Environmental Factors Influencing Stem Rot Development in Peanut: Predictors and Action Thresholds for Disease Management

Peanuts grown in tropical, subtropical, and temperate regions are susceptible to stem rot, which is a soilborne disease caused by Athelia rolfsii. Due to the lack of reliable environmental-based scheduling recommendations, stem rot control relies heavily on fungicides that are applied at predetermined intervals. We conducted inoculated field experiments for six site-years in North Florida to examine the relationship between germination of A. rolfsii sclerotia: the inoculum, stem rot symptom development in the peanut crop, and environmental factors such as soil temperature (ST), soil moisture, relative humidity (RH), precipitation, evapotranspiration, and solar radiation. Window-pane analysis with hourly and daily environmental data for 5- to 28-day periods before each disease assessment were evaluated to select model predictors using correlation analysis, regularized regression, and exhaustive feature selection. Our results indicated that within-canopy ST (at 0.05 m belowground) and RH (at 0.15 m aboveground) were the most important environmental variables that influenced the progress of mycelial activity in susceptible peanut crops. Decision tree analysis resulted in an easy-to-interpret one-variable model (adjusted R2 = 0.51, Akaike information criterion [AIC] = 324, root average square error [RASE] = 14.21) or two-variable model (adjusted R2 = 0.61, AIC = 306, RASE = 10.95) that provided an action threshold for various disease scenarios based on number of hours of canopy RH above 90% and ST between 25 and 35°C in a 14-day window. Coupling an existing preseason risk index for stem rot, such as Peanut Rx, with the environmentally based predictors identified in this study would be a logical next step to optimize stem rot management. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Peanut Yield Loss in the Presence of Defoliation Caused by Late or Early Leaf Spot

Late and early leaf spot, respectively caused by Nothopassalora personata and Passalora arachidicola, are damaging diseases of peanut (Arachis hypogaea) capable of defoliating canopies and reducing yield. Although one of these diseases may be more predominant in a given area, both are important on a global scale. To assist informed management decisions and quantify relationships between end-of-season defoliation and yield loss, meta-analyses were conducted over 140 datasets meeting established criteria. Slopes of proportion yield loss with increasing defoliation were estimated separately for Virginia and runner market type cultivars. Yield loss for Virginia types was described by an exponential function over the range of defoliation levels, with a loss increase of 1.2 to 2.2% relative to current loss levels per additional percent defoliation. Results for runner market type cultivars showed yield loss to linearly increase 2.2 to 2.8% per 10% increase in defoliation for levels up to approximately 95% defoliation, after which the rate of yield loss was exponential. Defoliation thresholds to prevent economic yield loss for Virginia and runner types were estimated at 40 and 50%, respectively. Although numerous factors remain important in mitigating overall yield losses, the integration of these findings should aid recommendations about digging under varying defoliation intensities and peanut maturities to assist in minimizing yield losses.

Refining a major QTL controlling spotted wilt disease resistance in cultivated peanut (Arachis hypogaea L.) and evaluating its contribution to the resistance variations in peanut germplasm

BACKGROUND

Spotted wilt, caused by tomato spotted wilt virus (TSWV), has been one of major diseases in cultivated peanut grown in the southeastern United States (US) since 1990. Previously a major quantitative trait locus (QTL) controlling spotted wilt disease resistance was mapped to an interval of 2.55 cM genetic distance corresponding to a physical distance of 14.4 Mb on chromosome A01 of peanut by using a segregating F₂ population. The current study focuses on refining this major QTL region and evaluating its contributions in the US peanut mini-core germplasm.

RESULTS

Two simple sequence repeat (SSR) markers associated with the major QTL were used to genotype F₅ individuals, and 25 heterozygous individuals were selected and developed into an F₆ segregating population. Based on visual evaluation in the field, a total of 194 susceptible F₆ individuals were selected and planted into F₇ generation for phenotyping. Nine SSR markers were used to genotype the 194 F₆ individuals, and QTL analysis revealed that a confidence interval of 15.2 Mb region had the QTL with 22.8% phenotypic variation explained (PVE). This QTL interval was further genotyped using the Amplicon-seq method. A total of 81 non-redundant single nucleotide polymorphism (SNP) and eight InDel markers were detected. No recombinant was detected among the F₆ individuals. Two InDel markers were integrated into the linkage group and helped to refine the confidence interval of this QTL into a 0.8 Mb region. To test the QTL contributes to the resistance variance in US peanut mini-core germplasm, two flanking SSR markers were used to genotype 107 mini-core germplasm accessions. No statistically significant association was observed between the genotype at the QTL region and spotted wilt resistance in the mini-core germplasm, which indicated that the resistance allelic region at this QTL didn't contribute to the resistance variance in the US peanut mini-core germplasm, thus was a unique resistance source.

