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Auxin signaling regulates growth and developmental processes in plants. The core of nuclear auxin signaling relies on just three components: TIR1/AFBs, Aux/IAAs, and ARFs. Each component is itself made up of several domains, all of which contribute to the regulation of auxin signaling. Studies of the structural aspects of these three core signaling components have deepened our understanding of auxin signaling dynamics and regulation. In addition to the structured domains of these components, intrinsically disordered regions within the proteins also impact auxin signaling outcomes. New research is beginning to uncover the role intrinsic disorder plays in auxin-regulated degradation and subcellular localization. Structured and intrinsically disordered domains affect auxin perception, protein degradation dynamics, and DNA binding. Taken together, subtle differences within the domains and motifs of each class of auxin signaling component affect signaling outcomes and specificity.

During evolution, chloroplasts, which originated by endosymbiosis of a prokaryotic ancestor of today’s cyanobacteria with a eukaryotic host cell, were established as the site for photosynthesis. Therefore, chloroplast organelles are loaded with transition metals including iron, copper, and manganese, which are essential for photosynthetic electron transport due to their redox capacity. Although transport, storage, and cofactor-assembly of metal ions in chloroplasts are tightly controlled and crucial throughout plant growth and development, knowledge on the molecular nature of chloroplast metal-transport proteins is still fragmentary. Here, we characterized the soluble, ATP-binding ABC-transporter subunits ABCI10 and ABCI11 in Arabidopsis thaliana, which show similarities to components of prokaryotic, multisubunit ABC transporters. Both ABCI10 and ABCI11 proteins appear to be strongly attached to chloroplast-intrinsic membranes, most likely inner envelopes for ABCI10 and possibly plastoglobuli for ABCI11. Loss of ABCI10 and ABCI11 gene products in Arabidopsis leads to extremely dwarfed, albino plants showing impaired chloroplast biogenesis and deregulated metal homeostasis. Further, we identified the membrane-intrinsic protein ABCI12 as potential interaction partner for ABCI10 in the inner envelope. Our results suggest that ABCI12 inserts into the chloroplast inner envelope membrane most likely with five predicted α-helical transmembrane domains and represents the membrane-intrinsic subunit of a prokaryotic-type, energy-coupling factor (ECF) ABC-transporter complex. In bacteria, these multisubunit ECF importers are widely distributed for the uptake of nickel and cobalt metal ions as well as for import of vitamins and several other metabolites. Therefore, we propose that ABCI10 (as the ATPase A-subunit) and ABCI12 (as the membrane-intrinsic, energy-coupling T-subunit) are part of a novel, chloroplast envelope-localized, AAT energy-coupling module of a prokaryotic-type ECF transporter, most likely involved in metal ion uptake.

Low temperature studies with winter-dormant buds are severely limited by the lack of a rapid,non-destructive assay for their viability. Investigations involving the winter harvest of ecodormant buds of woody subjects, including cryopreservation, are restricted if viability cannot be assessed until dormancy is broken. If post-treatment grafting indicates low survival of the harvested population then further collection and study has to be delayed until the next winter season. This study trials the use of a portable gas exchange system able to discriminate between live and dead buds rapidly, with the assay confirmed as non-destructive by subsequent micropropagation. Active respiration was recorded for 85% of a winter-dormant Malus domestica buds population that showed 91% viability when grafted (n = 45). Lethally stressed material gave no false positive results. When micropropagated after respiratory measurement, a population viability of 76% was recorded. There was a significant, positive correlation between respiration and fresh weight for buds of mass >10 mg, from a population with a mean fresh weight of 17 mg.

Anthracnose disease caused by Colletotrichum lindemuthianum (Sacc. and Magnus) Lams- -Scrib is one of the most devastating seed-borne diseases of common bean (Phaseolus vulgaris L.). In the present study, we evaluated the antifungal activity of Bunium persicum essential oil (EO) and its main constituents on mycelial growth, sporulation and spore germination inhibition of C. lindemuthianum. The main objective of this study was to investigate the effect of EO and its main constituents on decreasing the activity of cell wall degrading enzymes (CWDEs) produced by C. lindemuthianum, which are associated with disease progress. Also, the effects of seed treatment and foliar application of EO and its main constituent, cuminaldehyde, on anthracnose disease severity was investigated. The essential oil of B. persicum, was obtained by using a clevenger apparatus and its major constituents were identified by gas chromatography-mass spectrometry (GC-MS). The EO was characterized by the presence of major compounds such as cuminaldehyde (37.7%), γ-terpinene (17.1%) and β-pinene (15.4%), which indicated antifungal effects against C. lindemuthianum. This pathogen did not grow in the presence of EO, cuminaldehyde and γ-terpinene, β-pinene at 1,500; 1,010 and 1,835 ppm concentrations, respectively. Also, sporulation and spore germination of C. lindemuthianum was completely inhibited by EO and cuminaldehyde. Synergistic effects of the main constituents showed that combing γ-terpinene with cuminaldehyde induced a synergistic activity against C. lindemuthianum and in combination with β-pinene caused an additive effect. Activities of pectinase, cellulase and xylanase, as main CWDEs, were decreased by EO and its main constituents at low concentration without affecting mycelial growth. Seed treatment and foliar application of peppermint EO and/or cuminaldehyde significantly reduced the development of bean anthracnose. We introduced B. persicum EO and constituents, cuminaldehyde and γ-terpinene, as possible control agents for bean anthracnose.

Silicon (Si) is the second most abundant element present in the lithosphere, and it constitutes one of the major inorganic nutrient elements of many plants. Although Si is a nonessential nutrient element, its beneficial role in stimulating the growth and development of many plant species has been generally recognized. Silicon is known to effectively reduce disease severity in many plant pathosystems. The key mechanisms of Si-mediated increased plant disease resistance involve improving mechanical properties of cell walls, activating multiple signaling pathways leading to the expression of defense responsive genes and producing antimicrobial compounds. This article highlights the importance and applicability of Si fertilizers in integrated disease management for crops.

The homeodomain-leucine zipper (HD-Zip) family has been shown to perform a multitude of functions during plant development and stress responses; however, the family members and functions have not been identified in apple (Malus × domestica). In this study, 83 HD-Zips (MdHDZs) were identified in the apple genome. They were assembled into four subgroups according to the classification in Arabidopsis, where MdHDZs in the same subgroup had similar gene structures and conserved protein motifs. Putative cis-element analysis of MdHDZs promoter regions uncovered numerous elements related to the response of stress and plant hormones. In addition, twelve transcripts of the MdHDZs showed different expression patterns under salt, drought, low temperature and ABA stresses by quantitative reverse transcription-PCR (qRT-PCR) assay. To further explore the function of MdHDZs in apple, MdHDZ3 was selected to verify its function under salt, low temperature and ABA stresses; and genetic transformation was used to obtain MdHDZ3 transgenic apple calli. The results demonstrated that MdHDZ3 increased sensitivity to salt, low temperature and abscisic acid in apple calli, suggesting that MdHDZ3 plays an important role in response to stresses. Subcellular localization and three-dimensional structural analysis revealed that MdHDZ3 was a nuclear-localized protein. Taken together, these findings provide potential information for further identification of HD-Zip proteins in apple.

Boron (B) is an essential micronutrient for vascular plant growth. Both B deficiency and toxicity can impair tissue development in diverse plant species, but little is known about the effect of B on reproductive panicle development and grain yield. In this study, a mutant of Setaria italica exhibiting necrotic panicle apices was identified and designated as sibor1. Sequencing revealed a candidate gene, SiBOR1, with a G-to-A alteration at the seventh exon. Knockout transgenic lines generated by clustered regularly interspaced short palindromic repeats and their associated protein-9 also had necrotic panicles, verifying the function of SiBOR1. SiBOR1 encoded a membrane-localized B efflux transporter, co-orthologous to the rice BOR1 protein. SiBOR1 was dominantly expressed in panicles and displayed a distinct expression pattern from those of its orthologs in other species. The induced mutation in SiBOR1 caused a reduction in the B content of panicle primary branches, and B deficiency-associated phenotypes such as thicker cell walls and higher cell porosity compared with Yugu 1. Transcriptome analysis indicated that differentially expressed genes involved in cell wall biogenesis, jasmonic acid synthesis, and programmed cell death response pathways were enriched in sibor1. qPCR analysis identified several key genes, including phenylalanine ammonia-lyase (SiPAL) and jasmonate-ZIM-domain (SiJAZ) genes, responsive to B-deficient conditions. These results indicate that SiBOR1 helps to regulate panicle primary branch development to maintain grain yield in S. italica. Our findings shed light on molecular mechanisms underlying the relationship between B transport and plant development in S. italica.

