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Background: Breeding of lettuce (Lactuca sativa L.), the most important leafy vegetable worldwide, for enhanced disease resistance and resilience relies on multiple wild relatives to provide the necessary genetic diversity. In this study, we constructed a super-pangenome based on four Lactuca species (representing the primary, secondary and tertiary gene pools) and comprising 474 accessions. We include 68 newly sequenced accessions to improve cultivar coverage and add important foundational breeding lines., Results: With the super-pangenome we find substantial presence/absence variation (PAV) and copy-number variation (CNV). Functional enrichment analyses of core and variable genes show that transcriptional regulators are conserved whereas disease resistance genes are variable. PAV-genome-wide association studies (GWAS) and CNV-GWAS are largely congruent with single-nucleotide polymorphism (SNP)-GWAS. Importantly, they also identify several major novel quantitative trait loci (QTL) for resistance against Bremia lactucae in variable regions not present in the reference lettuce genome. The usability of the super-pangenome is demonstrated by identifying the likely origin of non-reference resistance loci from the wild relatives Lactuca serriola, Lactuca saligna and Lactuca virosa., Conclusions: The super-pangenome offers a broader view on the gene repertoire of lettuce, revealing relevant loci that are not in the reference genome(s). The provided methodology and data provide a strong basis for research into PAVs, CNVs and other variation underlying important biological traits of lettuce and other crops., (© 2024. The Author(s).)

Background: Alcohol dehydrogenase (ADH) is an enzyme that binds to zinc, facilitating the interconversion of ethanol and acetaldehyde or other corresponding alcohols/aldehydes in the pathway of ethanol fermentation. It plays a pivotal role in responding to environmental stress. However, the response of the ADH family to abiotic stress remains unknown in rapeseed., Result: In this study, we conducted a comprehensive genome-wide investigation of the ADH family in rapeseed, encompassing analysis of their gene structure, replication patterns, conserved motifs, cis-acting elements, and response to stress. A total of 47 ADH genes were identified within the rapeseed genome. Through phylogenetic analysis, BnADHs were classified into four distinct clades (I, II, IV, V). Prediction of protein domains revealed that all BnADH members possessed a GroES-like (ADH_N) domain and a zinc-bound (ADH_zinc_N) domain. Analysis of promoter sequences demonstrated that BnADHs contained numerous cis-acting elements associated with hormone and stress responses, indicating their widespread involvement in various biological regulatory processes. Expression profiling under different concentrations of salt stress treatments (0%, 0.4%, 0.8%, 1.0% NaCl) further highlighted the significant role played by the BnADH family in abiotic stress response mechanisms. Overexpression of BnADH36 in rapeseed significantly improved the salt tolerance of rapeseed., Conclusion: The features of the BnADH family in rapeseed was comprehensively characterized in this study, which could provide reference to the research of BnADHs in abiotic stress response., (© 2024. The Author(s).)

The two-component system (TCS) consists of histidine kinase (HK), histidine phosphate transfer protein (HP), and response regulatory factor (RR). It is one of the most crucial components of signal transduction in plants, playing a significant role in regulating plant growth, development, and responses to various abiotic stresses. Although TCS genes have been extensively identified in a variety of plants, the genome-wide recognition and examination of TCS in switchgrass remain unreported. Accordingly, this study identified a total of 87 TCS members in the genome of switchgrass, comprising 20 HK(L)s, 10 HPs, and 57 RRs. Detailed analyses were also conducted on their gene structures, conserved domains, and phylogenetic relationships. Moreover, this study analysed the gene expression profiles across diverse organs and investigated their response patterns to adverse environmental stresses. Results revealed that 87 TCS genes were distributed across 18 chromosomes, with uneven distribution. Expansion of these genes in switchgrass was achieved through both fragment and tandem duplication. PvTCS members are relatively conservative in the evolutionary process, but the gene structure varies significantly. Various cis-acting elements, varying in types and amounts, are present in the promoter region of PvTCSs, all related to plant growth, development, and abiotic stress, due to the TCS gene structure. Protein-protein interaction and microRNA prediction suggest complex interactions and transcriptional regulation among TCS members. Additionally, most TCS members are expressed in roots and stems, with some genes showing organ-specific expression at different stages of leaf and inflorescence development. Under conditions of abiotic stress such as drought, low temperature, high temperature, and salt stress, as well as exogenous abscisic acid (ABA), the expression of most TCS genes is either stimulated or inhibited. Our systematic analysis could offer insight into the characterization of the TCS genes, and further the growth of functional studies in switchgrass., (© 2024. The Author(s).)

The inflorescences morphology (IM) of sorghum (Sorghum bicolor L. Moench) affects its resistance to pests, diseases, and grain yields. However, the specific genetic factors underlying in IM are not yet fully elucidated. Here we conducted a comprehensive genome-wide association analysis (GWAS) to identify the stable and adaptive Quantitative Trait Loci (QTL) for five IM traits (panicle length, the number of cob nodes, the number of primary branches, the largest length of the primary branch, and panicle type) in a sorghum panel, which adapted to different environments from the south to north in China. Totally, 2,015,850 high quality single nucleotide polymorphisms (SNPs) were obtained. Population structure analysis showed that two distinct genetic sub-populations were divided according to their geographic origin. Seventy-one QTLs distributed in 41 genetic regions on 9 chromosomes were identified. These regions harbored 21 high-confident candidate genes that were homologous to rice domestication genes, including 7 related to IM. Two domestication-related genes (Sobic.003G052700 and Sobic.006G247700) were located into two major QTL regions (QTL3.4721839 and QTL6.58709500) which were identified in multi-environments. Allelic variations in the two genes displayed a geographical pattern, indicating that different IM traits were selected by south and north sorghum breeders, such as south sorghums had long and loose panicles in order to adapt the hot and humid climate, while north sorghums had short and compact panicle to increase planting density and grain yield per unit area due to dry climate. This work provides new breeding strategies and resources for developing locally adapted sorghum varieties., (© 2024. The Author(s).)

Background: Light is a critical environmental factor in plants, encompassing two vital aspects: intensity and quality. To assess the influence of different light intensities on Origanum majorana L., pots containing the herb were subjected to four levels of light intensity: 20, 50, 70, and 100% natural light. After a 60-day treatment period, the plants were evaluated for metabolite production, including total sugar content, protein, dry weight, antioxidant indices, expression of monoterpenes biosynthesis genes, and essential oil compounds. The experimental design followed a randomized complete blocks format, and statistical analysis of variance was conducted., Results: The results indicated a correlation between increased light intensity and elevated total sugar and protein content, which contributed to improved plant dry weight. The highest levels of hydrogen peroxide and malondialdehyde (MDA) were observed under 100% light intensity. Catalase and superoxide dismutase enzymes exhibited increased activity, with a 4.23-fold and 2.14-fold increase, respectively, under full light. In contrast, peroxidase and polyphenol oxidase enzyme activities decreased by 3.29-fold and 3.24-fold, respectively. As light intensity increases, the expression level of the 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) gene increases. However, beyond a light intensity of 70%, the DXR gene expression level decreased. Furthermore, the expression levels of the cytochrome P450 genes CYP71D178 and CYP71D179 exhibited an increasing trend in response to elevated light intensity. Essential oil content increased from 0.02 to 0.5% until reaching 70% light intensity. However, with further increases in light intensity, the essential oil content decreased by 54 to 0.23%., Conclusions: These findings emphasize the importance of balancing plant growth promotion and stress management under different light conditions. The research suggests that sweet marjoram plants thrive best in unshaded open spaces, resulting in maximum biomass. However, essential oil production decreases under the same conditions. For farmers in areas with an average light intensity of approximately 1700 µmol m -2 s -1 , it is recommended to cultivate sweet marjoram in shade-free fields to optimize biomass and essential oil production. Towards the end of the growth cycle, it is advisable to use shades that allow 70% of light to pass through. The specific duration of shade implementation can be further explored in future research., (© 2024. The Author(s).)

Background: The presence of potato cyst nematodes (PCN) causes a significant risk to potato crops globally, leading to reduced yields and economic losses. While the plant Solanum sisymbriifolium is known for its resistance to PCN and can be used as a trap crop, the molecular mechanisms behind this resistance remain poorly understood. In this study, genes differentially expressed were identified in control and infected plants during the early stages of the S. sisymbriifolium - G. pallida interaction., Results: Gene expression profiles were characterized for two S. sisymbriifolium cultivars, Melody and Sis6001, uninfected and infected by G. pallida. The comparative transcriptome analysis revealed a total of 4,087 and 2,043 differentially expressed genes (DEGs) in response to nematode infection in the cultivars Melody and Sis6001, respectively. Gene ontology (GO) enrichment analysis provided insights into the response of the plant to nematode infection, indicating an activation of the plant metabolism, oxidative stress leading to defence mechanism activation, and modification of the plant cell wall. Genes associated with the jasmonic and salicylic acid pathways were also found to be differentially expressed, suggesting their involvement in the plant's defence response. In addition, the analysis of NBS-LRR domain-containing transcripts that play an important role in hypersensitive response and programmed cell death led to the identification of ten transcripts that had no annotations from the databases, with emphasis on TRINITY_DN52667_C1_G1, found to be upregulated in both cultivars., Conclusions: These findings represent an important step towards understanding the molecular basis underlying plant resistance to nematodes and facilitating the development of more effective control strategies against PCN., (© 2024. The Author(s).)

