Zexi Cai

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Verified

Zexi verified their affiliation via an institutional email.

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• PhD
• Professor (Associate) at Aarhus University

Economic gain for sheep farmers is continually affected by incidences of copper intoxication and deficiency. This study assessed the ovine genome for differentially expressed genes (DEGs) influencing within-breed variation in hepatic copper content in Polish Merino sheep. To this end, we compared whole genome RNA sequence expression data from 12 fe...

Background Methane emissions from livestock, particularly from dairy cattle, represent a significant source of greenhouse gas, contributing to the global climate crisis. Understanding the complex interactions within the rumen microbiota that influence methane emissions is crucial for developing effective mitigation strategies. Results This study e...

Understanding the molecular and cellular mechanisms underlying complex traits in pigs is crucial for enhancing genetic gain via artificial selection and utilizing pigs as models for human disease and biology. Here, we conducted a comprehensive genome-wide association studies (GWAS) followed by cross-breed meta-analysis for 232 complex traits and wi...

The red seaweed Bonnemaisonia hamifera has shown potential as a CH4-mitigating feed additive in vitro, and hence, this pilot study aimed to investigate the potential of the seaweed when fed to dairy cows. The study was conducted as a 4 × 4 Latin square using 4 Danish Holstein cows with 4 periods of 7 d where the cows were placed in respiration cham...

Background Mastitis is a disease that incurs significant costs in the dairy industry. A promising approach to mitigate its negative effects is to genetically improve the resistance of dairy cattle to mastitis. A meta-analysis of genome-wide association studies (GWAS) across multiple breeds for clinical mastitis (CM) and its indicator trait, somatic...

Methane emissions from livestock, particularly from dairy cattle, represent a significant source of greenhouse gas (GHG), contributing to global climate crisis. This study employed Weighted Gene Co-expression Network Analysis (WGCNA) to investigate the complex interactions within the rumen microbiome that influence methane emissions. By integrating...

Systematic characterization of the molecular states of cells in livestock tissues is essential for understanding cellular and genetic mechanisms underlying economically and ecologically important physiological traits. This knowledge contributes to the advancement of sustainable and precision agriculture-food systems. Here, as part of the Farm anima...

The Farm Animal Genotype-Tissue Expression (FarmGTEx) project has been established to develop a public resource of genetic regulatory variants in livestock, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biological discovery and exploitation in animal breeding and human biomedicine. Here we show...

Understanding the molecular and cellular mechanisms that underlie complex traits in pigs is crucial for enhancing their genetic improvement program and unleashing their substantial potentials in human biomedicine research. Here, we conducted a meta-GWAS analysis for 232 complex traits with 28.3 million imputed whole-genome sequence variants in 70,3...

Identifying quantitative trait loci (QTL) associated with calf survival is essential for both reducing economic loss in cattle industry and understanding the genetic basis of the trait. To identify mutations and genes underlying young stock survival (YSS), we performed GWAS using de-regressed estimated breeding values of a YSS index and its compone...

We have previously demonstrated that pre- and early postnatal malnutrition in sheep induced depot- and sex-specific changes in adipose morphological features, metabolic outcomes, and transcriptome in adulthood, with perirenal (PER) as the major target followed by subcutaneous (SUB) adipose tissue. We aimed to identify co-expressed and hub genes in...

Genotype data from dairy cattle selection programs have greatly facilitated GWAS to identify variants related to economic traits. Results can enhance the accuracy of genomic prediction, analyze more complex models that go beyond additive effects, elucidate the genetic architecture of a trait, and finally, decipher the underlying biology of traits....

Microgravity changes the gene expression pattern in various cell types. This study focuses on the breast cancer cell lines MCF-7 (less invasive) and MDA-MB-231 (triple-negative, highly invasive). The cells were cultured for 14 days under simulated microgravity (s-µg) conditions using a random positioning machine (RPM). We investigated cytoskeletal...

Genome-wide association studies (GWAS) help identify polymorphic sites or genes linked to phenotypic variance, but a few identified genes and/or single nucleotide polymorphisms (SNPs) are unlikely to explain a large part of the phenotypic variability of complex traits. In this study, the focus was moved from single loci to functional units, express...

The Farm animal Genotype-Tissue Expression (FarmGTEx, https://www.farmgtex.org/) project has been established to develop a comprehensive public resource of genetic regulatory variants in domestic animal species, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biology discovery and exploitation in...

The Farm animal Genotype-Tissue Expression (FarmGTEx, https://www.farmgtex.org/) project has been established to develop a comprehensive public resource of genetic regulatory variants in domestic animal species, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biology discovery and exploitation in...

By their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. Previous studies identified biallelic single-nucleotide variants in the SRY, ZFY and DDX3Y genes, which in domestic goats identified four major Y-chromosomal haplotypes, Y1A, Y1B, Y2A and Y2B, with a marked geographi...

