combined effects of deficit irrigation and strobilurin application on gas exchange yield and water use efficiency in tomato solanum lycopersicum l

Abstract Water is the major factor limiting plant productivity in many regions of the world. The aim of this study was to evaluate the combined effect of deficit irrigation (restitution of 100%, 50% and 0% of plant consumption: WR100, WR50 and WR0, respectively) and strobilurin treatment (no agrochemical added vs azoxystrobin treatment) in two tomato genotypes, IT-22/025, a wild-type plant, and Ikram, a commercial hybrid. Water use efficiency (WUE), physiological, yield and quality parameters and the expression of ERD15, a gene involved in abiotic stress response were evaluated. The two genotypes showed a different behaviour in response to water stress. Stomatal conductance decrease from WR100 to WR50 was in mean 27.5% for IT-22/025 and 44.5% for Ikram. Moreover, in Ikram, water stress decreased transpiration more than assimilation rate, while the opposite occurred in IT-22/025. The ERD15 expression decrease from WR100 to WR50 was higher for IT-22/025. These effects corresponded to higher total fresh fruit yield and WUE for IT-22/025. Strobilurin determined lower stomata conductance, maintaining higher assimilation rate, leading to an increase in WUE in WR0. Finally, strobilurin caused an increase in ERD15 expression only in IT-22/025. This study underlines the possibility to reduce the water used in tomato crop, maintaining acceptable yield and quality, by using agronomic and genetic strategy

Genotyping-by-sequencing of a melon (Cucumis melo L.) germplasm collection from a secondary center of diversity highlights patterns of genetic variation and genomic features of different gene pools

Background: Melon (Cucumis melo L.) is one of the most important horticultural species, which includes several taxonomic groups. With the advent of next-generation sequencing, single nucleotide polymorphism (SNP) markers are widely used in the study of genetic diversity and genomics. Results: We report the first successful application of genotyping-by-sequencing (GBS) technology in melon. We detected 25,422 SNPs by the analysis of 72 accessions collected in Apulia, a secondary centre of diversity in Southern Italy. Analyses of genetic structure, principal components, and hierarchical clustering support the identification of three distinct subpopulations. One of them includes accessions known with the folk name of 'carosello', referable to the chate taxonomic group. This is one of the oldest domesticated forms of C. melo, once widespread in Europe and now exposed to the risk of genetic erosion. The second subpopulation contains landraces of 'barattiere', a regional vegetable production that was never characterized at the DNA level and we show was erroneously considered another form of chate melon. The third subpopulation includes genotypes of winter melon (C. melo var. inodorus). Genetic analysis within each subpopulation revealed patterns of diversity associated with fruit phenotype and geographical origin. We used SNP data to describe, for each subpopulation, the average linkage disequilibrium (LD) decay, and to highlight genomic regions possibly resulting from directional selection and associated with phenotypic variation. Conclusions: We used GBS to characterize patterns of genetic diversity and genomic features within C. melo. We provide useful information to preserve endangered gene pools and to guide the use of germplasm in breeding. Finally, our findings lay a foundation for molecular breeding approaches and the identification of genes underlying phenotypic traits

Genotyping-by-sequencing of a melon (Cucumis melo L.) germplasm collection from a secondary center of diversity highlights patterns of genetic variation and genomic features of different gene pool.

Melon (Cucumis melo L.) is one of the most important horticultural species, which includes several taxonomic groups. With the advent of next-generation sequencing, single nucleotide polymorphism (SNP) markers are widely used in the study of genetic diversity and genomics. Results: We report the first successful application of genotyping-by-sequencing (GBS) technology in melon. We detected 25,422 SNPs by the analysis of 72 accessions collected in Apulia, a secondary centre of diversity in Southern Italy. Analyses of genetic structure, principal components, and hierarchical clustering support the identification of three distinct subpopulations. One of them includes accessions known with the folk name of 'carosello', referable to the chate taxonomic group. This is one of the oldest domesticated forms of C. melo, once widespread in Europe and now exposed to the risk of genetic erosion. The second subpopulation contains landraces of 'barattiere', a regional vegetable production that was never characterized at the DNA level and we show was erroneously considered another form of chate melon. The third subpopulation includes genotypes of winter melon (C. melo var. inodorus). Genetic analysis within each subpopulation revealed patterns of diversity associated with fruit phenotype and geographical origin. We used SNP data to describe, for each subpopulation, the average linkage disequilibrium (LD) decay, and to highlight genomic regions possibly resulting from directional selection and associated with phenotypic variation. Conclusions: We used GBS to characterize patterns of genetic diversity and genomic features within C. melo. We provide useful information to preserve endangered gene pools and to guide the use of germplasm in breeding. Finally, our findings lay a foundation for molecular breeding approaches and the identification of genes underlying phenotypic traits

Merging genotyping-by-sequencing data from two ex situ collections provides insights on the pea evolutionary history

Pea (Pisum sativum L. subsp. sativum) is one of the oldest domesticated species and a widely cultivated legume. In this study, we combined next generation sequencing (NGS) data referring to two genotyping-by-sequencing (GBS) libraries, each one prepared from a different Pisum germplasm collection. The selection of single nucleotide polymorphism (SNP) loci called in both germplasm collections caused some loss of information; however, this did not prevent the obtainment of one of the largest datasets ever used to explore pea biodiversity, consisting of 652 accessions and 22 127 markers. The analysis of population structure reflected genetic variation based on geographic patterns and allowed the definition of a model for the expansion of pea cultivation from the domestication centre to other regions of the world. In genetically distinct populations, the average decay of linkage disequilibrium (LD) ranged from a few bases to hundreds of kilobases, thus indicating different evolutionary histories leading to their diversification. Genome-wide scans resulted in the identification of putative selective sweeps associated with domestication and breeding, including genes known to regulate shoot branching, cotyledon colour and resistance to lodging, and the correct mapping of two Mendelian genes. In addition to providing information of major interest for fundamental and applied research on pea, our work describes the first successful example of integration of different GBS datasets generated from ex situ collections - a process of potential interest for a variety of purposes, including conservation genetics, genome-wide association studies, and breeding