CONCLUSION

A major QTL related to spotted wilt disease resistance in peanut was refined to a 0.8 Mb region on A01 chromosome, which didn't relate to spotted wilt disease resistance in the US peanut mini-core germplasm and might be a unique genetic source.

Target enrichment sequencing in cultivated peanut (Arachis hypogaea L.) using probes designed from transcript sequences

Enabled by the next generation sequencing, target enrichment sequencing (TES) is a powerful method to enrich genomic regions of interest and to identify sequence variations. The objective of this study was to explore the feasibility of probe design from transcript sequences for TES application in calling sequence variants in peanut, an important allotetraploid crop with a large genome size. In this study, we applied an in-solution hybridization method to enrich DNA sequences of seven peanut genotypes. Our results showed that it is feasible to apply TES with probes designed from transcript sequences in polyploid peanut. Using a set of 31,123 probes, a total of 5131 and 7521 genes were targeted in peanut A and B genomes, respectively. For each genotype used in this study, the probe target capture regions were efficiently covered with high depth. The average on-target rate of sequencing reads was 42.47%, with a significant amount of off-target reads coming from genomic regions homologous to target regions. In this study, when given predefined genomic regions of interest and the same amount of sequencing data, TES provided the highest coverage of target regions when compared to whole genome sequencing, RNA sequencing, and genotyping by sequencing. Single nucleotide polymorphism (SNP) calling and subsequent validation revealed a high validation rate (85.71%) of homozygous SNPs, providing valuable markers for peanut genotyping. This study demonstrated the success of applying TES for SNP identification in peanut, which shall provide valuable suggestions for TES application in other non-model species without a genome reference available.

Identification of major QTLs underlying tomato spotted wilt virus resistance in peanut cultivar Florida-EP(TM) '113'

BACKGROUND

Spotted wilt caused by tomato spotted wilt virus (TSWV) is one of the major peanut (Arachis hypogaea L.) diseases in the southeastern United States. Occurrence, severity, and symptoms of spotted wilt disease are highly variable from season to season, making it difficult to efficiently evaluate breeding populations for resistance. Molecular markers linked to spotted wilt resistance could overcome this problem and allow selection of resistant lines regardless of environmental conditions. Florida-EP(TM) '113' is a spotted wilt resistant cultivar with a significantly lower infection frequency. However, the genetic basis is still unknown. The objective of this study is to map the major quantitative trait loci (QTLs) linked to spotted wilt resistance in Florida-EP(TM) '113'.

RESULTS

Among 2,431 SSR markers located across the whole peanut genome screened between the two parental lines, 329 were polymorphic. Those polymorphic markers were used to further genotype a representative set of individuals in a segregating population. Only polymorphic markers on chromosome A01 showed co-segregation between genotype and phenotype. Genotyping by sequencing (GBS) of the representative set of individuals in the segregating population also depicted a strong association between several SNPs on chromosome A01 and the trait, indicating a major QTL on chromosome A01. Therefore marker density was enriched on the A01 chromosome. A linkage map with 23 makers on chromosome A01 was constructed, showing collinearity with the physical map. Combined with phenotypic data, a major QTL flanked by marker AHGS4584 and GM672 was identified on chromosome A01, with up to 22.7 % PVE and 9.0 LOD value.

CONCLUSION

A major QTL controlling the spotted wilt resistance in Florida-EP(TM) '113' was identified. The resistance is most likely contributed by PI 576638, a hirsuta botanical-type line, introduced from Mexico with spotted wilt resistance. The flanking markers of this QTL can be used for further fine mapping and marker assisted selection in peanut breeding programs.

Molecular marker development from transcript sequences and germplasm evaluation for cultivated peanut (Arachis hypogaea L.)

