Mississippi Delta Community College

Two draft sequences of Gossypium hirsutum, the most widely cultivated cotton species, provide insights into genome structure, genome rearrangement, gene evolution and cotton fiber biology. Upland cotton is a model for polyploid crop domestication and transgenic improvement. Here we sequenced the allotetraploid Gossypium hirsutum L. acc. TM-1 genome by integrating whole-genome shotgun reads, bacterial artificial chromosome (BAC)-end sequences and genotype-by-sequencing genetic maps. We assembled and annotated 32,032 A-subgenome genes and 34,402 D-subgenome genes. Structural rearrangements, gene loss, disrupted genes and sequence divergence were more common in the A subgenome than in the D subgenome, suggesting asymmetric evolution. However, no genome-wide expression dominance was found between the subgenomes. Genomic signatures of selection and domestication are associated with positively selected genes (PSGs) for fiber improvement in the A subgenome and for stress tolerance in the D subgenome. This draft genome sequence provides a resource for engineering superior cotton lines.

Abstract Rice (Oryza sativa), a salt-sensitive species, has considerable genetic variation for salt tolerance within the cultivated gene pool. Two indica rice genotypes, FL478, a recombinant inbred line derived from a population developed for salinity tolerance studies, and IR29, the sensitive parent of the population, were selected for this study. We used the Affymetrix rice genome array containing 55,515 probe sets to explore the transcriptome of the salt-tolerant and salt-sensitive genotypes under control and salinity-stressed conditions during vegetative growth. Response of the sensitive genotype IR29 is characterized by induction of a relatively large number of probe sets compared to tolerant FL478. Salinity stress induced a number of genes involved in the flavonoid biosynthesis pathway in IR29 but not in FL478. Cell wall-related genes were responsive in both genotypes, suggesting cell wall restructuring is a general adaptive mechanism during salinity stress, although the two genotypes also had some differences. Additionally, the expression of genes mapping to the Saltol region of chromosome 1 were examined in both genotypes. Single-feature polymorphism analysis of expression data revealed that IR29 was the source of the Saltol region in FL478, contrary to expectation. This study provides a genome-wide transcriptional analysis of two well-characterized, genetically related rice genotypes differing in salinity tolerance during a gradually imposed salinity stress under greenhouse conditions.

Annual decreases in soybean (Glycine max L. Merrill) yield caused by diseases were estimated by surveying university-affiliated plant pathologists in 28 soybean-producing states in the United States and in Ontario, Canada, from 2010 through 2014. Estimated yield losses from each disease varied greatly by state or province and year. Over the duration of this survey, soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) was estimated to have caused more than twice as much yield loss than any other disease. Seedling diseases (caused by various pathogens), charcoal rot (caused by Macrophomina phaseolina (Tassi) Goid), and sudden death syndrome (SDS) (caused by Fusarium virguliforme O’Donnell & T. Aoki) caused the next greatest estimated yield losses, in descending order. The estimated mean economic loss due to all soybean diseases, averaged across U.S. states and Ontario from 2010 to 2014, was $60.66 USD per acre. Results from this survey will provide scientists, breeders, governments, and educators with soybean yield-loss estimates to help inform and prioritize research, policy, and educational efforts in soybean pathology and disease management.

Abstract Globally, flooding is one of the most damaging abiotic stresses, besides drought, that affects 17 million km 2 of land surface annually. Recent research indicates that climate change is resulting in more extreme weather events, such as flooding or soil waterlogging, that negatively affect crop production. Therefore, it is imperative to understand how flooding stress affects crops and to develop improved production practices that make cropping systems more resilient and able to cope with extreme weather events. This review paper summarizes the current state of knowledge on the impacts of flooding or soil waterlogging on crop production losses, nitrogen (N) losses, and provides potential management strategies to reduce these losses. The factors affecting the extent of flooding injury in plants as well as plant adaptations under waterlogging stress are also discussed briefly. For the purpose of this review, “flooding” refers to the situation when all or part of the plant is submerged under water, whereas “soil waterlogging” refers to the situation where soil pores are saturated with water. Soil waterlogging also promotes soil N losses through runoff, leaching, and denitrification. Potential management practices that can be used to mitigate soil waterlogging stress include the use of flood‐tolerant varieties, adjusting management practices, improving drainage, and practicing adaptive nutrient management strategies. However, these might be site‐ or crop‐specific management practices and they should be validated for their economic viability before developing future management plans that promote sustainable crop yields from waterlogged soils.

