Simultaneous improvement of grain yield and grain protein concentration in durum wheat by using association tests and weighted GBLUP

KEY MESSAGE

Simultaneous improvement for GY and GPC by using GWAS and GBLUP suggested a significant application in durum wheat breeding. Despite the importance of grain protein concentration (GPC) in determining wheat quality, its negative correlation with grain yield (GY) is still one of the major challenges for breeders. Here, a durum wheat panel of 200 genotypes was evaluated for GY, GPC, and their derived indices (GPD and GYD), under eight different agronomic conditions. The plant material was genotyped with the Illumina 25 k iSelect array, and a genome-wide association study was performed. Two statistical models revealed dozens of marker-trait associations (MTAs), each explaining up to 30%. phenotypic variance. Two markers on chromosomes 2A and 6B were consistently identified by both models and were found to be significantly associated with GY and GPC. MTAs identified for phenological traits co-mapped to well-known genes (i.e., Ppd-1, Vrn-1). The significance values (p-values) that measure the strength of the association of each single nucleotide polymorphism marker with the target traits were used to perform genomic prediction by using a weighted genomic best linear unbiased prediction model. The trained models were ultimately used to predict the agronomic performances of an independent durum wheat panel, confirming the utility of genomic prediction, although environmental conditions and genetic backgrounds may still be a challenge to overcome. The results generated through our study confirmed the utility of GPD and GYD to mitigate the inverse GY and GPC relationship in wheat, provided novel markers for marker-assisted selection and opened new ways to develop cultivars through genomic prediction approaches.

Breeding effects on durum wheat traits detected using GWAS and haplotype block analysis

Introduction

The recent boosting of genomic data in durum wheat (Triticum turgidum subsp. durum) offers the opportunity to better understand the effects of breeding on the genetic structures that regulate the expression of traits of agronomic interest. Furthermore, the identification of DNA markers useful for marker-assisted selection could also improve the reliability of technical protocols used for variety protection and registration.

Methods

Within this motivation context, 123 durum wheat accessions, classified into three groups: landraces (LR), ancient (OC) and modern cultivars (MC), were evaluated in two locations, for 34 agronomic traits, including UPOV descriptors, to assess the impact of changes that occurred during modern breeding.

Results

The association mapping analysis, performed with 4,241 SNP markers and six multi-locus-GWAS models, revealed 28 reliable Quantitative Trait Nucleotides (QTNs) related to plant morphology and kernel-related traits. Some important genes controlling flowering time and plant height were in linkage disequilibrium (LD) decay with QTNs identified in this study. A strong association for yellow berry was found on chromosome 6A (Q.Yb-6A) in a region containing the nadh-ubiquinone oxidoreductase subunit, a gene involved in starch metabolism. The Q.Kcp-2A harbored the PPO locus, with the associated marker (Ku_c13700_1196) in LD decay with Ppo-A1 and Ppo-A2. Interestingly, the Q.FGSGls-2B.1, identified by RAC875_c34512_685 for flag leaf glaucosity, mapped less than 1 Mb from the Epistatic inhibitors of glaucousness (Iw1), thus representing a good candidate for supporting the morphological DUS traits also with molecular markers. LD haplotype block approach revealed a higher diversity, richness and length of haploblocks in MC than OC and LR (580 in LR, 585 in OC and 612 in MC), suggesting a possible effect exerted by breeding programs on genomic regions associated with the agronomic traits.

Discussion

Our findings pave new ways to support the phenotypic characterization necessary for variety registration by using a panel of cost-effectiveness SNP markers associated also to the UPOV descriptors. Moreover, the panel of associated SNPs might represent a reservoir of favourable alleles to use in durum wheat breeding and genetics.

Genetic diversity and signature of divergence in the genome of grapevine clones of Southern Italy varieties

Sexual reproduction has contributed to a significant degree of variability in cultivated grapevine populations. However, the additional influence of spontaneous somatic mutations has played a pivotal role in shaping the diverse landscape of grapevine agrobiodiversity. These naturally occurring selections, termed 'clones,' represent a vast reservoir of potentially valuable traits and alleles that hold promise for enhancing grape quality and bolstering plant resilience against environmental and biotic challenges. Despite their potential, many of these clones remain largely untapped.In light of this context, this study aims to delve into the population structure, genetic diversity, and distinctive genetic loci within a collection of 138 clones derived from six Campanian and Apulian grapevine varieties, known for their desirable attributes in viticulture and winemaking. Employing two reduced representation sequencing methods, we extracted Single-Nucleotide Polymorphism (SNP) markers. Population structure analysis and fixation index (FST) calculations were conducted both between populations and at individual loci. Notably, varieties originating from the same geographical region exhibited pronounced genetic similarity.The resulting SNP dataset facilitated the identification of approximately two hundred loci featuring divergent markers (FST ≥ 0.80) within annotated exons. Several of these loci exhibited associations with essential traits like phenotypic adaptability and environmental responsiveness, offering compelling opportunities for grapevine breeding initiatives. By shedding light on the genetic variability inherent in these treasured traditional grapevines, our study contributes to the broader understanding of their potential. Importantly, it underscores the urgency of preserving and characterizing these valuable genetic resources to safeguard their intra-varietal diversity and foster future advancements in grapevine cultivation.

