Saeed Zerehdaran

The primary objective of this study was to develop and validate a unified genetic evaluation framework for Iranian Holstein dairy cattle integrating sire-by-herd (S-H) interactions, to account for macro-genotype-by-environment interaction (G*E), and refined Unknown Parent Groups (UPGs) to manage pedigree incompleteness. The analysis utilized a large-scale dataset of 305-day milk yield (MY) and calving interval (CI). To address pedigree gaps, UPGs were established and refined using an optimized Q-matrix conformation via the nadiv R library, following the diagnostic criteria of Legarra and Aguilar (2025). To account for environmental heterogeneity, an S-H interaction term was integrated into the linear mixed models. The impact of the S-H term on the ranking of elite animals was evaluated using Spearman rank correlation coefficients. The refinement process effectively reduced the number of UPG groups from 40 to 29 for MY and from 38 to 27 for CI, while maintaining precision within 0.5 genetic standard deviation (SD) and resolving high collinearity (r= -0.94) between adjacent groups. The inclusion of the S-H interaction term significantly improved model fit for both traits. Notably, a trait-specific response was observed: for the moderate heritability trait (MY), the S-H term led to a noticeable re-ranking of top sires and dams (r = 0.88 - 0.89), whereas for the low-heritability trait (CI), the ranking of elite animals remained highly stable (r = 0.99).The simultaneous integration of S-H interactions and refined UPGs provides a robust and statistically sound framework to accurately separate genetic potential from environmental factors. These findings demonstrate that neglecting macro-G*E can induce significant biases in the selection of elite animals, particularly for traits with moderate-to-high heritability. This integrated approach is recommended for national genetic evaluations in populations characterized by high environmental diversity and significant pedigree gaps.

Introduction: Identifying genomic regions under selection is the most challenging issue for improving important traits in animals. Few studies have focused on identifying genomic regions under selection in sheep. The aim of this study was to identify selective sweeps and to explore the relationship between these and quantitative trait loci (QTL) in both domestic and wild sheep species using single nucleotide polymorphism markers (SNPs).Methods: Genomic data were obtained from the NextGen project, which included genotyping 20 domestic and 14 wild sheep using the Illumina Ovine SNP50K BeadChip. The XP-EHH, iHS, and RSB methods were employed to detect signatures of positive selection.Results: The results of the iHS method indicated 405 and 275 selective sweeps in domestic and wild sheep, respectively. Additionally, RSB and XP-EHH analyses revealed approximately 398 and 479 selective sweeps in domestic and wild sheep, respectively. Some of the genes associated with important QTL traits in domestic sheep include ADGRB3, CADM1, CAPN2, GALNT10, MTR, RELN, and USP25, while in wild sheep, the relevant genes include ACAN, ACO1, GADL1, MGST3, and PRDM16. Selective sweeps identified in domestic sheep were associated with body weight, muscle weight, milk protein percentage, and milk yield. In contrast, selective sweeps found in wild sheep were linked to average daily gain, bone weight, carcass fat percentage, and dressing percentage.Discussion: These results indicate that selection by humans and the environment have largely progressed in harmony, highlighting the importance of both economic and environmental traits for survival. Additionally, the identification of potential candidate genes associated with economic traits and genomic regions that have experienced selection can be utilized in sheep breeding programs. However, due to the incomplete information regarding the functional annotation of genes in sheep and the limited sample size, further research with a larger sample group is essential to gain a deeper understanding of the candidate genes linked to economic traits in both domestic and wild sheep. Advancing knowledge in this area can significantly enhance the effectiveness of breeding strategies. The quantitative trait loci identified in this study have the potential to be incorporated into breeding plans for both domestic and wild sheep.

Despite the identification of candidate genes influencing milk protein, the connections between genes and regulatory pathways remains elusive. This study aimed integrate findings from genome-wide association studies (GWAS) and RNA sequencing (RNA-Seq) through meta-analysis to pinpoint single nucleotide polymorphisms (SNPs) and genes responsible for high and low protein yield in cows. Previous GWAS and RNA-Seq analyses had identified 663 SNPs and 1106 genes ( P < 0.05). Twenty SNPs from GWAS, 10 genes from RNA-Seq, and 49 SNP/gene associations from both datasets, were identified using meta-analysis. Meta-analysis validated several SNPs previously identified through GWAS, such as rs135549651 ( P = 2.6 × 10⁻²⁵⁶), rs109146371 ( P = 3.1 × 10⁻²⁰⁸), rs109350371 ( P = 4.0 × 10⁻²⁰⁷), and rs109774038 ( P = 8.6 × 10⁻⁵⁸⁷). Genes identified in RNA-Seq experiments, including NR4A1 ( P = 3.2 × 10⁻⁷), ATF3 ( P = 9.6 × 10⁻⁷), CDH16 ( P = 9.9 × 10⁻⁷), VEGFA ( P = 1.0 × 10⁻⁶), and SAA3 ( P = 7.3 × 10⁻¹¹), were confirmed. The combined GWAS and RNA-Seq datasets highlighted CCND2 ( P = 8.9 × 10⁻¹¹¹), MAPK15 ( P = 1.3 × 10⁻¹⁵¹), and CPSF1 ( P = 1.2 × 10⁻³⁰⁶) as the most significant genes. Additionally, significant gene ontology (GO) terms, including ionizing radiation ( P = 1.5 × 10⁻⁴), nuclear pore cytoplasmic filaments ( P = 9.4 × 10⁻⁵), and phenylalanine 4-monooxygenase activity ( P = 1.4 × 10⁻⁵), were identified. In conclusion, the integration of GWAS and RNA-Seq, coupled with GO enrichment, allowed identification of candidate SNPs and genes with higher accuracy. These findings improve our knowledge about genomic architecture of milk protein and enhance evaluation of Holstein cows.

