) the partition of genetic trends into that contributed by genotyped and non-genotyped individuals and by males and females.

Methods: We used data on 282,035 animals from a commercial maternal line of pigs, of which 32,856 were genotyped for 36,612 single nucleotide polymorphisms (SNPs) after quality control.

Genes and Pathways Affecting Sheep Productivity Traits: Genetic Parameters, Genome-Wide Association Mapping, and Pathway Enrichment Analysis.

Ewe productivity is a composite and maternal trait that is considered the most important economic trait in sheep meat production. The objective of this study was the application of alternative genome-wide association study (GWAS) approaches followed by gene set enrichment analysis (GSEA) on the ewes' genome to identify genes affecting pregnancy outcomes and lamb growth after parturition in Iranian Baluchi sheep. Three maternal composite traits at birth and weaning were considered.

Detecting effective starting point of genomic selection by divergent trends from best linear unbiased prediction and single-step genomic best linear unbiased prediction in pigs, beef cattle, and broilers.

Genomic selection has been adopted nationally and internationally in different livestock and plant species. However, understanding whether genomic selection has been effective or not is an essential question for both industry and academia. Once genomic evaluation started being used, estimation of breeding values with pedigree best linear unbiased prediction (BLUP) became biased because this method does not consider selection using genomic information.

Integration of single nucleotide variants and whole-genome DNA methylation profiles for classification of rheumatoid arthritis cases from controls.

This study evaluated the use of multiomics data for classification accuracy of rheumatoid arthritis (RA). Three approaches were used and compared in terms of prediction accuracy: (1) whole-genome prediction (WGP) using SNP marker information only, (2) whole-methylome prediction (WMP) using methylation profiles only, and (3) whole-genome/methylome prediction (WGMP) with combining both omics layers. The number of SNP and of methylation sites varied in each scenario, with either 1, 10, or 50% of these preselected based on four approaches: randomly, evenly spaced, lowest p value (genome-wide association or epigenome-wide association study), and estimated effect size using a Bayesian ridge regression (BRR) model.

Combining phenotype, genotype, and environment to uncover genetic components underlying water use efficiency in Persian walnut.

Walnut production is challenged by climate change and abiotic stresses. Elucidating the genomic basis of adaptation to climate is essential to breeding drought-tolerant cultivars for enhanced productivity in arid and semi-arid regions. Here, we aimed to identify loci potentially involved in water use efficiency (WUE) and adaptation to drought in Persian walnut using a diverse panel of 95 walnut families (950 seedlings) from Iran, which show contrasting levels of water availability in their native habitats.

Association of lipid-related genes implicated in conceptus elongation with female fertility traits in dairy cattle.

Elongation of the preimplantation conceptus is a requirement for pregnancy success in ruminants, and failures in this process are highly associated with subfertility in dairy cattle. Identifying genetic markers that are related to early conceptus development and survival and utilizing these markers in selective breeding can improve the reproductive efficiency of dairy herds. Here, we evaluated the association of 1,679 SNP markers within or close to 183 candidate genes involved in lipid metabolism of the elongating conceptus with different fertility traits in US Holstein cattle.

Economic values and selection indices for production and reproduction traits of Iranian buffaloes (Bubalus bubalis).

Iranian buffalo plays a critical role in supplying a portion of the income and the necessities of the rural population. The first step to design a breeding program is difinition of breeding goal (BG), a linear combination of breeding values for various traits and their economic values (EV). The current study was aimed at determining EVs for important traits of Iranian buffaloes, namely milk yield (MY), milk fat (MF), age at the first calving (AFC), and calving interval (CI), as well as at estimating the genetic response of applying various types of selection indices.

A review on breeding and genetic strategies in Iranian buffaloes (Bubalus bubalis).

The aim of current study was to review breeding progress and update information on genetic strategies in Iranian buffaloes. Iranian buffalo is one of the vital domestic animals throughout north, north-west, south and south-west of Iran with measurable characteristics both in milk and meat production. The species plays an important role in rural economy of the country due to its unique characteristics such as resistance to diseases and parasites, having long productive lifespan and showing higher capability of consuming low-quality forage.

Predicting bull fertility using genomic data and biological information.

The genomic prediction of unobserved genetic values or future phenotypes for complex traits has revolutionized agriculture and human medicine. Fertility traits are undoubtedly complex traits of great economic importance to the dairy industry. Although genomic prediction for improved cow fertility has received much attention, bull fertility largely has been ignored.

Differential contribution of genomic regions to marked genetic variation and prediction of quantitative traits in broiler chickens.

Background: Genome-wide association studies in humans have found enrichment of trait-associated single nucleotide polymorphisms (SNPs) in coding regions of the genome and depletion of these in intergenic regions. However, a recent release of the ENCyclopedia of DNA elements showed that ~80 % of the human genome has a biochemical function. Similar studies on the chicken genome are lacking, thus assessing the relative contribution of its genic and non-genic regions to variation is relevant for biological studies and genetic improvement of chicken populations.

The relation between the genetic architecture of quantitative traits and long-term genetic response.

The genetic architecture of a quantitative trait refers to the number of genetic variants, allele frequencies, and effect sizes of variants that affect a trait and their mode of gene action. This study was conducted to investigate the effect of four shapes of allelic frequency distributions (constant, uniform, L-shaped and U-shaped) and different number of trait-affecting loci (50, 100, 200, 500) on allelic frequency changes, long term genetic response, and maintaining genetic variance. To this end, a population of 440 individuals composed of 40 males and 400 females as well as a genome of 200 cM consisting of two chromosomes and with a mutation rate of 2.