Phenotypic evolution in durum wheat (Triticum durum Desf.) based on SNPs, morphological traits, UPOV descriptors and kernel-related traits

Durum wheat is a worldwide staple crop cultivated mainly in the Mediterranean basin. Progress in durum wheat breeding requires the exploitation of genetic variation among the gene pool enclosed in landraces, old cultivars and modern cultivars. The aim of this study was to provide a more comprehensive view of the genetic architecture evolution among 123 durum wheat accessions (41 landraces, 41 old cultivars and 41 modern cultivars), grown in replicated randomized complete block in two areas, Metaponto (Basilicata) and Foggia (Apulia), using the Illumina iSelect 15K wheat SNP array and 33 plant and kernel traits including the International Union for the Protection of new Varieties of Plants (UPOV) descriptors. Through DAPC and Bayesian population structure five groups were identified according to type of material data and reflecting the genetic basis and breeding strategies involved in their development. Phenotypic and genotypic coefficient of variation were low for kernel width (6.43%) and for grain protein content (1.03%). Highly significant differences between environments, genotypes and GEI (Genotype x Environment Interaction) were detected by mixed ANOVAs for agro-morphological-quality traits. Number of kernels per spike (h2 = 0.02) and grain protein content (h2 = 0.03) were not a heritability character and highly influenced by the environment. Nested ANOVAs revealed highly significant differences between DAPC clusters within environments for all traits except kernel roundness. Ten UPOV traits showed significant diversity for their frequencies in the two environments. By PCAmix multivariate analysis, plant height, heading time, spike length, weight of kernels per spike, thousand kernel weight, and the seed related traits had heavy weight on the differentiation of the groups, while UPOV traits discriminated moderately or to a little extent. The data collected in this study provide useful resources to facilitate management and use of wheat genetic diversity that has been lost due to selection in the last decades.

Genomics for Yield and Yield Components in Durum Wheat

In recent years, many efforts have been conducted to dissect the genetic basis of yield and yield components in durum wheat thanks to linkage mapping and genome-wide association studies. In this review, starting from the analysis of the genetic bases that regulate the expression of yield for developing new durum wheat varieties, we have highlighted how, currently, the reductionist approach, i.e., dissecting the yield into its individual components, does not seem capable of ensuring significant yield increases due to diminishing resources, land loss, and ongoing climate change. However, despite the identification of genes and/or chromosomal regions, controlling the grain yield in durum wheat is still a challenge, mainly due to the polyploidy level of this species. In the review, we underline that the next-generation sequencing (NGS) technologies coupled with improved wheat genome assembly and high-throughput genotyping platforms, as well as genome editing technology, will revolutionize plant breeding by providing a great opportunity to capture genetic variation that can be used in breeding programs. To date, genomic selection provides a valuable tool for modeling optimal allelic combinations across the whole genome that maximize the phenotypic potential of an individual under a given environment.

Varietal identification in pasta through an SSR-based approach: a case study

BACKGROUND

Pasta is a worldwide popular Italian food made exclusively of durum wheat. The choice of variety to be used to produce pasta is at the discretion of the producer based on the peculiar characteristics of each cultivar. The availability of analytical approaches for the tracking of specific varieties along the productive chain is becoming increasingly important to authenticate the pasta products and distinguish between fraudulent activities and cross-contaminations during the production process. Among the different methods, molecular approaches based on DNA markers are the most used for these purposes because of their ease of use and high reproducibility.

RESULTS

In the present study, we used an easy simple sequence repeats-based method to identify the durum wheat varieties used to produce 25 samples of semolina and commercial pasta comparing their molecular profile with those of the four varieties declared by the producer and other 10 durum wheat cultivars commonly used in pasta production. All of the samples showed the expected molecular profile; however, most of them present also a foreign allele indicating a possible cross-contamination. Moreover, we evaluated the accuracy of the proposed approach through the analysis of 27 hand-made mixtures with increasing amounts of a specific contaminant variety, allowing the estimation of the limit of detection of 5% (w/w).

CONCLUSION

We demonstrated the feasibility of the proposed method and its effectiveness in the detection of not declared varieties when these are present in a percentage equal to or higher than 5%. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Genetic approaches to exploit landraces for improvement of Triticum turgidum ssp. durum in the age of climate change

Addressing the challenges of climate change and durum wheat production is becoming an important driver for food and nutrition security in the Mediterranean area, where are located the major producing countries (Italy, Spain, France, Greece, Morocco, Algeria, Tunisia, Turkey, and Syria). One of the emergent strategies, to cope with durum wheat adaptation, is the exploration and exploitation of the existing genetic variability in landrace populations. In this context, this review aims to highlight the important role of durum wheat landraces as a useful genetic resource to improve the sustainability of Mediterranean agroecosystems, with a focus on adaptation to environmental stresses. We described the most recent molecular techniques and statistical approaches suitable for the identification of beneficial genes/alleles related to the most important traits in landraces and the development of molecular markers for marker-assisted selection. Finally, we outline the state of the art about landraces genetic diversity and signature of selection, already identified from these accessions, for adaptability to the environment.

Unlocking the molecular basis of wheat straw composition and morphological traits through multi-locus GWAS

BACKGROUND

Rapid reductions in emissions from fossil fuel burning are needed to curb global climate change. Biofuel production from crop residues can contribute to reducing the energy crisis and environmental deterioration. Wheat is a renewable source for biofuels owing to the low cost and high availability of its residues. Thus, identifying candidate genes controlling these traits is pivotal for efficient biofuel production. Here, six multi-locus genome-wide association (ML-GWAS) models were applied using 185 tetraploid wheat accessions to detect quantitative trait nucleotides (QTNs) for fifteen traits associated with biomass composition.