Sweet basil (Ocimum basilicum, 2n = 4x = 48) is susceptible to downy mildew caused by Peronospora belbahrii. The Pb1 gene exhibits complete resistance to the disease. However, Pb1 became prone to disease because of occurrence of new virulent races. Here, we show that Zambian accession PI 500950 (Ocimum americanum var. pilosum) is highly resistant to the new races. From an interspecies backcross between PI 500950 and the susceptible ‘Sweet basil’ we obtained, by embryo rescue, a population of 131 BC1F1 plants. This population segregated 73 resistant (58) and susceptible (1:1; P = 0.22) plants, suggesting that resistance is controlled by one incompletely dominant gene called Pb2. To determine whether allelic relationship exists between Pb1 and Pb2, we used two differential races: race 0, which is avirulent to both PI 500945 (Pb1) and PI 500950 (Pb2), and race 1, which is virulent to PI 500945 but avirulent to PI 500950. F1 plants obtained from ‘12-4-6’ (BC6F3 derived from PI 500945) and ‘56’ (BC3F3 derived from PI 500950) showed resistant superiority to both races through dominant complementary interaction. F2 plants segregated to race 0 as follows: 12:3:1 (immune/incomplete resistant/susceptible) as opposed to 9:3:4 to race 1, indicating that Pb1 and Pb2 are not alleles. Because joint action is contributed in F1 plants and in advanced [BC3F3(56) × BC6F3(12-4-6) F4] populations that carry both genes, it can be assumed that both accessions carry two unlinked genes but share a common signal transduction pathway, which leads to dominant complementation superiority of the resistance against different races of basil downy mildew.

Gray mold caused by Botrytis cinerea is one of the most widespread and damaging diseases in cannabis crops worldwide. With challenging restrictions on pesticide use and few effective control measures, biocontrol agents are needed to manage this disease. The aim of this study was to identify bacterial biocontrol agents with wide-spectrum activity against B. cinerea and other cannabis fungal pathogens. Twelve Bacillus and Pseudomonas strains were first screened with in vitro confrontational assays against 10 culturable cannabis pathogens, namely B. cinerea, Sclerotinia sclerotiorum, Fusarium culmorum, F. sporotrichoides, F. oxysporum, Nigrospora sphaerica, N. oryzae, Alternaria alternata, Phoma sp., and Cercospora sp. Six strains displaying the highest inhibitory activity, namely Bacillus velezensis LBUM279, FZB42, LBUM1082, Bacillus subtilis LBUM979, P. synxantha LBUM223, and P. protegens Pf-5, were further assessed in planta where all, except LBUM223, significantly controlled gray mold development on cannabis leaves. Notably, LBUM279 and FZB42 reduced disease severity by at least half compared with water-treated plants and prevented lesion development and/or sporulation up to 9 days after pathogen inoculation. Genomes of LBUM279, LBUM1082, and LBUM979 were sequenced de novo and taxonomic affiliations were determined to ensure nonrelatedness with pathogenic strains. Moreover, the genomes were exempt of detrimental genes encoding major toxins and virulence factors that could otherwise pose a biosafety risk when used on crops. Eighteen gene clusters of potential biocontrol interest were also identified. To our knowledge, this is the first reported attempt to control cannabis fungal diseases in planta by direct antagonism with beneficial bacteria.

Although open-central canopy (OCC) is popular in apple (Malus × domestica) orchards in Loess Plateau of China, its relevant photosynthetic mechanisms have not been elucidated. In this study, changes in photosynthetically active radiation (PAR), gas exchange, chlorophyll fluorescence quenching and fruit quality in apple trees were measured in OCC and compared with those in the conventional condensed round and large canopy (RLC). Results showed that light intercepted at different orientations was 44% higher by OCC than that by RLC. The improved light environment within OCC remarkably increased leaf maximum net photosynthetic rate (Pnmax) and significantly decreased stomatal limitation. Under high light, the ratio of photorespiratory rate to gross photosynthetic rate (Pr/Pg) in OCC was higher than that in RLC. Moreover, reversible component in non-photochemical quenching (r(qE)) was increased, while irreversible component (r(qI)) was decreased in OCC than in RLC. As a result, the fruit quality in OCC was greatly boosted as evidenced by the significantly increased single fruit weight, fruit flesh firmness and fruit soluble solid contents and the sharply decreased fruit titratable acid contents. PAR intercepted by the canopy and the fruit soluble solid contents, leaf Pnmax or single fruit weight were positively correlated, while PAR or Pnmax was negatively correlated with the fruit titratable acid contents. Accordingly, the improved crown light environment and the enhanced leaf photosynthetic performance and photoprotective capacity in OCC led to the boosted fruit quality.

Hormones play important roles in vegetative and reproductive processes; however, the regulatory roles of hormones in Nelumbo nucifera (Lotus) growth and development are unclear. In this study, nine types of endogenous hormones, including gibberellins (GA1, GA3, and GA4), indole-3-acetic acid (IAA), brassinolide (BR), ethylene (ETH), jasmonic acid (JA), abscisic acid (ABA), and zeatin (ZT) were detected in dormant shoot tips, vegetative shoot tips, developing leaf buds, and developing flower buds of lotus. The results indicated that GA, ETH, and BR signaling can promote vegetative and reproductive development of lotus. GA signaling regulates plant height and stimulates flower bud differentiation. GA levels were the highest in the flower buds; exogenous GA3+4 increased plant height by approximately 90%, increased flower quantity by nearly 40%, and advanced flowering by 4 d. Suppressing GA biosynthesis using paclobutrazol decreased plant height and flower quantity by 38% and 87.1%, respectively, and delayed flowering by 15.6 d. ETH signaling has positive regulatory effects on vegetative growth and flower development. The ETH concentration in the developing leaf buds was at least 50% higher than that in other samples. Ethephon spraying led to remarkable increases in plant height and leaf thickness and extended the flowering duration. BR signaling acts as a growth promoter during vegetative and reproductive development in lotus. The highest BR levels were detected in the vegetative shoot tips. External application of 28-epihomobrassinolide resulted in growth-promoting phenotypes including longer scapes, thicker leaves, and prolonged flowering.

In agriculture, LED light sources have increasingly replaced the standard luminescent lamps and have acquired an important role in plant micropropagation. We studied the effect of different light sources such as narrow-band LEDs (bright blue, blue, green, yellow, deep red, and red) and wide-band LEDs (cold white, white, warm white, full spectrum, and an artificial solar spectrum sun box constructed by us) on development of potato plantlets in vitro. White luminescent lamps were used as a control. The light intensity of 49 µmol • m−2 • s−1 was provided in all light treatments. We showed that the long-wave narrow-band light treatments were inapplicable for potato micropropagation, because plantlets were weak with small leaves, inhibited roots, and significantly elongated stems. Blue lights provided growth of shortened plantlets with large leaves, well-growing roots, and abundant green mass. The chlorophyll content was lower under blue and bright blue light and was at the same level in the remained treatments. Significant differences in the stomatal apparatus development were observed depending on the light source. These differences were not always reflected in the plantlet phenotype: e.g., plantlets under blue and bright blue lights showed no differences in any characteristics except stomatal density and size of stomatal guard cells. We found no significant effect of blue light portion in the white lights and full spectrum on plantlet growth. An artificial solar spectrum sun box was the most suitable for potato micropropagation, because it supported the development of plantlets with good fitness, uniform internodes length, abundant roots and green mass accumulation.

