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Finger millet is a key food security crop widely grown in eastern Africa, India and Nepal. Long considered a 'poor man's crop', finger millet has regained attention over the past decade for its climate resilience and the nutritional qualities of its grain. To bring finger millet breeding into the 21st century, here we present the assembly and annotation of a chromosome-scale reference genome. We show that this ~1.3 million years old allotetraploid has a high level of homoeologous gene retention and lacks subgenome dominance. Population structure is mainly driven by the differential presence of large wild segments in the pericentromeric regions of several chromosomes. Trait mapping, followed by variant analysis of gene candidates, reveals that loss of purple coloration of anthers and stigma is associated with loss-of-function mutations in the finger millet orthologs of the maize R1/B1 and Arabidopsis GL3/EGL3 anthocyanin regulatory genes. Proanthocyanidin production in seed is not affected by these gene knockouts.

Blackleg, caused by Leptosphaeria maculans, is a major oilseed rape disease present in many traditional growing regions worldwide and is also becoming increasingly important in Tunisia. Cultivation of oilseed rape varieties harbouring major blackleg resistance genes (R‐genes) in an integrated approach represents the most effective means of controlling this fungal threat; knowledge of the pathogen population structure is a prerequisite for its efficient use. Leptosphaeria spp. isolates (145) were collected and characterized during 2018–2020 from oilseed rape stubble originating from seven northern Tunisian regions. As in most other growing areas, L. maculans and L. biglobosa occurred together on diseased plants. Most isolates (78.6%, n = 114) were L. maculans. For those, a combination of differential set phenotyping and PCR‐based avirulence gene analyses was used to perform race typing. Overall, 30 races were identified, carrying at least two and up to eight of the 11 avirulence genes tested. The most predominant race (14.9%) carried AvrLm7, AvrLepR1 and AvrLepR2 and was detected each year and in six out of the seven regions sampled, indicating the effectiveness of major R‐genes Rlm7 and LepR1 in Tunisia. Rlm2 was overcome by all Tunisian L. maculans isolates, but most were avirulent on Rlm6 and LepR2 (>50%), suggesting that using these R‐genes would provide protection in Tunisia. Both mating types were identified, with MAT1‐2 being twice as frequent as MAT1‐1. These results endorse the need for regular race surveillance of the local pathogen population at temporal and regional scales to develop appropriate blackleg management strategies. [ABSTRACT FROM AUTHOR]

Rhizoctonia large patch (Rhizoctonia solani AG2-2 LP) significantly reduces turfgrass quality, aesthetics, and playability. Synthetic fungicides are commonly used for managing this disease, but they present high costs, potential for fungicide resistance, and environmental concerns. We conducted in vitro assays to test the effectiveness of three biofungicides, seven synthetic fungicides, and ten combinations against R. solani. We then assessed seven spray programs that included Bacillus subtilis QST713 and propiconazole, either alone or tank-mixed, on zoysiagrass 'El Toro' in a growth chamber and in field trials. Biofungicide B. subtilis QST713 reduced pathogen growth by up to 100% in vitro. B. subtilis QST713 alone or combined with synthetic fungicides and/or in rotation was as effective as the standalone synthetic fungicide, reducing disease severity and AUDPC by 81 and 77% (growth chamber) and by 71 and 52% (field), respectively, while maintaining acceptable turfgrass quality. Additionally, we screened zoysiagrass genotypes and advanced breeding lines against three R. solani isolates in growth chamber studies. Five genotypes and two breeding lines demonstrated resistance to Rhizoctonia large patch across isolates, highlighting their potential for developing disease-resistant cultivars. Our findings suggest that integrating biofungicides, resistant cultivars with chemical controls offer sustainable and effective strategies for managing Rhizoctonia large patch [ABSTRACT FROM AUTHOR]