RESULTS

Among the 470 QTNs, only 72 identified by at least two models were considered as reliable. Among these latter, 16 also showed a significant effect on the corresponding trait (p.value < 0.05). Candidate genes survey carried out within 4 Mb flanking the QTNs, revealed putative biological functions associated with lipid transfer and metabolism, cell wall modifications, cell cycle, and photosynthesis. Four genes encoded as Cellulose Synthase (CeSa), Anaphase promoting complex (APC/C), Glucoronoxylan 4-O Methyltransferase (GXM) and HYPONASTIC LEAVES1 (HYL1) might be responsible for an increase in cellulose, and natural and acid detergent fiber (NDF and ADF) content in tetraploid wheat. In addition, the SNP marker RFL_Contig3228_2154 associated with the variation in stem solidness (Q.Scsb-3B) was validated through two molecular methods (High resolution melting; HRM and RNase H²-dependent PCR; rhAMP).

CONCLUSIONS

The study provides new insights into the genetic basis of biomass composition traits on tetraploid wheat. The application of six ML-GWAS models on a panel of diverse wheat genotypes represents an efficient approach to dissect complex traits with low heritability such as wheat straw composition. The discovery of genes/genomic regions associated with biomass production and straw quality parameters is expected to accelerate the development of high-yielding wheat varieties useful for biofuel production.

Comparative Genetic Analysis of Durum Wheat Landraces and Cultivars Widespread in Tunisia

The durum wheat (Triticum turgidum L. ssp. durum Desf.) landraces constitute a useful natural germplasm to increase the genetic diversity in the modern durum cultivars. The Tunisian durum germplasm constitutes 28 accessions conserved in Genebank of Tunisia, which are still unexplored. In this study, a comparative genetic analysis was performed to investigate the relationships between the Tunisian durum lines and the modern cultivars and detect divergent loci involved in breeding history. The genetic diversity analyses carried out using nine morphological descriptors and the 25K single-nucleotide polymorphism (SNP) array allowed us to distinguish two groups of Tunisian landraces and one of durum cultivars. The analysis of molecular variance and diversity indices confirmed the genetic variability among the groups. A total of 529 SNP loci were divergent between Tunisian durum landraces and modern cultivars. Candidate genes related to plant and spike architecture, including FLOWERING LOCUS T (FT-B1), zinc finger CONSTANS, and AP2/EREBPs transcription factors, were identified. In addition, divergent genes involved in grain composition and biotic stress nucleotide-binding site and leucine-reach repeats proteins and disease resistance proteins (NBS-LRR and RPM) were found, suggesting that the Tunisian durum germplasm may represent an important source of favorable alleles to be used in future durum breeding programs for developing well-adapted and resilient cultivars.

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.

Whole-exome sequencing of selected bread wheat recombinant inbred lines as a useful resource for allele mining and bulked segregant analysis

Although wheat (Triticum aestivum L.) is the main staple crop in the world and a major source of carbohydrates and proteins, functional genomics and allele mining are still big challenges. Given the advances in next-generation sequencing (NGS) technologies, the identification of causal variants associated with a target phenotype has become feasible. For these reasons, here, by combining sequence capture and target-enrichment methods with high-throughput NGS re-sequencing, we were able to scan at exome-wide level 46 randomly selected bread wheat individuals from a recombinant inbred line population and to identify and classify a large number of single nucleotide polymorphisms (SNPs). For technical validation of results, eight randomly selected SNPs were converted into Kompetitive Allele-Specific PCR (KASP) markers. This resource was established as an accessible and reusable molecular toolkit for allele data mining. The dataset we are making available could be exploited for novel studies on bread wheat genetics and as a foundation for starting breeding programs aimed at improving different key agronomic traits.

Polyphenol oxidase genes as integral part of the evolutionary history of domesticated tetraploid wheat

Studying and understanding the genetic basis of polyphenol oxidases (PPO)-related traits plays a crucial role in genetic improvement of crops. A tetraploid wheat collection (T. turgidum ssp., TWC) was analyzed using the 90K wheat SNP iSelect assay and phenotyped for PPO activity. A total of 21,347 polymorphic SNPs were used to perform genome-wide association analysis (GWA) in TWC and durum wheat sub-groups, detecting 23 and 85 marker-trait associations (MTA). In addition, candidate genes responsible for PPO activity were predicted. Based on the 23 MTAs detected in TWC, two haplotypes associated with low and high PPO activity were identified. Four SNPs were developed and validated providing one reliable marker (IWB75732) for marker assisted selection. The 23 MTAs were used to evaluate the genetic divergence (F_ST > 0.25) between the T. turgidum subspecies, providing new information important for understanding the domestication process of Triticum turgidum ssp. and in particular of ssp. carthlicum.

QTL Analysis of Five Morpho-Physiological Traits in Bread Wheat Using Two Mapping Populations Derived from Common Parents

Traits such as plant height (PH), juvenile growth habit (GH), heading date (HD), and tiller number are important for both increasing yield potential and improving crop adaptation to climate change. In the present study, these traits were investigated by using the same bi-parental population at early (F₂ and F₂-derived F₃ families) and late (F₆ and F₇, recombinant inbred lines, RILs) generations to detect quantitative trait loci (QTLs) and search for candidate genes. A total of 176 and 178 lines were genotyped by the wheat Illumina 25K Infinium SNP array. The two genetic maps spanned 2486.97 cM and 3732.84 cM in length, for the F₂ and RILs, respectively. QTLs explaining the highest phenotypic variation were found on chromosomes 2B, 2D, 5A, and 7D for HD and GH, whereas those for PH were found on chromosomes 4B and 4D. Several QTL detected in the early generations (i.e., PH and tiller number) were not detected in the late generations as they were due to dominance effects. Some of the identified QTLs co-mapped to well-known adaptive genes (i.e., Ppd-1, Vrn-1, and Rht-1). Other putative candidate genes were identified for each trait, of which PINE1 and PIF4 may be considered new for GH and TTN in wheat. The use of a large F₂ mapping population combined with NGS-based genotyping techniques could improve map resolution and allow closer QTL tagging.