Molecular markers are important tools for genotyping in genetic studies and molecular breeding. The SSR and SNP are two commonly used marker systems developed from genomic or transcript sequences. The objectives of this study were to: (1) assemble and annotate the publicly available ESTs in Arachis and the in-house short reads, (2) develop and validate SSR and SNP markers, and (3) investigate the genetic diversity and population structure of the peanut breeding lines and the U.S. peanut mini core collection using developed SSR markers. An NCBI EST dataset with 252,951 sequences and an in-house 454 RNAseq dataset with 288,701 sequences were assembled separately after trimming. Transcript sequence comparison and phylogenetic analysis suggested that peanut is closer to cowpea and scarlet bean than to soybean, common bean and Medicago. From these two datasets, 6455 novel SSRs and 11,902 SNPs were identified. Of the discovered SSRs, 380 representing various SSR types were selected for PCR validation. The amplification rate was 89.2 %. Twenty-two (6.5 %) SSRs were polymorphic between at least one pair of four genotypes. Sanger sequencing of PCR products targeting 110 SNPs revealed 13 true SNPs between tetraploid genotypes and 193 homoeologous SNPs within genotypes. Eight out of the 22 polymorphic SSR markers were selected to evaluate the genetic diversity of Florida peanut breeding lines and the U.S. peanut mini core collection. This marker set demonstrated high discrimination power by displaying an average polymorphism information content value of 0.783, a combined probability of identity of 10(-11), and a combined power of exclusion of 0.99991. The structure analysis revealed four sub-populations among the peanut accessions and lines evaluated. The results of this study enriched the peanut genomic resources, provided over 6000 novel SSR markers and the credentials for true peanut SNP marker development, and demonstrated the power of newly developed SSR markers in genotyping peanut germplasm and breeding materials.

Calcium dependent protein kinase (CDPK) expression during fruit development in cultivated peanut (Arachis hypogaea) under Ca²⁺-sufficient and -deficient growth regimens

Adequate soil calcium (Ca²⁺) levels are crucial for sustained reproductive development of peanut (Arachis hypogaea). A role for calcium dependent protein kinase was evaluated during peanut fruit development under sufficient and deficient soil Ca²⁺ conditions. Quantitative RT-PCR and protein gel blot analyses confirmed transcriptional upregulation of CDPK in seeds developing under inadequate soil Ca²⁺ regimen, as well as spatiotemporal regulation of CDPK expression during early mitotic growth and later during the storage phase of seed development. However, a consistent basal level of CDPK was present during similar developmental stages of pod tissue, irrespective of the soil Ca²⁺ status. Immunolocalization data showed CDPK decoration primarily in the outer most cell layers of the pericarp and around vascular bundles linked by lateral connections in developing pods, as well as the single vascular trace supplying nutrients to the developing seed. Finally, carbohydrate analyses and qRT-PCR data are provided for peanut genes encoding enzymes involved in sucrose cleavage (orthologs of Vicia faba, VfCWI1 and VfCWI2) and utilization (AhSuSy and AhSpS), and oleosin gene transcripts (AhOleo17.8 and AhOleo18.5) validating a role for CDPK in the establishment and maintenance of sink strength, and subsequent onset of storage product biosynthetic phase during seed maturation.

Interactive Effects of Planting Date and Cultivar on Tomato Spotted Wilt of Peanut

Field experiments were conducted at Gainesville and Marianna, FL in 2004 and 2005 in which severity of spotted wilt, caused by Tomato spotted wilt virus, and pod yield were compared in six peanut (Arachis hypogaea) cultivars. The six cultivars included the moderately field resistant cultivars ANorden, C-99R, and Georgia Green; the highly field resistant cultivars AP-3 and DP-1; and the susceptible cultivar SunOleic 97R. There were four trials at each location, with four planting dates that ranged from late March to early June. Tomato spotted wilt severity in moderately resistant and susceptible cultivars was lower at Gainesville than at Marianna in both years in moderately resistant and susceptible cultivars. Trends in incidence for the two locations were less evident for AP-3 and DP-1. At Gainesville, there were few differences in tomato spotted wilt severity, and severity ratings were similar for Georgia Green and SunOleic 97R in two of four trials in 2004 and across all trials in 2005. At Marianna, severity ratings were lower for Georgia Green than for SunOleic 97R in six of the eight trials, and severity of tomato spotted wilt was lower for AP-3, C-99R, and DP-1 than for Georgia Green in all eight trials. In 2004, there was a trend toward decreasing severity ratings for Georgia Green and SunOleic 97R with later planting dates, but not for AP-3 or DP-1 at Marianna. Split-plot field experiments were also conducted at Tifton, GA in 2005 through 2007 in which incidence of tomato spotted wilt and pod yield were compared for peanut cultivars AP-3 and Georgia Green across planting dates ranging from late April through late May. Incidence of tomato spotted wilt was lower for AP-3 than for Georgia Green within each planting date of all years, and planting date effects were smaller in AP-3, if observed at all, than in Georgia Green. In most planting dates of all three trials, yields were higher for AP-3 than for Georgia Green. The relationships between yield and planting date were not consistent. These results indicate that the level of field resistance in AP-3 and DP-1 cultivars is sufficient to allow planting in late April without greatly increasing the risk of losses to tomato spotted wilt.