Phytophthora sojae, the causal agent of Phytophthora root and stem rot of soybean, has been managed with single Rps genes since the 1960s but has subsequently adapted to many of these resistance genes, rendering them ineffective. The objective of this study was to examine the pathotype and genetic diversity of P. sojae from soil samples across Illinois, Indiana, Kentucky, and Ohio by assessing which Rps genes were still effective and identifying possible population clusters. There were 218 pathotypes identified from 473 P. sojae isolates with an average of 6.7 out of 15 differential soybean lines exhibiting a susceptible response for each isolate. Genetic characterization of 103 P. sojae isolates from across Illinois, Indiana, Kentucky, and Ohio with 19 simple sequence repeat markers identified 92 multilocus genotypes. There was a moderate level of population differentiation between these four states, with pairwise FSTvalues ranging from 0.026 to 0.246. There were also moderate to high levels of differentiation between fields, with pairwise FSTvalues ranging from 0.071 to 0.537. Additionally, cluster analysis detected the presence of P. sojae population structure across neighboring states. The level of pathotype and genetic diversity, in addition to the identification of population clusters, supports the hypothesis of occasional outcrossing events that allow an increase in diversity and the potential to select for a loss in avirulence to specific resistance genes within regions. The trend of suspected gene flow among neighboring fields is expected to be an ongoing issue with current agricultural practices.

Capacity for dispersal is a fundamental fitness component of plant pathogens. Characterization of plant pathogen dispersal is important for understanding how pathogen populations change in time and space. We devised a systematic approach to measure and analyze rain splash-driven dispersal of plant pathogens in field conditions, using the major fungal wheat pathogen Zymoseptoria tritici as a case study. We inoculated field plots of wheat ( Triticum aestivum) with two distinct Z. tritici strains. Next, we measured disease intensity as counts of fruiting bodies (pycnidia) using automated image analysis. These measurements characterized primary disease gradients, which we used to estimate effective dispersal of the pathogen population. Genotyping of reisolated pathogen strains with strain-specific PCR confirmed the conclusions drawn from phenotypic data. Consistently with controlled environment studies, we found that the characteristic scale of dispersal is tens of centimeters. We analyzed the data using a spatially explicit mathematical model that incorporates the spatial extent of the source, rather than assuming a point source, which allows for a more accurate estimation of dispersal kernels. We employed bootstrapping methods for statistical testing and adopted a two-dimensional hypotheses test based on kernel density estimation, enabling more robust inference compared with standard methods. We report the first estimates of dispersal kernels of the pathogen in field conditions. However, repeating the experiment in other environments would lead to more robust conclusions. We put forward advanced methodology that paves the way for further measurements of plant pathogen dispersal in field conditions, which can inform spatially targeted plant disease management. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

Cotton architecture is partly determined by shoot branching and flowering patterns. GhBRC1 was previously identified by RNA-seq analysis of nulliplex-branching and normal-branching cotton. However, the roles of GhBRC1 in cotton remain unclear. In the present study, investigations of nuclear localization and transcriptional activity indicated that GhBRC1 has characteristics typical of transcription factors. Gene expression analysis showed that GhBRC1 was highly expressed in axillary buds but displayed different expression patterns between the two branching types. Overexpression of GhBRC1 in Arabidopsis significantly inhibited the number of branches and promoted flowering. In contrast, silencing GhBRC1 in cotton significantly promoted seedling growth. GhBRC1 was induced by multiple hormones, including strigolactones, which promoted seedling growth and seed germination of Arabidopsis plants overexpressing GhBRC1. Consistent with these findings, RNA-seq analysis of virus-induced gene silencing treated cotton revealed that a large number of genes were differentially expressed between GhBRC1-silenced and control plants, and these genes were significantly enriched in plant hormone signalling pathways. Together, our data indicates that GhBRC1 regulates plant branching and flowering through multiple regulatory pathways, especially those regulating plant hormones, with functions partly differing from those of Arabidopsis BRC1. These results provide insights into the molecular mechanisms controlling plant architecture, which is important for breeding cotton with ideal plant architecture and high yield.

Sugar transportation and sugar-to-starch metabolism are considered important processes in seed development and embryo viability. A few plant SWEET proteins acting as sugar transporters have been reported to function in inflorescence and/or seed development. Here, we identified seven members of the 21 OsSWEET genes in rice that play essential roles in sugar transportation and sugar-to-starch conversion in seed development. Nineteen OsSWEET genes exhibiting different expression patterns during inflorescence and seed development were knocked out individually by CRISPR/Cas9. One third of the mutants showed decreased fertile pollen viability and shriveled mature caryopses, resulting in weakened seed traits. Grain fill-related genes but not representative grain shape-regulating genes showed attenuated expression in the mutants. Seed of each of these mutants accumulated more sucrose, glucose or fructose but less starch. Among all OsSWEET genes, OsSWEET4 and OsSWEET11 had major effects on caryopsis development. The sugar-to-starch metabolic pathway was significantly altered in ossweet11 mutants based on differential expression analysis in RNA sequencing assays, confirming that OsSWEET11 functions as a sugar transporter with a key role in seed development. These results help to decipher the multiple functions of OsSWEET genes and to show how they might be used in genetic improvement of rice.

Soybean (Glycine max [L.] Merr.) is a food and oil crop whose growth and yield are influenced by root and nodule development. In the present study, GmNMHC5 was found to promote the formation of nodules in overexpressing mutants. In contrast, the number of nodules in Gmnmhc5 edited with CRISPR/Cas9 decreased sharply. In 35S:GmNMHC5 mutants, expression levels of genes involved in nodulation were significantly up-regulated. Both in vitro and in vivo biochemical analyses showed that GmNMHC5 directly interacted with GmGAI (a DELLA protein), and the content of gibberellin 3 (GA3) in overexpressing mutants was lower than that in the wild type. These results revealed that GmNMHC5 participates in the classical GA signaling pathway, and may regulate the content of GA3 to match the optimal concentration required for nodule formation, thereby promoting nodulation by directly interacting with GmGAI. A model illustrating the mechanism by which GmNMHC5 promotes soybean nodulation is presented.

Fusarium oxysporum f. sp. apii race 4, which is in F. oxysporum species complex (FOSC) Clade 2, causes a new Fusarium wilt of celery. We compared F. oxysporum f. sp. apii race 4 with race 2, which causes Fusarium yellows of celery and is in FOSC Clade 3. Optimal temperatures for celery yield are 16 to 18°C. Soil temperatures in California celery production areas can range up to 26°C, and the maximal rate of hyphal extension of F. oxysporum f. sp. apii races 2 and 4 in culture are 25 and 28°C, respectively. Here, we compared the effect of temperatures from 16 to 26°C on growth of F. oxysporum f. sp. apii races 4 and 2 in two celery cultivars: Challenger, which is resistant to F. oxysporum f. sp. apii race 2 and susceptible to race 4; and Sonora, which is susceptible to both F. oxysporum f. sp. apii races 2 and 4. Based on linear regressions, as temperature increases, there is an increase in the log of F. oxysporum f. sp. apii race 4 DNA concentration in celery crowns and in the reduction in plant height. Based on logistic regressions, as temperature increases, the incidence of vascular discoloration increases in celery with either F. oxysporum f. sp. apii race 2 or 4 infection. In both cultivars, temperatures of 22°C and above resulted in a significantly (α = 0.05) greater concentration of F. oxysporum f. sp. apii race 4 than race 2 in planta. The concentration of F. oxysporum f. sp. apii race 2 in crowns in ‘Challenger’ is temperature-independent and comparatively low; consequently, ‘Challenger’ is, at least partly, resistant rather than tolerant to F. oxysporum f. sp. apii race 2.