Annual decreases in corn yield caused by diseases were estimated by surveying members of the Corn Disease Working Group in 22 corn-producing states in the United States and in Ontario, Canada, from 2012 through 2015. Estimated loss from each disease varied greatly by state and year. In general, foliar diseases such as northern corn leaf blight, gray leaf spot, and Goss's wilt commonly caused the largest estimated yield loss in the northern United States and Ontario during non-drought years. Fusarium stalk rot and plant-parasitic nematodes caused the most estimated loss in the southern-most United States. The estimated mean economic loss due to yield loss by corn diseases in the United States and Ontario from 2012 to 2015 was $76.51 USD per acre. The cost of disease-mitigating strategies is another potential source of profit loss. Results from this survey will provide scientists, breeders, government, and educators with data to help inform and prioritize research, policy, and educational efforts in corn pathology and disease management. Accepted for publication 26 August 2016.

Abstract The aquaculture industry is under increasing pressure to make production more resource efficient and environmentally responsible. Application of better management practices is the main approach for improving the environmental performance of aquaculture. There are, however, few numerical indicators for comparing resource use and waste generation for culture of common species and by different grow-out techniques. Indicators are proposed for evaluating the efficiency with which feed, protein, fish meal, nutrients, liming materials, water, land, and energy are used in aquaculture. In addition, methods for evaluating amounts of nutrients and other possible pollutants generated by production facilities are suggested. The indicators are designed to reveal the quantities of resources used, or of waste discharged, per tonne of production. This will simplify comparisons among species and production systems and facilitate comparisons with other kinds of animal agriculture. Keywords: aquaculture and environmentsustainable aquacultureaquaculture BMPsaquaculture certification Notes 1$1.72/kg live weight. 2$1.79/kg live weight. 3$0.50/kg live weight.

Soybean (Glycine max L. Merrill) is an economically important commodity for United States agriculture. Nonetheless, the profitability of soybean production has been negatively impacted by soybean diseases. The economic impacts of 23 common soybean diseases were estimated in 28 soybean-producing states in the U.S., from 1996 to 2016 (the entire data set consisted of 13,524 data points). Estimated losses were investigated using a variety of statistical approaches. The main effects of state, year, pre- and post-discovery of soybean rust, region, and zones based on yield, harvest area, and production, were significant on "total economic loss" as a function of diseases. Across states and years, the soybean cyst nematode, charcoal rot, and seedling diseases were the most economically damaging diseases while soybean rust, bacterial blight, and southern blight were the least economically damaging. A significantly greater mean loss (51%) was observed in states/years after the discovery of soybean rust (2004 to 2016) compared to the pre-discovery (1996 to 2003). From 1996 to 2016, the total estimated economic loss due to soybean diseases in the U.S. was $95.48 billion, with $80.89 billion and $14.59 billion accounting for the northern and southern U.S. losses, respectively. Over the entire time period, the average annual economic loss due to soybean diseases in the U.S. reached nearly $4.55 billion, with approximately 85% of the losses occurring in the northern U.S. Low yield/harvest/production zones had significantly lower mean economic losses due to diseases in comparison to high yield/harvest/production zones. This observation was further bolstered by the observed positive linear correlation of mean soybean yield loss (in each state, due to all diseases considered in this study, across 21 years) with the mean state wide soybean production (MT), mean soybean yield (kg ha-1), and mean soybean harvest area (ha). Results of this investigation provide useful insights into how research, policy, and educational efforts should be prioritized in soybean disease management.

