The genomic landscape of short tandem repeats in cattle.

Short tandem repeats (STRs) are abundant and have high mutation rates across cattle genomes; however, comprehensive exploration of cattle STRs is needed. Here, we constructed a comprehensive map of 467 553 polymorphic STRs (pSTRs) constructed from 423 cattle genomes representing 59 breeds worldwide. We observed that pSTRs in coding sequences and 5'UTRs (Untranslated Regions) were under strong selective constraints and exhibited a relatively low level of diversity.

Inference of Genetic Diversity, Population Structure, and Selection Signatures in Xiangxi White Buffalo of China Through Whole-Genome Resequencing.

(1) Background: Buffaloes are crucial livestock species for food and service in tropical and subtropical regions. Buffalo genetics, particularly in indigenous Chinese breeds such as the Xiangxi white buffalo (XWB), remains an intriguing area of study due to its unique traits and regional significance. (2) Methods: This investigation utilized the whole-genome sequences of twenty XWBs (newly sequenced), along with eighty published whole-genome sequences of other buffalo breeds (including Guizhou white buffalo, river buffalo, and Chinese buffalo in the Yangtze River).

A Whole-Genome Scan Revealed Genomic Features and Selection Footprints of Mengshan Cattle.

(1) Background: Mengshan cattle from the Yimeng mountainous region in China stand out as a unique genetic resource, known for their adaptive traits and environmental resilience. However, these cattle are currently endangered and comprehensive genomic characterization remains largely unexplored. This study aims to address this gap by investigating the genomic features and selection signals in Mengshan cattle.

CATSPER2 and SPEF2 are potential molecular markers for boar sperm quality: a population association study.

Purpose: This study investigates the role of cation channel sperm associated 2 (CATSPER2) and sperm flagella 2 (SPEF2) genes in boar spermatogenesis, focusing on their association with sperm quality traits in boars.

Methods: Utilizing targeted next-generation sequencing, we identified and genotyped two polymorphisms in CATSPER2 (rs341636020G > A, rs326912346G > T) and three variants in SPEF2 (rs320839956A > G, rs334209514C > A, rs325319860C > T) across three boar breeds (Duroc, n = 181; Landrace, n = 87; Large White, n = 52).

Results: Our results confirmed the presence of the specified single nucleotide polymorphisms (SNPs), adhering to association study criteria.

Identification of Heilongjiang crossbred beef cattle pedigrees and reveals functional genes related to economic traits based on whole-genome SNP data.

To enhance the beef cattle industry, Heilongjiang Province has developed a new Crossbred beef cattle variety through crossbreeding with exotic commercial breeds. This new variety exhibits relatively excellent meat quality, and efficient reproductive performance, catering to market demands. This study employed whole genome resequencing technology to analyze the genetic pedigree and diversity of 19 Heilongjiang Crossbred beef cattle, alongside 59 published genomes from East Asian, Eurasian, and European taurine cattle as controls.

Effect of dietary Chinese herbal preparation on dry matter intake, milk yield and milk composition, serum biochemistry, hematological profile, and reproductive efficiency of Holstein dairy cows in early postpartum period.

The present study investigated the effects of various inclusion levels of dietary Chinese herbal medicine (CHM) preparation on feed consumption, milk yield and milk composition, serum biochemistry, hematological profile, and reproductive efficiency of Holstein dairy cows. A total of 117 lactating Holstein cows were randomly divided into four groups as control ( = 27; without CHM supplementation) and treatment groups CHM-0.5 ( = 31), CHM-0.

Illuminating Genetic Diversity and Selection Signatures in Matou Goats through Whole-Genome Sequencing Analysis.

(1) Background: Matou goats, native to Hunan and Hubei provinces in China, are renowned for their exceptional meat and skin quality. However, a comprehensive whole-genome-based exploration of the genetic architecture of this breed is scant in the literature. (2) Methods: To address this substantial gap, we used whole-genome sequences of 20 Matou goats and compared them with published genomic data of 133 goats of different breeds across China.

