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Liu Z.,Huazhong Agricultural University | Liu Z.,Cold Spring Harbor Laboratory | Kumari S.,Cold Spring Harbor Laboratory | Zhang L.,Cold Spring Harbor Laboratory | And 3 more authors.

Waterlogging of plants leads to low oxygen levels (hypoxia) in the roots and causes a metabolic switch from aerobic respiration to anaerobic fermentation that results in rapid changes in gene transcription and protein synthesis. Our research seeks to characterize the microRNA-mediated gene regulatory networks associated with short-term waterlogging. MicroRNAs (miRNAs) are small non-coding RNAs that regulate many genes involved in growth, development and various biotic and abiotic stress responses. To characterize the involvement of miRNAs and their targets in response to short-term hypoxia conditions, a quantitative real time PCR (qRT-PCR) assay was used to quantify the expression of the 24 candidate mature miRNA signatures (22 known and 2 novel mature miRNAs, representing 66 miRNA loci) and their 92 predicted targets in three inbred Zea mays lines (waterlogging tolerant Hz32, mid-tolerant B73, and sensitive Mo17). Based on our studies, miR159, miR164, miR167, miR393, miR408 and miR528, which are mainly involved in root development and stress responses, were found to be key regulators in the post-transcriptional regulatory mechanisms under short-term waterlogging conditions in three inbred lines. Further, computational approaches were used to predict the stress and development related cis-regulatory elements on the promoters of these miRNAs; and a probable miRNA-mediated gene regulatory network in response to short-term waterlogging stress was constructed. The differential expression patterns of miRNAs and their targets in these three inbred lines suggest that the miRNAs are active participants in the signal transduction at the early stage of hypoxia conditions via a gene regulatory network; and crosstalk occurs between different biochemical pathways. Source

Peiffer J.A.,Cornell University | Peiffer J.A.,North Carolina State University | Flint-Garcia S.A.,University of Missouri | De Leon N.,University of Wisconsin - Madison | And 4 more authors.

Stalk strength is an important trait in maize (Zea mays L.). Strong stalks reduce lodging and maximize harvestable yield. Studies show rind penetrometer resistance (RPR), or the force required to pierce a stalk rind with a spike, is a valid approximation of strength. We measured RPR across 4,692 recombinant inbreds (RILs) comprising the maize nested association mapping (NAM) panel derived from crosses of diverse inbreds to the inbred, B73. An intermated B73×Mo17 family (IBM) of 196 RILs and a panel of 2,453 diverse inbreds from the North Central Regional Plant Introduction Station (NCRPIS) were also evaluated. We measured RPR in three environments. Family-nested QTL were identified by joint-linkage mapping in the NAM panel. We also performed a genome-wide association study (GWAS) and genomic best linear unbiased prediction (GBLUP) in each panel. Broad sense heritability computed on a line means basis was low for RPR. Only 8 of 26 families had a heritability above 0.20. The NCRPIS diversity panel had a heritability of 0.54. Across NAM and IBM families, 18 family-nested QTL and 141 significant GWAS associations were identified for RPR. Numerous weak associations were also found in the NCRPIS diversity panel. However, few were linked to loci involved in phenylpropanoid and cellulose synthesis or vegetative phase transition. Using an identity-by-state (IBS) relationship matrix estimated from 1.6 million single nucleotide polymorphisms (SNPs) and RPR measures from 20% of the NAM panel, genomic prediction by GBLUP explained 64±2% of variation in the remaining RILs. In the NCRPIS diversity panel, an IBS matrix estimated from 681,257 SNPs and RPR measures from 20% of the panel explained 33±3% of variation in the remaining inbreds. These results indicate the high genetic complexity of stalk strength and the potential for genomic prediction to hasten its improvement. Source

Zwickl D.J.,University of Arizona | Stein J.C.,Cold Spring Harbor Laboratory | Wing R.A.,University of Arizona | Ware D.,Cold Spring Harbor Laboratory | And 2 more authors.
Systematic Biology