The productivity of beef cows depends on early reproduction traits such as puberty and has an economic impact on the efficiency of production system. Imprinted genes modulate many important endocrine processes such as growth, the onset of puberty and maternal reproductive and behavior. The role of imprinted genes in puberty is a challenging subject since they show the reciprocal role of maternal and paternal genomes in progeny. Although, there are evidences of the involvement of imprint genes in puberty in human, the role of this type of genes in the onset of puberty in cattle has not been studied yet. Here we examined the expression of 27 imprinted genes in pre and post puberty in a bovine model to find differentially expressed imprinted genes in maternal-paternal purebreds and reciprocal crosses across eight tissues and discussed the task of these genes in this crucial process of development and in onset of puberty. DLK1 and MKRN3 that previously described as cause of the central precocious puberty (CPP) in human were differentially expressed in this study. Functional annotation analysis of differentially imprinted genes in different tissues showed significant biological processes of cellular response to growth factor stimulus, response to growth factor, response to parathyroid hormone, developmental growth and the importance of alternative splicing. The results of this study have implications in understanding the role of imprinted genes in the onset of puberty in cattle.

Central composite design (CCD; 3 levels and 3 factors) and response surface methodology (RSM) were used to evaluate the average daily body weight gain (ADG) and feed conversion ratio (FCR) in broiler chicks to different levels of dietary sugar beet pulp (SBP), tallow (T) and soybean oil (SO). A total of 60 battery brooder cages of 7 birds each were assigned to 15 diets of CCD containing 3 levels of SBP (0.00, 1.75, 3.50%), T (0.00, 0.50, 1.00%) and SO (0.00, 0.50, 1.00%), from 0 to 14 days of age. The testable outcomes of CCD were fitted with the quadratic model. The response surface analysis showed significant linear, quadratic, and interaction models for ADG and FCR from 0 to 7 and 7 to 14 days of age. At 7 days of age, maximum ADG and minimum FCR were observed with 0.00% of SBP, T, and SO in the diet. At 14 days of age, maximum ADG was obtained at 0.60%, 0.33% and 0.45% of SBP, T and SO in the diet, and the minimum FCR was observed with 0.98%, 0.00% and 1.00% of SBP, T and SO in diet, respectively. The results of this study showed that with increasing age and development of the gastrointestinal tract of broilers, adverse effects of soluble fibres are reduced, and response surface models can explain the correlation among dietary nutrient concentrations and young broiler performance to achieve the optimal target.

The objective of the study was to investigate the influence of maternal and parent of origin effects (POE) on genetic variation of Iranian native fowl on economic traits.Studied traits were body weights at birth (BW0), at eight (BW8) and twelve weeks of age (BW12), age (ASM) and weight at sexual maturity (WSM), egg number (EN) and average egg weight (AEW).Several models, including additive, maternal additive genetics, permanent environmental effects and POE were compared using Wombat software. Bayesian Information Criterion (BIC) was used to identify the best model for each trait. The chance of reranking of birds between models was investigated using Spearman correlation and Wilcoxon rank test.Based on the best model, direct heritability estimates for BW0, BW8, BW12, ASM, WSM, EN and AEW traits were 0.05, 0.21, 0.23, 0.30, 0.39, 0.22 and 0.38, respectively. Proportion of variance due to paternal POE for BW8 was 4% and proportion of variance due to maternal POE for BW12 was 5%.Estimated maternal h...

Genomic imprinting results in monoallelic expression of genes in mammals and flowering plants. Understanding the function of imprinted genes improves our knowledge of the regulatory processes in the genome. In this study, we have employed classification and clustering algorithms with attribute weighting to specify the unique attributes of both imprinted (monoallelic) and biallelic expressed genes. We have obtained characteristics of 22 known monoallelically expressed (imprinted) and 8 biallelic expressed genes that have been experimentally validated alongside 208 randomly selected genes in bovine (Bos taurus). Attribute weighting methods and various supervised and unsupervised algorithms in machine learning were applied. Unique characteristics were discovered and used to distinguish mono and biallelic expressed genes from each other in bovine. To obtain the accuracy of classification, 10-fold cross-validation with concerning each combination of attribute weighting (feature selection) and machine learning algorithms, was used. Our approach was able to accurately predict mono and biallelic genes using the genomics and proteomics attributes.

Imprinted genes display biased expression of paternal and maternal alleles in mammals. They are marked through epigenetic process during gametogenesis. Characterization of imprinted genes has expanded our understanding of the regulation and function of genes. In the current study, 22 experimentally validated imprinted genes in bovine (Bos Taurus) were analysed. Several supervised machine learning algorithms and attribute weighting methods were used to find characteristics of different types of imprinted genes and suggest a classification method for finding maternally and paternally expressed genes in bovine. For assessing the best model and comparing attributes in other organisms, we have also conducted a comparative analysis for human and sheep imprinted genes. According to the results of the present study, GC contents 10 and 100 kb upstream, Gly and Gln amino acids, Ile/ATC codon usage, LINE and SINE in 100kbup and length of first intron were significantly different between the maternal and paternal genes in cattle. Considering all species together, we found that GC content 100 kb up, LINE 100 kb up and the frequency of amino acids like Gly, Gln and Met were the most important attributes for identifying the paternal and maternal imprinted genes. These findings could imply conservation pattern in the attributes among these species.