Pyrenophora tritici-repentis causes tan spot, an important foliar disease of wheat. A collection of P. tritici-repentis isolates from Tunisia, located in one of the main secondary centers of diversification of durum wheat, was tested for phenotypic race classification based on virulence on a host differential set and for the presence of the necrotrophic effector (NE) genes ToxA, ToxB, and toxb by PCR analysis. While races 2, 4, 5, 6, 7, and 8 were identified according to their virulence phenotypes, PCR testing indicated the presence of “atypical” isolates that induced necrosis on the wheat differential ‘Glenlea,’ but lacked the expected ToxA gene, suggesting the involvement of other NEs in the P. tritici-repentis/wheat interaction. Genetic diversity and the P. tritici-repentis population structure were explored further by examining 59 Tunisian isolates and 35 isolates from Algeria, Azerbaijan, Canada, Iran, and Syria using 24 simple sequence repeat markers. Average genetic diversity, overall gene flow, and percentage polymorphic loci were estimated as 0.58, 2.09, and 87%, respectively. Analysis of molecular variance showed that 81% of the genetic variance occurred within populations and 19% occurred between populations. Cluster analysis by the unweighted pair group method indicated that ToxB– isolates grouped together and were distantly related to ToxB+ isolates. Based on Nei’s analysis, the global collection clustered into two distinct groups according to their region of origin. The results suggest that geographic origin and the host specificity imposed by different NEs can lead to differentiation among P. tritici-repentis populations.

Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici, is managed primarily with cultivar resistance and foliar fungicides. Quinone outside inhibitors (QoIs), which target the mitochondrial cytochrome b (cytb) gene, are one of the two main fungicide classes used on wheat. While European populations of B. graminis f. sp. tritici are widely insensitive to QoIs, largely because of the cytb mutation G143A, the QoI sensitivity of the U.S. B. graminis f. sp. tritici population had never been evaluated despite years of QoI use on U.S. wheat. A total of 381 B. graminis f. sp. tritici isolates from 15 central and eastern U.S. states were screened for sensitivity to QoI fungicides pyraclostrobin and picoxystrobin. A modest range of sensitivities was observed, with maximum resistance factors of 11.2 for pyraclostrobin and 5.3 for picoxystrobin. The F129L, G137R, and G143A cytb mutations were not detected in the U.S. B. graminis f. sp. tritici population, nor were mutations identified in the PEWY loop, a key part of the Qo site. Thus, no genetic basis for the observed quantitative variation in QoI sensitivity of U.S. B. graminis f. sp. tritici was identified. Isolate sporulation was weakly negatively associated with reduced QoI sensitivity, suggesting a fitness cost. In the course of the study, the complete B. graminis f. sp. tritici cytb gene sequence was determined for the first time in the isolate 96224 v. 3.16 reference genome. Contrary to previous reports, the gene has an intron that appears to belong to intron group II, which is unusual in fungi. The study was the first QoI sensitivity screening of a large, geographically diverse set of U.S. B. graminis f. sp. tritici isolates, and while the population as a whole remains relatively sensitive, some quantitative loss of efficacy was observed.

Rice is one of the most important food crops in the world. Weeds seriously affect the rice yield and grain quality. In recent years, there are tremendous progresses in the research and application of herbicide-resistant genes in rice worldwide. This article reviews the working mechanisms of six herbicides (glyphosate, glufosinate, acetolactate synthase inhibitor herbicides, acetyl-CoA carboxylase inhibitor herbicides, hydroxyhenylpyruvate dioxygenase (HPPD) inhibitor herbicides and dinitroaniline herbicides), the resistance mutations of the corresponding herbicide-target genes, and the herbicide detoxification mechanisms by non-target genes. Examples are provided on herbicide-resistant rice materials obtained by transformation of exogenous resistance genes, by artificial mutagenesis and mutant screening, and by modifying the target genes through gene editing. This paper also introduces the current application of herbicide-resistant rice, points out problems that may be caused by utilization of herbicide resistant rice and solutions to the problems, and discusses the future prospects for the development of herbicide-resistant rice.

The number of reports associated with wood dieback caused by fungi in the Botryosphaeriaceae in numerous perennial crops worldwide has significantly increased in the past years. In this study, we investigated the interactions between the canker pathogen Neofusicoccum parvum and the almond tree host (Prunus dulcis), with an emphasis on varietal resistance and host response at the cell wall biochemical and histological levels. Plant bioassays in a shaded house showed that among the four commonly planted commercial almond cultivars (‘Butte’, ‘Carmel’, ‘Monterey’, and ‘Nonpareil’), there was no significant varietal difference with respect to resistance to the pathogen. Gummosis was triggered only by fungal infection, not by wounding. A two-dimensional nuclear magnetic resonance and liquid chromatography determination of cell wall polymers showed that infected almond trees differed significantly in their glycosyl and lignin composition compared with healthy, noninfected trees. Response to fungal infection involved a significant increase in lignin, a decrease in glucans, and an overall enrichment in other carbohydrates with a profile similar to those observed in gums. Histological observations revealed the presence of guaiacyl-rich cell wall reinforcements. Confocal microscopy suggested that N. parvum colonized mainly the lumina of xylem vessels and parenchyma cells, and to a lesser extent the gum ducts. We discuss the relevance of these findings in the context of the compartmentalization of decay in trees model in almond and its potential involvement in the vulnerability of the host toward fungal wood canker diseases.

Numerous studies using a combination of confocal microscopic- and pharmacological-based approaches have demonstrated that the actin cytoskeleton dynamically responds to pathogen infection. Here, we observed that phalloidin treatment induced actin nucleation, resulting in enhanced resistance of wheat against the stripe rust pathogen Puccinia striiformis f. sp. tritici (Pst). To define the mechanism underpinning this process, we characterized a family of conserved actin-binding proteins, the actin related protein (ARP) family, which controls actin polymerization. Specifically, we identified and characterized a wheat ARPC gene (TaARPC5), which encodes a 136-amino acid protein containing a P16-Arc domain, the smallest subunit of the ARP2/3 complex. TaARPC5 mRNA accumulation was induced following the infection of plants with the avirulent Pst strain, and following the elicitation with flagellin (e.g., flg22) as well. Subcellular localization analysis revealed that TaARPC5 is primarily localized to the cortical actin cytoskeleton, and its precise cellular localizations suggest the proximity to processes correlated with the actin-organelle interface. Upon treatment with virulent Pst, TaARPC5-knockdown plants exhibited a significant reduction in the expression of PTI-specific mRNAs. Conversely, we observed enhanced induction of reactive oxygen species (ROS) accumulation and a decrease in TaCAT1 expression following infection with an incompatible Pst isolate. Together with yeast complementation assays, the current study demonstrates a role for TaARPC5 in resistance signaling in wheat against Pst infection by regulating the host actin cytoskeleton.

Crop yield loss due to soil salinization is an increasing threat to agriculture worldwide. Salt stress drastically affects the growth, development, and grain productivity of rice (Oryza sativa L.), and the improvement of rice tolerance to salt stress is a desirable approach for meeting increasing food demand. The main contributors to salt toxicity at a global scale are Na+ and Cl− ions, which affect up to 50% of irrigated soils. Plant responses to salt stress occur at the organismic, cellular, and molecular levels and are pleiotropic, involving (1) maintenance of ionic homeostasis, (2) osmotic adjustment, (3) ROS scavenging, and (4) nutritional balance. In this review, we discuss recent research progress on these four aspects of plant physiological response, with particular attention to hormonal and gene expression regulation and salt tolerance signaling pathways in rice. The information summarized here will be useful for accelerating the breeding of salt-tolerant rice.

