D. B. Weaver

Status of the USA cotton germplasm collection and crop vulnerability.

The National Plant Germplasm System (NPGS) is a cooperative effort among State, Federal and Private organizations aimed at preserving one of agriculture’s greatest assets: plant genetic diversity. The NPGS serves the scientific community by collecting, storing, and distributing germplasm as well as maintaining a searchable database of trait descriptors. Serving the NPGS, a Crop Germplasm Committee (CGC) is elected for each crop and is comprised of a group of scientists concerned with development, maintenance, characterization, and utilization of germplasm collections. Each CGC serves in an advisory role and provides a status report every seven years to determine scientific efforts, adequacy of germplasm base representation, and progress in breeding through utilization of germplasm. In addition, each committee can call attention to areas of concerns regarding facilities and staffing associated with the maintenance, collection, and taxonomic activities for a specific crop within the system. The following report was developed by the CGC for cotton and provides a record of collections, activities, concerns, crop vulnerabilities, and recommendations associated with the cotton collection for the period 1997–2005. Information provided within this document is a much expanded and detailed description of a report provided to the NPGS and includes the most exhaustive citation of germplasm depositions and research activity descriptions available anywhere in the USA for this time period. This documentation will be a valuable resource to breeders, geneticists, and taxonomists with an interest in this important food and fiber crop.

Performance of frogeye leaf spot-resistant and -susceptible near-isolines of soybean

Frogeye leaf spot (FLS) caused by Cercospora sojina Hara is a disease of soybean (Glycine max (L.) Merr.) that causes significant seed yield losses in warm, humid environments of southeastern United States. The Rcs3 gene in soybean has been reported to condition resistance to all known races of C. sojina. The objectives of this study were to determine the effectiveness of Rcs3 in limiting seed yield loss due to FLS and to compare the seed yield of the resistant and susceptible near-isolines (NILs) in the absence of significant FLS disease. Four pairs of NILs-Colquitt/Colquitt-Rcs3, Gordon/Gordon-Rcs3, Thomas/Thomas-Rcs3, and Wright/Wright-Rcs 3-were evaluated in 23 field experiments in Alabama, Florida, Georgia, Louisiana, Mississippi, and South Carolina during 1992 to 1994. The amount of damage to susceptible soybean caused by FLS was dependent on the specific environment. All four of the Rcs3 NILs were resistant to the prevalent races of FLS in all environments. In the absence of significant FLS disease, each of the Rcs3 NILs was at least equal to the respective susceptible line in its seed yield. In the presence of FLS infestation, the susceptible lines suffered significant seed yield loss (up to 31%) compared to their Rcs3 NILs. The effect of FLS on seed yield was dependent on cumulative disease severity over the growing season. Thus, the area under disease progress curve was more useful than percent of leaf area infected at the end of the growing season (R7 stage of development) in explaining the seed yield loss due to FLS.

Integrated signaling networks in plant responses to sedentary endoparasitic nematodes: a perspective.

Sedentary plant endoparasitic nematodes can cause detrimental yield losses in crop plants making the study of detailed cellular, molecular, and whole plant responses to them a subject of importance. In response to invading nematodes and nematode-secreted effectors, plant susceptibility/resistance is mainly determined by the coordination of different signaling pathways including specific plant resistance genes or proteins, plant hormone synthesis and signaling pathways, as well as reactive oxygen signals that are generated in response to nematode attack. Crosstalk between various nematode resistance-related elements can be seen as an integrated signaling network regulated by transcription factors and small RNAs at the transcriptional, posttranscriptional, and/or translational levels. Ultimately, the outcome of this highly controlled signaling network determines the host plant susceptibility/resistance to nematodes.

Transcriptome Analysis of Cotton (Gossypium hirsutum L.) Genotypes That Are Susceptible, Resistant, and Hypersensitive to Reniform Nematode (Rotylenchulus reniformis).

Reniform nematode is a semi-endoparasitic nematode species causing significant yield loss in numerous crops, including cotton (Gossypium hirsutum L.). An RNA-sequencing analysis was conducted to measure transcript abundance in reniform nematode susceptible (DP90 & SG747), resistant (BARBREN-713), and hypersensitive (LONREN-1) genotypes of cotton (Gossypium hirsutum L.) with and without reniform nematode infestation. Over 90 million trimmed high quality reads were assembled into 84,711 and 80, 353 transcripts using the G. arboreum and the G. raimondii genomes as references. Many transcripts were significantly differentially expressed between the three different genotypes both prior to and during nematode pathogenesis, including transcripts corresponding to the gene ontology categories of cell wall, hormone metabolism and signaling, redox reactions, secondary metabolism, transcriptional regulation, stress responses, and signaling. Further analysis revealed that a number of these differentially expressed transcripts mapped to the G. raimondii and/or the G. arboreum genomes within 1 megabase of quantitative trait loci that had previously been linked to reniform nematode resistance. Several resistance genes encoding proteins known to be strongly linked to pathogen perception and resistance, including LRR-like and NBS-LRR domain-containing proteins, were among the differentially expressed transcripts mapping near these quantitative trait loci. Further investigation is required to confirm a role for these transcripts in reniform nematode susceptibility, hypersensitivity, and/or resistance. This study presents the first systemic investigation of reniform nematode resistance-associated genes using different genotypes of cotton. The candidate reniform nematode resistance-associated genes identified in this study can serve as the basis for further functional analysis and aid in further development of reniform a nematode resistant cotton germplasm.