BackgroundAdvances in genomic technologies have expanded our ability to accurately and exhaustively detect natural genomic variants that can be applied in crop improvement and to increase our knowledge of plant evolution and adaptation. Switchgrass (Panicum virgatum L.), an allotetraploid (2n = 4× = 36) perennial C4 grass (Poaceae family) native to North America and a feedstock crop for cellulosic biofuel production, has a large potential for genetic improvement due to its high genotypic and phenotypic variation. In this study, we analyzed single nucleotide polymorphism (SNP) variation in 372 switchgrass genotypes belonging to 36 accessions for 12 genes putatively involved in biomass production to investigate signatures of selection that could have led to ecotype differentiation and to population adaptation to geographic zones.ResultsA total of 11,682 SNPs were mined from ~ 15 Gb of sequence data, out of which 251 SNPs were retained after filtering. Population structure analysis largely grouped upland accessions into one subpopulation and lowland accessions into two additional subpopulations. The most frequent SNPs were in homozygous state within accessions. Sixty percent of the exonic SNPs were non-synonymous and, of these, 45% led to non-conservative amino acid changes. The non-conservative SNPs were largely in linkage disequilibrium with one haplotype being predominantly present in upland accessions while the other haplotype was commonly present in lowland accessions. Tajima's test of neutrality indicated that PHYB, a gene involved in photoperiod response, was under positive selection in the switchgrass population. PHYB carried a SNP leading to a non-conservative amino acid change in the PAS domain, a region that acts as a sensor for light and oxygen in signal transduction.ConclusionsSeveral non-conservative SNPs in genes potentially involved in plant architecture and adaptation have been identified and led to population structure and genetic differentiation of ecotypes in switchgrass. We suggest here that PHYB is a key gene involved in switchgrass natural selection. Further analyses are needed to determine whether any of the non-conservative SNPs identified play a role in the differential adaptation of upland and lowland switchgrass.

Blue mold rot, caused by Penicillium expansum, is one of the most economically important post-harvest diseases of apple worldwide. The goals of this study were threefold: to evaluate the diversity of P. expansum isolates for mycelial growth, spore production and lesion diameter on apples; to estimate the effects of cold-storage facility conditions on P. expansum population structure; and to investigate the efficacy of three essential oils against P. expansum. The results showed that storage facilities applying fungicides and storing diverse fruit species selected for P. expansum isolates with a larger lesion diameter on apples. In addition, application of fungicides and diversification in stored fruit species significantly select for P. expansum isolates with higher levels of mycelial growth and spore production, respectively. Moreover, the diversity of host species of stored fruit accounted for 38% of the variability observed between storage facilities for the measured fitness parameters in P. expansum isolates and had a stronger effect on P. expansum population structure than fungicide treatment. Essential oils from Mentha pulegium and Syzygium aromaticum significantly decreased mycelial growth and spore production of P. expansum isolates in vitro. Mentha pulegium essential oil also significantly decreased the size of lesions associated with the blue mold rot of apples. Reducing the diversity of stored host species and applying M. pulegium essential oil may be useful in counter-selecting for aggressive P. expansum isolates and reducing losses due to blue mold rot during fruit storage.

Dollar spot caused by Clarireedia spp. (formerly Sclerotinia homoeocarpa) is an economically destructive fungal disease of turfgrass that can significantly compromise turf quality, playability, and aesthetic value. Fungicides are frequently used to manage the disease but are costly and potentially unfavorable to the environment. Repeated use of some active ingredients has resulted in reduced efficacy on C. jacksonii causing dollar spot in cool-season turfgrasses in the US. Experiments were conducted to study fungicide sensitivity of Clarireedia spp. as well as to develop alternatives to fungicides against dollar spot on warm-season turfgrass in Georgia. First, 79 isolates of Clarireedia spp. collected across the state were tested on fungicide-amended agar plates for their sensitivity to thiophanate-methyl (benzimidazole) and propiconazole (dimethyl inhibitor). Seventy-seven isolates (97.5%) were sensitive (0.001 to 0.654 mg/mL) and two isolates (2.5%) were found resistant (>1000 mg/mL) to thiophanate-methyl. However, in the case of propiconazole, 27 isolates (34.2%) were sensitive (0.005 to 0.098 mg/mL) while 52 isolates (65.8%) were resistant (0.101 to 3.820 mg/mL). Next, the efficacy of three bio- and six synthetic fungicides and ten different combinations were tested in vitro against C. monteithiana. Seven bio- and synthetic fungicide spray programs comprising Bacillus subtilis QST713 and propiconazole were further tested, either alone or in a tank mix in a reduced rate, on dollar spot infected bermudagrass 'TifTuf' in growth chamber and field environments. These fungicides were selected as they were found to significantly reduce pathogen growth up to 100% on in vitro assays. The most effective spray program in growth chamber assays was 100% B. subtilis QST713 in rotation with 75% B. subtilis QST713 + 25% propiconazole tank mix applied every 14 days. However, the stand-alone application of the biofungicide B. subtilis QST713 every seven days was an effective alternative and equally efficacious as propiconazole, suppressing dollar spot severity and AUDPC up to 75%, while resulting in acceptable turf quality (>7.0) in field experiments. Our study suggests that increased resistance of Clarireedia spp. to benzimidazoles and dimethyl inhibitors warrants continuous surveillance and that biofungicides hold promise to complement synthetic fungicides in an efficacious and environmentally friendly disease management program. [ABSTRACT FROM AUTHOR]