Reproductive stage frost poses a major constraint for wheat production in countries such as Australia. However, little progress has been made in identifying key genes to overcome the constraint. In the present study, a severe frost event hit two large-scale field trials consisting of six doubled haploid (DH) wheat populations at reproductive stage (young microspore stage) in Western Australia, leading to the identification of 30 robust frost QTL on 17 chromosomes. The major 18 QTL with the phenotype variation over 9.5% were located on 13 chromosomes including 2A, 2B, 2D, 3A, 4A, 4B, 4D, 5A, 5D, 6D, 7A, 7B and 7D. Most frost QTL were closely linked to the QTL of anthesis, maturity, Zadok stages as well as linked to anthesis related genes. Out of those, six QTL were repetitively detected on the homologous regions on 2B, 4B, 4D, 5A, 5D, 7A in more than two populations. Results showed that the frost damage is associated with alleles of Vrn-A1a, Vrn-D1a, Rht-B1b, Rht-D1b, and the high copy number of Ppd-B1. However, anthesis QTL and anthesis related genes of Vrn-B1a and TaFT3-1B on chromosomes 5B and 1B did not lead to frost damage, indicating that these early-flowering phenotype related genes are compatible with frost tolerance and thus can be utilised in breeding. Our results also indicate that wild-type alleles Rht-B1a and Rht-D1a can be used when breeding for frost-tolerant varieties without delaying flowering time.

The embryo in maize has a critical role in controlling kernel nutrition components and grain yield. We measured five embryo weight and size traits, six kernel weight and size traits, and five embryo-to-kernel ratio traits in a nested association mapping (NAM) population of 611 recombinant inbred lines (RILs) derived from four inbred lines including the high-oil, giant-embryo line BY815 as the common parent. Using three statistical methods, we identified 5–22 quantitative trait loci (QTL) for each trait, explaining 4.7%–46.7% of the phenotypic variation. The genetic architecture of maize embryo size and its related traits appeared to be dominated by multiple small-effect loci with little epistasis, and the genetic control underlying embryo size appeared to be distinct from that underlying kernel size. A trait–QTL association network included 205 nodes and 439 edges and revealed 28 key loci associated with at least three traits. Cloned maize genes including ZmUrb2, Emp12 and ZmBAM1d, maize orthologs of known rice genes that control seed size including BG1, XIAO and GS9, and 11 maize orthologs of Arabidopsis EMBRYO-DEFECTIVE (EMB) genes were identified as underlying these key loci. Further, the phenotypic and genetic relationships between embryo size and kernel size were evaluated, and genetic patterns for identified loci that control embryo size and its related traits were proposed. Our findings reveal distinct genetic architectures for embryo size, kernel size, and embryo-to-kernel ratio traits and establish a foundation for the improvement of embryo-size-mediated kernel nutrition and grain yield.

Manipulation of flowering time to develop cultivars with desired maturity dates is fundamental in plant breeding. It is desirable to generate polyploid rapeseed (Brassica napus L.) germplasm with varying flowering time controlled by a few genes. In the present study, BnaSVP, a rapeseed homolog of the Arabidopsis SVP (Short Vegetative Phase) gene, was characterized and a set of mutants was developed using a CRISPR/Cas9-based gene-editing tool. A single construct targeting multiple sites was successfully applied to precisely mutate four copies of BnaSVP. The induced mutations in these copies were stably transmitted to subsequent generations. Homozygous mutants with loss-of-function alleles and free transgenic elements were generated across the four BnaSVP homologs. All mutant T1 lines tested in two environments (summer and winter growing seasons) showed early-flowering phenotypes. The decrease in flowering time was correlated with the number of mutated BnaSVP alleles. The quadruple mutants showed the shortest flowering time, with a mean decrease of 40.6%–50.7% in length relative to the wild type under the two growth conditions. Our study demonstrates the quantitative involvement of BnaSVP copies in the regulation of flowering time and provides valuable resources for rapeseed breeding.

The main defense response to Soybean mosaic virus (SMV) infection in soybean [Glycine max (L.) Merr.] is thought to be blockage of intercellular virus transport by callose deposition on plasmodesmata. But the specific regulatory mechanism remains largely unknown. In this study, we found that hydrogen peroxide (H2O2) signal downstream of NO was associated with the regulation of callose accumulation. Abundant H2O2 was produced on the cell membrane and cell wall in the incompatible combination of soybean cultivar Jidou 7 and SMV strain N3, whereas no obvious H2O2 was observed in the compatible combination of Jidou 7 and strain SC-8. When H2O2 production was inhibited, callose accumulation induced by SMV infection decreased to a level insufficient to restrict virus transport in the incompatible combination. The H2O2-associated transcriptome dynamics of soybean during SMV infection was investigated. Transcriptome and functional analysis using virus-induced gene silencing showed that GmSEOB and GmPAP27, two genes regulated by H2O2, functioned in resistance by positively regulating the accumulation of callose in response to SMV infection. These results lay a foundation for further research on the signal transduction and molecular regulation of callose deposition during soybean resistance to SMV infection.

Heterosis, the phenomenon in which hybrids outperform their parents, has been utilized in maize (Zea mays L.) for over 100 years. To provide a more complete understanding of heterosis, we collected a comprehensive transcriptome and translatome dataset on seedling leaves for B73, Mo17, and their F1 hybrid, which provided a dynamic landscape of transcriptomic and translatomic variation in maize. Although additivity accounted for a large proportion of variation at two omics-levels, an elevated nonadditive effect was observed in the translatome, especially in the translated subgenome maize1 genes, and the genes that switched from additivity in the transcriptome to nonadditivity in the translatome were significantly enriched in the subgenome maize1. Many genes with allele-specific expression and translation show dramatic regulatory switches between the transcriptome and translatome, and partial genes with allele-specific translation underlying regulatory mechanism also exhibited subgenome bias. Interestingly, we found the translated isoforms show different expression patterns compared with transcriptome and more genes changed their dominant isoforms during the genetic flow from parents to the hybrid at the translatome level. The translated genes with switched dominant isoforms significantly biased to the subgenome maize2 while genes with conserved dominant isoforms significantly enriched in subgenome maize1. Together, the dynamic changed patterns in translatome across hybrid and parental lines show translational fractionation of the maize subgenomes, which may be associated with heterosis in maize and provides a potential theoretical basis for breeding.

Peronospora tabacina is an obligate parasite that causes blue mold of tobacco. The pathogen reproduces primarily by sporangia, whereas the sexual oospores are rarely observed. A collection of 122 isolates of P. tabacina was genotyped using nine microsatellites to assess the population structure of individuals from subpopulations collected from central, southern, and western Europe; the Middle East; Central America; North America; and Australia. Genetic variations among the six subpopulations accounted for ∼8% of the total variation, including moderate levels of genetic differentiation, high gene flow among these subpopulations, and a positive correlation between geographic and genetic distance (r = 0.225; P < 0.001). Evidence of linkage disequilibrium (P < 0.001) showed that populations contained partially clonal subpopulations but that subpopulations from Australia and Mediterranean Europe did not. High genetic variation and population structure among samples could be explained by continuous gene flow across continents via infected transplant exchange and/or long-distance dispersal of sporangia via wind currents. This study analyzed the most numerous P. tabacina collection and allowed conclusions regarding the migration, mutation, and evolutionary history of this obligate biotrophic oomycete. The evidence pointed to the species origin in Australia and identified intracontinental and intercontinental migration patterns of this important pathogen.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Soil inorganic phosphate (Pi) levels are frequently suboptimal for the growth and development of crop plants. Although MADS-box genes participate in diverse plant developmental processes, their involvement in phosphate starvation responses (PSRs) remains unclear. We identified a type I MADS-box transcription factor gene, TaMADS2-3D, which was rapidly induced under low-Pi stress in roots of wheat (Triticum aestivum). A TaMADS2-3D-GFP fusion protein was found located in the nucleus. Transgenic Arabidopsis plants overexpressing TaMADS2-3D (TaMADS2-3DOE) showed shortened primary roots, increased lateral root density, and retarded seedling growth under high-Pi (HP) conditions, accompanied by increased Pi contents in their shoots and roots. The Arabidopsis TaMADS2-3DOE plants showed similar PSR phenotypes under low Pi (LP) conditions. These results indicate constitutive activation of PSRs by overexpression of TaMADS2-3D in Arabidopsis. Reactive oxygen species (ROS), H2O2 and O2−, levels were increased in root tips of Arabidopsis TaMADS2-3DOE plants under HP conditions. Transcriptome analysis of Arabidopsis TaMADS2-3DOE plants under different Pi regimes revealed expression changes for a variety of PSR genes including AtZAT6. Overexpression of TaMADS2-3D in wheat also led to constitutive activation of PSRs. We propose that TaMADS2-3D regulates plant PSRs probably by modulating ROS homeostasis, root development, PSR gene expression, and Pi uptake. This study increases our understanding of plant PSR regulation and provides a valuable gene for improving phosphorus-use efficiency in wheat and other crops.

