Publications by authors named "Kimberly Davenport"

A central determinant of successful reproduction is pregnancy establishment and maintenance that relies on proper development of the conceptus (embryo/fetus and associated extraembryonic membranes including the placenta). Pregnancy loss in cattle can be caused by inadequate development and differentiation of the placenta. However, the cellular and molecular mechanisms regulating bovine placenta development and, particularly, trophoblast differentiation are not well understood.

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Article Synopsis
  • - The dairy industry needs efficient reproduction for successful milk production, with spontaneous abortion (SA) affecting different rates between heifers bred by artificial insemination (4.5%) and those receiving embryo transfer (31.6%).
  • - A genome-wide association analysis (GWAA) identified 216 loci and 413 candidate genes linked to SA in artificially inseminated Holstein heifers, while no significant loci were found for embryo transfer recipients.
  • - The discovered genetic loci related to SA in AI heifers can potentially aid in decreasing fetal loss through genomic selection strategies.
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This study aimed to identify loci (p < 1 × 10) and gene sets (normalized enrichment score (NES) ≥ 3.0) associated with the number of times a heifer is bred to attain a successful pregnancy (TBRD) for Holstein heifers bred by artificial insemination (AI, n = 2754) or that were embryo transfer (ET, n = 1566) recipients. Eight loci were associated (p < 1 × 10) with TBRD in AI bred heifers and four loci were associated with TBRD in ET recipients.

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Reference genomes of cattle and sheep have lacked contiguous assemblies of the sex-determining Y chromosome. Here, we assemble complete and gapless telomere to telomere (T2T) Y chromosomes for these species. We find that the pseudo-autosomal regions are similar in length, but the total chromosome size is substantially different, with the cattle Y more than twice the length of the sheep Y.

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Heifer conception rate to the first service (HCR1) is defined as the number of heifers that become pregnant to the first breeding service compared to the heifers bred. This study aimed to identify loci associated and gene sets enriched for HCR1 for heifers that were bred by artificial insemination (AI, = 2829) or were embryo transfer (ET, = 2086) recipients, by completing a genome-wide association analysis and gene set enrichment analysis using SNP data (GSEA-SNP). Three unique loci, containing four positional candidate genes, were associated ( < 1 × 10) with HCR1 for ET recipients, while the GSEA-SNP identified four gene sets (NES ≥ 3) and sixty-two leading edge genes (LEGs) enriched for HCR1.

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Advancements in single-cell sequencing have transformed the genomics field by allowing researchers to delve into the intricate cellular heterogeneity within tissues at greater resolution. While single-cell omics are more widely applied in model organisms and humans, their use in livestock species is just beginning. Studies in cattle, sheep, and goats have already leveraged single-cell and single-nuclei RNA-seq as well as single-cell and single-nuclei ATAC-seq to delineate cellular diversity in tissues, track changes in cell populations and gene expression over developmental stages, and characterize immune cell populations important for disease resistance and resilience.

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Reference genomes of cattle and sheep have lacked contiguous assemblies of the sex-determining Y chromosome. We assembled complete and gapless telomere to telomere (T2T) Y chromosomes for these species. The pseudo-autosomal regions were similar in length, but the total chromosome size was substantially different, with the cattle Y more than twice the length of the sheep Y.

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Article Synopsis
  • - The study provided a comprehensive functional annotation of the bovine genome, identifying 160,820 unique transcripts across various tissues, with 50% being protein-coding and a significant portion validated by multiple sequencing technologies.
  • - A large number of identified transcripts (69%) were unannotated, suggesting extensive undiscovered functional elements in the genome, and highlighted that many genes produced both coding and noncoding isoforms depending on the tissue type.
  • - The findings expanded existing gene annotations significantly and integrated with quantitative trait loci data, aiding in the exploration of tissue connections related to specific traits and establishing a new trait similarity network for bovine research.
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The uterus is vital for successful reproduction in mammals, and two different types of epithelia (luminal and glandular) are essential for embryo implantation and pregnancy establishment. However, the essential cellular and molecular factors and pathways governing postnatal epithelium maturation, determination, and differentiation in developing uterus are yet to be elucidated. Here, the epithelium of the neonatal mouse uterus was isolated and subjected to single-cell transcriptome (scRNA-seq) analysis.

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  • * Researchers used single-cell transcriptome analysis to examine the conceptus and chorion at different developmental stages (days 17, 24, 30, and 50), identifying various cell types involved, such as trophoblasts and immune cells.
  • * The study outlines the development and differentiation of uninucleate and binucleate trophoblast cells, highlighting important transcription factors and creating a digital atlas that can aid in future research on bovine reproductive health.
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Osteogenesis is a developmental process critical for structural support and the establishment of a dynamic reservoir for calcium and phosphorus. Changes in livestock breeding over the past 100 years have resulted in earlier bone development and increased physical size of cattle. Advanced skeletal maturity is now commonly observed at harvest, with heifers displaying more mature bone than is expected at 30 months of age (MOA).

