Genetics and Genomics Commons^™

Gene Mapping Via Bulked Segregant Rna-Seq (Bsr-Seq), Sanzhen Liu, Cheng-Ting Yeh, Ho Man Tang, Dan Nettleton, Patrick S. Schnable

Dan Nettleton

Bulked segregant analysis (BSA) is an efficient method to rapidly and efficiently map genes responsible for mutant phenotypes. BSA requires access to quantitative genetic markers that are polymorphic in the mapping population. We have developed a modification of BSA (BSR-Seq) that makes use of RNA-Seq reads to efficiently map genes even in populations for which no polymorphic markers have been previously identified. Because of the digital nature of next-generation sequencing (NGS) data, it is possible to conduct de novo SNP discovery and quantitatively genotype BSA samples by analyzing the same RNA-Seq data using an empirical Bayesian approach. In addition, analysis …

The Maize Brown Midrib2 (Bm2) Gene Encodes A Methylenetetrahydrofolate Reductase That Contributes To Lignin Accumulation, Ho Man Tang, Sanzhen Liu, Sarah Hill-Skinner, Wei Wu, Danielle Reed, Cheng-Ting Yeh, Dan Nettleton, Patrick S. Schnable

Dan Nettleton

The midribs of maize brown midrib (bm) mutants exhibit a reddish‐brown color associated with reductions in lignin concentration and alterations in lignin composition. Here, we report the mapping, cloning, and functional and biochemical analyses of the bm2 gene. The bm2 gene was mapped to a small region of chromosome 1 that contains a putative methylenetetrahydrofolate reductase (MTHFR) gene, which is down‐regulated in bm2 mutant plants. Analyses of multiple Mu‐induced bm2‐Mu mutant alleles confirmed that this constitutively expressed gene is bm2. Yeast complementation experiments and a previously published biochemical characterization show that the bm2 gene encodes a …

Extreme‐Phenotype Genome‐Wide Association Study (Xp‐Gwas): A Method For Identifying Trait‐Associated Variants By Sequencing Pools Of Individuals Selected From A Diversity Panel, Jinliang Yang, Haiying Jiang, Cheng-Ting Yeh, Jianming Yu, Jeffrey A. Jeddeloh, Dan Nettleton, Patrick S. Schnable

Dan Nettleton

Although approaches for performing genome‐wide association studies (GWAS) are well developed, conventional GWAS requires high‐density genotyping of large numbers of individuals from a diversity panel. Here we report a method for performing GWAS that does not require genotyping of large numbers of individuals. Instead XP‐GWAS (extreme‐phenotype GWAS) relies on genotyping pools of individuals from a diversity panel that have extreme phenotypes. This analysis measures allele frequencies in the extreme pools, enabling discovery of associations between genetic variants and traits of interest. This method was evaluated in maize (Zea mays) using the well‐characterized kernel row number trait, which was …

Estimation And Testing Of Gene Expression Heterosis, Tieming Ji, Peng Liu, Dan Nettleton

Dan Nettleton

Heterosis, also known as the hybrid vigor, occurs when the mean phenotype of hybrid offspring is superior to that of its two inbred parents. The heterosis phenomenon is extensively utilized in agriculture though the molecular basis is still unknown. In an effort to understand phenotypic heterosis at the molecular level, researchers have begun to compare expression levels of thousands of genes between parental inbred lines and their hybrid offspring to search for evidence of gene expression heterosis. Standard statistical approaches for separately analyzing expression data for each gene can produce biased and highly variable estimates and unreliable tests of heterosis. …

Extensive Tissue-Specific Transcriptomic Plasticity In Maize Primary Roots Upon Water Deficit, Nina Opitz, Caroline Marcon, Anja Paschold, Waqas Ahmed Malik, Andrew Lithio, Ronny Brandt, Hans-Peter Piepho, Dan Nettleton, Frank Hochholdinger