Background: Drought stress markedly constrains plant growth and diminishes crop productivity. Strigolactones (SLs) exert a beneficial influence on plant resilience to drought conditions. Nevertheless, the specific function of SLs in modulating cotton's response to drought stress remains to be elucidated., Results: In this study, we assess the impact of exogenous SL (rac-GR24) administration at various concentrations (0, 1, 5, 10, 20 µM) on cotton growth during drought stress. The findings reveal that cotton seedlings treated with 5 µM exogenous SL exhibit optimal mitigation of growth suppression induced by drought stress. Treatment with 5 µM exogenous SL under drought stress conditions enhances drought tolerance in cotton seedlings by augmenting photosynthetic efficiency, facilitating stomatal closure, diminishing reactive oxygen species (ROS) generation, alleviating membrane lipid peroxidation, enhancing the activity of antioxidant enzymes, elevating the levels of osmoregulatory compounds, and upregulating the expression of drought-responsive genes. The suppression of cotton SL biosynthesis genes, MORE AXILLARY GROWTH 3 (GhMAX3) and GhMAX4b, impairs the drought tolerance of cotton. Conversely, overexpression of GhMAX3 and GhMAX4b in respective Arabidopsis mutants ameliorates the drought-sensitive phenotype in these mutants., Conclusion: These observations underscore that SLs significantly bolster cotton's resistance to drought stress., (© 2024. The Author(s).)

Vitamin B6 (VB6), as an essential component involved in numerous biological activities of animals and plants, reflects the nutritional quality of cereal crops such as rice. Few studies have been conducted to mine the genes controlling the VB6 content in rice grains, and the available studies remain to be deepened. In this study, the recombinant inbred lines created from parents 'HZ' and 'Nekken2' served as the experimental materials. Based on QTL mapping, the initial screening identified ten candidate genes. The expression levels of LOC _ Os01g52450 , LOC _ Os01g52500 , LOC _ Os05g09500 , LOC _ Os05g09440 , LOC _ Os05g20570 , and LOC _ Os05g36270 showed significant differences between the parents. According to the gene expression and parental VB6 content, we hypothesized LOC _ Os05g09500 as the key gene affecting the VB6 content in rice grains, and the high expression of this gene significantly influenced the VB6 content. The results of this study fill a gap in the QTL mapping on the VB6 content of rice grains and provide theoretical support for elucidating the molecular genetic mechanisms and cloning the related genes of VB6 synthesis in rice. In addition, the findings have significant implications for identifying, screening, and breeding new rice cultivars with high VB6 content.

The root architecture, more seminal roots, and Deeper roots help the plants to uptake the resources from the deeper soil layer to ensure better growth. The Gibberellic acid-sensitive (GA-sensitive) Rht genes are well known for increasing drought tolerance in wheat. Much work has been performed on the effect of these genes on the plant agronomic traits and little work has been done on the effect of Rht genes on seminal roots and root architecture. This study was designed to evaluate 200 wheat genotypes under normal and osmotic stress. The genotypes were sown in the solution culture and laid under CRD factorial arrangement with three replications and two factors i.e., genotypes and treatments viz. normal and osmotic stress (20% PEG-6000) applied one week after germination. The data was recorded for the root traits. Results demonstrated that out of 200 genotypes, the GA-sensitive Rht13 gene was amplified in 21 genotypes with a fragment length of 1089 bp. In comparison, the GA-insensitive Rht1 gene was amplified in 24 genotypes with a band size of 228 bp. From 200 wheat genotypes, 122 genotypes produced 5 seminal roots, 4 genotypes 4 seminal roots, and 74 genotypes 3 seminal roots. The genotypes G-3 (EBW11TALL#1/WESTONIA-Rht5//QUAIU#1), G-6 (EBW01TALL#1/SILVERSTAR-Rht13B//ROLF07) and G-8 (EBW01TALL#1/SILVERSTAR-Rht13B//NAVJ07) produced 5 seminal roots and have longer coleoptile (> 4.0 cm), root (> 11.0 cm) and shoot (> 17 cm) under normal and osmotic stress. Furthermore, Ujala 16, Galaxy-13, and Fareed-06 produced 3 seminal roots and have short coleoptile (< 3 cm), root (< 9.0 cm) and shoot (< 10.0 cm). These results showed that the genotypes showing the presence of GA-sensitive Rht genes produced a greater number of seminal roots, increased root/shoot growth, and osmotic stress tolerance compared to the genotypes having GA-insensitive Rht genes. Thus, the Rht13 gene improved the root architecture which will help to uptake the nutrients from deeper soil layers. Utilization of Rht13 in wheat breeding has the potential to improve osmotic stress tolerance in wheat., (© 2024. The Author(s).)

Background: Wild jujube trees in Ningxia, China, demonstrate exceptional drought tolerance. The identification of quantitative trait loci (QTLs) associated with drought resistance and linked genes could significantly enhance molecular breeding efforts for this species. This study involved the measurement of nine drought resistance indicators were measured in 150 wild jujube trees from five regions in Ningxia. Genome-wide association studies (GWAS) were carried out using a range of mixed linear models to pinpoint SNP markers linked to drought resistance., Results: The coefficients of variation for the nine leaf traits in wild jujube trees ranged from 14.76 to 62.17%, with broad-sense heritability estimates falling between 0.84 and 0.99. Through GWAS analysis, a total of 12 significant SNPs and 162 potential genes associated with drought resistance were detected. This SNPs explained phenotypic variance ranging from 20.74 to 50.37%. Gene Ontology (GO) functional annotation highlighted five crucial candidate genes‒ZjMYB44, ZjUCLOC, ZjDnaJ50, ZjUCHL22 and ZjHSFB‒linked to drought tolerance in wild jujube. These genes demonstrated a positive correlation with drought tolerance within the wild jujube population., Conclusions: Our findings indicate that these five genes likely play a pivotal role in conferring drought tolerance in wild jujubes. This study offers new insights to support the development of drought-resistant jujube varieties, thereby contributing to sustainable agricultural practices and bolstering food security in arid regions., (© 2024. The Author(s).)

Background: Grapes are highly valued for their nutritional and economic benefits, and have been widely studied for their biological attributes such as fruit development, quality formation, and stress resistance. One significant threat to grape quality is gray mold, caused by Botrytis cinerea, which can infect the flowers, fruits, leaves, and stems. The quantitative real-time PCR (qRT-PCR), known for its high sensitivity and quantitative accuracy, is an essential tool for analyzing gene expression related to the pathogenesis of gray mold, thereby providing deeper insights into the disease., Result: In this study, we aim to identify stable internal reference genes crucial for accurate gene expression analysis via qRT-PCR. Utilizing transcriptome data from grapes under various disease stresses, we identified twelve candidate reference genes with consistently high expression levels. The stability of these genes was assessed through delta-CT, geNorm, NormFinder, BestKeeper, and RefFinder analyses after establishing the cycling thresholds (Ct) in different grape varieties treated with Botrytis cinerea., Conclusions: Our findings reveal that VIT-17s0000g02750 and VIT-06s0004g04280 exhibit stable expression and are suitable as new reference genes. This foundational work supports further research into the molecular mechanisms of grape biological processes., (© 2024. The Author(s).)

Background: Kiwiberry is an emerging edible fruit with market potential owing to its advantages of small size, thin and hairless skin, and sweet taste. However, kiwiberry is highly susceptible to softening after harvest, which poses a challenge for storage and transport. To reveal the underlying cause of kiwiberry softening, it is essential to investigate the characteristics of postharvest fruit and the molecular mechanisms that affect changes in fruit firmness., Results: Morphological observations and analysis of physical parameters showed that the skin of kiwiberry did not change markedly from the 1st to the 7th day after harvest, while the colour of the inner pericarp gradually turned yellow. By the 9th day of room temperature storage, the kiwiberries began to rot. The hardness decreased rapidly from the 1st to the 5th day postharvest, reaching the low level on the 5th day. The starch and pectin contents of kiwiberry showed a downward trend with increasing storage time. Transcriptome sequencing and weighted gene co-expression network analysis identified 29 key genes associated with the changes in the hardness of kiwiberry after harvest. Gene Ontology enrichment analysis indicated that these 29 genes are mainly involved in pectin metabolism, starch synthesis, starch decomposition, and starch metabolism. In addition, three transcription factors, AGL31, HAT14, and ALC, were identified to be strongly positively correlated with the 29 genes that affect the hardness changes of kiwiberry after harvest, and 28 of the 29 key genes were predicted to be regulated by HAT14., Conclusions: These results reveal the changes in morphological characteristics and physiological indicators during the postharvest ripening and softening of kiwiberry stored under room temperature conditions. Transcriptome analysis identified 29 key genes and three transcription factors that affect the firmness changes of postharvest kiwiberry. The results of this study thus provide insight into the transcriptional regulatory mechanism of kiwiberry softening during storage to improve the postharvest quality., (© 2024. The Author(s).)

