High-throughput genotyping arrays provide a standardized resource for plant breeding communities that are useful for a breadth of applications including high-density genetic mapping, genome-wide association studies (GWAS), genomic selection (GS), complex trait dissection, and studying patterns of genomic diversity among cultivars and wild accessions. We have developed the CottonSNP63K, an Illumina Infinium array containing assays for 45,104 putative intraspecific single nucleotide polymorphism (SNP) markers for use within the cultivated cotton species Gossypium hirsutum L. and 17,954 putative interspecific SNP markers for use with crosses of other cotton species with G. hirsutum. The SNPs on the array were developed from 13 different discovery sets that represent a diverse range of G. hirsutum germplasm and five other species: G. barbadense L., G. tomentosum Nuttal × Seemann, G. mustelinum Miers × Watt, G. armourianum Kearny, and G. longicalyx J.B. Hutchinson and Lee. The array was validated with 1,156 samples to generate cluster positions to facilitate automated analysis of 38,822 polymorphic markers. Two high-density genetic maps containing a total of 22,829 SNPs were generated for two F₂ mapping populations, one intraspecific and one interspecific, and 3,533 SNP markers were co-occurring in both maps. The produced intraspecific genetic map is the first saturated map that associates into 26 linkage groups corresponding to the number of cotton chromosomes for a cross between two G. hirsutum lines. The linkage maps were shown to have high levels of collinearity to the JGI G. raimondii Ulbrich reference genome sequence. The CottonSNP63K array, cluster file and associated marker sequences constitute a major new resource for the global cotton research community.

Cyclooxygenase-2 (COX-2) overexpression is an established factor linking chronic inflammation with metaplastic and neoplastic change in various tissues. We generated transgenic mice (BK5.COX-2) in which elevation of COX-2 and its effectors trigger a metaplasia-dysplasia sequence in exocrine pancreas. Histologic evaluation revealed a chronic pancreatitis-like state characterized by acinar-to-ductal metaplasia and a well-vascularized fibroinflammatory stroma that develops by 3 months. By 6 to 8 months, strongly dysplastic features suggestive of pancreatic ductal adenocarcinoma emerge in the metaplastic ducts. Increased proliferation, cellular atypia, and loss of normal cell/tissue organization are typical features in transgenic pancreata. Alterations in biomarkers associated with human inflammatory and neoplastic pancreatic disease were detected using immunohistochemistry. The abnormal pancreatic phenotype can be completely prevented by maintaining mice on a diet containing celecoxib, a well-characterized COX-2 inhibitor. Despite the high degree of atypia, only limited evidence of invasion to adjacent tissues was observed, with no evidence of distant metastases. However, cell lines derived from spontaneous lesions are aggressively tumorigenic when injected into syngeneic or nude mice. The progressive nature of the metaplastic/dysplastic changes observed in this model make it a valuable tool for examining the transition from chronic inflammation to neoplasia.

Establishment of pregnancy in ruminants requires blastocyst growth to form an elongated conceptus that produces interferon tau, the pregnancy recognition signal, and initiates implantation. Blastocyst growth and development requires secretions from the uterine endometrium. An early increase in circulating concentrations of progesterone (P4) stimulates blastocyst growth and elongation in ruminants. This study utilized sheep as a model to identify candidate genes and regulatory networks in the endometrium that govern preimplantation blastocyst growth and development. Ewes were treated daily with either P4 or corn oil vehicle from day 1.5 after mating to either day 9 or day 12 of pregnancy when endometrium was obtained by hysterectomy. Microarray analyses revealed many differentially expressed genes in the endometria affected by day of pregnancy and early P4 treatment. In situ hybridization analyses revealed that many differentially expressed genes were expressed in a cell-specific manner within the endometrium. The Database for Annotation, Visualization, and Integrated Discovery (DAVID) was used to identify functional groups of genes and biological processes in the endometrium that are associated with growth and development of preimplantation blastocysts. Notably, biological processes affected by day of pregnancy and/or early P4 treatment included lipid biosynthesis and metabolism, angiogenesis, transport, extracellular space, defense and inflammatory response, proteolysis, amino acid transport and metabolism, and hormone metabolism. This transcriptomic data provides novel insights into the biology of endometrial function and preimplantation blastocyst growth and development in sheep.