Background: Septoria tritici blotch (STB) remains a significant obstacle to durum wheat cultivation on a global scale. This disease remains a challenge for farmers, researchers, and breeders, who are collectively dedicated to reduce its damage and improve wheat resistance. Tunisian durum wheat landraces have been recognized as valuable genetic ressources that exhibit resistance to biotic and abiotic stresses and therefore play a crucial role in breeding program aimed at creating new wheat varieties resistant to fungal diseases as STB, as well as adapted to climate change constraints. Results: A total of 366 local durum wheat accessions were assessed for resistance to two virulent Tunisian isolates of Zymoseptoria tritici Tun06 and TM220 under field conditions. Population structure analysis of the durum wheat accessions, performed with 286 polymorphic SNPs (PIC > 0.3) covering the entire genome, identified three genetic subpopulations (GS1, GS2 and GS3) with 22% of admixed genotypes. Interestingly, all of the resistant genotypes were among GS2 or admixed with GS2. Conclusions: This study revealed the population structure and the genetic distribution of the resistance to Z. tritici in the Tunisian durum wheat landraces. Accessions grouping pattern reflected the geographical origins of the landraces. We suggested that GS2 accessions were mostly derived from eastern Mediterranean populations, unlike GS1 and GS3 that originated from the west. Resistant GS2 accessions belonged to landraces Taganrog, Sbei glabre, Richi, Mekki, Badri, Jneh Khotifa and Azizi. Furthermore, we suggested that admixture contributed to transmit STB resistance from GS2 resistant landraces to initially susceptible landraces such as Mahmoudi (GS1), but also resulted in the loss of resistance in the case of GS2 susceptible Azizi and Jneh Khotifa accessions. [ABSTRACT FROM AUTHOR]

Species distribution models are widely used to estimate the potential geographic distribution of species habitat. They are also used to predict the impact of climate change on species distributions. In this study, we examined the distribution of Mal Secco disease, an infective disease of citrus caused by the fungus Plenodomus tracheiphilus. To model the Mal Secco distribution under current and two future (2050 and 2070) climatic scenarios in the Mediterranean basin, eight climate variables were incorporated into the Maximum Entropy (MaxEnt) model. All three model distributions had high AUC values (0.97), indicating excellent performance. The precipitation during the wettest month and the minimum temperature during the coldest month contributed the most to the model. The suitable areas for the Mal Secco disease were predicted to decrease by up to 23% by the year 2070. For each of the three scenarios, the change in the proportion of suitable areas along the longitudinal (west–east) and latitudinal (south–north) geographical axes of the Mediterranean basin showed a similar trend. Our study highlights the supposition that while climate change is likely to reduce the extent of suitable areas, no range shift is expected to occur in the Mediterranean basin. [ABSTRACT FROM AUTHOR]

Abstract Background Costs of adaptation play an important role in host-parasite coevolution. For parasites, evolving the ability to circumvent host resistance may trade off with subsequent growth or transmission. Such costs of virulence (sensu plant pathology) limit the spread of all-infectious genotypes and thus facilitate the maintenance of genetic polymorphism in both host and parasite. We investigated costs of three virulence factors in Puccinia striiformis f.sp.tritici, a fungal pathogen of wheat (Triticum aestivum). Results In pairwise competition experiments, we compared the fitness of near-isogenic genotypes that differed by a single virulence factor. Two virulence factors (vir4, vir6) imposed substantial fitness costs in the absence of the corresponding resistance genes. In contrast, the vir9 virulence factor conferred a strong competitive advantage to several isolates, and this for different host cultivars and growing seasons. In part, the experimentally derived fitness costs and benefits are consistent with frequency changes of these virulence factors in the French pathogen population. Conclusion Our results illustrate the variation in the evolutionary trajectories of virulence mutations and the potential role of compensatory mutations. Anticipation of such variable evolutionary outcomes represents a major challenge for plant breeding strategies. More generally, we believe that agro-patho-systems can provide valuable insight in (co)evolutionary processes in host-parasite systems.