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.

Whole Genome Scan Reveals Molecular Signatures of Divergence and Selection Related to Important Traits in Durum Wheat Germplasm

The first breeding program in the world for durum wheat was conceived in Italy in the early 1900s. Over the decades, pressure exerted by natural and artificial selection could have progressively reduced the genetic diversity of the durum wheat germplasm. In the present study, a large panel of Italian durum wheat accessions that includes landraces, old and modern cultivars was subjected to genotyping using the Illumina iSelect 15K wheat SNP array. The aim was to assess the impact that selection has in shaping Italian durum wheat genetic diversity and to exploit the patterns of genetic diversity between populations to identify molecular signatures of divergence and selection. Relatively small differences in genetic diversity have been observed among accessions, which have been selected and cultivated in Italy over the past 150 years. Indeed, directional selection combined with that operated by farmers/breeders resulted in the increase of linkage disequilibrium (LD) and in changes of the allelic frequencies in DNA regions that control important agronomic traits. Results from this study also show that major well-known genes and/or QTLs affecting plant height (RHT), earliness (VRN, PPD) and grain quality (GLU, PSY, PSD, LYC, PPO, LOX3) co-localized with outlier SNP loci. Interestingly, many of these SNPs fall in genomic regions where genes involved in nitrogen metabolism are. This finding highlights the key role these genes have played in the transition from landraces to modern cultivars. Finally, our study remarks on the need to fully exploit the genetic diversity of Italian landraces by intense pre-breeding activities aimed at introducing a new source of adaptability and resistance in the genetic background of modern cultivars, to contrast the effect of climate change. The list of divergent loci and loci under selection associated with useful agronomic traits represents an invaluable resource to detect new allelic variants for target genes and for guiding new genomic selection programs in durum wheat.

Genotyping by Sequencing of Cultivated Lentil (Lens culinaris Medik.) Highlights Population Structure in the Mediterranean Gene Pool Associated With Geographic Patterns and Phenotypic Variables

Cultivated lentil (Lens culinaris Medik.) is one of the oldest domesticated crops and one of the most important grain legumes worldwide. The Mediterranean Basin holds large part of lentil biodiversity; however, no genetic structure was defined within the Mediterranean gene pool. In this study, we used high-throughput genotyping by sequencing to resolve the genetic structure of the Mediterranean ex situ lentil collection held at the Italian National Research Council. Sequencing of a 188-plex genotyping-by-sequencing library and bioinformatics treatment of data yielded 6,693 single nucleotide polymorphisms. Analysis of nonredundant genotypes with nonparametric and parametric methods highlighted the occurrence of five highly differentiated genetic clusters. Clustering could be related to geographic patterns and phenotypic traits, indicating that post-domestication routes introducing cultivation in Mediterranean countries and selection were major forces shaping lentil population structure. The estimation of the fixation index F_ST at individual single nucleotide polymorphism loci allowed the identification of distinctive alleles across clusters, suggesting the possibility to set up molecular keys for the assignment of lentil germplasm to specific genetic groups. Finally, significant associations between markers and phenotypic data were identified. Overall, the results of this study are of major importance for lentil conservation genetics and breeding and provide insights on the lentil evolutionary history.

Genetic Characterization of Apulian Olive Germplasm as Potential Source in New Breeding Programs

The olive is a fruit tree species with a century-old history of cultivation in theMediterranean basin. In Apulia (Southern Italy), the olive is of main social, cultural and economicimportance, and represents a hallmark of the rural landscape. However, olive cultivation in thisregion is threatened by the recent spread of the olive quick decline syndrome (OQDS) disease, thusthere is an urgent need to explore biodiversity and search for genetic sources of resistance. Herein,a genetic variation in Apulian olive germplasm was explored, as a first step to identify genotypeswith enhanced bio-agronomic traits, including resistance to OQDS. A preselected set of nuclearmicrosatellite markers allowed the acquisition of genotypic profiles, and to define geneticrelationships between Apulian germplasm and widespread cultivars. The analysis highlighted thebroad genetic variation in Apulian accessions and the presence of different unique genetic profiles.The results of this study lay a foundation for the organization of new breeding programs for olivegenetic improvement.

GBS-derived SNP catalogue unveiled wide genetic variability and geographical relationships of Italian olive cultivars

Information on the distribution of genetic variation is essential to preserve olive germplasm from erosion and to recover alleles lost through selective breeding. In addition, knowledge on population structure and genotype-phenotype associations is crucial to support modern olive breeding programs that must respond to new environmental conditions imposed by climate change and novel biotic/abiotic stressors. To further our understanding of genetic variation in the olive, we performed genotype-by-sequencing on a panel of 94 Italian olive cultivars. A reference-based and a reference-independent SNP calling pipeline generated 22,088 and 8,088 high-quality SNPs, respectively. Both datasets were used to model population structure via parametric and non parametric clustering. Although the two pipelines yielded a 3-fold difference in the number of SNPs, both described wide genetic variability among our study panel and allowed individuals to be grouped based on fruit weight and the geographical area of cultivation. Multidimensional scaling analysis on identity-by-state allele-sharing values as well as inference of population mixtures from genome-wide allele frequency data corroborated the clustering pattern we observed. These findings allowed us to formulate hypotheses about geographical relationships of Italian olive cultivars and to confirm known and uncover novel cases of synonymy.

