Ralstonia solanacearum causes bacterial wilt disease in solanaceous crops. Identification of avirulence type III-secreted effectors recognized by specific disease resistance proteins in host plant species is an important step toward developing durable resistance in crops. In the present study, we show that R. solanacearum effector RipJ functions as an avirulence determinant in Solanum pimpinellifolium LA2093. In all, 10 candidate avirulence effectors were shortlisted based on the effector repertoire comparison between avirulent Pe_9 and virulent Pe_1 strains. Infection assays with transgenic strain Pe_1 individually carrying a candidate avirulence effector from Pe_9 revealed that only RipJ elicits strong bacterial wilt resistance in S. pimpinellifolium LA2093. Furthermore, we identified that several RipJ natural variants do not induce bacterial wilt resistance in S. pimpinellifolium LA2093. RipJ belongs to the YopJ family of acetyltransferases. Our sequence analysis indicated the presence of partially conserved putative catalytic residues. Interestingly, the conserved amino acid residues in the acetyltransferase catalytic triad are not required for effector-triggered immunity. In addition, we show that RipJ does not autoacetylate its lysine residues. Our study reports the identification of the first R. solanacearum avirulence protein that triggers bacterial wilt resistance in tomato. We expect that our discovery of RipJ as an avirulence protein will accelerate the development of bacterial wilt-resistant tomato varieties in the future. [ ] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

In tomato cultivation, a rare natural mutation in the flowering repressor antiflorigen gene SELF-PRUNING (sp-classic) induces precocious shoot termination and is the foundation in determinate tomato breeding for open field production. Heterozygous single flower truss (sft) mutants in the florigen SFT gene in the background of sp-classic provide a heterosis-like effect by delaying shoot termination, suggesting the subtle suppression of determinacy by genetic modification of the florigen–antiflorigen balance could improve yield. Here, we isolated three new sp alleles from the tomato germplasm that show modified determinate growth compared to sp-classic, including one allele that mimics the effect of sft heterozygosity. Two deletion alleles eliminated functional transcripts and showed similar shoot termination, determinate growth, and yields as sp-classic. In contrast, amino acid substitution allele sp-5732 showed semi-determinate growth with more leaves and sympodial shoots on all shoots. This translated to greater yield compared to the other stronger alleles by up to 42%. Transcriptome profiling of axillary (sympodial) shoot meristems (SYM) from sp-classic and wild type plants revealed six mis-regulated genes related to the floral transition, which were used as biomarkers to show that the maturation of SYMs in the weaker sp-5732 genotype is delayed compared to sp-classic, consistent with delayed shoot termination and semi-determinate growth. Assessing sp allele frequencies from over 500 accessions indicated that one of the strong sp alleles (sp-2798) arose in early breeding cultivars but was not selected. The newly discovered sp alleles are potentially valuable resources to quantitatively manipulate shoot growth and yield in determinate breeding programs, with sp-5732 providing an opportunity to develop semi-determinate field varieties with higher yields.

The control of flowering time is a major contributing factor to the improvement of crop yield by optimizing plant growth in a crop cycle. Genetic variants that determine flowering time can provide insights into optimizing flowering time for higher yields and other beneficial traits in tomato crops. Here, we examined a collection of flowering time variants to assess their effects on biomass and total tomato yields. Five late flowering (lf), thirteen large plant (lp), and seven floral homeotic (fh) mutants were identified as flowering time variants that could be rearranged according to leaf production in the primary shoot meristem (PSM). A flowering time continuum of mutants was translated into a positive continuum of biomass yield with more leaves, branches, and floral organs. The flowering time continuum showed an optimal curve of fruit yield, indicating a certain late flowering time as optimal for fruit yield, with the yield gradually decreasing in both directions with earlier or later flowering times. We isolated lf1, lf10, lp22, and fh13 as high-yielding genotypes with optimal flowering time, showing a new balance between the vegetative and flowering phases of tomato. Additionally, lp8, fh8, and fh15 produced extremely high biomass in leaves, axillary shoots, and floral organs due to late flowering in shoot apices with additional production of floral organs and lateral shoot. Our new late-flowering variants provide new genetic resources that can be used to optimize crop yield by fine-tuning flowering time, and future molecular studies could be conducted by revisiting our yield model.

Root hairs play crucial roles in the roots, including nutrient uptake, water assimilation, and anchorage with soil, along with supporting rhizospheric microorganisms. In rice, ammonia uptake is mediated by a specialized ammonium transporter (AMT). AMT1;1, AMT1;2, and AMT1;3 have been extensively studied in relation to nitrogen signaling. Cellulose synthase-like D1 (CSLD1) is essential for cell expansion and is highly specific to root hair cells. csld1 mutants showed successful initiation but failed to elongate. However, when nitrogen was depleted, csld1 root hairs resumed elongation. Further experiments revealed that in the presence of ammonium (NH₄⁺), csld1 roots failed to elongate. csld1 elongated normally in the presence of nitrate (NO₃⁻). Expression analysis showed an increase in root hair-specific AMT1;2 expression in csld1. CSLD1 was positively co-expressed with AMT1;2 changing nitrogen concentration in the growth media. CSLD1 showed increased expression in the presence of both ammonium and nitrate. Methylammonium (MeA) treatment of CSLD1 overexpression lines suggests that CSLD1 does not directly participate in nitrogen transport. Further studies on the root hair elongation mutant sndp1 showed that nitrogen assimilation is unlikely to depend on root hair length. Therefore, these results suggest that CSLD1 is closely involved in nitrogen-dependent root hair elongation and regulation of AMT1;2 expression in rice roots.

Tomato fruit color is primarily influenced by the accumulation of pigments such as carotenoids and anthocyanins, which are regulated by a complex network of genes and environmental factors. The presence of anthocyanins, in particular, contributes to the purple phenotype in tomatoes, which has been associated with improved nutritional quality and disease resistance. Previous studies have identified key regulatory genes, including SlMYBATV and SlANT1, that control anthocyanin biosynthesis in tomatoes. A total of 48 tomato accessions were selected, including both anthocyanin-producing and non-producing cultivars, to assess genetic variation in relation to fruit color. GWAS analysis identified significant associations between single-nucleotide polymorphisms (SNPs) on chromosomes 7 and 10 and the purple fruit phenotype. These genomic regions contained key anthocyanin regulatory genes, SlMYBATV on chromosome 7 and SlANT1 on chromosome 10, confirming their roles in anthocyanin biosynthesis. Linkage disequilibrium (LD) analysis further revealed strong correlations between SNPs within these regions, facilitating the selection of representative SNPs for genotyping. The genotyping of SNPs Ch07_60981501 and Ch10_64354129 using HPM demonstrated clear differentiation between purple and non-purple cultivars based on melting temperature differences, validating the functional significance of the identified loci. The results confirmed that the nonfunctional SlMYBATV allele at the atv locus allows for enhanced anthocyanin accumulation by relieving repression of anthocyanin activators like SlANT1. This interaction between the Aft and atv loci drives light-dependent anthocyanin biosynthesis in purple tomatoes. HPM genotyping offers a cost-effective tool for allele identification, supporting breeding programs for anthocyanin-rich tomatoes. SNP markers enable marker-assisted selection (MAS) for improved nutritional and aesthetic traits. This study highlights SlMYBATV and SlANT1 in anthocyanin biosynthesis, advancing efforts to develop enriched tomato varieties and supporting agricultural productivity and health.