An Integrative Transcriptomics and Proteomics Approach to Identify Putative Genes Underlying Fruit Ripening in Tomato near Isogenic Lines with Long Shelf Life.

The elucidation of the ripening pathways of climacteric fruits helps to reduce postharvest losses and improve fruit quality. Here, we report an integrative study on tomato ripening for two near-isogenic lines (NIL115 and NIL080) with Solanum pimpinellifolium LA0722 introgressions. A comprehensive analysis using phenotyping, molecular, transcript, and protein data were performed. Both NILs show improved fruit firmness and NIL115 also has longer shelf life compared to the cultivated parent. NIL115 differentially expressed a transcript from the APETALA2 ethylene response transcription factor family (AP2/ERF) with a potential role in fruit ripening. E4, another ERF, showed an upregulated expression in NIL115 as well as in the wild parent, and it was located physically close to a wild introgression. Other proteins whose expression levels changed significantly during ripening were identified, including an ethylene biosynthetic enzyme (ACO3) and a pectate lyase (PL) in NIL115, and an alpha-1,4 glucan phosphorylase (Pho1a) in NIL080. In this study, we provide insights into the effects of several genes underlying tomato ripening with potential impact on fruit shelf life. Data integration contributed to unraveling ripening-related genes, providing opportunities for assisted breeding.

Increasing Fruit Weight by Editing a Cis-Regulatory Element in Tomato KLUH Promoter Using CRISPR/Cas9.

CRISPR/Cas-mediated genome editing is a powerful approach to accelerate yield enhancement to feed growing populations. Most applications focus on "negative regulators" by targeting coding regions and promoters to create nulls or weak loss-of-function alleles. However, many agriculturally important traits are conferred by gain-of-function alleles. Therefore, creating gain-of-function alleles for "positive regulators" by CRISPR will be of great value for crop improvement. CYP78A family members are the positive regulators of organ weight and size in crops. In this study, we engineered allelic variation by editing tomato KLUH promoter around a single-nucleotide polymorphism (SNP) that is highly associated with fruit weight. The SNP was located in a conserved putative cis-regulatory element (CRE) as detected by the homology-based prediction and the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq). Twenty-one mutant alleles with various insertion and deletion sizes were generated in the LA1589 background. Five mutant alleles (m2+4bp , m3+1bp , m5-1bp , m13-8bp , and m14-9bp ) showed a consistent increase in fruit weight and a significant decrease in the proportion of small fruits in all experimental evaluations. Notably, m2+4bp and m3+1bp homozygote significantly increase fruit weight by 10.7-15.7 and 8.7-16.3%, respectively. Further analysis of fruit weight based on fruit position on the inflorescence indicated that the five beneficial alleles increase the weight of all fruits along inflorescence. We also found that allele types and transcriptional changes of SlKLUH were poor predictors of the changes in fruit weight. This study not only provides a way of identifying conserved CRE but also highlights enormous potential for CRISPR/Cas-mediated cis-engineering of CYP78A members in yield improvement.

¿Quién está consumiendo productos dietéticos en Perú? Reporte de consumo de una encuesta transversal no probabilística

Objetivo: Identificar el perfil y la percepción de los consumidores de productos dietéticos en las poblaciones de Lima, Arequipa y Trujillo en Perú. Materiales y métodos: Estudio transversal analítico realizado en sujetos mayores de 18 años que eran residentes en las ciudades de Lima, Arequipa y Trujillo en Perú. El estudio se realizó en dos etapas. En la primera etapa, se realizaron entrevistas personales, para lo cual se empleó cuestionarios estructurados y estandarizados. En la segunda etapa, se diseñó un cuestionario estructurado con preguntas abiertas y cerradas relacionadas con los hábitos de uso y compra de productos dietéticos. Resultados: Se entrevistaron a 890 personas, de las cuales el 42 % señalaron que consumían productos dietéticos, de los cuales las vitaminas y los minerales eran los productos de mayor consumo. Se observó que los consumidores mantenían una frecuencia diaria y una antigüedad de consumo entre 3 y 12 meses. Además, se identificó que la recomendación de los familiares y amigos sobre el consumo de productos dietéticos tenía un nivel de confianza similar a las recomendaciones de médicos y nutricionistas. Conclusiones: Los resultados de este estudio en una muestra representativa obtenida en Lima, Arequipa y Trujillo nos indican que un alto porcentaje de la población se encuentra satisfecha consumiendo productos dietéticos con regularidad. Es importante señalar que no existen diferencias significativas entre el porcentaje de la población encuestada que consume productos dietéticos por recomendación de un nutricionista y la que los consume por sugerencia de familiares y amigos. Esto indica que es necesario mejorar los hábitos nutricionales con estrategias de educación sobre hábitos alimenticios y la adaptación del uso de productos dietéticos a una dieta balanceada. Estos resultados podrían permitir que la población haga un uso más eficaz de los productos dietéticos como herramienta para reducir deficiencias nutricionales.