Key Message: The soybean Rxp gene, encoding a bHLH transcription factor and an ACT-like domain, has an rxp allele producing a truncated protein that confers resistance to pustule-causing Xanthomonas axonopodis pv. glycines. In soybean, bacterial pustules caused by Xanthomonas axonopodis pv. glycines lead to premature defoliation and decreased yield in warm, wet climates. In the USA, approximately 70 years ago, bacterial pustules were eliminated by introducing a recessive resistance allele, rxp, of the Rxp gene, representing the first example of successful soybean breeding for durable disease resistance in North America. In this study, we isolated this historical Rxp gene from resistant soybean varieties using positional cloning. The 1.06 Mb region where Rxp was reported to reside was narrowed down to an 11.1 kb region containing a single gene, Glyma.17g090500. The resistance allele, rxp, contains a T insertion. A complementation test of the Rxp allele in resistant plants confirmed the identification of the Rxp gene. The product of the susceptible wild-type allele, Rxp, is presumed to be a basic helix-loop-helix (bHLH) transcription factor with an aspartate kinase, chorismate mutase, and TyrA (ACT)-like domain. This gene was mainly expressed in extended leaves, and its homologs were identified to be distributed in angiosperms. A total of six alleles were obtained: four from spontaneous variation, including the wild-type and three mutant alleles that encoded truncated proteins, and two from ethyl methanesulfonate mutants, including an allele that encoded a truncated protein and a missense allele. By evaluating the resistance of these six alleles, we found that the loss of function of RXP decreased the bacterial pustule lesions. This study provides important insights into the soybean rxp allele, which confers durable resistance to bacterial pustules., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Key Message: In summary, we characterized a maize semi-dwarf mutant, sdw9, and successfully isolated the responsible gene, which encodes a GRAS protein, through a combination of map-based cloning and Re-sequencing (Re-seq). Our findings demonstrate that the candidate gene ZmGRAS42 regulates BR signaling genes, thereby influencing internode development. This regulatory function likely involves processes such as cell division, cell cycle regulation and cell wall synthesis. Favorable variations of ZmGRAS42 identified in this study may hold promise for the development of lodging-resistant maize cultivars suitable for high-density planting, contributing to the improvement of maize breeding programs. Plant height and lateral root angle are crucial determinants of plant architecture in maize (Zea mays) which are closely related to lodging resistance at high planting density. These traits are intricately regulated by various phytohormones. Mutations affecting hormone biosynthesis and signaling often lead to reduced yield alongside diminished plant height, posing challenges in breeding dwarf maize varieties. In this study, the maize mutant sdw9 was characterized, which displays shorter stature and altered lateral root angle compared to WT, while showing potential to increase planting density and improve overall yield despite a slight reduction in single-ear yield. Employing positional cloning coupled with Re-seq techniques, we pinpointed a transposon insertion in the candidate gene ZmGRAS42, which encodes a GRAS transcription factor involved in BR signaling in maize. Transcriptome analysis revealed that ZmGRAS42 orchestrates the expression of several known dwarfing genes such as D8, Br2, and Na2, along with genes associated with cell wall organization, cell division, and cell cycle regulation, notably Cesa4, Cesa7, and Cyc11. Furthermore, identification of favorable ZmGRAS42 haplotypes linked to reduced plant height offers novel avenues for maize breeding strategies. These findings not only hold the potential for enhancing maize lodging resistance but also for optimizing land utilization through high-density planting practices., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Background: Evidence shows that full mycoheterotrophs and holoparasites often have reduced plastid genomes with rampant gene loss, elevated substitution rates, and deeply altered to conventional evolution in mitochondrial genomes, but mechanisms of cytonuclear evolution is unknown. Endoparasitic Sapria himalayana and mycoheterotrophic Gastrodia and Platanthera guangdongensis represent different heterotrophic types, providing a basis to illustrate cytonuclear evolution. Here, we focused on nuclear-encoded plastid / mitochondrial (N-pt / mt) -targeting protein complexes, including caseinolytic protease (ClpP), ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCo), oxidative phosphorylation system (OXPHOS), DNA recombination, replication, and repair (DNA-RRR) system, and pentatricopeptide repeat (PPR) proteins, to identify evolutionary drivers for cytonuclear interaction., Results: The severity of gene loss of N-pt PPR and pt-RRR genes was positively associated with increased degree of heterotrophy in full mycoheterotrophs and S. himalayana, while N-mt PPR and mt-RRR genes were retained. Substitution rates of organellar and nuclear genes encoding N-pt/mt subunits in protein complexes were evaluated, cytonuclear coevolution was identified in S. himalayana, whereas disproportionate rates of evolution were observed in the OXPHOS complex in full mycoheterotrophs, only slight accelerations in substitution rates were identified in N-mt genes of full mycoheterotrophs., Conclusions: Nuclear compensatory evolution was identified in protein complexes encoded by plastid and N-pt genes. Selection shaping codon preferences, functional constraint, mt-RRR gene regulation, and post-transcriptional regulation of PPR genes all facilitate mito-nuclear evolution. Our study enriches our understanding of genomic coevolution scenarios in fully heterotrophic plants., (© 2024. The Author(s).)

Background: Cabbage (Brassica oleracea L. var. capitata) is an important crop within the Brassica oleracea species and is extensively cultivated worldwide. In recent years, outbreaks of downy mildew caused by Hyaloperonospora parasitica have resulted in substantial losses in cabbage production. Despite this, there have been limited studies on genes associated with resistance to downy mildew in cabbage., Results: This study identified sister lines exhibiting significant differences in disease resistance and susceptibility. Using bulked segregant analysis followed by sequencing (BSA-seq) and linkage analysis, the cabbage resistance locus BoDMR2 was accurately mapped to an approximately 300 kb interval on chromosome 7. Among the candidate genes identified, several single nucleotide polymorphisms (SNPs) and a 3-bp insertion were found within the conserved domain of the Bo7g117810 gene, encoding a leucine-rich repeat domain protein, in susceptible genotypes. Additionally, real-time quantitative polymerase chain reaction (RT‒qPCR) analysis revealed that the expression level of Bo7g117810 in resistant specimens was 2.5-fold higher than that in susceptible specimens. An insertion‒deletion (InDel) marker was designed based on the identified insertion in susceptible materials, facilitating the identification and selection of downy mildew-resistant cabbage cultivars., Conclusions: This study identifies Bo7g117810 as a potential candidate gene associated with adult-stage resistance to downy mildew in cabbage, supported by observed differences in gene sequence and expression levels. Furthermore, the development of an InDel marker I1-3, based on its mutation, provides valuable resources for breeding resistant cabbage cultivars., (© 2024. The Author(s).)

Key Message: A stable QTL, GW3, controlling grain width was identified in two populations. Its causal gene LOC&#95;Os03g04680 was verified by gene-based haplotype analysis, expression analysis, gene knockout and complementation transgenic tests. Grain width (GW) is one of the key traits affecting grain size and determines grain yield and appearance quality in rice. Mining gene loci and elite alleles controlling GW is necessary. The GW phenotypes of the two populations were investigated in three environments, which showed abundant phenotypic variation. GW3, encoding a P450 subfamily protein, was identified and validated as a causal gene by gene-based haplotype analysis, expression analysis, gene knockout and complementation transgenic tests. The accessions with large GW values had high gene expression levels. In addition, the GW of the accessions with the GG allele was significantly greater than that of the accessions with the AA allele. The Hap 1 and Hap 3 were identified as elite haplotypes, which can increase GW. The expression levels of OsKO1, OsGA3ox1, OsGA20ox1 and OsGA20ox2 in the young panicle of A7444 were significantly greater than those in the young panicle of the mutants, indicating that GW3 may be involved in the gibberellins (GA) biosynthesis pathway to regulate GW. GA 4 content detection and electron scanning analysis revealed that GA 4 regulates GW by affecting glume cell size. These results provide new insights for studying the genetic mechanism of rice GW and provide a material basis for breeding high-yield rice varieties., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Key Message: The combination of a QTL on chromosome arm 4BL and Yr29 provides durable resistance with no significant yield penalty. Wheat stripe rust or yellow rust (YR), caused by Puccinia striiformis f. sp. tritici (Pst), causes substantial yield reductions globally, but losses can be minimized by using resistance genes. Chinese wheat cultivar Jing 411 (J411) has continued to display an acceptable level of adult-plant resistance (APR) to YR in varied field conditions since its release in the 1990s. A recombinant inbred line (RIL) population comprising 187 lines developed from a cross of J411 and Kenong 9204 (KN9204) was evaluated in multiple environments to identify genomic regions carrying genes for YR resistance. A total of five quantitative trait loci (QTL) on chromosome arm 1BL, 3BS, 4BL, 6BS, and 7BL from J411 and two QTL on 3DS and 7DL from KN9204 were detected using inclusive composite interval mapping with the wheat 660 K SNP array. QYr.nwafu-1BL.5 and QYr.nwafu-4BL.3 from J411 were robust and showed similar effects in all environments. QYr.nwafu-1BL.5 was likely the pleiotropic gene of Yr29/Lr46. QYr.nwafu-4BL.3 was located within a 1.0 cM interval delimited by KASP markers AX-111609222 and AX-89755491. Based on haplotype analysis, Yr29 and QYr.nwafu-4BL.3 were identified as genetic components of quantitative resistance in a number of wheat cultivars. Moreover, RILs with Yr29 and QYr.nwafu-4BL.3 individually or when combined showed higher resistance to YR in rust nurseries compared with RILs without them, and there was no negative effect of their presence on agronomic traits under rust-free conditions. These results suggest that effective polymerization strategy is important for breeding high yielding and durable resistance cultivars., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Bract coloration is one of the key ornamental traits in Bougainvillea, yet research has predominantly focused on phenotypic color traits and pigment composition, with limited understanding of the molecular mechanisms underlying color formation. This gap hinders the improvement and innovation in bract coloration. To elucidate the regulatory mechanisms of bract coloration in Bougainvillea and to enhance the utilization of its germplasm resources, this study employed the Illumina Novaseq 6000 sequencing platform to conduct transcriptomic sequencing on 21 samples of bracts exhibiting seven distinct phenotypes. Comparative analysis against Nr, Pfam, EggNOG, GO, and KEGG databases annotated 90,279 unigenes. The highest annotation rates were achieved with the Nr (40.13%), GO (30.44%), and EggNOG (25.64%) databases. Among the species annotated, Beta vulgaris (20.08%) and Chenopodium quinoa (14.58%) shared the highest homology with Bougainvillea bract transcriptomes. WGCNA analysis identified 12 positively correlated tissue-specific modules, of which 2 are related to bract color formation. By comparing transcriptome data and genes within these specific modules against the KEGG database, a total of 321 unigenes associated with bract color formation in Bougainvillea were discovered. Among these, 220 unigenes are involved in anthocyanin synthesis, 43 unigenes are involved in betalain synthesis, 23 unigenes are annotated as Chlorophyll a-b binding protein genes, and 35 unigenes participate in carotenoid synthesis. Quantitative real-time PCR (qRT-PCR) validation of 16 differentially expressed genes (DEGs) including PAL2, CHS1, ANS, BZ1, 6GT, CDOPA5GT, ANR, CHS2, and DOPA, revealed significant expression differences among magenta, yellow, white, and cherry-colored bracts, suggesting their potential as candidate genes for bract color development. This study not only enriches the transcriptomic data of Bougainvillea but also identifies genes associated with bract coloration, providing a valuable theoretical basis for future gene cloning, genetic engineering, and breeding efforts in Bougainvillea., (© 2024. The Author(s).)