By their paternal transmission, Y‐chromosomal haplotypes are sensitive markers of population history and male‐mediated introgression. Previous studies identified biallelic single‐nucleotide variants in the SRY, ZFY and DDX3Y genes, which in domestic goats identified four major Y‐chromosomal haplotypes, Y1A, Y1B, Y2A and Y2B, with a marked geographi...

Genome-Wide Association Studies (GWAS) help identify polymorphic sites or genes linked to phenotypic variance, but a few identified genes / Single Nucleotide Polymorphisms are unlikely to explain a large part of the phenotypic variability of complex traits. In this study, the focus was moved from single loci to functional units, expressed by the me...

By their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. Previous studies identified biallelic single-nucleotide variants in the SRY, ZFY, DDX3Y genes, which in domestic goats identified four major Y-chromosomal haplotypes Y1A, Y1B, Y2A and Y2B with a marked geographic par...

Background Imputation from genotyping array to whole-genome sequence variants using resequencing of representative reference populations enhances our ability to map genetic factors affecting complex phenotypes in livestock species. The accumulation of knowledge about gene function in human and laboratory animals can provide substantial advantage fo...

The functional annotation of livestock genomes is crucial for understanding the molecular mechanisms that underpin complex traits of economic importance, adaptive evolution and comparative genomics. Here, we provide the most comprehensive catalogue to date of regulatory elements in the pig (Sus scrofa) by integrating 223 epigenomic and transcriptom...

Background Early life malnutrition is known to target adipose tissue with varying impact depending on timing of the insult. This study aimed to identify differentially expressed genes in subcutaneous (SUB) and perirenal (PER) adipose tissue of 2.5-years old sheep to elucidate the biology underlying differential impacts of late gestation versus earl...

This work represents a novel mechanistic approach to simulate and study genomic networks with accompanying regulatory interactions and complex mechanisms of quantitative trait formation. The approach implemented in MeSCoT software is conceptually based on the omnigenic genetic model of quantitative (complex) trait, and closely imitates the basic in...

The functional annotation of livestock genomes is crucial for understanding the molecular mechanisms that underpin complex traits of economic importance, adaptive evolution and comparative genomics. Here, we provide the most comprehensive catalogue to date of regulatory elements in the pig (Sus scrofa) by integrating 223 epigenomic and transcriptom...

Background: Production and health traits are central in cattle breeding. Advances in next-generation sequencing technologies and genotype imputation have increased the resolution of gene mapping based on genome-wide association studies (GWAS). Thus, numerous candidate genes that affect milk yield, milk composition, and mastitis resistance in dairy...

Abstract Dyslipidemia is the primary cause of cardiovascular disease, which is a serious human health problem in large parts of the world. Therefore, it is important to understand the genetic and molecular mechanisms that regulate blood levels of cholesterol and other lipids. Discovery of genetic elements in the regulatory machinery is often based...

Whole genome sequencing of 217 animals from three Danish commercial pig breeds (Duroc, Landrace, and Yorkshire) was performed. Twenty-six million single nucleotide polymorphisms (SNPs) and 8 million insertions or deletions (indels) were uncovered. Among the SNPs, 493,099 variants were located in coding sequences, and 29,430 were predicted to have a...

Tarim red deer (Cervus elaphus yarkandensis) is the only subspecies of red deer (of 22 subspecies) from Central Asia. This species is a desert dweller of the Tarim Basin of southern Xinjiang, China, and exhibits some unique adaptations to the dry and extreme hot climate. We report here the assembly of a Tarim red deer genome employing a 10X Genomic...

Carrizo citrange [Citrus sinensis (L.) Osbeck × Poncirus trifoliata (L.) Raf., CC] is one of the most widely used rootstocks in citriculture worldwide, but its cytogenetic study has been hampered by its inherent small size, morphological similarity to mitotic chromosomes, and lack of accessible cytological landmarks. In our previous study, a sponta...

Background Cervids have evolved very successful means for survival and thriving to adapt to various climates and environments. One of these successful means might be the effective and efficient way of communication. To support this notion, cervids are well equipped with a variety of skin glands that distribute in different body regions. However, st...

Background: Genome-wide association studies (GWAS) have been successfully implemented in cattle research and breeding. However, moving from the associations to identify the causal variants and reveal underlying mechanisms have proven complicated. In dairy cattle populations, we face a challenge due to long-range linkage disequilibrium (LD) arising...

Background Genome-wide association studies (GWAS) are widely used to identify regions of the genome that harbor genetic determinants of quantitative traits. However, the multiple-testing burden from scanning tens of millions of whole-genome sequence variants reduces the power to identify associated variants, especially if sample size is limited. In...