Genetic flow among olive populations within the Mediterranean basin

Background

The olive tree is a typical crop of the Mediterranean basin where it shows a wide diversity, accounting for more than 2,600 cultivars. The ability to discriminate olive cultivars and determine their genetic variability is pivotal for an optimal exploitation of olive genetic resources.

Methods

We investigated the genetic diversity within 128 olive accessions belonging to four countries in the Mediterranean Basin (Italy, Algeria, Syria, and Malta), with the purpose of better understanding the origin and spread of the olive genotypes across Mediterranean Basin countries. Eleven highly polymorphic simple sequence repeat (SSR) markers were used and proved to be very informative, producing a total of 179 alleles.

Results

Cluster analysis distinguished three main groups according to their geographical origin, with the current sample of Maltese accessions included in the Italian group. Phylogenetic analysis further differentiated Italian and Maltese olive accessions, clarifying the intermediate position of Maltese accessions along the x/y-axes of principal coordinate analysis (PCoA). Model-based and neighbor clustering, PCoA, and migration analysis suggested the existence of two different gene pools (Algerian and Syrian) and that the genetic exchange occurred between the Syrian, Italian and Maltese populations.

Discussion

The close relationship between Syrian and Italian and Maltese olives was consistent with the historical domestication and migration of olive tree from the North Levant to eastern Mediterranean basin. This study lays the foundations for a better understanding of olive genetic diversity in the Mediterranean basin and represents a step toward an optimal conservation and exploitation of olive genetic resources.

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.

Impact of resection margin status on oncological outcomes after CO2 laser cordectomy

The management of positive resection margins in micro-endoscopic glottic laser surgery remains a controversial and critical point. This study aims to assess the impact of margin status after transoral laser surgery on local control, survival and organ preservation rates; the decision-making process and treatment options in cases with positive margins are also discussed. We retrospectively reviewed the clinical and histological records of 308 consecutive patients with primary early glottic carcinoma (T1a, T1b, selected T2) and treated with endoscopic laser cordectomy. Recurrence rates and survival related to margin status were analysed using the Kaplan-Meier method. Local relapses and disease-free-survival rates were significantly related to excision margin status (p < 0.001). In the T1a category (n = 228) no significant differences were observed in disease-free-survival (p = 0.889) and overall survival (p = 0.426) between patients submitted to further treatment (revision endoscopic surgery or radiotherapy) for positive excision margins and patients who were left untreated. In 20 of 24 (83%) patients with positive margins that were surgically re-excised, no residual carcinoma was detected. Margin status (mainly multifocal and deep positive margins) at first surgery was significantly related to the final organ preservation rate (p < 0.001). Margin status during laser cordectomy in early glottic cancer has a prognostic impact on local control of disease without compromising survival. Patients with multifocal and deep positive borders should be surgically retreated and strictly monitored to increase the organ preservation rates. Careful preparation and mapping of the surgical specimen enhances the accuracy of pathological examination by reducing the risk of overestimate positive margins.

Polyphenol Oxidases in Crops: Biochemical, Physiological and Genetic Aspects

Enzymatic browning is a colour reaction occurring in plants, including cereals, fruit and horticultural crops, due to oxidation during postharvest processing and storage. This has a negative impact on the colour, flavour, nutritional properties and shelf life of food products. Browning is usually caused by polyphenol oxidases (PPOs), following cell damage caused by senescence, wounding and the attack of pests and pathogens. Several studies indicated that PPOs play a role in plant immunity, and emerging evidence suggested that PPOs might also be involved in other physiological processes. Genomic investigations ultimately led to the isolation of PPO homologs in several crops, which will be possibly characterized at the functional level in the near future. Here, focusing on the botanic families of Poaceae and Solanaceae, we provide an overview on available scientific literature on PPOs, resulting in useful information on biochemical, physiological and genetic aspects.

Genetic variation of a global germplasm collection of chickpea (Cicer arietinum L.) including Italian accessions at risk of genetic erosion

Chickpea (Cicer arietinum L.) is one of the most important legumes worldwide. We addressed this study to the genetic characterization of a germplasm collection from main chickpea growing countries. Several Italian traditional landraces at risk of genetic erosion were included in the analysis. Twenty-two simple sequence repeat (SSR) markers, widely used to explore genetic variation in plants, were selected and yielded 218 different alleles. Structure analysis and hierarchical clustering indicated that a model with three distinct subpopulations best fits the data. The composition of two subpopulations, named K1 and K2, broadly reflects the commercial classification of chickpea in the two types desi and kabuli, respectively. The third subpopulation (K3) is composed by both desi and kabuli genotypes. Italian accessions group both in K2 and K3. Interestingly, this study highlights genetic distance between desi genotypes cultivated in Asia and Ethiopia, which respectively represent the chickpea primary and the secondary centres of diversity. Moreover, European desi are closer to the Ethiopian gene pool. Overall, this study will be of importance for chickpea conservation genetics and breeding, which is limited by the poor characterization of germplasm collection.

Genome-wide SNP discovery and population structure analysis in pepper (Capsicum annuum) using genotyping by sequencing

Background

Knowledge on population structure and genetic diversity in vegetable crops is essential for association mapping studies and genomic selection. Genotyping by sequencing (GBS) represents an innovative method for large scale SNP detection and genotyping of genetic resources. Herein we used the GBS approach for the genome-wide identification of SNPs in a collection of Capsicum spp. accessions and for the assessment of the level of genetic diversity in a subset of 222 cultivated pepper (Capsicum annum) genotypes.