Background: Plant A/T-rich protein and zinc-binding protein (PLATZ) transcription factors are pivotal regulators in various aspects of plant biology, including growth, development, and responses to environmental stresses. While PLATZ genes have been extensively studied and functionally characterized in various plants, limited information is available for these genes in barley., Results: Here, we discovered a total of 11 PLATZ genes distributed across seven chromosomes in barley. Based on phylogenetic and conserved motif analysis, we classified PLATZ into five subfamilies, comprising 3, 1, 2, 1 and 4 genes, respectively. Analysis of gene structure demonstrated that these 11 HvPLATZ genes typically possessed two to four exons. Most HvPLATZ genes were found to possess at least one ABRE cis-element in their promoter regions, and a few of them also contained LTR, CAT-box, MRE, and DRE cis-elements. Then, we conducted an exploration of the expression patterns of HvPLATZs, which displayed notable differences across various tissues and in response to abiotic stresses. Functional analysis of HvPLATZ6 and HvPLATZ8 in yeast cells showed that they may be involved in drought tolerance. Additionally, we constructed a regulatory network including miRNA-targeted gene predictions and identified two miRNAs targeting two HvPLATZs, such as hvu-miR5053 and hvu-miR6184 targeting HvPLATZ2, hvu-miR6184 targeting HvPLATZ10., Conclusion: In summary, these findings provide valuable insights for future functional verification of HvPLATZs and contribute to a deeper understanding of the role of HvPLATZs in response to stress conditions in barley., (© 2024. The Author(s).)

Exchangeable aluminum (Al) ions released from acidic soils with pH < 5.5 inhibit root elongation of crops, ultimately leading to yield reduced. It is necessary to identify the quantitative trait locus (QTLs) and candidate genes that confer toxicity resistance to understand the mechanism and improve tolerance of rapeseed. In this study, an F 2 segregating population was derived from a cross between Al-tolerance inbred line FDH188 (R178) and -sensitive inbred line FDH152 (S169), and the F 2:3 were used as materials to map QTLs associated with the relative elongation of taproot (RET) under Al toxicity stress. Based on bulked segregant analysis sequencing (BSA-seq), three QTLs ( qAT-A07-1 , qAT-A07-2 , and qAT-A09-1 ) were detected as significantly associated with RET, and 656 candidate genes were screened. By combined BSA and RNA-seq analysis, 55 candidate genes showed differentially expressed, including genes encoding ABC transporter G (ABCG), zinc finger protein, NAC, ethylene-responsive transcription factor (ERF), etc. These genes were probably positive factors in coping with Al toxicity stress in rapeseed. This study provides new insight into exploring the QTLs and candidate genes' response to Al toxicity stress by combined BSA-seq and RNA-seq and is helpful to further research on the mechanism of Al resistance in rapeseed.

Elaeagnus mollis is an important newly developing woody oil plant species and the vitamin E (VitE) content in its kernel oil is relatively high. In the present study, the VitE component content and functional genes involving in VitE biosynthesis in E. mollis kernel at different developmental stage were investigated. The VitE content increased with kernel development, reaching up to ~ 7.96 mg/g oil in kernel mature stage. The content of tocopherol was much higher than that of tocotrienol and γ-tocopherol became the dominant component. E. mollis kernel extracts had relatively strong antioxidant capacity. We identified 17 genes (16 VTEs and 1 homogentisic acid geranylgeranyl transferase (HGGT)) directly involving in VitE biosynthesis in RNA-Seq data. Phylogenetic and qRT-PCR results indicated that the annotation and reliability of the RNA-Seq were accurate. Transient overexpression of EmVTE3 and EmWRKY13 in tobacoo leaves increased and decreased the VitE content to 192.18 and 118.29 µg/g, respectively. Weighted gene co-expression analysis elucidated that the blue module showed significant correlation with tocopherol content. Co-expression network analysis revealed that 2-methyl-6-phytobenzoquinone methyltransferase (MPBQ-MT/VTE3) played a vital role and EmWRKY13 may be a key negative regulator in E. mollis VitE biosynthesis. This study not only revealed the traditional VitE biosynthesis pathway in E. mollis, but also set a solid foundation for future genetic breeding of this species., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

Improving the powdery mildew resistance of bitter gourd is highly important for achieving high yield and high quality. To better understand the genetic basis of powdery mildew resistance in bitter gourd, this study analyzed 300 lines of recombinant inbred lines (RILs) formed by hybridizing the powdery mildew-resistant material MC18 and the powdery mildew-susceptible material MC402. A high-density genetic map of 1222.04 cM was constructed via incorporating 1,996,505 SNPs generated by resequencing data from 180 lines, and quantitative trait locus (QTL) positioning was performed using phenotypic data at different inoculation stages. A total of seven QTLs related to powdery mildew resistance were identified on four chromosomes, among which qPm-3-1 was detected multiple times and at multiple stages after inoculation. By selecting 18 KASP markers that were evenly distributed throughout the region, 250 lines and parents were genotyped, and the interval was narrowed to 207.22 kb, which explained 13.91% of the phenotypic variation. Through RNA-seq analysis of the parents, 11,868 differentially expressed genes (DEGs) were screened. By combining genetic analysis, gene coexpression, and sequence comparison analysis of extreme materials, two candidate genes controlling powdery mildew resistance in bitter gourd were identified ( evm.TU.chr3.2934 (C3H) and evm.TU.chr3.2946 (F-box-LRR)). These results represent a step forward in understanding the genetic regulatory network of powdery mildew resistance in bitter gourd and lay a molecular foundation for the genetic improvement in powdery mildew resistance.

The southern root-knot nematode, Meloidogyne incognita, is a highly serious plant parasitic nematode species that causes significant economic losses in various crops, including cucumber (Cucumis sativus L.). Currently, there are no commercial cultivars available with resistance to M. incognita in cucumber. However, the African horned melon (Cucumis metuliferus Naud.), a semi-wild relative of cucumber, has shown high resistance to M. incognita. In this study, we constructed an ultrahigh-density genetic linkage bin-map using low-coverage sequences from an F 2 population generated through the cross between C. metuliferus inbred lines CM3 and CM27. Finally, we identified a QTL (quantitative trait locus, QTL3.1) with a LOD (logarithm of the odds) score of 3.84, explaining 8.4% of the resistance variation. Subsequently, by combining the results of qPCR (quantitative PCR) and VIGS (virus-induced gene silencing), we identified two genes, EVM0025394 and EVM0006042, that are potentially involved in the resistance to M. incognita in CM3. The identification of QTLs and candidate genes in this study serve as a basis for further functional analysis and lay the groundwork for harnessing this resistance trait., (© 2024. The Author(s).)