The recently constructed river buffalo whole-genome radiation hybrid panel (BBURH₅₀₀₀) has already been used to generate preliminary radiation hybrid (RH) maps for several chromosomes, and buffalo-bovine comparative chromosome maps have been constructed. Here, we present the first-generation whole genome RH map (WG-RH) of the river buffalo generated from cattle-derived markers. The RH maps aligned to bovine genome sequence assembly Btau_4.0, providing valuable comparative mapping information for both species. A total of 3990 markers were typed on the BBURH₅₀₀₀ panel, of which 3072 were cattle derived SNPs. The remaining 918 were classified as cattle sequence tagged site (STS), including coding genes, ESTs, and microsatellites. Average retention frequency per chromosome was 27.3% calculated with 3093 scorable markers distributed in 43 linkage groups covering all autosomes (24) and the X chromosomes at a LOD ≥ 8. The estimated total length of the WG-RH map is 36,933 cR₅₀₀₀. Fewer than 15% of the markers (472) could not be placed within any linkage group at a LOD score ≥ 8. Linkage group order for each chromosome was determined by incorporation of markers previously assigned by FISH and by alignment with the bovine genome sequence assembly (Btau_4.0). We obtained radiation hybrid chromosome maps for the entire river buffalo genome based on cattle-derived markers. The alignments of our RH maps to the current bovine genome sequence assembly (Btau_4.0) indicate regions of possible rearrangements between the chromosomes of both species. The river buffalo represents an important agricultural species whose genetic improvement has lagged behind other species due to limited prior genomic characterization. We present the first-generation RH map which provides a more extensive resource for positional candidate cloning of genes associated with complex traits and also for large-scale physical mapping of the river buffalo genome.

The purpose of this paper is to publish a table which correlates the previous nomenclature with marker genes mapped on cattle chromosomes. This table also presents the human correspondences and the chromosome measurements expressed as relative lengths.

It was hypothesized that a high-concentrate diet fed during early calfhood alters the expression of genes within the arcuate nucleus that subserve reproductive competence. Beef heifers (n = 12) were weaned at approximately 3 mo of age, and after acclimation, were allocated randomly to 1 of 2 nutritional groups: 1) High Concentrate/High Gain (HC/HG), a high concentrate diet fed to promote a gain of 0.91 kg/d; or 2) High Forage/Low Gain (HF/LG), a forage-based diet fed to promote a gain of 0.45kg/d. Experimental diets were fed under controlled intake for 91 d. At the end of 91 d, heifers were slaughtered by humane procedures, blood samples were collected, brains were removed, liver weights were determined, and rumen fluid was collected for VFA analyses. Tissue blocks containing the hypothalamus were dissected from the brains, frozen, and cut using a cryostat, and frozen sections were mounted on slides. Tissue from the arcuate nucleus (ARC) was dissected from sections for mRNA extraction. Microarray analysis was used to assess genome-wide transcription in the ARC using a 60-mer oligonucleotide 44K bovine expression array. The ADG was greater (P < 0.001) in heifers fed the HC/HG diet than in heifers fed the HF/LG diet. At slaughter, mean propionate to acetate ratios in the ruminal fluid and liver weight as a percentage of BW were increased (P < 0.005) in HC/HG compared with HF/LG heifers. Mean serum concentrations of insulin (P < 0.05) and IGF-1 (P < 0.005) were greater, and leptin tended to be greater (P = 0.1) in HC/HG heifers compared with HF/LG heifers. Approximately 345 genes were observed to be differentially expressed in the HC/HG group with approximately two-thirds of the genes exhibiting increased expression in the HC/HG group. Genes exhibiting decreased expression in the HC/HG group included agouti-related protein and neuropeptide Y, products of which are known to regulate feed intake and energy expenditure. Functional annotation of enriched Gene Ontology terms indicates that a number of biological processes within the hypothalamus are affected by consumption of high-concentrate diets, including those related to control of feed intake, regulation of cellular metabolic processes, receptor and intracellular signaling, and neuronal communication. In summary, dietary treatments shown previously to accelerate the timing of pubertal onset in heifers increased ruminal propionate, promoted enhanced metabolic hormone secretion, and altered gene expression in the ARC.