Wilson H. Faircloth

Gene expression profiling in peanut using high density oligonucleotide microarrays

BackgroundTranscriptome expression analysis in peanut to date has been limited to a relatively small set of genes and only recently has a significant number of ESTs been released into the public domain. Utilization of these ESTs for oligonucleotide microarrays provides a means to investigate large-scale transcript responses to a variety of developmental and environmental signals, ultimately improving our understanding of plant biology.ResultsWe have developed a high-density oligonucleotide microarray for peanut using 49,205 publicly available ESTs and tested the utility of this array for expression profiling in a variety of peanut tissues. To identify putatively tissue-specific genes and demonstrate the utility of this array for expression profiling in a variety of peanut tissues, we compared transcript levels in pod, peg, leaf, stem, and root tissues. Results from this experiment showed 108 putatively pod-specific/abundant genes, as well as transcripts whose expression was low or undetected in pod compared to peg, leaf, stem, or root. The transcripts significantly over-represented in pod include genes responsible for seed storage proteins and desiccation (e.g., late-embryogenesis abundant proteins, aquaporins, legumin B), oil production, and cellular defense. Additionally, almost half of the pod-abundant genes represent unknown genes allowing for the possibility of associating putative function to these previously uncharacterized genes.ConclusionThe peanut oligonucleotide array represents the majority of publicly available peanut ESTs and can be used as a tool for expression profiling studies in diverse tissues.

Determination of Maturity and Degree Day Indices and their Success in Predicting Peanut Maturity1

Abstract The ability to accurately assess and predict peanut maturity is a strong determinant of the economic return to the producer as it governs crop quality, flavor, and yield. However, the currently available methods used to predict peanut maturity are based on hull color determination and are somewhat labor-intensive and subject to the observers ability to finely discriminate color classes. The objectives in this study were: 1) create an index of maturity based on the distribution of peanut pods within the accepted maturity profile board classes that give the best quantifiable correlation with peanut yield, grade, and net value; and 2) test degree day models to determine their efficacy in predicting the optimum maturity index. Peanuts were harvested on 7 and 6 sequential dates in 2003 and 2004, respectively, at two sites in southwest Georgia, USA. Several maturity indices were calculated at each harvest based on the percentage of pods in each color class of the maturity profile board. For both sites...

Shotgun label-free quantitative proteomics of water-deficit-stressed midmature peanut (Arachis hypogaea L.) seed.

Legume seeds and peanuts, in particular, are an inexpensive source of plant proteins and edible oil. A comprehensive understanding of seed metabolism and the effects of water-deficit stress on the incorporation of the main storage reserves in seeds, such as proteins, fatty acids, starch, and secondary metabolites, will enhance our ability to improve seed quality and yield through molecular breeding programs. In the present study, we employed a label-free quantitative proteomics approach to study the functional proteins altered in the midmature (65-70 days postanthesis) peanut seed grown under water-deficit stress conditions. We created a pod-specific proteome database and identified 93 nonredundant, statistically significant, and differentially expressed proteins between well-watered and drought-stressed seeds. Mapping of these differential proteins revealed three candidate biological pathways (glycolysis, sucrose and starch metabolism, and fatty acid metabolism) that were significantly altered due to water-deficit stress. Differential accumulation of proteins from these pathways provides insight into the molecular mechanisms underlying the observed physiological changes, which include reductions in pod yield and biomass, reduced germination, reduced vigor, decreased seed membrane integrity, increase in storage proteins, and decreased total fatty acid content. Some of the proteins encoding rate limiting enzymes of biosynthetic pathways could be utilized by breeders to improve peanut seed production during water-deficit conditions in the field. The data have been deposited to the ProteomeXchange with identifier PXD000308.

Weed Management with Fomesafen Preemergence in Glyphosate-Resistant Cotton1

Field studies were conducted in Alabama in 1998 and 1999 to evaluate fomesafen preemergence (PRE) in glyphosate-resistant cotton. Fomesafen (0.3 and 0.4 kg ai/ha), fluometuron (1.4 kg ai/ha), and pyrithiobac (0.05 kg ai/ha) were applied alone or in tank mixtures. Glyphosate (0.4 kg ae/ha) was applied postemergence over-the-top (POT) and postemergence directed (PD). Regardless of PRE treatment, POT followed by (fb) PD applications of glyphosate were necessary for greater than 82% sicklepod control at midseason. In the absence of glyphosate, fomesafen, and fomesafen-containing tank mixtures controlled common cocklebur and Ipomoea species 77 and 72%, respectively, 14 d after PD application. However, two applications of glyphosate were needed for >94% season-long control of common cocklebur and Ipomoea species because of continued germination throughout the growing season. Postemergence applications of glyphosate added a 1,000 kg/ha seed cotton yield increase to all PRE treatments at both locations. Common cocklebur, Ipomoea species, and sicklepod control was not significantly increased by the addition of fomesafen PRE tank mixtures fb glyphosate postemergence as compared with glyphosate postemergence only. Nomenclature: Fluometuron; fomesafen; glyphosate; pyrithiobac; common cocklebur, Xanthium strumarium L. #3 XANST; Ipomoea species # IPOSS; sicklepod, Senna obtusifolia (L.) Irwin and Barneby # CASOB; cotton, Gossypium hirsutum L. ‘Deltapine 655 BG/RR’, ‘Paymaster 1220 BG/ RR’. Additional index words: CASOB, fluometuron, fomesafen, glyphosate, glyphosate timing, pyrithiobac, residual herbicide, Senna obtusifolia, soil-applied herbicide, transgenic cotton, XANST, Xanthium strumarium. Abbreviations: fb, followed by; PD, postemergence directed; POT, postemergence over-the-top; PRE, preemergence; SRS, Syngenta Research Site; WGS, Wiregrass Research and Education Center.