Results

GBS analysis generated a total of 7,568,894 master tags, of which 43.4% uniquely aligned to the reference genome CM334. A total of 108,591 SNP markers were identified, of which 105,184 were in C. annuum accessions. In order to explore the genetic diversity of C. annuum and to select a minimal core set representing most of the total genetic variation with minimum redundancy, a subset of 222 C. annuum accessions were analysed using 32,950 high quality SNPs. Based on Bayesian and Hierarchical clustering it was possible to divide the collection into three clusters. Cluster I had the majority of varieties and landraces mainly from Southern and Northern Italy, and from Eastern Europe, whereas clusters II and III comprised accessions of different geographical origins. Considering the genome-wide genetic variation among the accessions included in cluster I, a second round of Bayesian (K = 3) and Hierarchical (K = 2) clustering was performed. These analysis showed that genotypes were grouped not only based on geographical origin, but also on fruit-related features.

Conclusions

GBS data has proven useful to assess the genetic diversity in a collection of C. annuum accessions. The high number of SNP markers, uniformly distributed on the 12 chromosomes, allowed the accessions to be distinguished according to geographical origin and fruit-related features. SNP markers and information on population structure developed in this study will undoubtedly support genome-wide association mapping studies and marker-assisted selection programs.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3297-7) contains supplementary material, which is available to authorized users.

Leaf Metabolic, Genetic, and Morphophysiological Profiles of Cultivated and Wild Rocket Salad (Eruca and Diplotaxis Spp.)

Rocket salad (Diplotaxis spp., Eruca spp.) is a leafy vegetable rich in health-promoting compounds and widely consumed. In the present study, metabolic profiles of 40 rocket accessions mainly retrieved from gene banks were assessed. Seven glucosinolates (GLSs) and 15 flavonol compounds were detected across genotypes. Dimeric 4-mercaptobutyl-GLS and 4-(β-d-glucopyranosyldisulfanyl)butyl-GLS were the major components of the total glucosinolate content. Flavonols were different between genera, with the exception of isorhamnetin 3,4'-diglucoside. Morphoagronomic traits and color coordinates were also scored. Results showed a negative correlation between color and GLSs, indicating these last as responsible for the increase of the intensity of green and yellow pigments as well as for the darkness of the leaf, whereas agronomic traits showed positive correlation with GLSs. Genetic diversity was assessed using inter simple sequence repeat (ISSR) markers, allowing separation of the accessions on the basis of the species and elucidating the observations made by means of phenotypic data.

Genetic Diversity and Population Structure of Tetraploid Wheats (Triticum turgidum L.) Estimated by SSR, DArT and Pedigree Data

Levels of genetic diversity and population genetic structure of a collection of 230 accessions of seven tetraploid Triticum turgidum L. subspecies were investigated using six morphological, nine seed storage protein loci, 26 SSRs and 970 DArT markers. The genetic diversity of the morphological traits and seed storage proteins was always lower in the durum wheat compared to the wild and domesticated emmer. Using Bayesian clustering (K = 2), both of the sets of molecular markers distinguished the durum wheat cultivars from the other tetraploid subspecies, and two distinct subgroups were detected within the durum wheat subspecies, which is in agreement with their origin and year of release. The genetic diversity of morphological traits and seed storage proteins was always lower in the improved durum cultivars registered after 1990, than in the intermediate and older ones. This marked effect on diversity was not observed for molecular markers, where there was only a weak reduction. At K >2, the SSR markers showed a greater degree of resolution than for DArT, with their identification of a greater number of groups within each subspecies. Analysis of DArT marker differentiation between the wheat subspecies indicated outlier loci that are potentially linked to genes controlling some important agronomic traits. Among the 211 loci identified under selection, 109 markers were recently mapped, and some of these markers were clustered into specific regions on chromosome arms 2BL, 3BS and 4AL, where several genes/quantitative trait loci (QTLs) are involved in the domestication of tetraploid wheats, such as the tenacious glumes (Tg) and brittle rachis (Br) characteristics. On the basis of these results, it can be assumed that the population structure of the tetraploid wheat collection partially reflects the evolutionary history of Triticum turgidum L. subspecies and the genetic potential of landraces and wild accessions for the detection of unexplored alleles.

Genetic Diversity and Population Structure of Tetraploid Wheats (Triticum turgidum L.) Estimated by SSR, DArT and Pedigree Data

Levels of genetic diversity and population genetic structure of a collection of 230 accessions of seven tetraploid Triticum turgidum L. subspecies were investigated using six morphological, nine seed storage protein loci, 26 SSRs and 970 DArT markers. The genetic diversity of the morphological traits and seed storage proteins was always lower in the durum wheat compared to the wild and domesticated emmer. Using Bayesian clustering (K = 2), both of the sets of molecular markers distinguished the durum wheat cultivars from the other tetraploid subspecies, and two distinct subgroups were detected within the durum wheat subspecies, which is in agreement with their origin and year of release. The genetic diversity of morphological traits and seed storage proteins was always lower in the improved durum cultivars registered after 1990, than in the intermediate and older ones. This marked effect on diversity was not observed for molecular markers, where there was only a weak reduction. At K >2, the SSR markers showed a greater degree of resolution than for DArT, with their identification of a greater number of groups within each subspecies. Analysis of DArT marker differentiation between the wheat subspecies indicated outlier loci that are potentially linked to genes controlling some important agronomic traits. Among the 211 loci identified under selection, 109 markers were recently mapped, and some of these markers were clustered into specific regions on chromosome arms 2BL, 3BS and 4AL, where several genes/quantitative trait loci (QTLs) are involved in the domestication of tetraploid wheats, such as the tenacious glumes (Tg) and brittle rachis (Br) characteristics. On the basis of these results, it can be assumed that the population structure of the tetraploid wheat collection partially reflects the evolutionary history of Triticum turgidum L. subspecies and the genetic potential of landraces and wild accessions for the detection of unexplored alleles.

