Following the domestication of maize over past approximately 10,000 years, breeders have exploited extensive genetic diversity this species to mold its phenotype meet human needs. The extent structural variation, including copy number variation (CNV) and presence/absence (PAV), which are thought contribute extraordinary phenotypic plasticity important crop, not been elucidated. Whole-genome, array-based, comparative genomic hybridization (CGH) revealed a level between inbred lines B73 Mo17...

Abstract We have achieved routine transformation of maize (Zea mays) using an Agrobacterium tumefaciensstandard binary (non-super binary) vector system. Immature zygotic embryos the hybrid line Hi II were infected with A. tumefaciens strain EHA101 harboring a standard and cocultivated in presence 400 mg L−1 l-cysteine. Inclusion l-cysteine cocultivation medium lead to improvement transient β-glucuronidase expression observed targeted cells significant increase stable efficiency, but was...

Heterosis is the phenomenon whereby progeny of particular inbred lines have enhanced agronomic performance relative to both parents. Although several hypotheses been proposed explain this fundamental biological phenomenon, responsible molecular mechanisms not determined. The maize B73 and Mo17 produce a heterotic F1 hybrid. Global patterns gene expression were compared in seedlings these three genotypes by using microarray that contains 13,999 cDNAs. Using an estimated 15% false discovery...

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

Abstract Next generation sequencing technology provides a powerful tool for measuring gene expression (mRNA) levels in the form of RNA-sequence data. Method development identifying differentially expressed (DE) genes from RNA-seq data, which frequently includes many low-count integers and can exhibit severe overdispersion relative to Poisson or binomial distributions, is popular area ongoing research. Here we present quasi-likelihood methods with shrunken dispersion estimates based on an...

Abstract The syncytium is a unique plant root organ whose differentiation induced by plant-parasitic cyst nematodes to create source of nourishment. Syncytium formation involves the redifferentiation and fusion hundreds cells. underlying regulatory networks that control this change cell fate are not understood. Here, we report strong down-regulation Arabidopsis (Arabidopsis thaliana) microRNA396 (miR396) in cells giving rise coincides with initiation syncytial induction/formation phase...

Significance Plant leaves are heavily colonized by microorganisms, but the extent to which surface sites differ from interior in selecting for microbial colonization traits is poorly understood. Global gene-expression studies of foliar pathogen Pseudomonas syringae reveal that leaf specifically favor active exploration using flagellar motility, chemosensing, and chemotaxis. In contrast, production enzymes secondary compounds modulate bacterial interactions with plant its defense system....

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 root cells for formation specialized feeding called syncytia. To better understand molecular mechanisms lead development nematode cells, transcript profiling was conducted on developing syncytia induced by soybean cyst glycines in roots coupling...

Abstract Shoots can be regenerated from Arabidopsis (Arabidopsisthaliana) root explants in tissue culture through a two-step process requiring preincubation on an auxin-rich callus induction medium. Regenerating tissues directed along different developmental pathways leading to the formation of shoots, new roots, or by transferring appropriate organ Using gene-profiling methods, we identified groups genes that serve as molecular signatures processes, i.e. were specifically up- down-regulated...

Polyploidy has played a prominent role in shaping the genomic architecture of angiosperms. Through allopolyploidization, several modern Gossypium (cotton) species contain two divergent, although largely redundant genomes. Owing to this redundancy, these genomes can play host an array evolutionary processes that act on duplicate genes.We compared homoeolog (genes duplicated by polyploidy) contributions transcriptome natural allopolyploid and synthetic interspecific F1 hybrid, both derived...

The human hypoxia-inducible transcription factor HIF-1 is a critical regulator of cellular and systemic responses to low oxygen levels. When levels are high, the HIF-1alpha subunit hydroxylated targeted for degradation by von Hippel-Lindau tumor suppressor protein (VHL). This regulatory pathway evolutionarily conserved, Caenorhabditis elegans hif-1 vhl-1 genes encode homologs VHL. To understand describe more fully molecular basis hypoxia response in this important genetic model system, we...

Abstract Plant recognition of pathogen-derived molecules influences attack and counterattack strategies that affect the outcome host–microbe interactions. To ascertain global framework host gene expression during biotrophic pathogen invasion, we analyzed in parallel mRNA abundance 22,792 genes throughout 36 (genotype × time) interactions between barley (Hordeum vulgare) Blumeria graminis f. sp hordei (Bgh), causal agent powdery mildew disease. A split-split-plot design was used to...