Dan Nettleton

Water deficit is the most important environmental constraint severely limiting global crop growth and productivity. This study investigated early transcriptome changes in maize (Zea mays L.) primary root tissues in response to moderate water deficit conditions by RNA-Sequencing. Differential gene expression analyses revealed a high degree of plasticity of the water deficit response. The activity status of genes (active/inactive) was determined by a Bayesian hierarchical model. In total, 70% of expressed genes were constitutively active in all tissues. In contrast, <3% (50 genes) of water deficit-responsive genes (1915) were consistently regulated in all tissues, while >75% (1501 genes) were specifically regulated in a single root tissue. Water deficit-responsive genes were most numerous in the …

Parallel Genome-Wide Expression Profiling Of Host And Pathogen During Soybean Cyst Nematode Infection Of Soybean, Nagabhushana Ithal, Justin Recknor, Dan Nettleton, Leonard Hearne, Tom Maier, Thomas J. Baum, Melissa G. Mitchum

Dan Nettleton

Global analysis of gene expression changes in soybean (Glycine max) and Heterodera glycines (soybean cyst nematode [SCN]) during the course of infection in a compatible interaction was performed using the Affymetrix GeneChip soybean genome array. Among 35,611 soybean transcripts monitored, we identified 429 genes that showed statistically significant differential expression between uninfected and nematode-infected root tissues. These included genes encoding enzymes involved in primary metabolism; biosynthesis of phenolic compounds, lignin, and flavonoids; genes related to stress and defense responses; cell wall modification; cellular signaling; and transcriptional regulation. Among 7,431 SCN transcripts monitored, 1,850 genes showed statistically significant differential …

Sequence Mining And Transcript Profiling To Explore Cyst Nematode Parasitism, Axel A. Elling, Makedonka Mitreva, Xiaowu Gai, John Martin, Justin Recknor, Eric L. Davis, Richard S. Hussey, Dan Nettleton, James P. Mccarter, Thomas J. Baum

Dan Nettleton

Background: Cyst nematodes are devastating plant parasites that become sedentary within plant roots and induce the transformation of normal plant cells into elaborate feeding cells with the help of secreted effectors, the parasitism proteins. These proteins are the translation products of parasitism genes and are secreted molecular tools that allow cyst nematodes to infect plants.

Results: We present here the expression patterns of all previously described parasitism genes of the soybean cyst nematode, Heterodera glycines, in all major life stages except the adult male. These insights were gained by analyzing our gene expression dataset from experiments using the Affymetrix Soybean …

Mu Transposon Insertion Sites And Meiotic Recombination Events Co-Localize With Epigenetic Marks For Open Chromatin Across The Maize Genome, Sanzhen Liu, Cheng-Ting Yeh, Tieming Ji, Kai Ying, Haiyan Wu, Ho Man Tang, Yan Fu, Daniel S. Nettleton, Patrick S. Schnable

Dan Nettleton

The Mu transposon system of maize is highly active, with each of the ∼50–100 copies transposing on average once each generation. The approximately one dozen distinct Mutransposons contain highly similar ∼215 bp terminal inverted repeats (TIRs) and generate 9-bp target site duplications (TSDs) upon insertion. Using a novel genome walking strategy that uses these conserved TIRs as primer binding sites, Mu insertion sites were amplified from Mu stocks and sequenced via 454 technology. 94% of ∼965,000 reads carried Mu TIRs, demonstrating the specificity of this strategy. Among these TIRs, 21 novel Mu TIRs were discovered, revealing additional complexity of …

Flor Revisited (Again): Eqtl And Mutational Analysis Of Nb-Lrr Mediated Immunity To Powdery Mildew In Barley, Roger P. Wise, Priyanka Surana, Gregory S. Fuerst, Ruo Xu, Divya Mistry, Julie A. Dickerson, Dan Nettleton Dr.