Drought stress poses a critical threat to global crop yields and sustainable agriculture. The GASA genes are recognized for their pivotal role in stress tolerance and plant growth, but little is known about how they function in sunflowers. The investigation aimed to identify and elucidate the role of HaGASA genes in conferring sunflowers with drought tolerance. Twenty-seven different HaGASA gene family members were found in this study that were inconsistently located across eleven sunflower chromosomes. Phylogeny analysis revealed that the sunflower HaGASA genes were divided into five subgroups by comparing GASA genes with those from Arabidopsis, peanut, and soybean, with members within each subgroup displaying similar conserved motifs and gene structures. In-silico evaluation of cis-regulatory elements indicated the existence of specific elements associated with stress-responsiveness being the most abundant, followed by hormone, light, and growth-responsive elements. Transcriptomic data from the NCBI database was utilized to assess the HaGASA genes expression profile in different sunflower varieties under drought conditions. The HaGASA genes expression across ten sunflower genotypes under drought stress, revealed 14 differentially expressed HaGASA genes, implying their active role in the plant's stress response. The expression in different organs revealed that HaGASA2, HaGASA11, HaGASA17, HaGASA19, HaGASA21 and HaGASA26 displayed maximum expression in the stem. Our findings implicate HaGASA genes in mediating sunflower growth maintenance and adaptation to abiotic stress, particularly drought. The findings, taken together, provided a basic understanding of the structure and potential functions of HaGASA genes, setting the framework for further functional investigations into their roles in drought stress mitigation and crop improvement strategies., (© 2024. The Author(s).)

Key Message: Platanus acerifolia AIL genes PaAIL5a/b and PaAIL6b participate in FT-AP1/FUL-AIL pathways to regulate bud dormancy. In addition, PaAIL6a/b can promote flowering, and PaAIL5b and PaAIL6b affect floral development. Bud dormancy and floral induction are essential processes for perennial plants, they are both regulated by photoperiod, temperature, and hormones, indicating the existence of common regulators for both processes. AINTEGUMENTA-LIKE (AIL) genes regulate reproductive growth of annual plants, including floral induction and flower development, and their homologs in poplar and grape act downstream of the florigen gene FT and the floral meristem identity genes AP1/FUL and function to maintain growth and thus inhibit dormancy induction. However, it is not known whether AIL homologs participate in the reproduction processes in perennials and whether the Platanus acerifolia AIL genes are involved in dormancy. P. acerifolia is a perennial woody plant whose reproductive growth is strongly associated with dormancy. Here, we isolated four AIL homologs from P. acerifolia, PaAIL5a, PaAIL5b, PaAIL6a, and PaAIL6b, and systematically investigated their functions by ectopic-overexpression in tobacco. The findings demonstrate that PaAIL5a/b and PaAIL6b respond to short day, low temperature, and hormone signals and act as the components of the FT-AP1/FUL-AIL pathway to regulate the bud dormancy in P. acerifolia. Notably, PaAIL5a/b and PaAIL6b function downstream of PaFTL-PaFUL1/2/3 to inhibit the dormancy induction and downstream of PaFT-PaFUL2/3 to promote the dormancy release. In addition, PaAIL6a/b were found to accelerate flowering in transgenic tobacco, whereas PaAIL5b and PaAIL6b affected the flower development. Together, our results suggest that PaAIL genes may act downstream of different PaFT/PaFTL and PaFUL proteins to fulfill conservative and diverse roles in floral initiation, floral development, and dormancy regulation in P. acerifolia., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Temperature is an important limiting factor in the counter-seasonal cultivation of pepper. Currently, there are no studies on transcriptomic analysis of 'cold stress memory' in pepper. In this study, in order to understand the mechanism of 'cold stress memory' in pepper (Capsicum annuum L.), seedlings were subjected to the following treatments: normal temperature treatment (P0), the first cold treatment for 3 days (P3), the recovery temperature treatment for 3 days (R3), and another cold treatment for 3 days (RP3). The results showed that P3 plants wilted the most, RP3 the second and R3 the least. Leaf reactive oxygen species (ROS) and electrolyte leakage were the most in P3, the second in RP3 and the least in R3. In addition, RP3 had the highest accumulation of zeaxanthin, violaxanthin and β-cryptoxanthin, followed by P3, and R3 had the least. These results suggest that pepper seedlings are characterized by 'cold stress memory'. Transcriptomics was used to analyze the key genes and transcription factors involved in the biosynthesis of zeaxanthin, violaxanthin and β-cryptoxanthin during the formation of 'cold stress memory'. This study provides candidate genes and transcription factors for an in-depth study of the cold tolerance mechanism in pepper., (© 2024. The Author(s).)

A genome-wide association study (GWAS) identifies trait-associated loci, but identifying the causal genes can be a bottleneck, due in part to slow decay of linkage disequilibrium (LD). A transcriptome-wide association study (TWAS) addresses this issue by identifying gene expression-phenotype associations or integrating gene expression quantitative trait loci with GWAS results. Here, we used self-pollinated soybean (Glycine max [L.] Merr.) as a model to evaluate the application of TWAS to the genetic dissection of traits in plant species with slow LD decay. We generated RNA sequencing data for a soybean diversity panel and identified the genetic expression regulation of 29 286 soybean genes. Different TWAS solutions were less affected by LD and were robust to the source of expression, identifing known genes related to traits from different tissues and developmental stages. The novel pod-color gene L2 was identified via TWAS and functionally validated by genome editing. By introducing a new exon proportion feature, we significantly improved the detection of expression variations that resulted from structural variations and alternative splicing. As a result, the genes identified through our TWAS approach exhibited a diverse range of causal variations, including SNPs, insertions or deletions, gene fusion, copy number variations, and alternative splicing. Using this approach, we identified genes associated with flowering time, including both previously known genes and novel genes that had not previously been linked to this trait, providing insights complementary to those from GWAS. In summary, this study supports the application of TWAS for candidate gene identification in species with low rates of LD decay., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Background: Heterosis is a common phenomenon in plants and has been extensively applied in crop breeding. However, the superior traits in the hybrids can only be maintained in the first generation but segregate in the following generations. Maintaining heterosis in generations has been challenging but highly desirable in crop breeding. Recent study showed that maternally produced diploid seeds could be achieved in rice by knocking out three meiosis related genes, namely REC8, PAIR1, OSD1 to create MiMe in combination with egg cell specific expression of BBM transcription factor, a technology called clonal seeds. Interestingly, there has been very limited reports indicating the feasibility of this approach in other crops., Results: In this study, we aimed to test whether clonal seeds could be created in cotton. We identified the homologs of the three meiosis related genes in cotton and used the multiplex CRISPR/Cas9 gene editing system to simultaneously knock out these three genes in both A and D sub-genomes. More than 50 transgenic cotton plants were generated, and fragment analysis indicated that multiple gene knockouts occurred in the transgenic plants. However, all the transgenic plants were sterile apparently due to the lack of pollen. Pollination of the flowers of the transgenic plants using the wild type pollens could not generate seeds, an indication of defects in the formation of female sexual cells in the transgenic plants. In addition, we generated transgenic cotton plants expressing the cotton BBM gene driven by the Arabidopsis egg cell specific promoter pDD45. Two transgenic plants were obtained, and both showed severely reduced fertility., Conclusions: Overall, our results indicate that knockout of the clonal seeds related genes in cotton causes sterility and how to manipulate genes to create clonal seeds in cotton requires further research., (© 2024. The Author(s).)

Powdery mildew infection is a significant challenge in butternut squash ( Cucurbita moschata ) production during winter in Hainan, China. The tropical climate of Hainan promotes powdery mildew infection, resulting in substantial yield losses. By utilizing transcriptome and genome sequencing data, SNPs and potential genes associated with powdery mildew resistance in butternut squash were identified. The analysis of differentially expressed genes (DEGs) following powdery mildew infection revealed several genes involved in resistance, with particular focus on a resistance (R) gene cluster that may be linked to the observed resistance. Two MLO genes in clade V from Cucurbita moschata may not be directly associated with resistance in the two genotypes studied. These findings are expected to contribute to the development of genetic tools for improving powdery mildew resistance in Cucurbita crops, thereby reducing yield losses and enhancing the sustainability of butternut squash production in Hainan and other regions.

Background: TOBAMOVIRUS MULTIPLICATION 1 (TOM1) and its homolog TOBAMOVIRUS MULTIPLICATION 3 (TOM3) play a prominent role in the multiplication of tobacco mosaic virus (TMV) in higher plants. Although homologs of NtTOM1/TOM3 genes have been identified in several plant species, little is known about the characteristics and functions of NtTOM1/TOM3 at the genome-wide level in tobacco (Nicotiana tabacum L.)., Results: In this study, we performed genome-wide identification and expression pattern analysis of the tobacco NtTOM1/TOM3 gene family. Twelve NtTOM1/TOM3 genes were identified and classified into four groups based on phylogenetic analysis. Sequence and conserved domain analyses showed that all these genes contained a specific DUF1084 domain. Expression pattern analysis showed that NtTOM1a, NtTOM1b, NtTOM1d, NtTOM3a, NtTOM3b, and NtTOM3d were induced by TMV at 1-, 3-, and 9 dpi, whereas the expression of other genes was not responsive to TMV at the early infection stage. TMV virion accumulation showed no obvious difference in either nttom1a or nttom3a mutants compared with the wild type. However, the virus propagation was significantly, but not completely, inhibited in the nttom1atom3a double mutant, indicating that other gene family members may function redundantly, such as NtTOM1b and NtTOM1d. In addition, overexpression of NtTOM1a or NtTOM3a also inhibited the TMV replication to some extent., Conclusions: The present study performed genome-wide analysis of the NtTOM1/TOM3 gene family in tobacco, and identified NtTOM1a and NtTOM3a as important genes involved in TMV multiplication based on functional analysis. These results provide a theoretical basis for further improving TMV resistance in tobacco., (© 2024. The Author(s).)