Global analysis of gene expression changes in soybean (Glycine max) and Heterodera glycines (soybean cyst nematode [SCN]) during the course infection a compatible interaction was performed using Affymetrix GeneChip genome array. Among 35,611 transcripts monitored, we identified 429 genes that showed statistically significant differential between uninfected nematode-infected root tissues. These included encoding enzymes involved primary metabolism; biosynthesis phenolic compounds, lignin,...

The Mu transposon system of maize is highly active, with each the approximately 50-100 copies transposing on average once generation. one dozen distinct transposons contain 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, insertion sites were amplified from stocks sequenced via 454 technology. 94% 965,000 reads carried TIRs,...

With the availability of microarray technology, expression profiles thousands genes can be monitored simultaneously to help determine mechanisms these biological processes. We conducted Affymetrix GeneChip analyses Arabidopsis-cyst nematode interaction and employed a statistical procedure analyze resultant data, which allowed us identify significant gene changes. Quantitative real-time RT-PCR assays were used confirm analyses. The results profiling revealed 128 with altered steady-state mRNA...

The monogenic recessive maize (Zea mays) mutant rootless with undetectable meristems 1 (rum1) is deficient in the initiation of embryonic seminal roots and postembryonic lateral at primary root. Lateral root shoot-borne development aerial parts rum1 are not affected. displays severely reduced auxin transport a delayed gravitropic response. Exogenously applied does induce rum1. initiated specific cell type, pericycle. Cell-type-specific transcriptome profiling pericycle 64 h after...

Obligate biotrophic pathogens of plants must circumvent or counteract defenses to guarantee accommodation inside the host. To do so, they secrete a variety effectors that regulate host immunity and facilitate establishment pathogen feeding structures called haustoria. The barley powdery mildew fungus Blumeria graminis f. sp. hordei produces large number proteins predicted be secreted from Fifty these effector candidates (BEC) were screened by host-induced gene silencing (HIGS), eight...

Typically, F 1 -hybrids are more vigorous than their homozygous, genetically distinct parents, a phenomenon known as heterosis. In the present study, transcriptomes of reciprocal maize ( Zea mays L.) hybrids B73×Mo17 and Mo17×B73 parental inbred lines B73 Mo17 were surveyed in primary roots, early developmental manifestation heterotic root traits. The application statistical methods suitable experimental design established that 34,233 (i.e., 86%) all high-confidence genes expressed at least...

Abstract Mitogen-activated protein kinase (MAPK) cascades play important roles in disease resistance model plant species such as Arabidopsis (Arabidopsis thaliana) and tobacco (Nicotiana tabacum). However, the importance of MAPK signaling pathways crops is still largely uninvestigated. To better understand role soybean (Glycine max), 13, nine, 10 genes encoding distinct MAPKs, MAPKKs, MAPKKKs, respectively, were silenced using virus-induced gene silencing mediated by Bean pod mottle virus....

Bacterial leaf streak of rice, caused by Xanthomonas oryzae pv. oryzicola (Xoc) is an increasingly important yield constraint in this staple crop. A mesophyll colonizer, Xoc differs from X. (Xoo), which invades xylem to cause bacterial blight rice. Both produce multiple distinct TAL effectors, type III-delivered proteins that transactivate effector-specific host genes. effector finds its target(s) via a partially degenerate code whereby the modular amino acid sequence identifies nucleotide...

A-Maize-ing Maize is one of our oldest and most important crops, having been domesticated approximately 9000 years ago in central Mexico. Schnable et al. (p. 1112 ; see the cover) present results sequencing B73 inbred maize line. The findings elucidate how became diploid after an ancestral doubling its chromosomes reveals transposable element movement activity recombination. Vielle-Calzada 1078 ) have sequenced Palomero Toluqueño ( landrace, a highland popcorn from Mexico, which, when...

Little is known about the role of proteins that lack primary sequence homology with any motifs (proteins unknown functions, PUFs); these comprise more than 10% all proteins. This paper offers a generalized experimental strategy for identifying functions such proteins, particularly in relation to metabolism. Using this strategy, we have identified novel regulatory function Arabidopsis locus At3g30720 (which term QQS qua-quine starch). expression, revealed through global mRNA profiling,...

Abstract To gain new insights into the mechanism of soybean (Glycine max) resistance to cyst nematode (Heterodera glycines), we compared gene expression profiles developing syncytia in near-isogenic lines differing at Rhg1 (for Heterodera a major quantitative trait locus for resistance, by coupling laser capture microdissection with microarray analysis. Gene profiling revealed that 1,447 genes were differentially expressed between two lines. Of these, 241 (16.8%) stress- and defense-related...