Proteomics and Proteogenomics Analysis of Sweetpotato ( Ipomoea batatas) Leaf and Root.

Two complementary protein extraction methodologies coupled with an automated proteomic platform were employed to analyze tissue-specific proteomes and characterize biological and metabolic processes in sweetpotato. A total of 74 255 peptides corresponding to 4321 nonredundant proteins were successfully identified. Data were compared to predicted protein accessions for Ipomoea species and mapped on the sweetpotato transcriptome and haplotype-resolved genome. The two methodologies exhibited differences in the number and class of the unique proteins extracted. Overall, 39 916 peptides mapped to 3143 unique proteins in leaves, and 34 339 peptides mapped to 2928 unique proteins in roots. Primary metabolism and protein translation processes were enriched in leaves, whereas genetic pathways associated with protein folding, transport, sorting, as well as pathways in the primary carbohydrate metabolism were enriched in storage roots. A proteogenomics analysis successfully mapped 90.4% of the total uniquely identified peptides against the sweetpotato transcriptome and genome, predicted 741 new protein-coding genes, and specified 2056 loci where gene annotations can be further improved. The proteogenomics results provide evidence for the translation of new open reading frames (ORFs), alternative ORFs, exon extensions, and intronic ORF sequences. Data are available via ProteomeXchange with identifier PXD012999.

Effects of Subsurface Banding and Broadcast of Poultry Litter and Cover Crop on Soil Microbial Populations.

Agronomic management is aimed at managing the crop environment to maximize crop yield, but soil biology is often ignored. This study aimed to compare the application of poultry litter via broadcast and subsurface banding versus standard inorganic fertilizer to cotton ( L.) and their effects on soil bacterial populations and fecal indicator bacteria. The study comprised a randomized complete block design, with fertilizer and time of application as treatment effects and cover crop as a main effect. Soil cores were collected and analyzed from 2008 to 2014. Fecal indicator bacteria were at detection limits for all treatments, where the integron 1 gene was significantly elevated in litter plots. There were few differences between litter application approaches, but both significantly increased key biogeochemical genes over control plots, whereas a cover crop only increased soil moisture and urease C. Data suggested a positive residual effect of litter application with 16S, phosphatase A, and urease C genes elevated over controls, but similar to standard fertilizer plots. High-throughput 16S ribosomal RNA analysis suggested increased diversity and enrichment indices in litter and standard fertilizer over untreated control plots. Litter and standard fertilizer effects persisted 4 and 2 yr after application, respectively, as evidenced by residual library community structures. This study demonstrated the positive effects of litter application on the soil bacterial community when compared with untreated control plots. Some differences between standard fertilization and litter practices were noted and suggest that there is a positive residual effect on soil microbial populations associated with both practices.

Drought, Low Nitrogen Stress, and Ultraviolet-B Radiation Effects on Growth, Development, and Physiology of Sweetpotato Cultivars during Early Season.

Drought, ultraviolet-B (UV-B), and nitrogen stress are significant constraints for sweetpotato productivity. Their impact on plant growth and development can be acute, resulting in low productivity. Identifying phenotypes that govern stress tolerance in sweetpotatoes is highly desirable to develop elite cultivars with better yield. Ten sweetpotato cultivars were grown under nonstress (100% replacement of evapotranspiration (ET)), drought-stress (50% replacement of ET), UV-B (10 kJ), and low-nitrogen (20% LN) conditions. Various shoot and root morphological, physiological, and gas-exchange traits were measured at the early stage of the crop growth to assess its performance and association with the storage root number. All three stress factors caused significant changes in the physiological and root- and shoot-related traits. Drought stress reduced most shoot developmental traits (29%) to maintain root growth. UV-B stress increased the accumulation of plant pigments and decreased the photosynthetic rate. Low-nitrogen treatment decreased shoot growth (11%) and increased the root traits (18%). The highly stable and productive cultivars under all four treatments were identified using multitrait stability index analysis and weighted average of absolute scores (WAASB) analyses. Further, based on the total stress response indices, 'Evangeline', 'O'Henry', and 'Beauregard B-14' were identified as vigorous under drought; 'Evangeline', 'Orleans', and 'Covington' under UV-B; and 'Bonita', 'Orleans', and 'Beauregard B-14' cultivars showed greater tolerance to low nitrogen. The cultivars 'Vardaman' and 'NC05-198' recorded a low tolerance index across stress treatments. This information could help determine which plant phenotypes are desirable under stress treatment for better productivity. The cultivars identified as tolerant, sensitive, and well-adapted within and across stress treatments can be used as source materials for abiotic stress tolerance breeding programs.

Sweetpotato cultivars responses to interactive effects of warming, drought, and elevated carbon dioxide.

Plants are sensitive to changes projected in climates, such as elevated carbon dioxide (eCO2), high temperature (T), and drought stress (DS), which affect crop growth, development, and yield. These stresses, either alone or in combination, affect all aspects of sweetpotato plant growth and development, including storage root development and yield. We tested three sweetpotato cultivars (Beauregard, Hatteras, and LA1188) responses to eight treatments (Control, DS, T, eCO2, DS + T, T + eCO2, DS + eCO2, DS + T + eCO2). All treatments were imposed 36 days after transplanting (DAP) and continued for 47 days. Treatments substantially affected gas exchange, photosynthetic pigments, growth, and storage root components. Cultivars differed considerably for many of the measured parameters. The most significant negative impact of DS was recorded for the shoot and root weights. The combination of DS + T had a significant negative effect on storage root parameters. eCO2 alleviated some of the damaging effects of DS and high T in sweetpotato. For instance, eCO2 alone or combined with DS increased the storage root weights by 22% or 42% across all three cultivars, respectively. Based on the stress response index, cultivar "Hatteras" was most tolerant to individual and interactive stresses, and "LA 1188" was sensitive. Our findings suggest that eCO2 negates the negative impact of T or DS on the growth and yield of sweetpotato. We identified a set of individual and interactive stress-tolerant traits that can help select stress cultivars or breed new lines for future environments.