Oil and protein content and fatty acid composition are quality traits in peanut. Elucidating the genetic mechanisms underlying these traits may help researchers to obtain improved cultivars by molecular breeding. Whole-genome resequencing of a recombinant inbred population of 318 lines was performed to construct a high-density linkage map and identify QTL for peanut quality. The map, containing 4561 bin markers, covered 2032 cM with a mean marker density of 0.45 cM. A total of 110 QTL for oil and protein content, and fatty acid composition were mapped on the 18 peanut chromosomes. The QTL qA05.1 was detected in four environments and showed a major phenotypic effect on the contents of oil, protein, and six fatty acids. The genomic region spanned by qA05.1, corresponding to a physical interval of approximately 1.5 Mb, contains two SNPs polymorphic between the parents that could cause missense mutations. The two SNP sites were employed as KASP markers and validated using lines with extremely high and low oil contents. These sites may be useful in the marker-assisted breeding of peanut cultivars with high oil contents.

The two most important activities in maize breeding are the development of inbred lines with high values of general combining ability (GCA) and specific combining ability (SCA), and the identification of hybrids with high yield potentials. Genomic selection (GS) is a promising genomic tool to perform selection on the untested breeding material based on the genomic estimated breeding values estimated from the genomic prediction (GP). In this study, GP analyses were carried out to estimate the performance of hybrids, GCA, and SCA for grain yield (GY) in three maize line-by-tester trials, where all the material was phenotyped in 10 to 11 multiple-location trials and genotyped with a mid-density molecular marker platform. Results showed that the prediction abilities for the performance of hybrids ranged from 0.59 to 0.81 across all trials in the model including the additive effect of lines and testers. In the model including both additive and non-additive effects, the prediction abilities for the performance of hybrids were improved and ranged from 0.64 to 0.86 across all trials. The prediction abilities of the GCA for GY were low, ranging between − 0.14 and 0.13 across all trials in the model including only inbred lines; the prediction abilities of the GCA for GY were improved and ranged from 0.49 to 0.55 across all trials in the model including both inbred lines and testers, while the prediction abilities of the SCA for GY were negative across all trials. The prediction abilities for GY between testers varied from − 0.66 to 0.82; the performance of hybrids between testers is difficult to predict. GS offers the opportunity to predict the performance of new hybrids and the GCA of new inbred lines based on the molecular marker information, the total breeding cost could be reduced dramatically by phenotyping fewer multiple-location trials.

Plum pox virus (PPV) is a significant pathogen of Prunus worldwide and is known for having a broad experimental host range. Many of these hosts represent epidemiological risks as potential wild viral reservoirs. A comparative study of the PPV reservoir capacity of three commonly found native North American species, western choke cherry (Prunus virginiana var. demissa), black cherry (Prunus serotina), and American plum (Prunus americana) was conducted. Pennsylvania isolates of PPV-D were transmitted from the original host peach (Prunus persica cv. GF305) to all three species. Viral accumulation and transmission rates to alternative hosts and peach were monitored over the course of five vegetative growth and cold induced dormancy (CID) cycles. The three alternative host species demonstrated differences in their ability to maintain PPV-D and the likelihood of transmission to additional alternative hosts or back transmission to peach. Western choke cherry had low (5.8%) initial infection levels, PPV-D was not transmissible to additional western choke cherry, and transmission of PPV-D from western choke cherry to peach was only possible before the first CID cycle. Black cherry had intermediate initial infection levels (26.6%) but did not maintain high infection levels after repeated CID cycles. Conversely, American plum had a high level (50%) of initial infection that was not significantly different from initial infection in peach (72.2%) and maintained moderate levels (15 to 25%) of infection and PPV-D transmission to both American plum and peach through all five cycles of CID. Our results indicate that American plum has the greatest potential to act as a reservoir host for Pennsylvania isolates of PPV-D.

Botryosphaeria dothidea causes white rot, which is among the most devastating diseases affecting apple crops globally. In this study, we assessed B. dothidea resistance to carbendazim by collecting samples from warts on the infected branches of apple trees or from fruits exhibiting evidence of white rot. All samples were collected from different orchards in nine provinces of China in 2018 and 2019. In total, 440 B. dothidea isolates were evaluated, of which 19 isolates from three provinces were found to exhibit carbendazim resistance. We additionally explored the fitness and resistance stability of these isolates, revealing that they were no less fit than carbendazim-sensitive isolates in terms of pathogenicity, sporulation, and mycelial growth and that the observed carbendazim resistance was stable. Sequencing of the β-tubulin gene in carbendazim-resistant isolates showed the presence of a substitution at codon 198 (GAG to GCG) that results in an alanine substitution in place of glutamic acid (E198A) in all 19 resistant isolates. A loop-mediated isothermal amplification (LAMP) method was then developed to rapidly and specifically identify this E198A mutation. This LAMP method offers value as a tool for rapidly detecting carbendazim-resistant isolates bearing this E198A mutation and can thus be used for the widespread monitoring of apple crops to detect and control the development of such resistance.

Loquat (Eriobotrya japonica Lindl.) is an evergreen fruit tree species of the Rosaceae, and its unique flowering time greatly hinders its production. To explore the artificial regulation of loquat flowering time, we removed the main inflorescence (by cutting it) to induce reflowering. For different loquat tree cultivars with different stages, the inflorescence was removed by cutting the main floral axis at two alternative positions: the upper or the lower position beneath the inflorescence, and it was found that the proportion of reflowering resulting from removing the upper position of the main floral axis of yellow-flesh loquat cultivars during the full-bloom stage was the highest. In addition, compared with those of the normal-growing panicles, the number of flower buds and branch axes of the reflowering panicles decreased significantly after cutting. Importantly, these newly produced inflorescences flowered 2–4 months later than normal-growing inflorescences did, effectively prolonging both the flowering and fruiting time. In addition, qRT-PCR results showed that EjFT1, EjFT2, EjAP1-1 and EjAP1-2 were highly expressed in the floral axis. These findings highlighted a new method for extending the production cycle of loquat and provided a reference for the flowering regulation of loquat and other economically important fruit tree species.

DNA barcoding is a supplementary tool in plant systematics, extensively used to resolve the species level controversies. This paper details the identification of DNA barcodes for seven species of Momordica, using the chloroplast gene matK. Since the species M. cymbalaria has been confused as a member of the genus Luffa, 26 accessions of Momordica belonging to seven Indian species and two accessions of Luffa acutangula were included in this study. Analysis of matK sequences has yielded distinct barcodes in M. charantia var. charantia, M. subangulata subsp. renigera, M. cochinchinensis, M. balsamina, M. cymbalaria and also in Luffa acutangula. Evolutionary status of each species was reflected as nucleotide polymorphisms in each sequence. The wild species M. dioica and M. sahyadrica have yielded one barcode but failed to get differentiated. Further, this study provides conclusive proof that M. cymbalaria is a member of Momordica genus. The phylogram generated was successful to distinguish the monoecious species of this genus, M. charantia, M. balsamina and M. cymbalaria, from the dioecious species M. dioica, M. sahyadrica, M. subangulata subsp. renigera and M. cochinchinensis. Thus, matK locus, by accumulating the evolutionary sequence variations, is proven efficient to differentiate the Momordica species and to reveal their relatedness.