The sugar and organic acid content significantly impacts the flavor quality of star fruit, and it undergoes dynamic changes during development. However, the metabolic network and molecular mechanisms governing the formation of sugar and organic acid in star fruit remain unclear. In this study, 23 of 743 components were detected by metabonomic analysis. The highest metabolites contents were organic acids and derivatives. The highest sugar content in the fruit was fructose and glucose, followed by sucrose, which proved that A. carambola is a hexose accumulation type fruit. Genome identification preliminarily screened 141 genes related to glucose metabolism and 67 genes related to acid metabolism. A total of 7,881 unigenes were found in transcriptome data, 6,124 differentially expressed genes were screened, with more up-regulated than down-regulated genes. Transcriptome and metabolome association analysis screened seven core candidate genes related to glucose metabolism and 17 core genes highly related to organic acid pathway, and eight differentially expressed sugar and acid genes were selected for qRT-PCR verification. In addition, 29 bHLHs and eight bZIPs transcription factors were predicted in the glucose metabolism pathway, and 23 MYBs, nine C2H2s transcription factors and one GRAS transcription factor was predicted in the acid metabolism pathway, and transcription factors have both positive and negative regulatory effects on sugar and acid structure genes. This study increased our understanding of A. carambola fruit flavor and provided basic information for further exploring the ornamental and edible values of star fruit., (© 2024. The Author(s).)

The organosulfur compound dimethylsulfoniopropionate (DMSP) has key roles in stress protection, global carbon and sulfur cycling, chemotaxis, and is a major source of climate-active gases. Saltmarshes are global hotspots for DMSP cycling due to Spartina cordgrasses that produce exceptionally high concentrations of DMSP. Here, in Spartina anglica, we identify the plant genes that underpin high-level DMSP synthesis: methionine S-methyltransferase (MMT), S-methylmethionine decarboxylase (SDC) and DMSP-amine oxidase (DOX). Homologs of these enzymes are common in plants, but differences in expression and catalytic efficiency explain why S. anglica accumulates such high DMSP concentrations and other plants only accumulate low concentrations. Furthermore, DMSP accumulation in S. anglica is consistent with DMSP having a role in oxidative and osmotic stress protection. Importantly, administration of DMSP by root uptake or over-expression of Spartina DMSP synthesis genes confers plant tolerance to salinity and drought offering a route for future bioengineering for sustainable crop production., (© 2024. The Author(s).)

Background: Nitric oxide (NO) is pivotal in regulating the activity of NBS-LRR specific R genes, crucial components of the plant's immune system. It is noteworthy that previous research has not included a genome-wide analysis of NO-responsive NBS-LRR genes in plants., Results: The current study examined 29 NO-induced NBS-LRR genes from Arabidopsis thaliana, along with two monocots (rice and maize) and two dicots (soybean and tomato) using genome-wide analysis tools. These NBS-LRR genes were subjected to comprehensive characterization, including analysis of their physio-chemical properties, phylogenetic relationships, domain and motif identification, exon/intron structures, cis-elements, protein-protein interactions, prediction of S-Nitrosylation sites, and comparison of transcriptomic and qRT-PCR data. Results showed the diverse distribution of NBS-LRR genes across chromosomes, and variations in amino acid number, exons/introns, molecular weight, and theoretical isoelectric point, and they were found in various cellular locations like the plasma membrane, cytoplasm, and nucleus. These genes predominantly harbor the NB-ARC superfamily, LRR, LRR&#95;8, and TIR domains, as also confirmed by motif analysis. Additionally, they feature species-specific PLN00113 superfamily and RX-CC&#95;like domain in dicots and monocots, respectively, both responsive to defense against pathogen attacks. The NO-induced NBS-LRR genes of Arabidopsis reveal the presence of cis-elements responsive to phytohormones, light, stress, and growth, suggesting a wide range of responses mediated by NO. Protein-protein interactions, coupled with the prediction of S-Nitrosylation sites, offer valuable insights into the regulatory role of NO at the protein level within each respective species., Conclusion: These above findings aimed to provide a thorough understanding of the impact of NO on NBS-LRR genes and their relationships with key plant species., (© 2024. The Author(s).)

Three Hordeum spontaneum-derived resistances (referred to as 145L2, 41T1 and 40Y5) have demonstrated long-term effectiveness against barley scald, caused by Rhynchosporium commune, in western Canada. Genetic mapping of these resistances in three populations, and the use of five barley genome assemblies, revealed they co-located to a narrowly defined 0.58-1.2 Mbp region of chromosome 6HS containing the Rrs13 scald resistance gene. Differential disease reactions among the three resistances and a Rrs13 carrier (AB6) to a panel of 24 scald isolates indicated that the four resistances were unique from one another. A marker created to target the 6HS scald locus was screened across a panel of barley germplasm that included H. vulgare, H. spontaneum and H. bulbosum lines. The marker showed specificity to H. vulgare lines known to carry the 6HS scald resistances and to two H. spontaneum lines that trace their origins to Jordan. Within the 0.58-1.2 Mbp region were 2-7 tandemly repeated leucine-rich repeat receptor-like proteins (LRR-RLP) and one lectin receptor-like kinase (Lec-RLK) genes with abundant sequence variation between them. The well-defined role that RLP and RLK genes play in plant defense responses make them logical candidate resistance genes, with one possible hypothesis being that each unique scald resistance may be encoded by a different RLP that interacts with a common RLK. It is suggested the three scald resistances be temporarily named Rrs13 145L2 , Rrs13 41T1 and Rrs13 40Y5 to recognize their co-location to the Rrs13 locus until it is determined whether these resistances represent unique genes or alleles of the same gene., (© 2024. The Author(s).)

The oil content of maize kernels is essential to determine its nutritional and economic value. A multiparent population (MPP) consisting of five recombinant inbred line (RIL) subpopulations was developed to elucidate the genetic basis of the total oil content (TOC) in maize. The MPP used the subtropical maize inbred lines CML312 and CML384, along with the tropical maize inbred lines CML395, YML46, and YML32 as the female parents, and Ye107 as the male parent. A genome-wide association study (GWAS) was performed using 429 RILs of the multiparent population across three environments, employing 584,847 high-quality single nucleotide polymorphisms (SNPs). Furthermore, linkage analysis was performed in the five subpopulations to identify quantitative trait loci (QTL) linked to TOC in maize. Through QTL mapping and GWAS, 18 QTLs and 60 SNPs that were significantly associated with TOC were identified. Two novel candidate genes, Zm00001d029550 and Zm00001d029551 , related to TOC in maize and located on chromosome 1 were reported, which have not been previously reported. These genes are involved in biosynthesis, lipid signal transduction, plant development and metabolism, and stress responses, potentially influencing maize TOC. Haplotype analysis of Zm00001d029550 and Zm00001d029551 revealed that Hap3 could be considered a superior haplotype for increasing TOC in maize. A co-located SNP (SNP-75791466) on chromosome 1, located 5648 bp and 11,951 bp downstream of the candidate genes Zm00001d029550 and Zm00001d029551 , respectively, was found to be expressed in various maize tissues. The highest expression was observed in embryos after pollination, indicating that embryos are the main tissue for oil accumulation in maize. This study provides a theoretical basis for understanding the genetic mechanisms underlying maize TOC and developing high-quality, high-oil maize varieties.

Pedicel length is a crucial agronomic trait of cucumbers. Fruit deformation can occur When the pedicel is too long or too short. Moreover, an appropriate pedicel length is advantageous for mechanized harvesting. Therefore, it is essential to investigate the molecular regulatory mechanisms underlying cucumber pedicel length. In the current study, we obtained a short pedicel mutant through EMS mutagenesis and discovered that the reduced cell number was the primary cause of the shortened pedicel. Upon analyzing the hormone content, we found that the level of trans zeatin in the long-pedicel material was significantly higher than that in the short-pedicel material. Further transcriptome sequencing analysis revealed that differentially expressed genes were enriched in cytokinin synthesis-related pathways. Based on these results, the present study concluded that cucumber pedicel length is regulated by genes related to the cytokinin synthesis pathway and that differences in length result from differences in zeatin content and cell number., (© 2024. The Author(s).)