Dan Nettleton

Genes encoding early signaling events in pathogen defense often are identified only by their phenotype. Such genes involved in barley-powdery mildew interactions include Mla, specifying race-specific resistance; Rar1 (Required for Mla12-specified resistance1), and Rom1 (Restoration of Mla-specified resistance1). The HSP90-SGT1-RAR1 complex appears to function as chaperone in MLA-specified resistance, however, much remains to be discovered regarding the precise signaling underlying plant immunity. Genetic analyses of fast-neutron mutants derived from CI 16151 (Mla6) uncovered a novel locus, designated Rar3 (Required for Mla6-specified resistance3). Rar3 segregates independent of Mla6 and Rar1, and rar3 mutants are susceptible to Blumeria graminis f. sp. hordei …

Identification Of Differentially Expressed Gene Categories In Microarray Studies Using Nonparametric Multivariate Analysis, Dan Nettleton, Justin Recknor, James M. Reecy

Dan Nettleton

The field of microarray data analysis is shifting emphasis from methods for identifying differentially expressed genes to methods for identifying differentially expressed gene categories. The latter approaches utilize a priori information about genes to group genes into categories and enhance the interpretation of experiments aimed at identifying expression differences across treatments. While almost all of the existing approaches for identifying differentially expressed gene categories are practically useful, they suffer from a variety of drawbacks. Perhaps most notably, many popular tools are based exclusively on gene-specific statistics that cannot detect many types of multivariate expression change. We have developed a nonparametric …

Developmental Transcript Profiling Of Cyst Nematode Feeding Cells In Soybean Roots, Nagabhushana Ithal, Justin Recknor, Dan Nettleton, Tom Maier, Thomas J. Baum, Melissa G. Mitchum

Dan Nettleton

Cyst nematodes of the genus Heterodera are obligate, sedentary endoparasites that have developed highly evolved relationships with specific host plant species. Successful parasitism involves significant physiological and morphological changes to plant root cells for the formation of specialized feeding cells called syncytia. To better understand the molecular mechanisms that lead to the development of nematode feeding cells, transcript profiling was conducted on developing syncytia induced by the soybean cyst nematode Heterodera glycines in soybean roots by coupling laser capture microdissection with high-density oligonucleotide microarray analysis. This approach has identified pathways that may play intrinsic roles in syncytium induction, formation, and …

Differentially Expressed Genes In Blood From Young Pigs Between Two Swine Lines Divergently Selected For Feed Efficiency: Potential Biomarkers For Improving Feed Efficiency, Haibo Liu, Yet T. Nguyen, Daniel S. Nettleton, Jack C. M. Dekkers, Christopher K. Tuggle

Dan Nettleton

The goal of this study was to find potential gene expression biomarkers in blood of piglets that can be used to predict pigs’ future feed efficiency. Using RNA-seq technology, we found 453 genes were differentially expressed (false discovery rate (FDR) ≤ 0.05) in the blood of two Yorkshire lines of pigs divergently selected for feed efficiency (FE) based on residual feed intake (RFI). Genes involved in several biosynthetic processes were overrepresented among genes more highly expressed in the low RFI line compared to the high RFI line. Weighted gene co-expression network analysis (WGCNA) also revealed genes involved in some of …

66th National Poultry Breeder Roundtable Poster_Jibin Zhang.Pdf, Jibin Zhang, Carl J. Schmidt, Susan J. Lamont

Jibin Zhang

Pag 2017 Poster _ Jibin Zhang.Pdf, Jibin Zhang, Michael G. Kaiser, Melissa S. Herrmann, Rodrigo A. Gallardo, David A. Bunn, Terra R. Kelly, Jack C. M. Dekkers, Huaijun Zhou, Susan J. Lamont

Jibin Zhang

Gene Expression Response To Heat Stress In Two Broiler Lines, Jibin Zhang, Carl J. Schmidt, Susan J. Lamont

Jibin Zhang

The fast growth rate and increased body weight of modern broilers makes them susceptible to heart failure and sensitive to heat stress. To find the genetic causes of these problems, gene expression was measured in hearts of two broiler lines that differed in their response to heat stress. Each line was separated into two groups that were kept under heat stress or at ambient temperature. The comparison of gene expression between the two lines and heat treatments suggests that expression of 325 genes were significantly changed in modern broilers under heat stress, while only 3 genes changed their expression in …