The Complexity of Posttranscriptional Small RNA Regulatory Networks Revealed by In Silico Analysis of Gossypium arboreum L. Leaf, Flower and Boll Small Regulatory RNAs

MicroRNAs (miRNAs) and secondary small interfering RNAs (principally phased siRNAs or trans-acting siRNAs) are two distinct subfamilies of small RNAs (sRNAs) that are emerging as key regulators of posttranscriptional gene expression in plants. Both miRNAs and secondary-siRNAs (sec-siRNAs) are processed from longer RNA precursors by DICER-LIKE proteins (DCLs). Gossypium arboreum L., also known as tree cotton or Asian cotton, is a diploid, possibly ancestral relative of tetraploid Gossypium hirsutum L., the predominant type of commercially grown cotton worldwide known as upland cotton. To understand the biological significance of these gene regulators in G. arboreum, a bioinformatics analysis was performed on G. arboreum small RNAs produced from G. arboreum leaf, flower, and boll tissues. Consequently, 263 miRNAs derived from 353 precursors, including 155 conserved miRNAs (cs-miRNAs) and 108 novel lineage-specific miRNAs (ls-miRNAs). Along with miRNAs, 2,033 miRNA variants (isomiRNAs) were identified as well. Those isomiRNAs with variation at the 3’-miRNA end were expressed at the highest levels, compared to other types of variants. In addition, 755 pha-siRNAs derived 319 pha-siRNA gene transcripts (PGTs) were identified, and the potential pha-siRNA initiators were predicted. Also, 2,251 non-phased siRNAs were found as well, of which 1,088 appeared to be produced by so-called cis- or trans-cleavage of the PGTs observed at positions differing from pha-siRNAs. Of those sRNAs, 148 miRNAs/isomiRNAs and 274 phased/non-phased siRNAs were differentially expressed in one or more pairs of tissues examined. Target analysis revealed that target genes for both miRNAs and pha-siRNAs are involved a broad range of metabolic and enzymatic activities. We demonstrate that secondary siRNA production could result from initial cleavage of precursors by both miRNAs or isomiRNAs, and that subsequently produced phased and unphased siRNAs could result that also serve as triggers of a second round of both cis- and trans-cleavage of additional siRNAs, leading to the formation of complex sRNA regulatory networks mediating posttranscriptional gene silencing. Results from this study extended our knowledge on G. arboreum sRNAs and their biological importance, which would facilitate future studies on regulatory mechanism of tissue development in cotton and other plant species.

Disease Management in Soybean: Use of Cultural Techniques and Genetic Resistance

The soybean is a good host for many fungal, bacterial, viral, and nematode pathogens. Environmental and economic concerns often dictate that cultural practices and genetic resistance are the only disease management options open to a grower. Primary cultural options include crop rotation and burial of crop residue by tillage. Crop rotation is very effective in reducing yield loss to diseases and nematodes, but is not always economically feasible. One of the most stable, economical, and environmentally safe disease and nematode management strategies is the use of genetic resistance. Genetically resistant cultivars are available for a variety of diseases and nernatodes, including Phytophthora rot, brown stem rot, stem canker, frogeye leaf spot, soybean cyst nematodes, and rootknot nematodes. Vertical resistance is widely used for a number of diseases and is a major objective in a number of breeding programs. Horizontal resistance and tolerance are used to a lesser extent.

Nitrogen mineralization from ‘AU Golden' sunn hemp residue

ABSTRACT The tropical legume sunn hemp (Crotalaria juncea L.) cultivar ‘AU Golden’ has the potential to provide substantial nitrogen (N) to subsequent crops to reduce recommended application rates of synthetic N fertilizers. A mineralization field trial was conducted to measure mass decomposition and N and carbon (C) amounts remaining from sunn hemp residue following three planting dates (May, June, and July) during the 2013 growing season at the Tennessee Valley (TVS) and Coastal Plain (WGS) locations of AL. Residue from June and July plantings contained 50.0% and 61.1% N at WGS and 41.5% and 66.5% N at TVS by the end of their respective incubation periods compared to residue from the May planting, which contained 21.1% N at WGS and 47.8% at TVS. In order to create a more synchronous relationship between ‘AU Golden’ residue N mineralization and crop demand, termination must be delayed until approximate planting of the following crop.