Bovine Functional Genomics Laboratory

Beltsville, MD, United States

Bovine Functional Genomics Laboratory

Beltsville, MD, United States

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News Article | May 1, 2017
Site: phys.org

Catfish is an important dietary protein source and is the third most commonly farmed fish worldwide. While more than 2,500 species of catfish are known to exist, the channel catfish dominates U.S. aquaculture, accounting for more than 60 percent of fish and seafood production. In 2015, production sales for U.S. catfish growers totaled $361 million, up 3 percent from the previous year, according to USDA's National Agricultural Statistics Service. Research at the Agricultural Research Service (ARS) Warmwater Aquaculture Research Unit (WARU) in Stoneville, Mississippi, helps catfish producers improve the quality and quantity of their products. Recently, a team led by WARU molecular biologist Geoff Waldbieser and Auburn University scientist John Liu produced the first genome-sequence assembly for the channel catfish. It's also the first for any type of catfish. The total complement of DNA in the cell is called the "genome," and the catfish genome, like an instruction manual, contains the information needed to make and "operate" each fish. The catfish genome-sequence assembly gives scientists the ability to read the instruction manual for each individual catfish and look for differences that make some animals grow faster or resist disease better. Waldbieser used a special breeding technique called "gynogenesis" to produce the genome donor, Coco, so that she contained two copies of DNA—like other animals—except that both copies were completely identical. "I named her after Coco Chanel, because she's Channel No. 1," Waldbieser says. Collaborating with ARS scientists at the Genomics and Bioinformatics Research Unit in Stoneville and the Bovine Functional Genomics Laboratory in Beltsville, Maryland, Waldbieser produced about 800 million DNA sequences from Coco's DNA. "Those sequences were like puzzle pieces. It took 2 months on a 64-processor computer workstation to align them and produce the genome assembly," Waldbieser says. Waldbieser and WARU geneticist Brian Bosworth recently used Coco's genome to identify variation in DNA sequences between individual catfish within the Delta Select line—an improved catfish line being developed at WARU for use by farmers. "Now that we know where the genetic variations in the DNA sequences are located, we will be able to analyze different parts of the genome inherited by different individual catfish," Waldbieser says. "We can identify those segments, propagate them to our fish population, and improve meat production and production efficiency for farmers." This is important, because improving catfish growth rate, fillet yield, meat quality, and disease resistance will greatly benefit fish farmers, Waldbieser adds. More information: Qifan Zeng et al. Development of a 690 K SNP array in catfish and its application for genetic mapping and validation of the reference genome sequence, Scientific Reports (2017). DOI: 10.1038/srep40347


PubMed | Bovine Functional Genomics Laboratory, Biocontrol, U.S. Department of Agriculture and University of Maryland Extension
Type: Journal Article | Journal: Journal of dairy science | Year: 2014

Brown marmorated stink bug (BMSB; Halyomorpha halys) is an emerging invasive species of grave concern to agriculture as a polyphagous plant pest with potential negative effects on the dairy industry. The purpose of this study was to determine the risk of including BMSB-contaminated silage in lactating dairy cow rations. First, 6 dairies, either highly infested (n=3; 30 to 100 bugs per stalk) or not infested (n=3), were sampled to assess the prevalence of bug secretion compounds tridecane (major component) and E-2-decenal (stink odor component) in silage and milk. Second, using wild BMSB, a mini-silo dose-response experiment (adding 100, 50, 25, 10, and 1 freshly crushed bugs/0.5kg of chopped corn) was conducted to assess the effect of ensiling on BMSB stink odor compounds. Finally, synthetic BMSB stink odor compounds (10g of tridecane and 5g of E-2-decenal) were ruminally infused twice daily over 3 d, and samples of milk, urine, and rumen fluid were collected to evaluate disposition. Bug stink odor compounds were sampled by solid-phase microextraction (SPME) and analyzed by gas chromatography-mass spectrometry (GC-MS). Milk production and feed composition were unaffected when BMSB-contaminated silage was fed. Moreover, no E-2-decenal was detected in silage or milk (detection threshold = 0.00125g/mL). The dose-response of tridecane in mini-silo samples exhibited a linear relationship (R(2)=0.78) with the amount of BMSB added; however, E-2-decenal was completely decomposed and undetectable in spiked mini-silos after ensiling. Both synthetic secretion compounds infused into rumen were undetectable in all milk and urine samples. E-2-Decenal was not detectable in rumen fluid, whereas tridecane was detected only at 15 min postinfusion but not present thereafter. Feed intake was unaffected by infusion treatment and BMSB secretion compounds (E-2-decenal and tridecane) were not observed in milk. E-2-Decenal and tridecane from the metathoracic gland of BMSB are not able to contaminate milk either due to the ensiling process or because of metabolism within the rumen. Concern over BMSB stink odor compounds contaminating the fluid milk supply, even on highly infested farms, is not warranted.