Whole-genome resequencing reveals diversity and selective signals in the Wuxue goat.

Animal genetic resources are crucial for ensuring global food security. However, in recent years, a noticeable decline in the genetic diversity of livestock has occurred worldwide. This decline is pronounced in developing countries, where the management of these resources is insufficient.

Whole-genome resequencing deciphers patterns of genetic diversity, phylogeny, and evolutionary dynamics in Kashmir cattle.

Kashmir cattle, which were kept by local pastoralists for centuries, are exceptionally resilient and adaptive to harsh environments. Despite its significance, the genomic characteristics of this cattle breed remain elusive. This study utilized whole genome sequences of Kashmir cattle (n = 20; newly sequenced) alongside published whole genomes of 32 distinct breeds and seven core cattle populations (n = 135).

Comprehensive whole-genome resequencing unveils genetic diversity and selective signatures of the Xiangdong black goat.

Xiangdong black goats, indigenous to Hunan Province, China, exhibit remarkable adaptation to challenging environments and possess distinct black coat coloration alongside exceptional meat quality attributes. Despite their significance, comprehensive genomic investigations of this breed have been notably lacking. This study involved a comprehensive examination of population structure, genomic diversity, and regions of selection in Xiangdong black goats utilizing whole-genome sequencing data from 20 samples of this breed and 139 published samples from six other Chinese goat breeds.

Unraveling genomic diversity and positive selection signatures of Qaidam cattle through whole-genome re-sequencing.

Qaidam cattle are a typical Chinese native breed inhabiting northwest China. They bear the characteristics of high cold and roughage tolerance, low-oxygen adaptability and good meat quality. To analyze the genetic diversity of Qaidam cattle, 60 samples were sequenced using whole-genome resequencing technology, along with 192 published sets of whole-genome sequencing data of Indian indicine cattle, Chinese indicine cattle, North Chinese cattle breeds, East Asian taurine cattle, Eurasian taurine cattle and European taurine cattle as controls.

Temperature adaptation patterns in Chinese cattle revealed by gene mutation analysis.

Cattle are sensitive to temperature fluctuations but adapt well to inclement weather conditions. When environmental temperatures exceed specific thresholds, heat stress becomes a critical concern for cattle. The gene, which resides on cattle chromosome 1 encodes a TRP channel protein, holding a unique capacity to sense temperature changes and facilitate rapid response to avoid heat stress.

Exploring testicular miRNA profiles during developmental stages in Dezhou donkeys: A preliminary insight.

Testicular development and spermatogenesis are complex phenomena controlled by various genetic factors, including miRNA-based post-transcriptional gene expression regulation. Exploring the miRNA expression patterns during testicular development in Dezhou donkeys would enhance our understanding of equine fertility and spermatogenesis. In this investigation, we examined the testicular miRNA profiles at various stages of development.

Global dispersal and adaptive evolution of domestic cattle: a genomic perspective.

Domestic cattle have spread across the globe and inhabit variable and unpredictable environments. They have been exposed to a plethora of selective pressures and have adapted to a variety of local ecological and management conditions, including UV exposure, diseases, and stall-feeding systems. These selective pressures have resulted in unique and important phenotypic and genetic differences among modern cattle breeds/populations.

The genetic secrets of adaptation: decoding the significance of the 30-bp insertion in the gene for Chinese cattle.

The gene is a type II epithelial cell α-keratin gene family member that plays a crucial role in animal epidermal and coat formation. This study aimed to investigate the relationship between the gene and the adaptability of Chinese cattle in varying environments by exploring the distribution of an exon insertion of the gene in different cattle populations. Our analysis involved amplifying and sequencing DNA samples from 362 individuals from 24 cattle breeds in China.

Administration of melatonin prior to modified synchronization protocol improves the productive and reproductive efficiency of Chinese crossbred buffaloes in low breeding season.