Pancreatic pseudocyst: case report and short literature review

We report a case of pancreatic pseudocyst secondary to acute necrotizing pancreatitis treated with open cystogastrostomy. Following a literature review, we stress the enormous benefits offered by modern diagnostic techniques, and especially imaging techniques, for the diagnosis and monitoring of this disease. Treatment should be delayed for at least six weeks, following which the drainage by open surgery offers the best results and lowest morbidity and mortality, followed by laparoscopy and endoscopy, indicated in particular cases and in patients where open surgery is contraindicated.

Liver trauma. Diagnosis and treatment

The authors summarize the essential steps in liver surgery. Modern imaging techniques are of great help in establishing a circumstantiated diagnosis of post-traumatic lesions of the intra-abdominal parenchymatous organs, and especially the liver. Such diagnosis must always be based on the AAST (American Association for the Surgery of Trauma) classification, essential for a correct approach. Each therapeutic choice must be based on a careful clinical evaluation to establish whether emergency exploration of the abdomen or simple patient monitoring is indicated. Organ injuries and consequent hemoperitoneum must be found and quantified. In any case, diagnosis and treatment must only begin once all measures have been taken to ensure the maintenance of vital functions and the normalization of the main blood chemistry parameters.

Mucocele of the appendix. Two case reports

The authors present two cases of mucocele of the appendix and discuss them in relation to the literature and the clinical features of this disease. They clarify the definition of mucocele as an intraluminal accumulation of mucus in the appendix, and concentrate on the observable pathological processes, agreeing on the higher frequency of mucinous cystadenoma and the possibility that mucocele can develop into peritoneal pseudomyxoma or degenerate into cystadenocarcinoma. They also note that most diagnoses are made intra-operatively during appendectomy, and that, in cases suspected preoperatively, thorough investigation with imaging techniques is very important in order to plan the best treatment.

[Acute typhlitis associated with taxane-based chemotherapy]

A rare case of acute typhlitis is reported. The patient had undergone chemotherapy for a breast cancer. Clinical and diagnostic tools as well as general and topical care are examined.

[Recanalizing entero-rectal fistula post-colostomy for inoperable rectal cancer]

The Authors report a case of a spontaneous intestinal 'recanalization' after 1 year since the palliative surgery (definitive colostomy) for rectal cancer in a 79 years-old patient.

Chondrosarcoma of the larynx: a case report

Chondrosarcomas of the larynx are rare cancers and are more frequently located at cricoid cartilage level. They are characterised by a low tendency to metastatic diffusion (low grade). The treatment of choice is surgery, which may be endoscopic or "open partial surgery", if extension of the cancer is limited. Prognosis is generally good. In this report, a case of low malignancy chondrosarcoma of the larynx is presented, which was treated surgically with a glottic-hypoglottic laryngectomy according to Serafini-Bartual. Chondrosarcoma of the larynx shows a slow and painless growth, the first symptom is often an ingravescent dysphonia. Laryngoscopy reveals tumefaction of the larynx, covered by intact mucosa. Computerized tomography imaging with contrast and magnetic resonance imaging defines not only coarse calcifications, pathognomonic of chondromatous neo-formations but also the relationship of the neoformation with the surrounding tissues. However, histology remains the gold standard for diagnostic purposes. Treatment is essentially surgical; it must allow eradication of the cancer between specific safety margins and, it must, at the same time, be functional, if the lesion does not extend beyond half of the cricoid circle and if histological grade is low.

Amyand's hernia: case report and review of the literature

The authors report a case of gangrenous acute appendicitis in the sac of an inguinal hernia (Amyand's hernia). After a review of the literature, they emphasise the extreme rarity of the case reported, they underline how the clinical picture is highly similar to that of a strangulated inguinal hernia. They affirm that appendicectomy and hernioplasty may be performed at the same time, since the repair of the hernia should be performed without prosthesis implantation due to the contamination of the operating field.

[Surgery of inguinal hernia in the elderly]

The authors report their 14 years experiences with inguinal hernia repair in elderly. The result were compared with young (< 75 years old), and confirmed that there were no significant differences between the 2 groups. The study confirmed the safety and effectiveness of the "tension-free" technique under local anaesthesia, which is proposed as the treatment of choice in elderly.

Vascular complications of native arteriovenous fistulas for hemodialysis: role of microsurgery

This article describes the treatment of 56 early and late vascular complications of native arteriovenous fistula (AVF) in patients with end-stage renal disease, between January 1987 and January 1999. Twenty-six were arteriovenous aneurysms and 2 pseudoaneurysms; 25 were thromboses. We also observed two cases of periarteritis associated with systemic lupus erythematosus (SLE) and one complex iatrogenic lesion caused by an attempt at percutaneous restoration of potency. We applied microsurgical principles, instruments, and techniques. It was possible to restore a vascular access at the original site, using the same vessels in 45 cases (80.4%). In 10.7% of cases, we were able to rescue the original AVF by microsurgical revision. A new vascular access had to be created proximally in the same limb or in the contralateral forearm in 11 cases of aneurysms (19.6% of the total, 42% of the aneurysms). After a minimum follow-up of 8 months, a total of four patients had to be reoperated for further complications (7.2%). Our data support the idea that microsurgical treatment of vascular complications of native AVF is highly successful compared with results obtained by conventional surgery and, in a defined subgroup of patients, permits salvage of the fistula.

