Deciphering genetic factors contributing to enhanced resistance against Cercospora leaf blight in soybean (Glycine max L.) using GWAS analysis.

Cercospora leaf blight (CLB), caused by Cercospora cf. flagellaris, C. kikuchii, and C. cf. sigesbeckiae, is a significant soybean [Glycine max (L.) Merr.] disease in regions with hot and humid conditions causing yield loss in the United States and Canada. There is limited information regarding resistant soybean cultivars, and there have been marginal efforts to identify the genomic regions underlying resistance to CLB. A Genome-Wide Association Study was conducted using a diverse panel of 460 soybean accessions from maturity groups III to VII to identify the genomic regions associated to the CLB disease. These accessions were evaluated for CLB in different regions of the southeastern United States over 3 years. In total, the study identified 99 Single Nucleotide Polymorphism (SNPs) associated with the disease severity and 85 SNPs associated with disease incidence. Across multiple environments, 47 disease severity SNPs and 23 incidence SNPs were common. Candidate genes within 10 kb of these SNPs were involved in biotic and abiotic stress pathways. This information will contribute to the development of resistant soybean germplasm. Further research is warranted to study the effect of pyramiding desirable genomic regions and investigate the role of identified genes in soybean CLB resistance.

Genome resources for three modern cotton lines guide future breeding efforts.

Cotton (Gossypium hirsutum L.) is the key renewable fibre crop worldwide, yet its yield and fibre quality show high variability due to genotype-specific traits and complex interactions among cultivars, management practices and environmental factors. Modern breeding practices may limit future yield gains due to a narrow founding gene pool. Precision breeding and biotechnological approaches offer potential solutions, contingent on accurate cultivar-specific data. Here we address this need by generating high-quality reference genomes for three modern cotton cultivars ('UGA230', 'UA48' and 'CSX8308') and updating the 'TM-1' cotton genetic standard reference. Despite hypothesized genetic uniformity, considerable sequence and structural variation was observed among the four genomes, which overlap with ancient and ongoing genomic introgressions from 'Pima' cotton, gene regulatory mechanisms and phenotypic trait divergence. Differentially expressed genes across fibre development correlate with fibre production, potentially contributing to the distinctive fibre quality traits observed in modern cotton cultivars. These genomes and comparative analyses provide a valuable foundation for future genetic endeavours to enhance global cotton yield and sustainability.

Characterization of QoI-Fungicide Resistance in Cercospora Isolates Associated with Cercospora Leaf Blight of Soybean from the Southern United States.

Cercospora leaf blight (CLB) of soybean, caused by Cercospora cf. flagellaris, C. kikuchii, and C. cf. sigesbeckiae, is an economically important disease in the southern United States. Cultivar resistance to CLB is inconsistent; therefore, fungicides in the quinone outside inhibitor (QoI) class have been relied on to manage the disease. Approximately 620 isolates from plants exhibiting CLB were collected between 2018 and 2021 from 19 locations in eight southern states. A novel polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay based on two genes, calmodulin and histone h3, was developed to differentiate between the dominant species of Cercospora, C. cf. flagellaris, and C. cf. sigesbeckiae. A multilocus phylogenetic analysis of actin, calmodulin, histone h3, ITS rDNA, and transcription elongation factor 1-α was used to confirm PCR-RFLP results and identify remaining isolates. Approximately 80% of the isolates collected were identified as C. cf. flagellaris, while 15% classified as C. cf. sigesbeckiae, 2% as C. kikuchii, and 3% as previously unreported Cercospora species associated with CLB in the United States. PCR-RFLP of cytochrome b (cytb) identified QoI-resistance conferred by the G143A substitution. Approximately 64 to 83% of isolates were determined to be QoI-resistant, and all contained the G143A substitution. Results of discriminatory dose assays using azoxystrobin (1 ppm) were 100% consistent with PCR-RFLP results. To our knowledge, this constitutes the first report of QoI resistance in CLB pathogen populations from Alabama, Arkansas, Kentucky, Mississippi, Missouri, Tennessee, and Texas. In areas where high frequencies of resistance have been identified, QoI fungicides should be avoided, and fungicide products with alternative modes-of-action should be utilized in the absence of CLB-resistant soybean cultivars.

Deciphering the genetic architecture of resistance to Corynespora cassiicola in soybean (Glycine max L.) by integrating genome-wide association mapping and RNA-Seq analysis.