Invasion Dynamics and Genotypic Diversity of Cogongrass (Imperata cylindrica) at the Point of Introduction in the Southeastern United States

Abstract Nine sites of cogongrass were included in a study of genotypic diversity and spread dynamics at the point of introduction and its adjacent areas in the southern United States. Clones evaluated with two primer pairs yielded a total of 137 amplified fragment length polymorphism (AFLP) loci of which 102 (74.4%) were polymorphic. Genetic diversity was measured as the percentage of polymorphic, Shannons information index, Neis gene diversity, and panmictic heterozygosity. Neis gene diversity (HS) across all nine sites was estimated to be 0.11 and within site gene diversity ranged from 0.06 to 0.16. Bayesian estimate of gene diversity and Shannons information index were higher (0.17 and 0.17, respectively). The samples from the point of introduction (Pi) had the lowest genetic diversity for all types of estimates. Within site variance accounted for 56% of the total variation and among site variance 44% (P < 0.05). Differentiation among sites was assessed using FST. The greatest difference was found between the Pi and the others. No relationship was found between genetic and geographic distances. Principal component analysis as well as cluster analysis separated individuals into three main clusters. The Pi formed a separate subcluster. Gene flow (Nm), inferred from Φ-statistics describing the genetic differentiation between pairs of sites ranged from 0.6 to 5.55. The lack of significant relationship between gene flow and geographic distance as well as genetic and geographic distances suggests that the invasion dynamics of cogongrass into the southern United States is primarily through anthropogenic activities and to the lesser extent through natural forces. Nomenclature: cogongrass, Imperata cylindrica (L.) P. Beauv; Brazilian satintail, Imperata braziliensis Trin.; satintail, Imperata brevifolia Vasey; satsuma orange, Citrus reticulata L.; CTAB, cetyltrimethyl ammonium bromide; DNA, deoxyribonucleic acid.

Economic Returns of Irrigated and Non-Irrigated Peanut Based Cropping Systems

Proper crop rotation is essential to maintaining high peanut yield and quality. However, the economic considerations of sustainable cropping systems must incorporate commodity prices, production costs, and yield responses of the crops within the cropping system. Research was conducted at the USDA/ARS National Peanut Research Laboratorys Multi-crop Irrigation Research Farm in Shellman, Georgia to determine the average net returns of irrigated and non-irrigated cropping systems consisting of peanut (Arachis hypogea L.), cotton (Gossypium hirsutum L.), and corn (Zea mays L.). Five replicated cropping systems provided data on yield responses from irrigated and non-irrigated rotation sequences defined as: continuous peanuts (PPP), cotton/peanuts/cotton (CPC), corn/peanuts/corn (MPM), cotton/cotton/peanuts (CCP), and cotton/corn/peanuts (CMP). The peanut yield in the PPP rotation was 3300 kg/ha in the non-irrigated treatment. Non-irrigated yields in CPC and MPM rotation sequences were 3940 and 3890 kg/ha, respectively and yields in CCP and CMP rotation sequences were 4770 and 4710 kg/ha, respectively. The peanut yield in the PPP rotation was 4080 kg/ha in the irrigated treatment. Irrigated yields in CPC and MPM rotation sequences were 5280 and 5230 kg/ha, respectively and yields in CCP and CMP rotation sequences were 5940 and 6010 kg/ha, respectively. The economic returns of the cropping systems were analyzed for 3 different price level combinations. Production costs (variable and fixed) were obtained from partial budgets. Returns were defined as the 3 year average net returns of each cropping system and were calculated for each price level combination which resulted in 57 comparable average net returns for the irrigated and non-irrigated treatments. Net returns were influenced by rotation sequence, price, and irrigation.

Interaction of Tillage System and Irrigation Amount on Peanut Performance in the Southeastern U.S

Abstract A five-year study to investigate the potential interaction of conservation tillage with reduced irrigation amounts was conducted near Dawson, GA on peanut (Arachis hypogaea L.). Conventional tillage was compared to two conservation tillage programs (wide-strip and narrow-strip tillage) under four irrigation levels (100, 66, 33, and 0% of a recommended amount). Peanut yield did not exhibit a tillage by irrigation interaction as expected, although the main effects of irrigation and tillage were each significant by year due to weather variations. Peanut yield in narrow-strip tillage or wide-strip tillage were individually superior to conventional tillage in three seasons out of five, however only in one year did both conservation tillage systems outperform the conventional system. No detrimental effects on yields could be attributed to conservation tillage. Peanut quality and digging loss were dependent on the tillage by year effect as well as the main effect of irrigation. Irrigation increased tota...

Weed-Control Systems for Peanut Grown as a Biofuel Feedstock

Abstract Peanuts are not often used as a true oilseed crop, especially for the production of fuel. However, peanut could be a feedstock for biodiesel, especially in on-farm or small cooperative businesses, where producers can dictate the cost of making their own fuel. Field studies were conducted in 2005 and 2006 to assess low-cost weed-control systems for peanuts that would facilitate the economic viability of peanut biodiesel. Four preselected herbicide costs ranging from

Effects of Irrigation Method and Tillage Regime on Peanut (Arachis hypogaea L.) Reproductive Processes

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Effect of Cover Crop Management and Preemergence Herbicides on the Control of ALS-Resistant Palmer Amaranth (Amaranthus palmeri) in Peanut

62/ha and two application timings were compared with nontreated (