Objective: To identify the profile and perception of dietary supplement users in the population of Lima, Arequipa and Trujillo, Peru. Materials and methods: An analytical cross-sectional study conducted with subjects over 18 years of age residing in the cities of Lima, Arequipa and Trujillo, Peru. The study was performed in two steps. In the first step, personal interviews were held using structured and standardized surveys. In the second step, a structured survey was designed with open and closed questions related to the purchasing and consumption habits of dietary supplements. Results: Eight hundred ninety (890) people were interviewed, out of which 42 % reported to be dietary supplement users, being vitamins and minerals the most commonly used products. It was observed that these users had been taking daily doses of dietary supplements for 3 to 12 months. Additionally, it was found that family and friends served as a source of information on dietary supplements similar to the one provided by doctors and nutritionists. Conclusions: The results of this study conducted with a representative sample from Lima, Arequipa and Trujillo showed that a high percentage of the population was satisfied with using dietary supplements regularly. It is important to point out that there were no significant differences between the percentage of the surveyed population that used dietary supplements recommended by nutritionists and the one which used them on family and friends' recommendation. This suggests that it is necessary to improve nutritional habits with educational strategies on eating habits and adapt the use of dietary supplements to a balanced diet. These results could allow the population to use dietary supplements more effectively as a tool to reduce nutritional deficiencies.

Fruit quality and DNA methylation are affected by parental order in reciprocal crosses of tomato.

KEY MESSAGE: Reciprocal effects were found for tomato fruit quality and DNA methylation. The epigenetic identity of reciprocal hybrids indicates that DNA methylation might be one of the mechanisms involved in POEs. Crosses between different genotypes and even between different species are commonly used in plant breeding programs. Reciprocal hybrids are obtained by changing the cross direction (or the sexual role) of parental genotypes in a cross. Phenotypic differences between these hybrids constitute reciprocal effects (REs). The aim of this study was to evaluate phenotypic differences in tomato fruit traits and DNA methylation profiles in three inter- and intraspecific reciprocal crosses. REs were detected for 13 of the 16 fruit traits analyzed. The number of traits with REs was the lowest in the interspecific cross, whereas the highest was found in the cross between recombinant inbred lines (RILs) derived from the same interspecific cross. An extension of gene action analysis was proposed to incorporate parent-of-origin effects (POEs). Maternal and paternal dominance were found in four fruit traits. REs and paternal inheritance were found for epiloci located at coding and non-coding regions. The epigenetic identity displayed by the reciprocal hybrids accounts for the phenotypic differences among them, indicating that DNA methylation might be one of the mechanisms involved in POEs.

Selected genome regions for fruit weight and shelf life in tomato RILs discernible by markers based on genomic sequence information.

Fruit weight (FW) and shelf life (SL) are important traits in commercial fresh market tomatoes. A tomato RIL population was developed by antagonistic and divergent selection for both traits from an interspecific cross between the Solanum lycopersicum L. cv. "Caimanta" and the S. pimpinellifolium L. accession "LA0722". The objective of this work was to evaluate phenotypic and genetic components for FW and SL. Phenotypic data from RILs were collected during 3-year trials. Sixteen SSR, 62 InDels developed based on the genome sequences of "Caimanta" and "LA0722", and four functional markers for fruit size genes were used. FW and SL had a significant genetic variability, and both traits showed a genotype by year interaction. Genome-wide molecular characterization of the population demonstrated that is genetically structured according to FW. Marker data was used to study changes on allelic frequencies at loci between the phenotypic extreme group of RILs for FW and SL. Twenty four markers were associated to FW, the LC gene in chromosome 2 and other six markers in chromosomes 1, 2, 6, and 11 presented the most significant associations. Finally, we reported three new genomic regions located on chromosomes 9, 10 and 12 that underlie SL in tomato.

Network Analyses Reveal Shifts in Transcript Profiles and Metabolites That Accompany the Expression of SUN and an Elongated Tomato Fruit.

SUN controls elongated tomato (Solanum lycopersicum) shape early in fruit development through changes in cell number along the different axes of growth. The gene encodes a member of the IQ domain family characterized by a calmodulin binding motif. To gain insights into the role of SUN in regulating organ shape, we characterized genome-wide transcriptional changes and metabolite and hormone accumulation after pollination and fertilization in wild-type and SUN fruit tissues. Pericarp, seed/placenta, and columella tissues were collected at 4, 7, and 10 d post anthesis. Pairwise comparisons between SUN and the wild type identified 3,154 significant differentially expressed genes that cluster in distinct gene regulatory networks. Gene regulatory networks that were enriched for cell division, calcium/transport, lipid/hormone, cell wall, secondary metabolism, and patterning processes contributed to profound shifts in gene expression in the different fruit tissues as a consequence of high expression of SUN. Promoter motif searches identified putative cis-elements recognized by known transcription factors and motifs related to mitotic-specific activator sequences. Hormone levels did not change dramatically, but some metabolite levels were significantly altered, namely participants in glycolysis and the tricarboxylic acid cycle. Also, hormone and primary metabolite networks shifted in SUN compared with wild-type fruit. Our findings imply that SUN indirectly leads to changes in gene expression, most strongly those involved in cell division, cell wall, and patterning-related processes. When evaluating global coregulation in SUN fruit, the main node represented genes involved in calcium-regulated processes, suggesting that SUN and its calmodulin binding domain impact fruit shape through calcium signaling.