Gene expression during the early stages of fiber cell development and in allopolyploid crops is poorly understood. Here we report computational and expression analyses of 32 789 high-quality ESTs derived from Gossypium hirsutum L. Texas Marker-1 (TM-1) immature ovules (GH_TMO). The ESTs were assembled into 8540 unique sequences including 4036 tentative consensus sequences (TCs) and 4504 singletons, representing approximately 15% of the unique sequences in the cotton EST collection. Compared with approximately 178 000 existing ESTs derived from elongating fibers and non-fiber tissues, GH_TMO ESTs showed a significant increase in the percentage of genes encoding putative transcription factors such as MYB and WRKY and genes encoding predicted proteins involved in auxin, brassinosteroid (BR), gibberellic acid (GA), abscisic acid (ABA) and ethylene signaling pathways. Cotton homologs related to MIXTA, MYB5, GL2 and eight genes in the auxin, BR, GA and ethylene pathways were induced during fiber cell initiation but repressed in the naked seed mutant (N1N1) that is impaired in fiber formation. The data agree with the known roles of MYB and WRKY transcription factors in Arabidopsis leaf trichome development and the well-documented phytohormonal effects on fiber cell development in immature cotton ovules cultured in vitro. Moreover, the phytohormonal pathway-related genes were induced prior to the activation of MYB-like genes, suggesting an important role of phytohormones in cell fate determination. Significantly, AA sub-genome ESTs of all functional classifications including cell-cycle control and transcription factor activity were selectively enriched in G. hirsutum L., an allotetraploid derived from polyploidization between AA and DD genome species, a result consistent with the production of long lint fibers in AA genome species. These results suggest general roles for genome-specific, phytohormonal and transcriptional gene regulation during the early stages of fiber cell development in cotton allopolyploids.

Abstract Cyanobacteria (blue‐green algae) in the genera Anabaena, Aphanizomenon, Microcystis , and Oscillatoria often form extensive and persistent blooms in freshwater aquaculture ponds. Bloom‐forming cyanobacteria are undesirable in aquaculture ponds because: 1) they are a relatively poor base for aquatic food chains; 2) they are poor oxygenators of the water and have undesirable growth habits; 3) some species produce odorous metabolites that impart undesirable flavors to the cultured animal; and 4) some species may produce compounds that are toxic to aquatic animals. Development of cyanobacterial blooms is favored under conditions of high nutrient loading rates (particularly if the availability of nitrogen is limited relative to phosphorus), low rates of vertical mixing, and warm water temperatures. Under those conditions, dominance of phytoplankton communities by cyanobacteria is the result of certain unique physiological attributes (in particular, N 2 fixation and buoyancy regulation) that allow cyanobacteria to compete effectively with other phytoplankton. The ability to fix N 2 provides a competitive advantage under severe nitrogen limitation because it allows certain cyanobacterial species to make use of a source of nitrogen unavailable to other phytoplankton. The ability to regulate cell buoyancy through environmentally‐controlled collapse ad reformation of intracellular gas vacuoles is perhaps the primary reason for the frequent dominance of aquaculture pond phytoplankton communities by cyanobacteria. Cyanobacteria that can regulate their position in the water column gain a distinct advantage over other phototrophs in poorly mixed bodies of water. In addition to the physicochemical interactions that influence phytoplankton community dynamics, cyanobacterial‐microbial associations may play an important regulatory role in determining community structure. Cyanobacteria are always found in close association with a diverse array of microorganisms, including eubacteria, fungi, and protozoans. These associations, which in the past have often been viewed as antagonistic, are increasingly seen as mutualistic and may function in a positive manner during bloom development.

High-throughput genotyping arrays provide a standardized resource for plant breeding communities that are useful for a breadth of applications including high-density genetic mapping, genome-wide association studies (GWAS), genomic selection (GS), complex trait dissection, and studying patterns of genomic diversity among cultivars and wild accessions. We have developed the CottonSNP63K, an Illumina Infinium array containing assays for 45,104 putative intraspecific single nucleotide polymorphism (SNP) markers for use within the cultivated cotton species Gossypium hirsutum L. and 17,954 putative interspecific SNP markers for use with crosses of other cotton species with G. hirsutum. The SNPs on the array were developed from 13 different discovery sets that represent a diverse range of G. hirsutum germplasm and five other species: G. barbadense L., G. tomentosum Nuttal × Seemann, G. mustelinum Miers × Watt, G. armourianum Kearny, and G. longicalyx J.B. Hutchinson and Lee. The array was validated with 1,156 samples to generate cluster positions to facilitate automated analysis of 38,822 polymorphic markers. Two high-density genetic maps containing a total of 22,829 SNPs were generated for two F2 mapping populations, one intraspecific and one interspecific, and 3,533 SNP markers were co-occurring in both maps. The produced intraspecific genetic map is the first saturated map that associates into 26 linkage groups corresponding to the number of cotton chromosomes for a cross between two G. hirsutum lines. The linkage maps were shown to have high levels of collinearity to the JGI G. raimondii Ulbrich reference genome sequence. The CottonSNP63K array, cluster file and associated marker sequences constitute a major new resource for the global cotton research community.

