The Sm gene conferring resistance to gray leaf spot disease encodes an NBS-LRR (nucleotide-binding site-leucine-rich repeat) plant resistance protein in tomato

Chromosome-level genome assembly of Solanum pimpinellifolium

Solanum pimpinellifolium, the closest wild relative of the domesticated tomato, has high potential for use in breeding programs aimed at developing multi-pathogen resistance and quality improvement. We generated a chromosome-level genome assembly of S. pimpinellifolium LA1589, with a size of 833 Mb and a contig N50 of 31 Mb. We anchored 98.80% of the contigs into 12 pseudo-chromosomes, and identified 74.47% of the sequences as repetitive sequences. The genome evaluation revealed BUSCO and LAI score of 98.3% and 14.49, respectively, indicating high quality of this assembly. A total of 41,449 protein-coding genes were predicted in the genome, of which 89.17% were functionally annotated. This high-quality genome assembly serves as a valuable resource for accelerating the biological discovery and molecular breeding of this important horticultural crop.

Identification of Gene Responsible for Conferring Resistance against Race KN2 of Podosphaera xanthii in Melon

Powdery mildew caused by Podosphaera xanthii is a serious fungal disease which causes severe damage to melon production. Unlike with chemical fungicides, managing this disease with resistance varieties is cost effective and ecofriendly. But, the occurrence of new races and a breakdown of the existing resistance genes poses a great threat. Therefore, this study aimed to identify the resistance locus responsible for conferring resistance against P. xanthii race KN2 in melon line IML107. A bi-parental F2 population was used in this study to uncover the resistance against race KN2. Genetic analysis revealed the resistance to be monogenic and controlled by a single dominant gene in IML107. Initial marker analysis revealed the position of the gene to be located on chromosome 2 where many of the resistance gene against P. xanthii have been previously reported. Availability of the whole genome of melon and its R gene analysis facilitated the identification of a F-box type Leucine Rich Repeats (LRR) to be accountable for the resistance against race KN2 in IML107. The molecular marker developed in this study can be used for marker assisted breeding programs.

Transcriptome and Metabolome Provide Insights into Fruit Ripening of Cherry Tomato (Solanum lycopersicum var. cerasiforme)

Insights into flavor formation during fruit ripening can guide the development of breeding strategies that balance consumer and producer needs. Cherry tomatoes possess a distinctive taste, yet research on quality formation is limited. Here, metabolomic and transcriptomic analyses were conducted on different ripening stages. The results revealed differentially accumulated metabolites during fruit ripening, providing candidate metabolites related to flavor. Interestingly, several key flavor-related metabolites already reached a steady level at the mature green stage. Transcriptomic analysis revealed that the expression levels of the majority of genes tended to stabilize after the pink stage. Enrichment analysis demonstrated that changes in metabolic and biosynthetic pathways were evident throughout the entire process of fruit ripening. Compared to disease resistance and fruit color genes, genes related to flavor and firmness may have a broader impact on the accumulation of metabolites. Furthermore, we discovered the interconversion patterns between glutamic acid and glutamine, as well as the biosynthesis patterns of flavonoids. These findings contribute to our understanding of fruit quality formation mechanisms and support breeding programs aimed at improving fruit quality traits.

Mapping of the Cladosporium fulvum resistance gene Cf-16, a major gene involved in leaf mold disease in tomato