Almond diversity and homozygosity define structure, kinship, inbreeding, and linkage disequilibrium in cultivated germplasm, and reveal genomic associations with nut and seed weight

Almond [Prunus dulcis Miller (D.A. Webb)] is the main tree nut species worldwide. Here, genotyping-by-sequencing (GBS) was applied to 149 almond cultivars from the ex situ collections of the Italian Council for Agricultural Research (CREA) and the Spanish National Research Council (CSIC), leading to the detection of 93,119 single-nucleotide polymorphisms (SNPs). The study of population structure outlined four distinct genetic groups and highlighted diversification between the Mediterranean and Californian gene pools. Data on SNP diversity and runs of homozygosity (ROHs) allowed the definition of kinship, inbreeding, and linkage disequilibrium (LD) decay in almond cultivated germplasm. Four-year phenotypic observations, gathered on 98 cultivars of the CREA collection, were used to perform a genome-wide association study (GWAS) and, for the first time in a crop species, homozygosity mapping (HM), resulting in the identification of genomic associations with nut, shell, and seed weight. Both GWAS and HM suggested that loci controlling nut and seed weight are mostly independent. Overall, this study provides insights on the almond cultivation history and delivers information of major interest for almond genetics and breeding. In a broader perspective, our results encourage the use of ROHs in crop science to estimate inbreeding, choose parental combinations minimizing the risk of inbreeding depression, and identify genomic footprints of selection for specific traits

A Distinct Genetic Cluster in Cultivated Chickpea as Revealed by Genome-wide Marker Discovery and Genotyping

The accurate description of plant biodiversity is of utmost importance to efficiently address efforts in conservation genetics and breeding. Herein, we report the successful application of a genotyping-by-sequencing (GBS) approach in chickpea ( L.), resulting in the characterization of a cultivated germplasm collection with 3187 high-quality single nucleotide polymorphism (SNP) markers. Genetic structure inference, principal component analysis, and hierarchical clustering all indicated the identification of a genetic cluster corresponding to black-seeded genotypes traditionally cultivated in Southern Italy. Remarkably, this cluster was clearly distinct at both genetic and phenotypic levels from germplasm groups reflecting commercial chickpea classification into and seed types. Fixation index estimates for individual polymorphisms pointed out loci and genomic regions that might be of significance for the diversification of agronomic and commercial traits. Overall, our findings provide information on genetic relationships within cultivated chickpea and highlight a gene pool of great interest for the scientific community and chickpea breeding, which is limited by the low genetic diversity available in the primary gene pool

CAPS technology as a tool for the development of genic and functional markers: Study in peas

DNA markers linked to economically important alleles are often used in plant breeding in order to replace/assist traditional phenotypic selection. Thanks to growing advances in agricultural genetics and genomics, it is possible today to develop genic markers and functional markers, the latter targeting polymorphisms, within a certain gene, directly responsible for the phenotype. It is known that allelic variation is commonly due to single nucleotide polymorphisms (SNPs) and small insertion/deletions (In/Del). In both cases restriction endonucleases recognition sites can be created or disrupted. Thus, cleaved amplified polymorphic sequence (CAPS) technology is particularly suitable for the development of genic and functional markers. In recent activities, we developed a series of CAPS and derived CAPS (dCAPS) functional markers which target all SNP mutations in a gene of cultivated pea (Pisum sativum L.) known to determine resistance to the powdery mildew pathogen Erysiphe pisi. Molecular markers other than CAPS, including those based on next generation sequencing methods, can be today used to target SNPs and In/Del polymorphisms. However, considering their ease of obtainment without the need of costly equipment, CAPS might be still the markers of choice for breeding programs which do not make use of genome-wide screenings and for species whose genetic/genomic information is limited

DNA occurrence in organic matter fractions isolated from amended, agricultural soils

The persistence of soil organic matter (SOM) constituents as a function of their recalcitrance has been recently questioned, with several papers showing the influence of the combined action of physical protection and chemical stabilization mechanisms as the main factors affecting SOM mean residence time. Using a physical fractionation method, SOM located between aggregates (FR), occluded within macro- (MA) and micro-aggregates (MI), and associated with the mineral fractions (MIN) were isolated from an agricultural soil differently amended (using compost, sewage sludge and biochar), and the occurrence of (total, bacterial and plant) DNA in these SOM pools was investigated. Following physical fractionation, total DNA (tDNA) was recovered from all SOM pools and from all treatments. Independently from the amendment, most tDNA accumulates in the FR fraction (30\u201370%), followed by the MIN pool (25\u201355%). The positive correlation between tDNA contents and C/N ratios (both tending to decrease following the order FR, MA and MI) observed for the light SOM fractions, together with the opposite pattern characterizing the heavy, MIN fraction (characterized by relatively high tDNA contents and low C/N ratios), suggests a different origin of the latter SOM pool, i.e., new molecules resulting from microbial transformations rather than highly degraded litter inputs. Therefore, tDNA may represent a promising proxy of organic matter dynamics in mineral soils. Finally, the MI fraction shows the highest number of microbial taxa and diversity, and seems to constitute a separate microbial niche in which different bacterial communities carry out their activity