Foye-Jackson O.T.,U.S. Department of Agriculture | Foye-Jackson O.T.,Office of Applied Research and Safety Assessment | Long J.A.,U.S. Department of Agriculture | Bakst M.R.,U.S. Department of Agriculture | And 5 more authors.
Poultry Science | Year: 2011

The sperm storage tubules (SST) of theturkey hen, which are located in the uterovaginal junction(UVJ) of the oviduct, maintain viable sperm for upto 10 wk after a single insemination. The mechanisms ofthis in vivo sperm storage are poorly understood. Ourobjective was to evaluate mRNA and protein expressionof avidin and 2 avidin-associated factors, avidinrelatedprotein-2 (AVR2) and progesterone receptor, inthe oviducts of 2 different lines to determine the extentto which they were sperm responsive and tissue specific.At 38 wk of age, Hybrid Grade Maker and Converterturkey hens were artificially inseminated with dilutedsemen (AI) or were sham-inseminated with extenderalone (SI). Forty-eight hours after insemination, total RNA was extracted from the UVJ epithelium (containingSST) and vaginal epithelium (VGE) of SI and AIhens. Real time-polymerase chain reaction data showeda clear tissue region-specific effect on gene expressionin the turkey hen oviduct, with much greater (P <0.0001) expression in the UVJ compared with VGE regionfor avidin and AVR2 mRNA in both lines and forprogesterone receptor mRNA in the Converter line. Incontrast to real-time PCR data, in situ hybridizationof SI and AI tissues showed that the presence of spermincreased avidin mRNA in the SST and UVJ surfaceepithelium in the Converter hens. Immunohistochemistryconfirmed the presence of avidin protein in theepithelium of the UVJ in both lines; however, whereasavidin protein was localized in the SST of SI-GradeMaker hens, this protein was not detected in the SST ofConverter hens. The upregulation of avidin and AVR2 mRNA within the sperm storage region indicates theinvolvement of avidin, and perhaps avidin analogs, inthe sustained storage of sperm in the SST, possiblythrough the binding of biotin to avidin. The absenceof avidin protein in the SST and VGE of Converterhens in the presence of increased mRNA may indicatea rapid turnover of protein. © 2011 Poultry Science Association Inc.


Huang Y.-Z.,Northwest University, China | Sun J.-J.,Northwest University, China | Zhang L.-Z.,Northwest University, China | Li C.-J.,Bovine Functional Genomics Laboratory | And 7 more authors.
Scientific Reports | Year: 2014

DNA methylation is a key epigenetic modification in mammals and plays important roles in muscle development. We sampledlongissimusdorsimuscle (LDM) fromawell-known elite native breed of Chinese Qinchuan cattle living within the same environment but displaying distinct skeletal muscle at the fetal and adult stages. We generated and provided a genome-wide landscape of DNA methylomes and their relationship with mRNA and miRNA for fetal and adult muscle studies. Integration analysis revealed a total of 77 and 1,054 negatively correlated genes with methylation in the promoter and gene body regions, respectively, in both the fetal and adult bovine libraries. Furthermore, we identified expression patterns of high-read genes that exhibit a negative correlation between methylation and expression from nine different tissues at multiple developmental stages of bovine muscle-related tissue or organs. In addition, we validated the MeDIP-Seq results by bisulfite sequencing PCR (BSP) in some of the differentially methylated promoters. Together, these results provide valuable data for future biomedical research and genomic and epigenomic studies of bovine skeletal muscle that may help uncover the molecular basis underlying economically valuable traits in cattle. This comprehensive map also provides a solid basis for exploring the epigenetic mechanisms of muscle growth and development.