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  • The study focuses on how the uterus develops after birth, specifically how undifferentiated cells turn into specialized uterine cells, which is influenced by interactions between different cell types and specific genetic factors.
  • Researchers used mouse models and lab-grown organoids to examine these processes, finding that normal (wild-type) organoids formed a typical single layer of epithelial cells, while organoids lacking a certain gene developed an abnormal multilayered structure.
  • Additionally, when the abnormal organoids were mixed with normal uterine cells, the development of unwanted basal cells was reduced, and treatment with estrogen further affected the types of cells formed, indicating that the gene in question plays a crucial role in maintaining proper epithelial development in the uterus.
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The hypothesis that CSF2 plays a role in the preimplantation development of the bovine embryo was tested by evaluating consequences of inactivation of CSF2RA (the functional receptor in the embryo) for development of embryos in utero. CRISPR/Cas9 was used to alter sequences on exon 5 and intron 5 of CSF2RA, Control embryos were injected with Cas9 mRNA only. Embryos > 16 cells at day 5 after insemination were transferred to synchronized recipient females in groups of 7 to 24.

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Ruminants have a semi-invasive placenta, which possess highly vascularized placentomes formed by maternal endometrial caruncles and fetal placental cotyledons and required for fetal development to term. The synepitheliochorial placenta of cattle contains at least two trophoblast cell populations, including uninucleate (UNC) and binucleate (BNC) cells that are most abundant in the cotyledonary chorion of the placentomes. The interplacentomal placenta is more epitheliochorial in nature with the chorion developing specialized areolae over the openings of uterine glands.

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  • * A study involving 480 sheep utilized advanced genotyping methods to analyze genetic variations linked to monocyte counts in their blood, identifying significant genetic markers on specific chromosomes.
  • * The findings highlight genes associated with cytokine production and immune responses, suggesting that further research could enhance understanding of sheep immunity and its implications for animal health management.
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Background: The domestic sheep (Ovis aries) is an important agricultural species raised for meat, wool, and milk across the world. A high-quality reference genome for this species enhances the ability to discover genetic mechanisms influencing biological traits. Furthermore, a high-quality reference genome allows for precise functional annotation of gene regulatory elements.

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Bitter taste perception in sheep can lead to avoidance of specific types of forage, such as sagebrush, which is present on many rangeland grazing systems in the Intermountain West. In humans, bitter taste perception is influenced by variation in several TAS2R genes, including more extensively studied and . We hypothesize that variation in taste receptor genes in sheep is associated with bitter taste.

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The Ovine Functional Annotation of Animal Genomes (FAANG) project, part of the broader livestock species FAANG initiative, aims to identify and characterize gene regulatory elements in domestic sheep. Regulatory element annotation is essential for identifying genetic variants that affect health and production traits in this important agricultural species, as greater than 90% of variants underlying genetic effects are estimated to lie outside of transcribed regions. Histone modifications that distinguish active or repressed chromatin states, CTCF binding, and DNA methylation were used to characterize regulatory elements in liver, spleen, and cerebellum tissues from four yearling sheep.

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Bison are an icon of the American West and an ecologically, commercially, and culturally important species. Despite numbering in the hundreds of thousands today, conservation concerns remain for the species, including the impact on genetic diversity of a severe bottleneck around the turn of the 20th century and genetic introgression from domestic cattle. Genetic diversity and admixture are best evaluated at genome-wide scale, for which a high-quality reference is necessary.

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Article Synopsis
  • The study focuses on improving livestock reproduction efficiency, which is essential for sustainable animal agriculture, specifically looking at beef heifers' fertility traits.
  • Researchers conducted two genome-wide association studies (GWAS) to identify genetic variations related to antral follicle count (AFC) and reproductive tract scores (RTS) in a sample of crossbred beef heifers.
  • Key findings revealed significant genetic loci on several chromosomes (2, 3, 8, 10, and 11) correlated to fertility traits; however, further investigation is required to fully understand the genetic mechanisms involved.
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Genomics research has relied principally on the establishment and curation of a reference genome for the species. However, it is increasingly recognized that a single reference genome cannot fully describe the extent of genetic variation within many widely distributed species. Pangenome representations are based on high-quality genome assemblies of multiple individuals and intended to represent the broadest possible diversity within a species.

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Meiotic recombination is an important contributor to genetic variation and ensures proper chromosome segregation during gametogenesis. Previous studies suggest that at least 1 crossover (CO) per chromosome arm is important to avoid mis-segregation. While the total number of COs per spermatocyte is known to differ in mice, this is only beginning to be evaluated in sheep.

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We report here the complete mitochondrial genome sequence of a Rocky Mountain bighorn sheep () in the United States. The circular genome has a size of 16,466 bp and contains 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes.

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