Cytokinins are a class of phytohormones that promote cell division and differentiation and are thought to affect plant immunity to multiple pathogens. However, a comprehensive analysis of cytokinin dehydrogenase/oxidase (CKX) family genes in cabbage has not been reported. In this study, a total of 36 CKX genes were identified using a genome-wide search method. Phylogenetic analysis classified these genes into three groups. They were distributed unevenly across nine chromosomes in B. oleracea, and 15 of them did not contain any introns. The results of colinearity analysis showed that 36 CKX gene in Arabidopsis was present in several copies in the Brassica oleracea genome. An analysis of cis-acting elements indicated that all genes possessed at least one stress or hormone responsive cis-acting element. A heatmap of CKX gene expression showed the patterns of expression of these genes in various tissues and organs. Three genes (Bol028363, Bol031036 and Bol018140) were relatively highly expressed in all of the investigated tissues under normal conditions, showing the expression profile of housekeeping genes. Generally, the expression patterns of CKX genes in Jingfeng 1 and Xiangan 336 were quite different under the same treatment. Notably, three genes (Bol020547, Bol028392 and Bol045724) were significantly down-regulated and up-regulated in the susceptible and resistant material, respectively, after inoculation, which may indicate their crucial roles in resistance to clubroot disease. The results provide insights for better understanding the roles of CKX genes in the B. oleracea–P. brassicae interaction.

Tomato brown rugose fruit virus (ToBRFV), belonging to the genus Tobamovirus, is a highly virulent emerging virus, causing disease outbreaks and significant crop losses worldwide. The growing number of ToBRFV epidemic episodes prompted the investigation of the role of seeds in the dissemination of the virus as an important aspect in the overall disease management. Therefore, the objectives of this study were to determine the localization of ToBRFV within tomato seeds and to evaluate its seed transmission characteristics. Seeds extracted from naturally ToBRFV-infected tomato fruits were tested for the presence of the virus using serological, molecular, and biological assays. Three immunolocalization techniques were used to determine the localization and distribution of ToBRFV within the different tissues and parts of tomato seeds. To evaluate seed transmission of ToBRFV, two grow-out experiments were conducted to assess the rate of both vertical (seeds to progeny seedlings) and possible horizontal transmission (plant to plant) based on serological and molecular assays. Seeds extracted from ToBRFV-infected fruits had a 100% contamination rate. The localization of ToBRFV in tomato seeds is only external on the seed coat (testa). Seed transmission rate from seeds to their seedlings was very low (0.08%), while no transmission was recorded from plants to plants in a small-scale greenhouse experimental setup. In conclusion, ToBRFV is a seedborne virus located externally on tomato seed coat and transmitted mechanically from ToBRFV-contaminated tomato seeds to seedlings, which could initiate a disease foci and eventually drive further dissemination and spread of the disease in a new growing area.

Huanglongbing, or citrus greening disease, is the most serious disease of citrus worldwide and is associated with plant infection by ‘Candidatus Liberibacter asiaticus’ (CLas) and other Liberibacter species. CLas is transmitted by Diaphorina citri, the Asian citrus psyllid, in a circulative propagative manner. Circulative propagative transmission is a complex process comprising at least three steps: movement of the pathogen into vector tissues, translocation and replication of the pathogen within the vector host, and pathogen inoculation of a new host by the vector. In this work, we describe an excised leaf CLas acquisition assay, which enables precise measurements of CLas acquisition by D. citri in a streamlined laboratory assay. Briefly, healthy fourth and fifth instar D. citri nymphs acquire CLas from excised CLas-positive leaves, where the insects also complete their developmental cycle. CLas titer in the resulting adults is measured using quantitative PCR and CLas-specific 16S rRNA gene primers. We observed positive correlations between CLas titer in each leaf replicate and the CLas titer that developed in the insects after acquisition (rs = 0.78; P = 0.0002). This simple assay could be used to detect CLas acquisition phenotypes and their underlying genotypes, facilitate assessment of plant factors that impact acquisition, and screen for compounds that interfere with CLas acquisition by delivering these compounds through the excised leaf.

Winged bean [Psophocarpus tetragonolobus (L.) DC.] is a vegetable legume crop. The center of origin, diversity and domestication of this crop are not known. This study assessed the genetic diversity and population structure of 457 accessions of winged bean collected from six geographical regions (North, Northeast, East, West, and central, and South) in Thailand using 14 simple sequence repeat (SSR) markers. In total, the SSR markers detected only 55 alleles with an average of 3.9 alleles per locus. Observed heterozygosity was relatively high (0.15) and overall gene diversity was moderate (0.487). Gene diversity, allelic richness and observed heterozygosity in the six regions were comparable while the estimated out-crossing rate was relatively high (16.4%). STRUCTURE analysis grouped the 457 winged bean accessions into three sub-populations. Neighbor-joining (NJ) analysis grouped all the accessions into two major clusters. Genetic groups identified by both STRUCTURE analysis and NJ analysis were unrelated to geographical origins. Principal coordinate analysis revealed no clear clustering of the winged bean accessions from different regions widely distributed and overlapping. Although genetic groups were not unrelated to geographical origins, most of the winged bean accessions with long pods (30 cm or higher in length) or having purple seed coats or purple young pods were grouped together. This suggested that the winged beans with long pods or with purple seed or purple young pods may have a single origin. Altogether, these results demonstrated that the genetic diversity of winged bean in Thailand was moderate with high genetic admixture. We argue that the high genetic admixture of the winged bean in Thailand is due to seed migration and relatively high outcrossing rate.

Indigenous crops also known as orphan crops are key contributors to food security, which is becoming increasingly vulnerable with the current trend of population growth and climate change. They have the major advantage that they fit well into the general socio-economic and ecological context of developing world agriculture. However, most indigenous crops did not benefit from the Green Revolution, which dramatically increased the yield of major crops such as wheat and rice. Here, we describe the Tef Improvement Project, which employs both conventional- and molecular-breeding techniques to improve tef—an orphan crop important to the food security in the Horn of Africa, a region of the world with recurring devastating famines. We have established an efficient pipeline to bring improved tef lines from the laboratory to the farmers of Ethiopia. Of critical importance to the long-term success of this project is the cooperation among participants in Ethiopia and Switzerland, including donors, policy makers, research institutions, and farmers. Together, European and African scientists have developed a pipeline using breeding and genomic tools to improve the orphan crop tef and bring new cultivars to the farmers in Ethiopia. We highlight a new variety, Tesfa, developed in this pipeline and possessing a novel and desirable combination of traits. Tesfa’s recent approval for release illustrates the success of the project and marks a milestone as it is the first variety (of many in the pipeline) to be released., Euphytica, 214 (2), ISSN:0014-2336, ISSN:1573-5060

Lentil (Lens culinaris Medik.) is a self-pollinating, diploid, annual, cool-season, food legume crop that is cultivated throughout the world. Ascochyta blight (AB), caused by Ascochyta lentis Vassilievsky, is an economically important and widespread disease of lentil. Development of cultivars with high levels of durable resistance provides an environmentally acceptable and economically feasible method for AB control. A detailed understanding of the genetic basis of AB resistance is hence highly desirable, in order to obtain insight into the number and influence of resistance genes. Genetic linkage maps based on single nucleotide polymorphisms (SNP) and simple sequence repeat (SSR) markers have been developed from three recombinant inbred line (RIL) populations. The IH × NF map contained 460 loci across 1461.6 cM, while the IH × DIG map contained 329 loci across 1302.5 cM and the third map, NF × DIG contained 330 loci across 1914.1 cM. Data from these maps were combined with a map from a previously published study through use of bridging markers to generate a consensus linkage map containing 689 loci distributed across seven linkage groups (LGs), with a cumulative length of 2429.61 cM at an average density of one marker per 3.5 cM. Trait dissection of AB resistance was performed for the RIL populations, identifying totals of two and three quantitative trait loci (QTLs) explaining 52 and 69% of phenotypic variation for resistance to infection in the IH × DIG and IH × NF populations, respectively. Presence of common markers in the vicinity of the AB_IH1- and AB_IH2.1/AB_IH2.2-containing regions on both maps supports the inference that a common genomic region is responsible for conferring resistance and is associated with the resistant parent, Indianhead. The third QTL was derived from Northfield. Evaluation of markers associated with AB resistance across a diverse lentil germplasm panel revealed that the identity of alleles associated with AB_IH1 predicted the phenotypic responses with high levels of accuracy (~86%), and therefore have the potential to be widely adopted in lentil breeding programs. The availability of RIL-based maps, a consensus map, and validated markers linked to AB resistance provide important resources for lentil improvement.