PubMed | Jiangsu University, Northwest Agriculture and Forestry University, Texas A&M University and Bovine Functional Genomics Laboratory
Type: | Journal: Scientific reports | Year: 2014

DNA methylation is a key epigenetic modification in mammals and plays important roles in muscle development. We sampled longissimus dorsi muscle (LDM) from a well-known elite native breed of Chinese Qinchuan cattle living within the same environment but displaying distinct skeletal muscle at the fetal and adult stages. We generated and provided a genome-wide landscape of DNA methylomes and their relationship with mRNA and miRNA for fetal and adult muscle studies. Integration analysis revealed a total of 77 and 1,054 negatively correlated genes with methylation in the promoter and gene body regions, respectively, in both the fetal and adult bovine libraries. Furthermore, we identified expression patterns of high-read genes that exhibit a negative correlation between methylation and expression from nine different tissues at multiple developmental stages of bovine muscle-related tissue or organs. In addition, we validated the MeDIP-Seq results by bisulfite sequencing PCR (BSP) in some of the differentially methylated promoters. Together, these results provide valuable data for future biomedical research and genomic and epigenomic studies of bovine skeletal muscle that may help uncover the molecular basis underlying economically valuable traits in cattle. This comprehensive map also provides a solid basis for exploring the epigenetic mechanisms of muscle growth and development.


Zhou Y.,Northwest University, China | Sun J.,Northwest University, China | Li C.,Bovine Functional Genomics Laboratory | Wang Y.,Jiangsu University | And 6 more authors.
PLoS ONE | Year: 2014

Background: Adipose tissue has long been recognized to play an extremely important role in development. In bovines, it not only serves a fundamental function but also plays a key role in the quality of beef and, consequently, has drawn much public attention. Age and sex are two key factors that affect the development of adipose tissue, and there has not yet been a global study detailing the effects of these two factors on expressional differences of adipose tissues. Results: In this study, total RNA from the back fat of fetal bovines, adult bulls, adult heifers and adult steers were used to construct libraries for Illumina next-generation sequencing. We detected the expression levels of 12,233 genes, with over 3,000 differently expressed genes when comparing fetal and adult patterns and an average of 1000 differently expressed genes when comparing adult patterns. Multiple Gene Ontology terms and pathways were found to be significantly enriched for these differentially expressed genes. Of the 12,233 detected genes, a total of 4,753 genes (38.85%) underwent alternative splicing events, and over 50% were specifically expressed in each library. Over 4,000 novel transcript units were discovered for one library, whereas only approximately 30% were considered to have coding ability, which supplied a large amount of information for the lncRNA study. Additionally, we detected 56,564 (fetal bovine), 65,154 (adult bull), 78,061 (adult heifer) and 86,965 (adult steer) putative single nucleotide polymorphisms located in coding regions of the four pooled libraries. Conclusion: Here, we present, for the first time, a complete dataset involving the spatial and temporal transcriptome of bovine adipose tissue using RNA-seq. These data will facilitate the understanding of the effects of age and sex on the development of adipose tissue and supply essential information towards further studies on the genomes of beef cattle and other related mammals.


Zhang L.,Northwest University, China | Jia S.,Northwest University, China | Jia S.,King Abdullah University of Science and Technology | Yang M.,Northwest University, China | And 10 more authors.
BMC Genomics | Year: 2014

Background: Copy number variations (CNVs) are a main source of genomic structural variations underlying animal evolution and production traits. Here, with one pure-blooded Angus bull as reference, we describe a genome-wide analysis of CNVs based on comparative genomic hybridization arrays in 29 Chinese domesticated bulls and examined their effects on gene expression and cattle growth traits.Results: We identified 486 copy number variable regions (CNVRs), covering 2.45% of the bovine genome, in 24 taurine (Bos taurus), together with 161 ones in 2 yaks (Bos grunniens) and 163 ones in 3 buffaloes (Bubalus bubalis). Totally, we discovered 605 integrated CNVRs, with more " loss" events than both " gain" and " both" ones, and clearly clustered them into three cattle groups. Interestingly, we confirmed their uneven distributions across chromosomes, and the differences of mitochondrion DNA copy number (gain: taurine, loss: yak & buffalo). Furthermore, we confirmed approximately 41.8% (253/605) and 70.6% (427/605) CNVRs span cattle genes and quantitative trait loci (QTLs), respectively. Finally, we confirmed 6 CNVRs in 9 chosen ones by using quantitative PCR, and further demonstrated that CNVR22 had significantly negative effects on expression of PLA2G2D gene, and both CNVR22 and CNVR310 were associated with body measurements in Chinese cattle, suggesting their key effects on gene expression and cattle traits.Conclusions: The results advanced our understanding of CNV as an important genomic structural variation in taurine, yak and buffalo. This study provides a highly valuable resource for Chinese cattle's evolution and breeding researches. © 2014 Zhang et al.; licensee BioMed Central Ltd.