Target spot caused by Corynespora cassiicola is a problematic disease in tropical and subtropical soybean (Glycine max) growing regions. Although resistant soybean genotypes have been identified, the genetic mechanisms underlying target spot resistance has not yet been studied. To address this knowledge gap, this is the first genome-wide association study (GWAS) conducted using the SoySNP50K array on a panel of 246 soybean accessions, aiming to unravel the genetic architecture of resistance. The results revealed significant associations of 14 and 33 loci with resistance to LIM01 and SSTA C. cassiicola isolates, respectively, with six loci demonstrating consistent associations across both isolates. To identify potential candidate genes within GWAS-identified loci, dynamic transcriptome profiling was conducted through RNA-Seq analysis. The analysis involved comparing gene expression patterns between resistant and susceptible genotypes, utilizing leaf tissue collected at different time points after inoculation. Integrating results of GWAS and RNA-Seq analyses identified 238 differentially expressed genes within a 200 kb region encompassing significant quantitative trait loci (QTLs) for disease severity ratings. These genes were involved in defense response to pathogen, innate immune response, chitinase activity, histone H3-K9 methylation, salicylic acid mediated signaling pathway, kinase activity, and biosynthesis of flavonoid, jasmonic acid, phenylpropanoid, and wax. In addition, when combining results from this study with previous GWAS research, 11 colocalized regions associated with disease resistance were identified for biotic and abiotic stress. This finding provides valuable insight into the genetic resources that can be harnessed for future breeding programs aiming to enhance soybean resistance against target spot and other diseases simultaneously.

Comparative Transcriptome Profiling Unfolds a Complex Defense and Secondary Metabolite Networks Imparting Corynespora cassiicola Resistance in Soybean (Glycine max (L.) Merrill).

Target spot is caused by Corynespora cassiicola, which heavily affects soybean production areas that are hot and humid. Resistant soybean genotypes have been identified; however, the molecular mechanisms governing resistance to infection are unknown. Comparative transcriptomic profiling using two known resistant genotypes and two susceptible genotypes was performed under infected and control conditions to understand the regulatory network operating between soybean and C. cassiicola. RNA-Seq analysis identified a total of 2571 differentially expressed genes (DEGs) which were shared by all four genotypes. These DEGs are related to secondary metabolites, immune response, defense response, phenylpropanoid, and flavonoid/isoflavonoid pathways in all four genotypes after C. cassiicola infection. In the two resistant genotypes, additional upregulated DEGs were identified affiliated with the defense network: flavonoids, jasmonic acid, salicylic acid, and brassinosteroids. Further analysis led to the identification of differentially expressed transcription factors, immune receptors, and defense genes with a leucine-rich repeat domain, dirigent proteins, and cysteine (C)-rich receptor-like kinases. These results will provide insight into molecular mechanisms of soybean resistance to C. cassiicola infection and valuable resources to potentially pyramid quantitative resistance loci for improving soybean germplasm.

Characterizing the vector competence of Aphis gossypii, Myzus persicae and Aphis craccivora (Hemiptera: Aphididae) to transmit cotton leafroll dwarf virus to cotton in the United States.

Cotton leafroll dwarf virus (CLRDV) is a yield-limiting, aphid-transmitted virus that was identified in cotton, Gossypium hirsutum L., in the United States of America in 2017. CLRDV is currently classified in the genus Polerovirus, family Solemoviridae. Although 8 species of aphids (Hemiptera: Aphididae) are reported to infest cotton, Aphis gossypii Glover is the only known vector of CLRDV to this crop. Aphis gossypii transmits CLRDV in a persistent and nonpropagative manner, but acquisition and retention times have only been partially characterized in Brazil. The main objectives of this study were to characterize the acquisition access period, the inoculation access period, and retention times for a U.S. strain of CLRDV and A. gossypii population. A sub-objective was to test the vector competence of Myzus persicae Sulzer and Aphis craccivora Koch. In our study, A. gossypii apterous and alate morphs were able to acquire CLRDV in 30 min and 24 h, inoculate CLRDV in 45 and 15 min, and retain CLRDV for 15 and 23 days, respectively. Neither M. persicae nor A. craccivora acquired or transmitted CLRDV to cotton.

QTL mapping and identification of candidate genes linked to red rot resistance in sugarcane.

Sugarcane (Saccharum species hybrid) is one of the most important commercial crops cultivated worldwide for products like white sugar, bagasse, ethanol, etc. Red rot is a major sugarcane disease caused by a hemi-biotrophic fungus, Colletotrichum falcatum Went., which can potentially cause a reduction in yield up to 100%. Breeding for red rot-resistant sugarcane varieties has become cumbersome due to its complex genome and frequent generation of new pathotypes of red rot fungus. In the present study, a genetic linkage map was developed using a selfed population of a popular sugarcane variety CoS 96268. A QTL linked to red rot resistance (qREDROT) was identified, which explained 26% of the total phenotypic variation for the trait. A genotype-phenotype network analysis performed to account for epistatic interactions, identified the key markers involved in red rot resistance. The differential expression of the genes located in the genomic region between the two flanking markers of the qREDROT as well as in the vicinity of the markers identified through the genotype-phenotype network analysis in a set of contrasting genotypes for red rot infection further confirmed the mapping results. Further, the expression analysis revealed that the plant defense-related gene coding 26S protease regulatory subunit is strongly associated with the red rot resistance. The findings can help in the screening of disease resistant genotypes for developing red rot-resistant varieties of sugarcane. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-023-03481-7.

First Report of Tomato Yellow Leaf Curl Virus Infecting Upland Cotton (Gossypium hirsutum) in Alabama, USA.

