DNA methylation analysis to differentiate reference, breed, and parent-of-origin effects in the bovine pangenome era.

Background: Most DNA methylation studies have used a single reference genome with little attention paid to the bias introduced due to the reference chosen. Reference genome artifacts and genetic variation, including single nucleotide polymorphisms (SNPs) and structural variants (SVs), can lead to differences in methylation sites (CpGs) between individuals of the same species. We analyzed whole-genome bisulfite sequencing data from the fetal liver of Angus (Bos taurus taurus), Brahman (Bos taurus indicus), and reciprocally crossed samples.

Asymmetric growth-limiting development of the female conceptus.

Introduction: Sex differences in prenatal growth may contribute to sex-dependent programming effects on postnatal phenotype.

Methods: We integrated for the first time phenotypic, histomorphological, clinico-chemical, endocrine and gene expression analyses in a single species, the bovine conceptus at mid-gestation.

Results: We demonstrate that by mid-gestation, before the onset of accelerated growth, the female conceptus displays asymmetric lower growth compared to males.

MicroRNA breed and parent-of-origin effects provide insights into biological pathways differentiating cattle subspecies in fetal liver.

MicroRNAs (miRNAs) play a crucial role in regulating gene expression during key developmental processes, including fetal development. Brahman () and Angus () cattle breeds represent two major cattle subspecies with strikingly different phenotypes. We analyzed miRNA expression in liver samples of purebred and reciprocal crosses of Angus and Brahman to investigate breed and parent-of-origin effects at the onset of accelerated fetal growth.

Long read isoform sequencing reveals hidden transcriptional complexity between cattle subspecies.

The Iso-Seq method of full-length cDNA sequencing is suitable to quantify differentially expressed genes (DEGs), transcripts (DETs) and transcript usage (DTU). However, the higher cost of Iso-Seq relative to RNA-seq has limited the comparison of both methods. Transcript abundance estimated by RNA-seq and deep Iso-Seq data for fetal liver from two cattle subspecies were compared to evaluate concordance.

Gaur genome reveals expansion of sperm odorant receptors in domesticated cattle.

Background: The gaur (Bos gaurus) is the largest extant wild bovine species, native to South and Southeast Asia, with unique traits, and is listed as vulnerable by the International Union for Conservation of Nature (IUCN).

Results: We report the first gaur reference genome and identify three biological pathways including lysozyme activity, proton transmembrane transporter activity, and oxygen transport with significant changes in gene copy number in gaur compared to other mammals. These may reflect adaptation to challenges related to climate and nutrition.