Soybean (Glycine max [L.] Merrill) yield losses as a result of plant diseases were estimated by university and government plant pathologists in 29 soybean producing states in the United States and in Ontario, Canada, from 2015 through 2019. In general, the estimated losses that resulted from each of 28 plant diseases or pathogens varied by state or province as well as year. Soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) caused more than twice as much loss as any other disease during the survey period. Seedling diseases (caused by various pathogens), Sclerotinia stem rot (white mold) (caused by Sclerotinia sclerotiorum [Lib.] de Bary), and sudden death syndrome (caused by Fusarium virguliforme O’Donnell & T. Aoki) caused the next greatest yield losses, in descending order. Following SCN, the most damaging diseases in the northern United States and Ontario differed from those in the southern United States. The estimated mean economic loss from all soybean diseases, averaged across the United States and Ontario, Canada was US$45 per acre (US$111 per hectare). The outcome from the current survey will provide pertinent information regarding the important soybean diseases and their overall severity in the soybean crop and help guide future research and Extension efforts on managing soybean diseases.

Abstract Agriculture has been very successful in addressing the food and fiber needs of today's world population. However, there are increasing concerns about the economic, environmental and social costs of this success. Integrated agricultural systems may provide a means to address these concerns while increasing sustainability. This paper reviews the potential for and challenges to integrated agricultural systems, evaluates different agricultural systems in a hierarchical systems framework, and provides definitions and examples for each of the systems. This paper also describes the concept of dynamic-integrated agricultural systems and calls for the development of principles to use in developing and researching integrated agricultural systems. The concepts in this paper have arisen from the first in a series of planned workshops to organize common principles, criteria and indicators across physiographic regions in integrated agricultural systems. Integrated agricultural systems have multiple enterprises that interact in space and time, resulting in a synergistic resource transfer among enterprises. Dynamic-integrated agricultural systems have multiple enterprises managed in a dynamic manner. The key difference between dynamic-integrated agricultural systems and integrated agricultural systems is in management philosophy. In an integrated agricultural system, management decisions, such as type and amount of commodities to produce, are predetermined. In a dynamic-integrated system, decisions are made at the most opportune time using the best available knowledge. We developed a hierarchical scheme for agricultural systems ranging from basic agricultural production systems, which are the simplest system with no resource flow between enterprises, to dynamic-integrated agricultural systems. As agricultural systems move up in the hierarchy, their complexity, amount of management needed, and sustainability also increases. A key aspect of sustainability is the ability to adapt to future challenges. We argue that sustainable systems need built-in flexibility to achieve this goal.

Annual reductions in corn (Zea mays L.) yield caused by diseases were estimated by university Extension-affiliated plant pathologists in 26 corn-producing states in the United States and in Ontario, Canada, from 2016 through 2019. Estimated loss from each disease varied greatly by state or province and year. Gray leaf spot (caused by Cercospora zeae-maydis Tehon & E.Y. Daniels) caused the greatest estimated yield loss in parts of the northern United States and Ontario in all years except 2019, and Fusarium stalk rot (caused by Fusarium spp.) also greatly reduced yield. Tar spot (caused by Phyllachora maydis Maubl.), a relatively new disease in the United States, was estimated to cause substantial yield loss in 2018 and 2019 in several northern states. Gray leaf spot and southern rust (caused by Puccinia polysora Underw.) caused the most estimated yield losses in the southern United States. Unfavorable wet and delayed harvest conditions in 2018 resulted in an estimated 2.5 billion bushels (63.5 million metric tons) of grain contaminated with mycotoxins. The estimated mean economic loss due to reduced yield caused by corn diseases in the United States and Ontario from 2016 to 2019 was US$55.90 per acre (US$138.13 per hectare). Results from this survey provide scientists, corn breeders, government agencies, and educators with data to help inform and prioritize research, policy, and educational efforts in corn pathology and disease management.