Cotton (Gossypium hirsutum L.) is used as a non-host of tomato yellow leaf curl virus (TYLCV) (family Geminiviridae, genus Begomovirus) in many studies (Ghanim and Czosnek 2000; Legarrea et al. 2015; Zeidan and Czosnek 1991), but only one reports methods used to determine host-status (Sinisterra et al. 2005), and there is one contradictory report from China stating cotton is a host of TYLCV (Li et al. 2014). In October 2018, cotton was screened for the presence of begomoviruses in Elmore, Escambia and Macon Counties, AL, where infestations of its whitefly vector (Bemisia tabaci Genn.) occurred in August. DNA was extracted from fully expanded leaves from the upper 1/3 of the canopy using a DNeasy® Plant Mini Kit (QIAGEN, Hilden, Germany) and amplified with primers V324/C889 targeting a 575 bp coat protein fragment of begomoviruses (Brown et al. 2001). Five out of 200 cotton samples tested positive, and sequences recovered from three samples revealed 98-99% identity to TYLCV isolates in NCBI (Accession Nos. MT947801-03); sequences from the other two samples were of low quality and inconclusive. These samples were not available for additional tests, therefore, we proceeded to confirm host status using a monopartite clone of TYLCV-Israel (Reyes et al. 2013) reported in the US (Polston et al. 1999). All experiments were conducted in growth chambers with 16:8 light:dark cycle at 25.0℃ and 50% RH. Cotton seedlings (DeltaPine 1646 B2XF) at the 2-3 true leaf stage and tomatoes (Solanum lycopersicum L., var. 'Florida Lanai') at the 4 true leaf stage were agroinoculated at the stem tissue between the apical meristem and the first node (Reyes et al. 2013). Tomato served as a positive control; tomato and cotton mock inoculated with an empty vector were negative controls. A hole-punch was used to collect 4 leaf discs along midveins of the three, uppermost fully expanded leaves. DNA was extracted 28 days after inoculation as described above. A 390 bp segment of the intergenic region of TYLCV-A was amplified using primers PTYIRc287/PTYIRv21 (Nakhla et al., 1993). PCR results from agroinoculated plants confirmed (2/18) cotton plants, (5/5) tomatoes and (0/10) mock inoculated controls were infected with TYLCV. Whitefly transmission to cotton was confirmed using a leaf-disc bioassay for rapid testing (Czosnek et al. 1993). Bemisia tabaci MEAM-1 reared on eggplant (non-host of TYLCV) were placed on agroinoculated TYLCV-infected tomato/span> plants for a 96-h acquisition access period. Cohorts of 10 viruliferous B. tabaci were aspirated into 30mL cups each containing a 2.5cm healthy cotton leaf disc set in plant agar. After a 48-h inoculation access period, adults and their eggs were removed from the leaf discs. Leaf discs were held another 96-h before they were tested for TYLCV using the methods described above. TYLCV-infection was confirmed in (9/20) cotton leaf discs, demonstrating the viral load delivered by whiteflies was high enough to initiate local infection in cotton. No obvious begomovirus symptoms were observed on cotton plants in the field or laboratory. Field collection of samples was prompted by symptoms attributed to cotton leafroll dwarf virus (Avelar et al. 2017). TYLCV infection of cotton does not appear to be of economic importance. Additional information is needed to determine the frequency of infection in the field, specificity of TYLCV isolate x cotton genotype interactions leading to successful infection, and underlying causes of conflicting host-status reports in previously published studies.

Correction to: Improved lint yield under field conditions in cotton over-expressing transcription factors regulating fibre initiation.

Due to an unfortunate misunderstanding, an extra middle initial erroneously appeared in the original publication and the full name of the first author should read Shi Ming Liu.

Improved lint yield under field conditions in cotton over-expressing transcription factors regulating fibre initiation.

Only a few transcription factors (TFs) regulating which cells of the ovule epidermis differentiate into lint fibres have been identified in cotton (Gossypium hirsutum L.). In this study, the effect on lint yield and fibre quality of over-expressing three TFs in cotton, GhHD-1, GhMYB25 and GhMYB25Like, and their double and triple combinations, were evaluated in field experiments over two seasons. The expression of single or stacked TFs were all driven either by an ovule-specific promoter, FBP 7, or a constitutive promoter, Stunt 7, in a Coker 315 background. TF type, either singly or in combination, was found to be the most significant factor affecting lint yield. Among 64 transgenic lines tested, seven were higher yielding than null segregant lines in one or both seasons and were all from the sets with single and double over-expressed TF combinations. A reduced yield was associated with the set of triple combinations. The two most stable high yielding lines across the seasons recorded 12-22% higher yields than the nulls, although were not competitive to locally adapted commercial controls. Over-expression of TFs singly or in combination did not significantly alter fibre length and strength, but sometimes increased fibre micronaire. There were positive relationships between lint yield and lint percentage and lint yield and fibre density amongst the transgenic lines. Our preliminary results suggest that manipulating TF expression, either singly or in pairs, can increase the density of fibres initiated on developing seeds and fibre yields under field conditions while maintaining overall fibre quality.