[Indications for preventive tracheostomy in the surgical treatment of non-neoplastic thyroid disease]

In thyroid surgery, an emergency tracheostomy is mandatory, as is well known, in acute pre- and postoperative asphyxia due to obstruction of the upper airways, especially in cases of malignant tumours. In particular conditions, in the presence of benign thyroid disease and when there is no reduction in the laryngo-tracheal lumen, tracheostomy has an important precautionary function following total thyroidectomy. The authors describe their experience with 6 patients treated by precautionary tracheostomy after total thyroidectomy for benign thyroid disease, analysing the indications and the advantages of this method.

Brunner's adenoma, esophageal reflux and gastric ulcer. A case report

In this work the authors report a clinical case of Brunner's adenoma, which was responsible for the onset of other pathologies in the upper gastrointestinal tract, such as gastroesophageal reflux (GER), esophagitis and ulcerations of the antral mucosa. The preoperative diagnostic procedure (endoscopy, esophageal manometry, gastric emptying) and the follow-up at 3, 6 and 12 months from the surgery confirmed the relationship between the Brunner's adenoma and the alterations of the lower esophageal sphyncter (LES) tone and the gastric emptying. After a review of the international literature and a short analysis of the physiopathologic alterations, the authors point out the different therapeutical approach, in according to the size and implantation (sessile or peduncolated) of the lesion and to the related pathologies.

[Internal abdominal hernia. Unusual cause of intestinal occlusion]

Internal abdominal hernias are an unusual cause of intestinal occlusion. They are responsible for 2% of all the intestinal obstructions. Various types of hernia have been described. The diagnosis is difficult, but should be suspected in patients suffering from intestinal obstruction who have undergone earlier laparotomy. Diagnosis is even more difficult in cases of congenital internal hernia. The authors report a case of left paraduodenal hernia (congenital), and a case of transmesenteric hernia (acquired). Both patients complained of a short history of abdominal pain and characteristic symptoms of acute abdomen (nausea, vomit, cramps and obstipation). Emergency surgery using laparotomy enabled diagnosis and treatment. The authors underline the difficulty of diagnosing these hernias and emphasise the diagnostic and therapeutic importance of emergency surgery.

The recurrent laryngeal nerve related to thyroid surgery

BACKGROUND

Iatrogenic injury of inferior laryngeal nerve is one of the most serious concerns in thyroid surgery. Paralysis of vocal cords is a common sequela of thyroidectomy. It represents a serious complication inducing, when bilateral, serious functional sequelae such as phonatory, respiratory and psychological problems that limit working capacities and social relationships of patients. We carried out an intraoperative study aimed to define anatomical relationships between the recurrent laryngeal nerve and the adjacent structures (the inferior thyroid artery in particular), intraoperative identification of which may allow prevention of iatrogenic injuries of the laryngeal nerve.

METHODS

One hundred ninety-two patients (165 females, 27 males whose age was between 18 and 90 years, median age 55) who had undergone thyroidectomy in our department in the last 3 years. Among them, 179 patients underwent total extracapsular thyroidectomy, and of the 13 remaining, 12 were completions of thyroidectomy in patients who had previously undergone a first thyroid surgical intervention and underwent istmo-lobectomy.

RESULTS

Despite a systematic intraoperative search, we identified the recurrent laryngeal nerve in 158 of 192 patients (82.3%), while in the remaining 34 (17.7%), the recurrent laryngeal nerve was not identified. In 122 out of the 158 patients (77.2%) in whom the recurrent laryngeal nerve had been detected, the nerve was identified bilaterally: in 19 of 158 (12%) only on the right side; in 17 of 158 (10.7%) only on the left. Concerning the postoperative results we noticed only one case (0.5%) of recurrent laryngeal nerve injury for neoplastic infiltration of its own branch, one case (0.5%) of monolateral cordal hypomotility, and two cases (1.04%) of bilateral cordal hypomotility with temporary disphonia, which regressed in 6 months of time.

CONCLUSION

The results of our study may confirm that iatrogenic injury to the recurrent laryngeal nerve, or to its branches, might be better avoided by searching, identifying, and exposing the nerve itself and by following its course with care. In our view, total extracapsular thyroidectomy, with systematic search for the nerve, is the best approach. We believe that deep knowledge of the thyroid region's surgical anatomy and the awareness of the extremely varying course of the recurrent laryngeal nerve and the inferior thyroid artery and their relations should be taken into account by surgeons.

[Microsurgical approach to epididymal neoplasms. Our experience]

In the period from January 1st 1988 to January 15th 1994 inclusive, we observed 36 patients with epididymal neoformations. In patients with a considerable oligospermia, we associated microsurgical extirpation of neoformations, with the "testis biopsy" operation, to assess eventual histologic alterations of the interstice and seminiferous tubulus. The authors show as the application of microsurgical techniques with the help of magnifying optical instruments, permits to remove these neoformations with respect to near by structures besides consenting the accurate reconstruction of structures operated and maintenance or recovery of functionality mostly in young people, where fertility recovery is obligatory.

[Hemorrhagic pseudocysts of the spleen]

After a short introduction regarding the physiopathology of secondary spleen cysts, the authors describe a personally observed case of voluminous hemorrhagic pseudocyst. They underline the rarity of the orientation towards radical surgery, having in mind the post-splenectomy risks determined by deficiency of important spleen functions. The authors, with respect to this, underline the importance of reimplanting splenic tissue fragment into omentum, promoting to use, in selected cases, this treatment that needs, however, further clinical findings.