Variation In Avian Pathogenic Escherichia Coli Colonization Levels In Chickens, Melissa Monson, Michael Kaiser, Susan Lamont

Melissa Monson

Colonization levels in five tissues after avian pathogenic Escherichia coli (APEC) inoculation were investigated in chickens to generate phenotypic data for a genome wide association study (GWAS). Bacterial loads were measured in 370 birds and varied among individuals and tissues. Mean bacterial levels were significantly different between tissues (right lung > spleen > left lung and liver > blood). There were also significant correlations in bacterial load between tissues. These data suggest that colonization levels could be used as phenotypes in GWAS and could help identify markers associated with poultry resistance to APEC infections. After verification, these markers could be used for genetic …

Draft Genome Sequence Of Xylella Fastidiosa Pear Leaf Scorch Strain In Taiwan, C.-C. Su, W.-L. Deng, F.-J. Jan, C.-J. Chang, Hong Huang, J. Chen

Hong Huang

The draft genome sequence of Xylella fastidiosa pear leaf scorch strain PLS229, isolated from the pear cultivar Hengshan (Pyrus pyrifolia) in Taiwan, is reported here. The bacterium has a genome size of 2,733,013 bp, with a G+C content of 53.1%. The PLS229 genome was annotated and has 3,259 open reading frames and 50 RNA genes.

Differential Expression Of Cyb5a In Chinese And European Pig Breeds Due To Genetic Variations In The Promoter Region..Pdf, Ying Bai, Jibin Zhang, Y Xue, Yl Peng, Gang Chen, Meiying Fang

Jibin Zhang

Characterization Of Physical, Thermal And Structural Properties Of Chromium (Vi) Oxide Powder: Impact Of Biofield Treatment, Mahendra Kumar Trivedi, Rama Mohan Tallapragada, Alice Branton, Dahryn Trivedi, Gopal Nayak, Omprakash Latiyal, Snehasis Jana

Mahendra Kumar Trivedi

Influence Of Biofield Treatment On Physicochemical Properties Of Hydroxyethyl Cellulose And Hydroxypropyl Cellulose, Mahendra Kumar Trivedi, Gopal Nayak, Shrikant Patil, Rama Mohan Tallapragada, Rakesh K. Mishra

Mahendra Kumar Trivedi

Differential Expression Of Cell Cycle Regulators During Hyperplastic And Hypertrophic Growth Of Broiler Subcutaneous Adipose Tissue.Pdf, Jibin Zhang, Yeunsu Suh, Young Min Choi, Paula Chen, Michael Davis, Kichoon Lee

Jibin Zhang

Identification Of Ctla2a, Defb29, Wfdc15b, Serpina1f And Mup19 As Novel Tissue-Specific Secretory Factors In Mouse..Pdf, Jibin Zhang, Jinsoo Ahn, Yeunsu Suh, Seongsoo Hwang, Michael E. Davis, Kichoon Lee

Jibin Zhang

Connecting Through Consilience: Ecology, Society, Culture And Technology, Ruth Mirams, Alexander Hayes

Alexander Hayes Mr.

Amongst linguistic, cultural and geographic diversity, humanity is characterised by inquisitiveness, communication and a deep desire to connect with each other. Despite our advanced intelligence and technological capacity, we are creatures of nature - a species which occupies a habitat, depends on consumable resources and fragile in many ways. As a species, we currently face challenges including overpopulation, diminishing resources and habitat degradation. In essence, we are exhausting the resources we depend on. [1] Resource depletion, disruption, famine, growth and sustainability are all observable in other species and natural systems. Human societies and systems can be described through the same …

Differential Expression Of Cyclin G2, Cyclin Dependent Kinase Inhibitor 2c And Peripheral Myelin Protein 22 Genes During Adipogenesis..Pdf, Jibin Zhang, Yeunsu Suh, Young Min Choi, Jinsoo Ahn, Michael E. Davis, Kichoon Lee