Coix lacryma-jobi L., a plant species closely related to Zea and Sorghum, is an important food and medicinal crop in Asia. However, no reference genome of this species has been reported, and its exact phylogeny within the Andropogoneae remains unresolved. Here, we generated a high-quality genome assembly of coix comprising ∼1.73 Gb with 44,485 pred...

Background Mithun (Bos frontalis), also called gayal, is an endangered bovine species, under the tribe bovini with 2n = 58 XX chromosome complements and reared under the tropical rain forests region of India, China, Myanmar, Bhutan and Bangladesh. However, the origin of this species is still disputed and information on its genomic architecture is s...

Centromeres are indispensable functional units of chromosomes. The evolutionary mechanisms underlying the rapid evolution of centromeric repeats, especially those following polyploidy, remain unknown. In this study, we isolated centromeric sequences of Brassica nigra, a model diploid progenitor (B genome) of the allopolyploid species B. juncea (AB...

Background: An unfavorable genetic correlation between milk production and fertility makes simultaneous improvement of milk production and fertility difficult in cattle breeding. Rapid genetic improvement in milk production traits in dairy cattle has been accompanied by decline in cow fertility. The genetic basis of this correlation remains poorly...

Blood orange [Citrus sinensis (L.) Osbeck] has been increasingly appreciated by consumers worldwide owing to its brilliant red color, abundant anthocyanin and other health-promoting compounds. However, there is still relatively little known about its cytogenetic characteristics, probably because of the small size and similar morphology of metaphase...

Sweet potato is one of the most important crops worldwide; however, basic research in this crop is limited. In this study, we aimed to construct a detailed karyotype of six species of Ipomoea (hexaploid Ipomoea batatas and five related species, namely, one tetraploid, I. tabascana and four diploids, I. splendor-sylvae, I. trifida, I. tenuissima, an...

Background Clementine mandarin (Citrus clementina Hort. ex Tan.) is one of the most famous and widely grown citrus cultivars worldwide. Variations in relation to the composition and distribution of repetitive DNA sequences that dominate greatly in eukaryote genomes are considered to be species-, genome-, or even chromosome-specific. Repetitive DNA-...

Background: Genome-wide association studies (GWAS) have been successfully implemented in cattle research and breeding. However, moving from the associations to identifying the causal variants and revealing underlying mechanisms have proven complicated. In dairy cattle populations, we face a challenge due to long-range linkage disequilibrium (LD) a...

Background Identification of genes underlying production traits is a key aim of the mink research community. Recent availability of genomic tools have opened the possibility for faster genetic progress in mink breeding. Availability of mink genome assembly allows genome-wide association studies in mink. Results In this study, we used genotyping-by...

Background: Improving resistance to mastitis, one of the costliest diseases in dairy production, has become an important objective in dairy cattle breeding. However, mastitis resistance is influenced by many genes involved in multiple processes, including the response to infection, inflammation, and post-infection healing. Low genetic heritability...

The American mink (Neovison vison) is a semiaquatic species of mustelid native to North America. It’s an important animal for the fur industry. Many efforts have been made to locate genes influencing fur quality and color, but this search has been impeded by the lack of a reference genome. Here we present the first draft genome of mink. In our stud...

In the subtribe Maydeae, Tripsacum and Zea are closely related genera. Tripsacum is a horticultural crop widely used as pasture forage. Previous studies suggested that Tripsacum might play an important role in maize origin and evolution. However, our understanding of the genomics and the evolution of Tripsacum remains limited. In this study, two di...

Radish (Raphanus sativus L., 2n = 2x = 18) is a major root vegetable crop especially in eastern Asia. Radish root contains various nutritions which play an important role in strengthening immunity. Repetitive elements are primary components of the genomic sequence and the most important factors in genome size variations in higher eukaryotes. To dat...

Coix, Sorghum and Zea are closely related plant genera in the subtribe Maydeae. Coix comprises 9-11 species with different ploidy levels (2n = 10, 20, 30, and 40). The exclusively cultivated C. lacryma-jobi L. (2n = 20) is widely used in East and Southeast Asia for food and medicinal applications. Three fertile cytotypes (2n = 10, 20, and 40) have...

Coix L., including many species, distributes across the Southeast Asia. The cultivar Coix lacryma-jobi L. is a traditional medical and tonic herb in Asia, especially in China. In recent years, the reports on the extract of Coix lacryma-jobi L. can help treat and prevent cancer attract extensive attention. Evolutionary, Coix L. consists of close rel...

The synaptonemal complex (SC) is a super protein lattice that connects paired homologous chromosomes in most meiotic systems. This special organization is related to the meiosis processes such as homologous chromosomes pairing, synapsis, recombination, segregation, etc. Flaws of it would lead the meiocytes to apoptosis, which contributes to sterili...