We describe new methods for characterizing gene tree discordance in phylogenomic data sets, which screen for deviations from neutral expectations, summarize variation in statistical support among gene trees, and allowcomparison of the patterns of discordance induced by various analysis choices. Using an exceptionally complete set of genome sequences for the short armof chromosome 3 in Oryza (rice) species,we applied these methods to identify the causes and consequences of differing patterns of discordance in the sets of gene trees inferred using a panel of 20 distinct analysis pipelines.We found that discordance patterns were strongly affected by aspects of data selection, alignment, and alignment masking. Unusual patterns of discordance evident when using certain pipelines were reduced or eliminated by using alternative pipelines, suggesting that theywere the product of methodological biases rather than evolutionary processes. In some cases, once such biaseswere eliminated, evolutionary processes such as introgression could be implicated.Additionally, patterns of gene tree discordance had significant downstream impacts on species tree inference. For example, inference from supermatrices was positivelymisleading when pipelines that led to biased gene treeswere used. Several resultsmay generalize to other data sets: we found that gene tree and species tree inference gave more reasonable results when intron sequence was included during sequence alignment and tree inference, the alignment software PRANK was used, and detectable "block-shift" alignment artifacts were removed. We discuss our findings in the context of well-established relationships in Oryza and continuing controversies regarding the domestication history of O. sativa. © The Author(s) 2014. Source

Bouis H.E.,International Food Policy Research Institute | Welch R.M.,Robert lley Center For Agriculture And Health
Crop Science

Minerals and vitamins in food staples eaten widely by the poor may be increased either through conventional plant breeding or through use of transgenic techniques, a process known as biofortification. HarvestPlus seeks to develop and distribute cultivars of food staples (rice [Oryza sativa L.], wheat [Triticum aestivum L.], maize [Zea mays L.], cassava [Manihot esculenta Crantz], pearl millet [Pennisetum americanum Leeke], beans [Phaseolus vulgaris L.], sweet potato [Ipomoea batatas L.]) that are high in Fe, Zn, and provitamin A through an interdisciplinary global alliance of scientific institutions and implementing agencies in developing and developed countries. Biofortified crops offer a rural-based intervention that, by design, initially reaches these more remote populations, which comprise a majority of the undernourished in many countries, and then penetrates to urban populations as production surpluses are marketed. Thus, biofortification complements fortification and supplementation programs, which work best in centralized urban areas and then reach into rural areas with good infrastructure. Initial investments in agricultural research at a central location can generate high recurrent benefits at low cost as adapted biofortified cultivars become widely available in countries across time at low recurrent costs. Overall, three things must happen for biofortification to be successful. First, the breeding must be successful—high nutrient density must be combined with high yields and high profitability. Second, efficacy must be demonstrated—the micronutrient status of human subjects must be shown to improve when consuming the biofortified cultivars as normally eaten. Third, the biofortified crops must be adopted by farmers and consumed by those suffering from micronutrient malnutrition in significant numbers. © Crop Science Society of America. Source

Park D.H.,Cornell University | Mirabella R.,University of Amsterdam | Bronstein P.A.,Cornell University | Bronstein P.A.,Robert lley Center For Agriculture And Health | And 5 more authors.
Plant Journal

Pseudomonas syringae pv. tomato DC3000 is a bacterial pathogen of Arabidopsis and tomato that grows in the apoplast. The non-protein amino acid γ-amino butyric acid (GABA) is produced by Arabidopsis and tomato and is the most abundant amino acid in the apoplastic fluid of tomato. The DC3000 genome harbors three genes annotated as gab TGABA transaminases. A DC3000 mutant lacking all three gabT genes was constructed and found to be unable to utilize GABA as a sole carbon and nitrogen source. In complete minimal media supplemented with GABA, the mutant grew less well than wild-type DC3000 and showed strongly reduced expression of hrpL and avrPto, which encode an alternative sigma factor and effector, respectively, associated with the type III secretion system. The growth of the gabT triple mutant was weakly reduced in Arabidopsis ecotype Landberg erecta (Ler) and strongly reduced in the Ler pop2-1 GABA transaminase-deficient mutant that accumulates higher levels of GABA. Much of the ability to grow on GABA-amended minimal media or in Arabidopsis pop2-1 leaves could be restored to the gabT triple mutant by expression in trans just gabT2. The ability of DC3000 to elicit the hypersensitive response (HR) in tobacco leaves is dependent upon deployment of the type III secretion system, and the gabT triple mutant was less able than wild-type DC3000 to elicit this HR when bacteria were infiltrated along with GABA at levels of 1 mM or more. GABA may have multiple effects on P. syringae-plant interactions, with elevated levels increasing disease resistance. © 2010 Blackwell Publishing Ltd. Source

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