Introduction: Melatonin is a neurohormone involving various biological processes, including restoration of cyclicity in animals with seasonal breeding patterns. The use of melatonin in different forms has gained broader acceptance in different species, particularly in summer anestrous buffaloes.

Objectives: The objective of the current study was to evaluate the melatonin effect on the reproductive and productive performance of crossbred buffaloes during the low breeding season.

A missense mutation of the gene affects cold tolerance in Chinese domestic cattle.

Inclement weather conditions, especially cold stress, have threatened the cattle industry. Cattle exposed to cold environments for a longer time suffer developmental delay, immunity decline, and eventually death. is a member of With-no-lysine kinases (s), widely expressed in animal organs and tissues.

Improvement of carbon source composition reduces antibiotic resistance genes in the ectopic fermentation system.

Effectively reduce antibiotic resistance genes (ARGs) in ectopic fermentation system (EFS) is essential for practical production. In this study, three experiments were performed to explore how to remove ARGs in EFS effectively. Results demonstrated that ARGs were easily enriched in rice-husk-sawdust padding; simultaneous addition of laccase and cellulase suppressed the ARGs, mainly by increasing soluble carbohydrate concentration and promoting humic acid concentration; addition of corn stalks into rice-husk-sawdust decreased the abundance of ARGs by improving the carbon source structure and enhancing cellulase activity.

Genome-wide analysis emancipates genomic diversity and signature of selection in Altay white-headed cattle of Xinjiang, China.

Altay white-headed cattle have not received enough attention for several reasons. Due to irrational breeding and selection practices, the number of pure Altay white-headed cattle has decreased significantly and the breed is now on the eve of extinction. The genomic characterization will be a crucial step towards understanding the genetic basis of productivity and adaptability to survival under native Chinese agropastoral systems; nevertheless, no attempt has been made in Altay white-headed cattle.

Analysis of genomic copy number variations through whole-genome scan in Chinese Qaidam cattle.

Qaidam cattle (CDM) are indigenous breed inhabiting Northwest China. In the present study, we newly sequenced 20 Qaidam cattle to investigate the copy number variants (CNVs) based on the ARS-UMD1.2 reference genome.

Administration of GnRH at day 20 of AI and embryonic losses in synchronized crossbred buffalo.

Introduction: Following the application of different artificial insemination and synchronization protocols, the synchronized buffaloes had a higher incidence of early embryonic or fetal death, thus impairing reproductive performance. Therefore, there is a need to devise a synchronizing program that can improve conception, allow early pregnancy diagnosis, reduce early embryonic losses, and provide an early clue for pregnancy diagnosis and establishment. The present study aimed (1) to determine the effect of administration of different GnRH doses at day 20 of artificial insemination (AI) on the reproductive performance of buffaloes and (2) to observe the influence of synchronization protocol, parity, age, milk production, and body condition score (BCS) on early embryonic loss and progesterone (P4) levels in crossbred buffaloes.

Analysis of genetic diversity and selection signals in Chaling cattle of southern China using whole-genome scan.

China has diversified resources of indigenous cattle, which are classified into Northern, Central, and Southern groups according to their geographical distribution. Chaling cattle belong to Southern group. This breed is famous for the production of good quality meat with elite meat grades.

Whole-genome resequencing reveals genetic diversity, differentiation, and selection signatures of yak breeds/populations in Qinghai, China.

The Qinghai Province of China is located in the northeast region of the Qinghai-Tibetan Plateau (QTP) and carries abundant yak genetic resources. Previous investigations of archaeological records, mitochondrial DNA, and Y chromosomal markers have suggested that Qinghai was the major center of yak domestication. In the present study, we examined the genomic diversity, differentiation, and selection signatures of 113 Qinghai yak, including 42 newly sequenced Qinghai yak and 71 publicly available individuals, from nine yak breeds/populations (wild, Datong, Huanhu, Xueduo, Yushu, Qilian, Geermu, Tongde, and Huzhu white) using high-depth whole-genome resequencing data.