Jibin Zhang

Jibin Zhang's Ppt For Midwest Meeting.Pdf, Jibin Zhang, Yeunsu Suh, Young Min Choi, Michael E. Davis, Kichoon Lee

Jibin Zhang

A Comprehensive Microrna Expression Profile Of The Backfat Tissue From Castrated And Intact Full-Sib Pair Male Pigs.Pdf, Ying Bai, Jinming Huang, Gang Liu, Jibin Zhang, Jianying Wang, Chengkun Liu, Meiying Fang

Jibin Zhang

Genetic Character Of Cyb5 Gene Among Different Pig Breeds.Pdf, Ying Bai, Jibin Zhang, Meiying Fang

Jibin Zhang

Genetic Parameters For Concentrations Of Minerals In Longissimus Muscle And Their Associations With Palatability Traits In Angus Cattle, R. G. Mateescu, A. J. Garmyn, Richard G. Tait Jr., Qing Duan, Q. Liu, Mary S. Mayes, Dorian J. Garrick, A. L. Van Eenennaam, D. L. Vanoverbeke, G. G. Hilton, Donald C. Beitz, James M. Reecy

Richard G. Tait Jr.

The objective of this study was to estimate genetic parameters for concentrations of minerals in LM and to evaluate their associations with beef palatability traits. Samples of LM from 2,285 Angus cattle were obtained and fabricated into steaks for analysis of mineral concentrations and for trained sensory panel assessments. Nine minerals, including calcium, copper, iron, magnesium, manganese, phosphorus, potassium, sodium, and zinc, were quantified. Restricted maximum likelihood procedures were used to obtain estimates of variance and covariance components under a multiple-trait animal model. Estimates of heritability for mineral concentrations in LM varied from 0.01 to 0.54. Iron and sodium were …

Evaluation Of Fixed Sources Of Variation And Estimation Of Genetic Parameters For Incidence Of Bovine Respiratory Disease In Preweaned Calves And Feedlot Cattle, M. J. Schneider, Richard G. Tait Jr., Marshall V. Ruble, W. Darrell Busby, James M. Reecy

Richard G. Tait Jr.

The primary objective of this study was to estimate variance components and heritability of bovine respiratory disease (BRD) incidence in beef calves before weaning and during the finishing phase. The second objective was to investigate the impact of BRD incidence and treatment frequency on performance and carcass traits. Bovine respiratory disease is the biggest and most costly health challenge facing the cattle industry. The 2 populations used consisted of 1,519 preweaned calves and 3,277 head of feedlot cattle. The incidence rate of BRD in preweaned calves was 11.39%, and among treated cattle, 82.1% were treated once, 13.9% were treated twice, …

Genetic Parameters For Carnitine, Creatine, Creatinine, Carnosine, And Anserine Concentration In Longissimus Muscle And Their Association With Palatability Traits In Angus Cattle, R. G. Mateescu, A. J. Garmyn, M. A. O'Neil, Richard G. Tait Jr., Almass A. Abuzaid, Mary S. Mayes, Dorian J. Garrick, A. L. Van Eenennaam, D. L. Vanoverbeke, G. G. Hilton, Donald C. Beitz, James M. Reecy

Richard G. Tait Jr.

The objective of this study was to estimate genetic parameters for carnitine, creatine, creatinine, carnosine, and anserine concentration in LM and to evaluate their associations with Warner-Bratzler shear force (WBSF) and beef palatability traits. Longissimus muscle samples from 2,285 Angus cattle were obtained and fabricated into steaks for analysis of carnitine, creatine, creatinine, carnosine, anserine, and other nutrients, and for trained sensory panel and WBSF assessments. Restricted maximum likelihood procedures were used to obtain estimates of variance and covariance components under a multiple-trait animal model. Estimates of heritability for carnitine, creatine, creatinine, carnosine, and anserine concentrations in LM from Angus …