Tomato (Solanum lycopersicum) is widely cultivated and consumed worldwide. Tomato leaf mold, caused by Cladosporium fulvum, is one of the most devastating diseases in tomato production. At present, some tomato leaf mold resistance (Cf series) genes used in production gradually lose resistance due to the continuous and rapid differentiation of C. fulvum physiological races. The Cf-16 gene derived from the "Ontario7816" tomato cultivar has shown effective resistance in field trials for many years, but few studies have reported on the mapping of the Cf-16 gene, which has not been cloned, limiting its utilization in tomato breeding. Here, we mapped Cf-16 using a novel comprehensive strategy including bulk segregation analysis (BSA), genome resequencing and SSR molecular markers. A genetic analysis revealed that Cf-16 resistance in "Ontario7816" is controlled by one major dominant locus. The Cf-16 gene was mapped in a region of 2.6 cM at chromosome 6 between two markers, namely, TGS447 and TES312, by using an F2 population from a cross between the resistant cultivar "Ontario7816" and susceptible line "Moneymaker." Two nucleotide-binding-site-leucine-rich repeat (NBS-LRR) resistance genes, namely, XM_004240667.3 and XM_010323727.1, were identified in this interval. They are strong candidates for the Cf-16 gene. The mapping of Cf-16 may speed up its utilization for breeding resistant tomato varieties and represents an important step forward in our understanding of the mechanism underlying resistance to tomato leaf mold.

High-resolution mapping of SrTm4, a recessive resistance gene to wheat stem rust

KEY MESSAGE

The diploid wheat recessive stem rust resistance gene SrTm4 was fine-mapped to a 754-kb region on chromosome arm 2A^mL and potential candidate genes were identified. Race Ug99 of Puccinia graminis f. sp. tritici (Pgt), the causal agent of wheat stem (or black) rust is one of the most serious threats to global wheat production. The identification, mapping, and deployment of effective stem rust resistance (Sr) genes are critical to reduce this threat. In this study, we generated SrTm4 monogenic lines and found that this gene confers resistance to North American and Chinese Pgt races. Using a large mapping population (9522 gametes), we mapped SrTm4 within a 0.06 cM interval flanked by marker loci CS4211 and 130K1519, which corresponds to a 1.0-Mb region in the Chinese Spring reference genome v2.1. A physical map of the SrTm4 region was constructed with 11 overlapping BACs from the resistant Triticum monococcum PI 306540. Comparison of the 754-kb physical map with the genomic sequence of Chinese Spring and a discontinuous BAC sequence of DV92 revealed a 593-kb chromosomal inversion in PI 306540. Within the candidate region, we identified an L-type lectin-domain containing receptor kinase (LLK1), which was disrupted by the proximal inversion breakpoint, as a potential candidate gene. Two diagnostic dominant markers were developed to detect the inversion breakpoints. In a survey of T. monococcum accessions, we identified 10 domesticated T. monococcum subsp. monococcum genotypes, mainly from the Balkans, carrying the inversion and showing similar mesothetic resistant infection types against Pgt races. The high-density map and tightly linked molecular markers developed in this study are useful tools to accelerate the deployment of SrTm4-mediated resistance in wheat breeding programs.

Stemphylium lycopersici Nep1-like Protein (NLP) Is a Key Virulence Factor in Tomato Gray Leaf Spot Disease

The fungus Stemphylium lycopersici (S. lycopersici) is an economically important plant pathogen that causes grey leaf spot disease in tomato. However, functional genomic studies in S. lycopersici are lacking, and the factors influencing its pathogenicity remain largely unknown. Here, we present the first example of genetic transformation and targeted gene replacement in S. lycopersici. We functionally analyzed the NLP gene, which encodes a necrosis- and ethylene-inducing peptide 1 (Nep1)-like protein (NLP). We found that targeted disruption of the NLP gene in S. lycopersici significantly compromised its virulence on tomato. Moreover, our data suggest that NLP affects S. lycopersici conidiospore production and weakly affects its adaptation to osmotic and oxidative stress. Interestingly, we found that NLP suppressed the production of reactive oxygen species (ROS) in tomato leaves during S. lycopersici infection. Further, expressing the fungal NLP in tomato resulted in constitutive transcription of immune-responsive genes and inhibited plant growth. Through gene manipulation, we demonstrated the function of NLP in S. lycopersici virulence and development. Our work provides a paradigm for functional genomics studies in a non-model fungal pathogen system.