Photosynthesis is the only yield-related trait not yet substantially improved by plant breeding. Previously, we have established H. incana as the model plant for high photosynthetic light-use efficiency (LUE). Now we aim to unravel the genetic basis of this trait in H. incana, potentially contributing to the improvement of photosynthetic LUE in other species. Here, we compare its transcriptomic response to high light with that of Arabidopsis thaliana, Brassica rapa, and Brassica nigra, 3 fellow Brassicaceae members with lower photosynthetic LUE. We built a high-light, high-uniformity growing environment, in which the plants developed normally without signs of stress. We compared gene expression in contrasting light conditions across species, utilizing a panproteome to identify orthologous proteins. In-depth analysis of 3 key photosynthetic pathways showed a general trend of lower gene expression under high-light conditions for all 4 species. However, several photosynthesis-related genes in H. incana break this trend. We observed cases of constitutive higher expression (like antenna protein LHCB8), treatment-dependent differential expression (as for PSBE), and cumulative higher expression through simultaneous expression of multiple gene copies (like LHCA6). Thus, H. incana shows differential regulation of essential photosynthesis genes, with the light-harvesting complex as the first point of deviation. The effect of these expression differences on protein abundance and turnover, and ultimately the high photosynthetic LUE phenotype is relevant for further investigation. Furthermore, this transcriptomic resource of plants fully grown under, rather than briefly exposed to, a very high irradiance, will support the development of highly efficient photosynthesis in crops., Competing Interests: Conflicts of interest The author(s) declare no conflicts of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)

The interaction of plant mitochondrial and nuclear genetic systems is exemplified by mitochondria-encoded cytoplasmic male sterility (CMS) under the control of nuclear restorer-of-fertility genes. The S type of CMS in maize is characterized by a pollen collapse phenotype and a unique paradigm for fertility restoration in which numerous nuclear restorer-of-fertility lethal mutations rescue pollen function but condition homozygous-lethal seed phenotypes. Two nonallelic restorer mutations recovered from Mutator transposon-active lines were investigated to determine the mechanisms of pollen fertility restoration and seed lethality. Mu Illumina sequencing of transposon-flanking regions identified insertion alleles of nuclear genes encoding mitochondrial ribosomal proteins RPL6 and RPL14 as candidate restorer-of-fertility lethal mutations. Both candidates were associated with lowered abundance of mitochondria-encoded proteins in developing maize pollen, and the rpl14 mutant candidate was confirmed by independent insertion alleles. While the restored pollen functioned despite reduced accumulation of mitochondrial respiratory proteins, normal-cytoplasm plants heterozygous for the mutant alleles showed a significant pollen transmission bias in favor of the nonmutant Rpl6 and Rpl14 alleles. CMS-S fertility restoration affords a unique forward genetic approach to investigate the mitochondrial requirements for, and contributions to, pollen and seed development., Competing Interests: Conflicts of interest The author(s) declare no conflict of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)

Flavonoids are secondary metabolites associated with plant seed coat and flower color. These compounds provide health benefits to humans as anti-inflammatory and antioxidant compounds. The expression of the late biosynthetic genes in the flavonoid pathway is controlled by a ternary MBW protein complex consisting of interfacing MYB, beta-helix-loop-helix (bHLH), and WD40 Repeat (WDR) proteins. P, the master regulator gene of the flavonoid expression in common bean (Phaseolus vulgaris L.), was recently determined to encode a bHLH protein. The T and Z genes control the distribution of color in bean seeds and flowers and have historically been considered regulators of the flavonoid gene expression. T and Z candidates were identified using reverse genetics based on genetic mapping, phylogenetic analysis, and mutant analysis. Domain and AlphaFold2 structure analyses determined that T encodes a seven-bladed β-propeller WDR protein, while Z encodes a R2R3 MYB protein. Deletions and SNPs in T and Z mutants, respectively, altered the 3D structure of these proteins. Modeling of the Z MYB/P bHLH/T WDR MBW complex identified interfacing sequence domains and motifs in all three genes that are conserved in dicots. One Z MYB motif is a possible beta-molecular recognition feature (β-MoRF) that only appears in a structured state when Z MYB is modeled as a component of a MBW complex. Complexes containing mutant T and Z proteins changed the interaction of members of the complex in ways that would alter their role in regulating the expression of genes in the flavonoid pathway., Competing Interests: Conflicts of interest The authors declare no conflict of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)

Objective: This research aims to analyze the presence and distribution of resistance genes in the avium and fruticosa subgenomes of Prunus cerasus through computational methods and bioinformatics tools., Results: Analysis of genome and transcriptome sequencing data revealed a total of 19,570 transcripts with at least one resistance gene domain in Prunus cerasus subgenome avium and 19,142 in Prunus cerasus subgenome fruticosa. Key findings include the identification of 804 "complete" resistance gene transcripts in Prunus cerasus subgenome avium and 817 in Prunus cerasus subgenome fruticosa, with distinct distributions of resistance gene classes observed between the subgenomes. Phylogenetic analysis showed clustering of resistance genes, and unique resistance proteins were identified in each subgenome. Functional annotation comparisons with Arabidopsis thaliana highlighted shared and unique resistance genes, emphasizing the complexity of disease resistance in cherry species. Additionally, a higher diversity of RLKs and RLPs was observed, with 504 transcripts identified and 18 showing similarity to known reference genes., (© 2024. The Author(s).)

Recessive genic male sterility (RGMS) provides an effective approach for the commercial exploitation of heterosis, especially in Brassica crops. Although some artificial RGMS mutants have been reported in B. rapa, no causal genes derived from these natural mutants have been identified so far. In this study, a spontaneous RGMS mutant Bcajh97-01A derived from the 'Aijiaohuang' line traced back to the 1980 s was identified. Genetic analysis revealed that the RGMS trait was controlled by a single locus in the Bcajh97-01A/B system. Bulk segregant analysis (BSA) in combination with linkage analysis was employed to delimit the causal gene to an approximate 129 kb interval on chromosome A02. The integrated information of transcriptional levels and the predicted genes in the target region indicated that the Brmmd1 (BraA02g017420) encoding a PHD-containing nuclear protein was the most likely candidate gene. A 374 bp miniature inverted-repeat transposable element (MITE) was inserted into the first exon to prematurely stop the Brmmd1 gene translation, thus blocking the normal expression of this gene at the tetrad stage in the Bcajh97-01A. Additionally, a co-segregating structure variation (SV) marker was developed to rapidly screen the RGMS progenies from Bcajh97-01A/B system. Our findings reveal that BraA02g017420 is the causal gene responsible for the RGMS trait. This study lays a foundation for marker-assisted selection and further molecular mechanism exploration of pollen development in B. rapa., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

Background: Vegetable soybean is rich in nutrients and has a unique flavor. It is highly preferred by people because of its pharmacological activities, including those that regulate the intestines and lower blood pressure. The pod color of vegetable soybeans is an important quality that indicates their freshness and has a significant impact on their commercialization., Results: In this study, pod color was evaluated in 301 vegetable soybean accessions collected from various regions. Genome-wide association analysis was carried out using the Mixed linear model (MLM), a total of 18 quantitative trait loci including 117 SNPs were detected. Two significant QTLs located on chromosomes 6 (qGPCL4 /qGPCa1/qGPCb2) and 18 (qGPCL10/qGPCb3) were consistently detected across different variables. Based on gene functional annotation, 30 candidate genes were identified in these two candidate intervals. Combined with transcriptome analysis, Glyma.18g241700 has been identified as a candidate gene for regulating pod color in vegetable soybeans. Glyma.18g241700 encodes a chlorophyll photosystem I subunit XI. which localizes to the chloroplast named GmPsaL, qRT-PCR analysis showed that GmPsaL was specifically highly expressed in developing pods. Furthermore, overexpression of GmPsaL in transgenetic Arabidopsis plants produced dark green pods., Conclusions: These findings may be useful for clarifying the genetic basis of the pod color of vegetable soybeans. The identified candidate genes may be useful for the genetic improvement of the appearance quality of vegetable soybeans., (© 2024. The Author(s).)

Key Message: Two small fragment translocation lines (T4DS·4DL-4EL and T5AS·5AL-4EL) showed high resistance to stripe rust and resistance gene Yr4EL was localized to an about 35 Mb region at the end of chr arm 4EL. Stripe rust, caused by the fungus Puccinia striiformis f. sp. tritici, is a devastating wheat disease worldwide. Deployment of disease resistance (R) genes in wheat cultivars is the most effective way to control the disease. Previously, the all-stage stripe rust R gene Yr4EL from tetraploid Thinopyrum elongatum was introduced into common wheat as 4E(4D) substitution and T4DS·4EL translocation lines. To further map and utilize Yr4EL, Chinese Spring (CS) mutant pairing homoeologous gene ph1b was used in crossing to induce recombination between chromosome (chr) 4EL and wheat chromosomes. Two small fragment translocation lines T4DS·4DL-4EL and T5AS·5AL-4EL with Yr4EL resistance were selected using molecular markers and confirmed by genomic in situ hybridization (GISH), fluorescence in situ hybridization (FISH), and Wheat 660 K SNP array analyses. We mapped Yr4EL to an about 35 Mb region at the end of chr 4EL, corresponding to 577.76-612.97 Mb based on the diploid Th. elongatum reference genome. In addition, two competitive allele-specific PCR (KASP) markers co-segregating with Yr4EL were developed to facilitate molecular marker-assisted selection in breeding. The T4DS·4DL-4EL lines were crossed and backcrossed with wheat cultivars SM482 and CM42, and the resulting pre-breeding lines showed high stripe rust resistance and potential for wheat breeding with good agronomic traits. These lines represent new germplasm for wheat stripe rust resistance breeding, as well as providing a solid foundation for Yr4EL fine mapping and cloning., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Background: Potato is the fourth largest food crop in the world, but potato cultivation faces serious threats from various diseases and pests. Despite significant advancements in research on potato disease resistance, these findings are scattered across numerous publications. For researchers, obtaining relevant knowledge by reading and organizing a large body of literature is a time-consuming and labor-intensive process. Therefore, systematically extracting and organizing the relationships between potato genes and diseases from the literature to establish a potato gene-disease knowledge base is particularly important. Unfortunately, there is currently no such gene-disease knowledge base available., Methods: In this study, we constructed a Potato Gene-Disease Knowledge Base (PotatoG-DKB) using natural language processing techniques and large language models. We used PubMed as the data source and obtained 2,906 article abstracts related to potato biology, extracted entities and relationships between potato genes and related disease, and stored them in a Neo4j database. Using web technology, we also constructed the Potato Gene-Disease Knowledge Portal (PotatoG-DKP), an interactive visualization platform., Results: PotatoG-DKB encompasses 22 entity types (such as genes, diseases, species, etc .) of 5,206 nodes and 9,443 edges between entities (for example, gene-disease, pathogen-disease, etc .). PotatoG-DKP can intuitively display associative relationships extracted from literature and is a powerful assistant for potato biologists and breeders to understand potato pathogenesis and disease resistance. More details about PotatoG-DKP can be obtained at https://www.potatogd.com.cn/., Competing Interests: The authors declare that they have no competing interests., (© 2024 Xie et al.)