Response of New Field-Resistant Peanut Cultivars to Twin-Row Pattern or In-Furrow Applications of Phorate for Management of Spotted Wilt

Field experiments were conducted at Marianna, FL in 2006 and Tifton, GA in 2006 and 2007 to compare new peanut (Arachis hypogaea) cultivars to the moderately resistant cv. Georgia Green and the highly resistant cv. AP-3 for field resistance to Tomato spotted wilt virus (TSWV), genus Tospovirus, and to determine the effects of in-furrow application of phorate insecticide and use of twin-row versus single-row patterns on incidence of spotted wilt in these cultivars. Cvs. Georgia Green, AP-3, Georgia-03L, Georgia-01R, Florida-07, McCloud, and York were evaluated in all five experiments, and Tifguard was added in experiments at Tifton. All cultivars except McCloud had lower incidence of spotted wilt than Georgia Green in all experiments. McCloud was intermediate in resistance to TSWV and had lower incidence of spotted wilt than Georgia Green in four of five experiments. Use of the twin-row pattern also reduced incidence of spotted wilt in McCloud in both years. On Georgia Green, phorate reduced incidence of spotted wilt in 2007 and twin-row pattern reduced incidence in both years. Phorate had no effect on spotted wilt in AP-3, Georgia-03L, McCloud, Georgia-01R, or Tifguard in either year. Twin-row pattern reduced either final incidence or area under the disease progress curve in all cultivars in at least 1 year of the study. All of these new cultivars should reduce the risk of losses to spotted wilt compared with Georgia Green. In highly resistant cultivars, especially AP-3, York, and Tifguard, use of phorate insecticide or twin-row pattern may not be necessary, and may not provide noticeable benefit in reduction of spotted wilt or increased yield.

Yield Loss Caused by Bacterial Streak in Winter Wheat

The relationship between severity of bacterial streak and yield in winter wheat was studied in field plots and using a single-tiller method. Regression analysis from single-tiller studies showed that the grain weight per spike decreased as bacterial streak severity increased in cvs. Florida 304 and Savannah. The number of kernels per spike decreased as bacterial streak severity increased in Savannah but not in Florida 304. There was no difference in slope of the regression line between different years, locations, or cultivars for grain weight per spike. However, grain weight per spike at 0% bacterial streak (intercept) was different for different years, locations, and cultivars. The average reduction in grain weight per spike was 0.012 g for every 1% increase in bacterial streak severity. Using this relationship for cv. Savannah, average bacterial streak severity of 10% would result in about a 9% reduction in the grain weight per spike. In Florida 304, bacterial streak severity of 10% would result in about a 7% reduction in the grain weight per spike. During 1993-94, the largest difference in bacterial streak severity between inoculated and noninoculated plots was 4% in cv. Pioneer 2548, and the smallest difference was less than 1% in cvs. Terral 101 and Florida 304. There were no yield differences between inoculated and noninoculated treatments for any genotype. In field plot studies at two locations during 1989-90, bacterial streak severity did not differ between inoculated and noninoculated plots in Alexandria, Louisiana; but in Winnsboro, Louisiana, bacterial streak severity was 18 to 40% in inoculated plots and less than 5% in noninoculated plots. Differences in yield between inoculated and noninoculated plots ranged from 1,370 kg/ha (24% loss) to -121 kg/ha in Winns-boro. During the three seasons in which these studies were conducted, bacterial streak severity averaged about 10% or less in susceptible cultivars in all experiments except one. Based on the relationships derived from single-tiller studies, this suggests that yield loss is likely to be low most years. As indicated by the experiment in Winnsboro, however, more severe yield reductions could occur in a susceptible cultivar if weather conditions are favorable for disease development.