PubMed | CAS Northwest Institute of Plateau Biology, Bovine Functional Genomics Laboratory and Northwest University, China
Type: Journal Article | Journal: Genome biology and evolution | Year: 2015

Copy number variation (CNV) is an important component of genomic structural variation and plays a role not only in evolutionary diversification but also in domestication. Chinese cattle were derived from Bos taurus and Bos indicus, and several breeds presumably are of hybrid origin, but the evolution of CNV regions (CNVRs) has not yet been examined in this context. Here, we of CNVRs, mtDNA D-loop sequence variation, and Y-chromosomal single nucleotide polymorphisms to assess the impact of maternal and paternal B. taurus and B. indicus origins on the distribution of CNVRs in 24 Chinese domesticated bulls. We discovered 470 genome-wide CNVRs, only 72 of which were shared by all three Y-lineages (B. taurus: Y1, Y2; B. indicus: Y3), whereas 265 were shared by inferred taurine or indicine paternal lineages, and 228 when considering their maternal taurine or indicine origins. Phylogenetic analysis uncovered eight taurine/indicine hybrids, and principal component analysis on CNVs corroborated genomic exchange during hybridization. The distribution patterns of CNVRs tended to be lineage-specific, and correlation analysis revealed significant positive or negative co-occurrences of CNVRs across lineages. Our study suggests that CNVs in Chinese cattle partly result from selective breeding during domestication, but also from hybridization and introgression.


Li R.W.,Bovine Functional Genomics Laboratory | Wu S.,University of California at San Diego | Baldwin VI R.L.,Bovine Functional Genomics Laboratory | Li W.,University of California at San Diego | Li C.,Bovine Functional Genomics Laboratory
PLoS ONE | Year: 2012

The capacity of the rumen microbiota to produce volatile fatty acids (VFAs) has important implications in animal well-being and production. We investigated temporal changes of the rumen microbiota in response to butyrate infusion using pyrosequencing of the 16S rRNA gene. Twenty one phyla were identified in the rumen microbiota of dairy cows. The rumen microbiota harbored 54.5±6.1 genera (mean ± SD) and 127.3±4.4 operational taxonomic units (OTUs), respectively. However, the core microbiome comprised of 26 genera and 82 OTUs. Butyrate infusion altered molar percentages of 3 major VFAs. Butyrate perturbation had a profound impact on the rumen microbial composition. A 72 h-infusion led to a significant change in the numbers of sequence reads derived from 4 phyla, including 2 most abundant phyla, Bacteroidetes and Firmicutes. As many as 19 genera and 43 OTUs were significantly impacted by butyrate infusion. Elevated butyrate levels in the rumen seemingly had a stimulating effect on butyrate-producing bacteria populations. The resilience of the rumen microbial ecosystem was evident as the abundance of the microorganisms returned to their pre-disturbed status after infusion withdrawal. Our findings provide insight into perturbation dynamics of the rumen microbial ecosystem and should guide efforts in formulating optimal uses of probiotic bacteria treating human diseases.


PubMed | Jiangsu University, Northwest Agriculture and Forestry University and Bovine Functional Genomics Laboratory
Type: Journal Article | Journal: PloS one | Year: 2014

Adipose tissue has long been recognized to play an extremely important role in development. In bovines, it not only serves a fundamental function but also plays a key role in the quality of beef and, consequently, has drawn much public attention. Age and sex are two key factors that affect the development of adipose tissue, and there has not yet been a global study detailing the effects of these two factors on expressional differences of adipose tissues.In this study, total RNA from the back fat of fetal bovines, adult bulls, adult heifers and adult steers were used to construct libraries for Illumina next-generation sequencing. We detected the expression levels of 12,233 genes, with over 3,000 differently expressed genes when comparing fetal and adult patterns and an average of 1000 differently expressed genes when comparing adult patterns. Multiple Gene Ontology terms and pathways were found to be significantly enriched for these differentially expressed genes. Of the 12,233 detected genes, a total of 4,753 genes (38.85%) underwent alternative splicing events, and over 50% were specifically expressed in each library. Over 4,000 novel transcript units were discovered for one library, whereas only approximately 30% were considered to have coding ability, which supplied a large amount of information for the lncRNA study. Additionally, we detected 56,564 (fetal bovine), 65,154 (adult bull), 78,061 (adult heifer) and 86,965 (adult steer) putative single nucleotide polymorphisms located in coding regions of the four pooled libraries.Here, we present, for the first time, a complete dataset involving the spatial and temporal transcriptome of bovine adipose tissue using RNA-seq. These data will facilitate the understanding of the effects of age and sex on the development of adipose tissue and supply essential information towards further studies on the genomes of beef cattle and other related mammals.

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