Maize is one of the main food crops in the world, and cultivating high-yield and high-quality maize varieties is of great significance in addressing food security issues. Leaves are crucial photosynthetic organs in maize, and leaf senescence can result in the degradation of chlorophyll. This, in turn, impacts photosynthetic activity and the accumulation of photosynthetic products. Delaying leaf senescence and increasing carbon assimilation can enhance grain yield and biomass production. The stay green of maize is an important trait closely related to yield, feed quality and resistance. Therefore, this study employed multi-generation joint analysis of major genes and a polygene model to investigate the genetic inheritance of stay green-related traits. Four populations (P1, P2, F1 and F2) were obtained by crossing T01 (stay green) × Xin3 (non-stay green) and T01 (stay green) × Mo17 (non-stay green) under two environments. Six stay green-related traits, including visual stay green (VSG), number of green leaves (GLNM), SPAD value of ear leaf at anthesis (SPADS), SPAD value of ear leaf at maturity (SPADM), absolute green leaf area (GLAD), grain yield per plant (GYP), displayed continuous variations with kurtosis and skewness values of absolute value less than 1 and distribution close to normal. They were characterized by typical inheritance of quantitative traits, with these traits demonstrating the transgressive segregation. The correlation analysis among the traits revealed that five stay green traits have a positive impact on yield. VSG, GLNM and SPADM in the two populations were regulated by the two major genes of additive effects plus additive-dominance polygene model with a major gene heritability varying from 89.03 to 95.95% in the F2 generation. GLAD in TMF2 was controlled by two major genes of equal-additive dominance effects with high heritability (93.47%). However, in TXF2, GLAD was regulated by two major genes of additive-dominance interaction effects plus additive-dominance polygene model. These results provide important genetic information for breeding, which could guide the improvement of stay green-related traits. They also lay a foundation for quantitative trait loci mapping of the stay stay-green traits in maize., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Zheng et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The subgenus Tillandsia (Bromeliaceae) belongs to one of the fastest radiating clades in the plant kingdom and is characterized by the repeated evolution of Crassulacean acid metabolism (CAM). Despite its complex genetic basis, this water-conserving trait has evolved independently across many plant families and is regarded as a key innovation trait and driver of ecological diversification in Bromeliaceae. By producing high-quality genome assemblies of a Tillandsia species pair displaying divergent photosynthetic phenotypes, and combining genome-wide investigations of synteny, transposable element (TE) dynamics, sequence evolution, gene family evolution, and temporal differential expression, we were able to pinpoint the genomic drivers of CAM evolution in Tillandsia. Several large-scale rearrangements associated with karyotype changes between the 2 genomes and a highly dynamic TE landscape shaped the genomes of Tillandsia. However, our analyses show that rewiring of photosynthetic metabolism is mainly obtained through regulatory evolution rather than coding sequence evolution, as CAM-related genes are differentially expressed across a 24-h cycle between the 2 species but are not candidates of positive selection. Gene orthology analyses reveal that CAM-related gene families manifesting differential expression underwent accelerated gene family expansion in the constitutive CAM species, further supporting the view of gene family evolution as a driver of CAM evolution., Competing Interests: Conflict of interest statement. None declared., (© The Author(s) 2024. Published by Oxford University Press on behalf of American Society of Plant Biologists.)

Duplicated genes are thought to follow one of three evolutionary trajectories that resolve their redundancy: neofunctionalization, subfunctionalization, or pseudogenization. Differences in expression patterns have been documented for many duplicated gene pairs and interpreted as evidence of subfunctionalization and a loss of redundancy. However, little is known about the functional impact of such differences and about their molecular basis. Here, we investigate the genetic and molecular basis for the partial loss of redundancy between the two BLADE-ON-PETIOLE genes BOP1 and BOP2 in red shepherd's purse (Capsella rubella) compared to Arabidopsis (Arabidopsis thaliana). While both genes remain almost fully redundant in A. thaliana, BOP1 in C. rubella can no longer ensure wild-type floral organ numbers and suppress bract formation, due to an altered expression pattern in the region of the cryptic bract primordium. We use two complementary approaches, transgenic rescue of A. thaliana atbop1 atbop2 double mutants and deletions in the endogenous AtBOP1 promoter, to demonstrate that several BOP1 promoter regions containing conserved noncoding sequences interact in a nonadditive manner to control BOP1 expression in the bract primordium and that changes in these interactions underlie the evolutionary divergence between C. rubella and A. thaliana BOP1 expression and activity. Similarly, altered interactions between cis-regulatory regions underlie the divergence in functional promoter architecture related to the control of floral organ abscission by BOP1. These findings highlight the complexity of promoter architecture in plants and suggest that changes in the interactions between cis-regulatory elements are key drivers for evolutionary divergence in gene expression and the loss of redundancy., Competing Interests: Conflict of interest statement. None declared., (© The Author(s) 2024. Published by Oxford University Press on behalf of American Society of Plant Biologists.)

Following whole-genome duplication (WGD), duplicate gene pairs (homoeologs) can evolve varying degrees of expression divergence. However, the determinants influencing these relative expression level differences (RFPKM) between homoeologs remain elusive. In this study, we analyzed the RFPKM between homoeologs in 3 angiosperms, Nymphaea colorata, Nelumbo nucifera, and Acorus tatarinowii, all having undergone a single WGD since the origin of angiosperms. Our results show significant positive correlations in RFPKM of homoeologs among tissues within the same species, and among orthologs across these 3 species, indicating convergent expression balance/bias between homoeologous gene copies following independent WGDs. We linked RFPKM between homoeologs to gene attributes associated with dosage-balance constraints, such as protein-protein interactions, lethal-phenotype scores in Arabidopsis (Arabidopsis thaliana) orthologs, domain numbers, and expression breadth. Notably, homoeologs with lower RFPKM often had more interactions and higher lethal-phenotype scores, indicating selective pressures favoring balanced expression. Also, homoeologs with lower RFPKM were more likely to be retained after WGDs in angiosperms. Within Nelumbo, greater RFPKM between homoeologs correlated with increased cis- and trans-regulatory differentiation between species, highlighting the ongoing escalation of gene expression divergence. We further found that expression degeneration in 1 copy of homoeologs is inclined toward nonfunctionalization. Our research highlights the importance of balanced expression, shaped by dosage-balance constraints, in the evolutionary retention of homoeologs in plants., Competing Interests: Conflict of interest statement. None declared., (© The Author(s) 2024. Published by Oxford University Press on behalf of American Society of Plant Biologists. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Background: Tomato leaf curl New Delhi virus (ToLCNDV) (family Geminiviridae, genus Begomovirus) is a significant threat to cucumber (Cucumis sativus) production in many regions. Previous studies have reported the genetic mapping of loci related to ToLCNDV resistance, but no resistance genes have been identified., Results: We conducted map-based cloning of the ToLCNDV resistance gene in cucumber accession No.44. Agroinfiltration and graft-inoculation analyses confirmed the resistance of No.44 to ToLCNDV isolates from the Mediterranean and Asian countries. Initial mapping involving two rounds of phenotyping with two independent F 2 populations generated by crossing the begomovirus-susceptible cultivar SHF and No.44 consistently detected major quantitative trait loci (QTLs) on chromosomes 1 and 2 that confer resistance to ToLCNDV. Fine-mapping of Cy-1, the dominant QTL on chromosome 1, using F 3 populations narrowed the candidate region to a 209-kb genomic segment harboring 24 predicted genes. Among these genes, DFDGD-class RNA-dependent RNA polymerase (CsRDR3), an ortholog of Ty-1/Ty-3 of tomato and Pepy-2 of capsicum, was found to be a strong candidate conferring ToLCNDV resistance. The CsRDR3 sequence of No.44 contained multiple amino acid substitutions; the promoter region of CsRDR3 in No.44 had a large deletion; and the CsRDR3 transcript levels were greater in No.44 than in SHF. Virus-induced gene silencing (VIGS) of CsRDR3 using two chromosome segment substitution lines harboring chromosome 1 segments derived from No.44 compromised resistance to ToLCNDV., Conclusions: Forward and reverse genetic approaches identified CsRDR3, which encodes a DFDGD-class RNA-dependent RNA polymerase, as the gene responsible for ToLCNDV resistance at the major QTL Cy-1 on chromosome 1 in cucumber. Marker-assisted breeding of ToLCNDV resistance in cucumber will be expedited by using No.44 and the DNA markers developed in this study., (© 2024. The Author(s).)