Rice yield is most sensitive to salinity stress imposed during the panicle initiation (PI) stage. In this study, we have focused on physiological and transcriptional responses of four rice genotypes exposed to salinity stress during PI. The genotypes selected included a pair of indicas (IR63731 and IR29) and a pair of japonica (Agami and M103) rice subspecies with contrasting salt tolerance. Physiological characterization showed that tolerant genotypes maintained a much lower shoot Na+ concentration relative to sensitive genotypes under salinity stress. Global gene expression analysis revealed a strikingly large number of genes which are induced by salinity stress in sensitive genotypes, IR29 and M103 relative to tolerant lines. We found 19 probe sets to be commonly induced in all four genotypes. We found several salinity modulated, ion homeostasis related genes from our analysis. We also studied the expression of SKC1, a cation transporter reported by others as a major source of variation in salt tolerance in rice. The transcript abundance of SKC1 did not change in response to salinity stress at PI stage in the shoot tissue of all four genotypes. However, we found the transcript abundance of SKC1 to be significantly higher in tolerant japonica Agami relative to sensitive japonica M103 under control and stressed conditions during PI stage.

The influence of environmental factors on germination and emergence of horseweed was examined in growth chamber experiments. Germination was highest (61%) under 24/20 C day/night temperature under light. Horseweed seed germination was observed under both light (13 h photoperiod) and complete darkness (24 h), but germination under continuous darkness was only 0 to 15% compared with 0 to 61% under light. All other experiments were conducted under 24/20 C and 13-h light conditions. Germination was 19 to 36% over a pH range from 4 to 10, with a trend toward higher germination under neutral-to-alkaline conditions. Horseweed germination was > 20% at < 40 mM NaCl concentration and lowest (4%) at 160 mM NaCl. These data suggest that even at high soil salinity conditions, horseweed can germinate. Germination of horseweed decreased from 25% to 2% as osmotic potential increased from 0 (distilled water) to −0.8 MPa, indicating that germination can still occur under moderate water stress conditions. Horseweed seedling emergence was at its maximum on the soil surface, and no seedlings emerged from seeds placed at a depth of 0.5 cm or higher.

Field, laboratory, and greenhouse experiments were conducted to determine the seed production potential and effect of environmental factors on germination, emergence, and survival of texasweed. Texasweed produced an average of 893 seed per plant, and 90% were viable. Seed exhibited dormancy, and prechilling did not release dormancy. Percent germination ranged from 56% for seed subjected to no prechilling to 1% for seed prechilled at 5 C for 140 d. Seed remained viable during extended prechilling conditions, with 80% of seed viable after 140 d of prechilling. Texasweed seed germinated over a range of 20 to 40 C, with optimum germination (54%) occurring with a fluctuating 40/30 C temperature regime. Seed germinated with fluctuating 12-h light/dark and constant dark conditions. Texasweed seed germinated over a broad range of pH, osmotic potential, and salt concentrations. Seed germination was 31 to 62% over a pH range from 4 to 10. Germination of texasweed ranged from 9 to 56% as osmotic potential decreased from − 0.8 MPa to 0 (distilled water). Germination was greater than 52% at less than 40 mM NaCl concentrations and lowest (27%) at 160 mM NaCl. Texasweed seedlings emerged from soil depths as deep as 7.5 cm (7% emergence), but emergence was > 67% for seed placed on the soil surface or at a 1-cm depth. Texasweed seed did not germinate under saturated or flooded conditions, but seed survived flooding and germinated (23 to 25%) after flood removal. Texasweed seedlings 2.5 to 15 cm tall were not affected by emersion in 10-cm-deep flood for up to 14 d. These results suggest that texasweed seed is capable of germinating and surviving in a variety of climatic and edaphic conditions, and that flooding is not a viable management option for emerged plants of texasweed.