BACKGROUND: Grapevine (Vitis vinifera L.) as basis for winemaking is one of the most economically important plants in modern agriculture. As requirements in viticulture are increasing due to changing environments, terroir and pests, classical agriculture techniques reach their limits. OBJECTIVE: We summarize the impact of modern “omics” technologies on modern grapevine breeding and cultivation, as well as for dealing with challenges in viniculture caused by environmental or terroir changes and pests and diseases. In this review, we give an overview on current research on the influence of “omics” technologies on modern viticulture. RESULTS: Considerable advances in bioinformatics and analytical techniques such as next generation sequencing or mass spectrometry fueled new molecular biological studies. Modern “omics” technologies such as “genomics”, “transcriptomics”, “proteomics” and “metabolomics” allow the investigation on a large-scale data basis and the identification of key markers. Holistic understanding of genes, proteins and metabolites in combination with external biotic and abiotic factors improves vine and wine quality. CONCLUSION: The rapid evolution in wine quality was only enabled by the progress of modern biotechnological methods developing enology from a handcraft to science.

Lodging is a major problem limiting maize yield worldwide. However, the mechanisms of lodging resistance remain incompletely understood for maize. Here, we evaluated 443 maize accessions for lodging resistance in the field. Five lodging-resistant accessions and five lodging-sensitive accessions were selected for further research. The leaf number, plant height, stem diameter, and rind penetrometer resistance were similar between lodging-resistant and -sensitive inbred lines. The average thickness of sclerenchymatous hypodermis layer was thicker and the vascular area was larger in the lodging-resistant lines compared with lodging-sensitive lines. Although total lignin content in stem tissue did not significantly differ between lodging-resistant and -sensitive lines, phloroglucinol staining revealed that the lignin content of the cell wall in the stem cortex and in the stem vascular tissue near the cortex was higher in the lodging-resistant lines than in the lodging-sensitive lines. Analysis of strand-specific RNA-seq transcriptome showed that a total of 793 genes were up-regulated and 713 genes were down-regulated in lodging-resistant lines relative to lodging-sensitive lines. The up-regulated genes in lodging-resistant lines were enriched in cell wall biogenesis. These results indicated that modification of cell wall biosynthesis would contribute to lodging resistance of maize.

Resistance to late blight caused by Phytophthora infestans clonal lineage US-23 in 217 old and modern potato cultivars was evaluated in field trials in 2016 and 2017 in Pennsylvania. Significant differences in resistance were found among these cultivars (P < 0.0001). Significant interaction between cultivars and environments was found (P < 0.0001). The values of relative area under the disease progress curve ranged from 0 to 0.5841 in 2016 and from 0 to 0.5469 in 2017. Broad-sense heritability of late blight resistance was estimated to be 0.91, with a 95% confidence interval of 0.88 to 0.93. Cluster analysis classified the cultivars into five groups: resistant, moderately resistant, intermediate, moderately susceptible, and susceptible. Thirty cultivars showing resistance and 32 cultivars showing moderate resistance were identified. The 217 cultivars were also evaluated for foliar maturity, tuber yield, and resistance to early blight caused by Alternaria solani. A few cultivars with late blight resistance independent of late maturity were found. Late blight resistance and early blight resistance were positively correlated, and 17 cultivars possessed resistance to both diseases. Yield trade-off associated with late blight resistance was not observed among the cultivars in the absence of disease pressure.

Erratic rainfall often results in intermittent drought and/or waterlogging and limits maize (Zea mays L.) productivity in many parts of the Asian tropics. Developing climate-resilient maize germplasm possessing tolerance to these key abiotic stresses without a yield penalty under optimal growing conditions is a challenge for breeders working in stress-vulnerable agro-ecologies in the region. Breeding stress-resilient maize for rainfed stress-prone ecologies is identified as one of the priority areas for CIMMYT-Asia maize program. We applied rapid cycle genomic selection (RCGS) on two multiparent yellow synthetic populations (MYS-1 and MYS-2) to improve grain yield simultaneously under drought and waterlogging conditions using genomic-estimated breeding values (GEBVs). Also, the populations were simultaneously advanced using recurrent phenotypic selection (PS) by exposing them to managed drought and waterlogging and intermating tolerant plants from the two selection environments. Selection cycles per se (C1, C2, and C3) of the two populations developed using RCGS and PS approach and their test-cross progenies were evaluated separately in multilocation trials under managed drought, waterlogging, and optimal moisture conditions. Significant genetic gains were observed with both GS and PS, except with PS in MYS-2 under drought and with GS in MYS-1 under waterlogging. Realized genetic gains from GS were relatively higher under drought conditions (110 and 135 kg ha−1 year−1) compared to waterlogging (38 and 113 kg ha−1 year−1) in both MYS-1 and MYS-2, respectively. However, under waterlogging stress PS showed at par or better than GS as gain per year with PS was 80 and 90 kg ha−1, whereas with GS it was 90 and 43 kg ha−1 for MYS-1 and MYS-2, respectively. Our findings suggested that careful constitution of a multiparent population by involving trait donors for targeted stresses, along with elite high-yielding parents from diverse genetic background, and its improvement using RCGS is an effective breeding approach to build multiple stress tolerance without compromising yield when tested under optimal conditions.

Cotton bacterial blight (CBB), caused by Xanthomonas citri pv. malvacearum, was a major disease of cotton in the United States in the early part of the twentieth century. The reemergence of CBB revealed many gaps in our understanding of this important disease. In this study, we employed a wild-type (WT) field isolate of X. citri pv. malvacearum from Georgia (U.S.A.) to generate a nonpathogenic hrcV mutant lacking a functional type-III secretion system (T3SS−). We tagged the WT and T3SS− strains with an auto-bioluminescent Tn7 reporter and compared colonization patterns of CBB-susceptible and CBB-resistant cotton seedlings using macroscopic image analysis and bacterial load enumeration. WT and T3SS− X. citri pv. malvacearum strains colonized cotton cotyledons of CBB-resistant and CBB-susceptible cotton cultivars. However, X. citri pv. malvacearum populations were significantly higher in CBB-susceptible seedlings inoculated with the WT strain. Additionally, WT and T3SS− X. citri pv. malvacearum strains systemically colonized true leaves, although at different rates. Finally, we observed that seed-to-seedling transmission of X. citri pv. malvacearum may involve systemic spread through the vascular tissue of cotton plants. These findings yield novel insights into potential X. citri pv. malvacearum reservoirs for CBB outbreaks.

Appearance and cooked rice elongation are key quality traits of rice. Although some QTL for these traits have been identified, understanding of the genetic relationship between them remains limited. In the present study, large phenotypic variation was observed in 760 accessions from the 3K Rice Genomes Project for both appearance quality and cooked rice elongation. Most component traits of appearance quality and cooked rice elongation showed significant pairwise correlations, but a low correlation was found between appearance quality and cooked rice elongation. A genome-wide association study identified 74 QTL distributed on all 12 chromosomes for grain length, grain width, length to width ratio, degree of endosperm with chalkiness, rice elongation difference, and elongation index. Thirteen regions containing QTL stably expressed in multiple environments and/or exerting pleiotropic effects on multiple traits were detected. By gene-based association analysis and haplotype analysis, 46 candidate genes, including five cloned genes, and 49 favorable alleles were identified for these 13 QTL. The effect of the candidate gene Wx on rice elongation difference was validated by a transgenic strategy. These results shed light on the genetic bases of appearance quality and cooked rice elongation and provide gene resources for improving rice quality by molecular breeding.