BACKGROUND: In recent years, outbreaks of the brown planthopper, Nilaparvata lugens (Stål), have occurred more frequently in China. The objective of this study was to determine the susceptibility of N. lugens to neonicotinoids and other insecticides in major rice production areas in China. RESULTS: Results indicated that substantial variations in the susceptibility to different insecticides existed in N. lugens. Field populations had developed variable resistance levels to neonicotinoids, with a high resistance level to imidacloprid (RR: 135.3-301.3-fold), a medium resistance level to imidaclothiz (RR: 35-41.2-fold), a low resistance level to thiamethoxam (up to 9.9-fold) and no resistance to dinotefuran, nitenpyram and thiacloprid (RR < 3-fold). Further examinations indicated that a field population had developed medium resistance level to fipronil (up to 10.5-fold), and some field populations had evolved a low resistance level to buprofezin. In addition, N. lugens had been able to develop 1424-fold resistance to imidacloprid in the laboratory after the insect was selected with imidacloprid for 26 generations. CONCLUSION: Long-term use of imidacloprid in a wide range of rice-growing areas might be associated with high levels of resistance in N. lugens. Therefore, insecticide resistance management strategies must be developed to prevent further increase in resistance.

Soybean [Glycine max (L.) Merr.] seed composition and yield are a function of genetics (G), environment (E), and management (M) practices, but contribution of each factor to seed composition and yield are not well understood. The goal of this synthesis-analysis was to identify the main effects of G, E, and M factors on seed composition (protein and oil concentration) and yield. The entire dataset (13,574 data points) consisted of 21 studies conducted across the United States (US) between 2002 and 2017 with varying treatments and all reporting seed yield and composition. Environment (E), defined as site-year, was the dominant factor accounting for more than 70% of the variation for both seed composition and yield. Of the crop management factors: i) delayed planting date decreased oil concentration by 0.007 to 0.06 % per delayed week (R2~0.70) and a 0.01 to 0.04 Mg ha-1 decline in seed yield per week, mainly in northern latitudes (40-45oN); ii) crop rotation (corn-soybean) resulted in an overall positive impact for both seed composition and yield (1.60 Mg ha-1 positive yield difference relative to continuous soybean); and iii) other management practices such as no-till, seed treatment, foliar nutrient application, and fungicide showed mixed results. Fertilizer N application in lower quantities (10-50 kg N ha-1) increased both oil and protein concentration, but seed yield was improved with rates above 100 kg N ha-1. At southern latitudes (30-35oN), trends of reduction in oil and increases in protein concentrations with later maturity groups (MG, from 3 to 7) was found. Continuing coordinated research is critical to advance our understanding of G x E x M interactions.

The competitive effects of common cocklebur ( Xanthium pensylvanicum Wallr.) on soybeans [Glycine max (L.) Merr. ‘Lee 68′] were studied on Dundee silty clay loam soil from 1970 to 1972. Full-season competition by common cocklebur at 3,300, 6,600, 13,000, and 26,000 plants/ha reduced the 2-year average soybean seed yields 10, 28, 43, and 52%, respectively. Competition from common cocklebur at 100,000 plants/ha for 4, 6, 8, 10, 12, and 16 weeks after soybean emergence reduced soybean seed yields 10, 36, 40, 60, 80, and 80%, respectively. A reduction in soybean stand occurred after 12 or more weeks competition, and an increase in soybean plant height occurred after 10 or more weeks competition. When common cockleburs were removed during the first 4 weeks after soybean emergence, no further removal was required to obtain maximum soybean yield. Bentazon [3-isopropyl-1 H -2,1,3-benzothiadiazin-(4)3 H -one 2,2-dioxide] at 1.1 to 2.2 kg/ha applied over-the-top of common cockleburs and soybeans was as effective as hand removal in terminating competition provided common cocklebur plants were not flowering.

Journal Article Male Sterility From Gossypium harknessii Get access VESTA G. MEYER VESTA G. MEYER Delta Branch, Mississippi Agricultural and Forestry Experiment StationStoneville, Mississippi 38776 Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Heredity, Volume 66, Issue 1, January 1975, Pages 23–27, https://doi.org/10.1093/oxfordjournals.jhered.a108566 Published: 01 January 1975