An S-RNase-based gametophytic self-incompatibility (GSI) system, a mechanism that forces outbreeding by preventing self-fertilization, characterizes the genus Malus. Knowledge of the self-incompatibility (S) genotypes of apple cultivars is crucial for choosing pollen donors for fruit production and breeding. Even though the S-allele of most commercial apple cultivars has already been identified, limited information is available about the S-allele diversity within local germplasm collections. In this study, 67 S-allele combinations of local apple accessions were identified. The allele S3 was the most common among local apple accessions followed by S1 and S7. The main aim of this study is to provide new information on cultivar compatibility, and these results will be used to set up new parent selection in apple breeding programmes as well as pollinator selection for the commercial orchard.

Apricot breeding programs could be strongly improved by the availability of molecular markers linked to the main fruit quality traits. Fruit acidity is one of the key factors in consumer acceptance, but despite its importance, the molecular bases of this trait are still poorly understood. In order to increase the genetic knowledge on the fruit acidity, an F1 apricot population ('Lito' × 'BO81604311') has been phenotyped for titratable acidity and juice pH for the three following years. In addition, the contents of the main organic acids of the juice (malate, citrate, and quinate) were also evaluated. A Gaussian distribution was observed for most of the traits in this progeny, confirming their quantitative inheritance. An available simple sequence repeat (SSR)-based molecular map, implemented with new markers in specific genomic regions, was used to perform a quantitative trait loci (QTL) analysis. The molecular map was also anchored to the recently published apricot genome sequence of 'Stella.' Several major QTLs linked to fruit acidity-related traits have been identified both in the 'Lito' (no. 21) and 'BO81604311' (no. 13), distributed in five linkage groups (LG 4, 5, 6, 7, and 8). Some of these QTLs show good stability between years and their linked markers were used to identify candidate genes in specific QTLs genomic regions.

The efficient use of sorghum as a renewable energy source requires high biomass yields and reduced agricultural inputs. Hybridization of Sorghum bicolor with wild Sorghum halepense can help meet both requirements, generating high-yielding and environment friendly perennial sorghum cultivars. Selection efficiency, however, needs to be improved to exploit the genetic potential of the derived recombinant lines and remove weedy and other wild traits. In this work, we present the results from a Genome-Wide Association Study conducted on a diversity panel made up of S. bicolor and an advanced population derived from S. bicolor × S. halepense multi-parent crosses. The objective was to identify genetic loci controlling biomass yield and biomass-relevant traits for breeding purposes. Plants were phenotyped during four consecutive years for dry biomass yield, dry mass fraction of fresh material, plant height and plant maturity. A genotyping-by-sequencing approach was implemented to obtain 92,383 high quality SNP markers used in this work. Significant marker-trait associations were uncovered across eight of the ten sorghum chromosomes, with two main hotspots near the end of chromosomes 7 and 9, in proximity of dwarfing genes Dw1 and Dw3. No significant marker was found on chromosomes 2 and 4. A large number of significant marker loci associated with biomass yield and biomass-relevant traits showed minor effects on respective plant characteristics, with the exception of seven loci on chromosomes 3, 8, and 9 that explained 5.2-7.8% of phenotypic variability in dry mass yield, dry mass fraction of fresh material, and maturity, and a major effect (R 2 = 16.2%) locus on chromosome 1 for dry mass fraction of fresh material which co-localized with a zinc-finger homeodomain protein possibly involved in the expression of the D (Dry stalk) locus. These markers and marker haplotypes identified in this work are expected to boost marker-assisted selection in sorghum breeding.

The genus Pyrus is characterized by an S-RNase-based gametophytic self-incompatibility (GSI) system, a mechanism that promotes outbreeding and prevents self-fertilization. While the S-genotype of the most widely known pear cultivars was already described, little is known on the S-allele variability within local accessions. The study was conducted on 86 accessions encompassing most of the local Sicilian varieties selected for their traits of agronomic interest and complemented with some accessions of related wild species (P. pyrifolia Nakai, P. amygdaliformis Vill.) and some national and international cultivars used as references. The employment of consensus and specific primers enabled the detection of 24 S-alleles combined in 48 S-genotypes. Results shed light on the distribution of the S-alleles among accessions, with wild species and international cultivars characterized by a high diversity and local accessions showing a more heterogeneous distribution of the S-alleles, likely reflecting a more complex history of hybridization. The S-allele distribution was largely in agreement with the genetic structure of the studied collection. In particular, the “wild” genetic background was often characterized by the same S-alleles detected in P. pyrifolia and P. amygdaliformis. The analysis of the S-allele distribution provided novel insight into the contribution of the wild and international cultivars to the genetic background of the local Sicilian or national accessions. Furthermore, these results provide information that can be readily employed by breeders for the set-up of novel mating schemes.

Sorghum is widely used for producing food, feed, and biofuel, and it is increasingly grown to produce grains rich in health-promoting antioxidants. The conventional use of grain color as a proxy to indirectly select against or for antioxidants polyphenols in sorghum grain was hampered by the lack of consistency between grain color and the expected antioxidants concentration. Marker-assisted selection built upon significant loci identified through linkage disequilibrium studies showed interesting potential in several plant breeding and animal husbandry programs, and can be used in sorghum breeding for consumer-tailored antioxidant production. The purpose of this work was therefore to conduct genome-wide association study of sorghum grain antioxidants using single nucleotide polymorphisms in a novel diversity panel of Sorghum bicolor landraces and S. bicolor × S. halepense recombinant inbred lines. The recombinant inbred lines outperformed landraces for antioxidant production and contributed novel polymorphism. Antioxidant traits were highly correlated and showed very high broad-sense heritability. The genome-wide association analysis uncovered 96 associations 55 of which were major quantitative trait loci (QTLs) explaining 15 to 31% of the observed antioxidants variability. Eight major QTLs localized in novel chromosomal regions. Twenty-four pleiotropic major effect markers and two novel functional markers (Chr9_1550093, Chr10_50169631) were discovered. A novel pleiotropic major effect marker (Chr1_61095994) explained the highest proportion (R2 = 27-31%) of the variance observed in most traits evaluated in this work, and was in linkage disequilibrium with a hotspot of 19 putative glutathione S-transferase genes conjugating anthocyanins into vacuoles. On chromosome four, a hotspot region was observed involving major effect markers linked with putative MYB-bHLH-WD40 complex genes involved in the biosynthesis of the polyphenol class of flavonoids. The findings in this work are expected to help the scientific community particularly involved in marker assisted breeding for the development of sorghum cultivars with consumer-tailored antioxidants concentration.

Sorghum is grown for several purposes including biomass for producing energy and fodder, and grain for producing health-promoting foods. Sorghum is a drought resistant cereal with low input requirements, making it one of the most promising crops under the world’s tropics and higher latitudes. Crop monitoring, one of the leading activities in smart farming, can help cut production costs and more so under climate change. In this study, Sentinel 2A and 2B-derived fAPAR and NDVI data were used to monitor sorghum phenology, foliar diseases, and to predict aboveground biomass yields months before harvest, using machine learning approaches including Bayesian methods and region-convolutional neural network. The results obtained in this work were encouraging. We were able to predict biomass yields up to 6 months before harvest with mean absolute percentage error (MAPE) < 0.2, while diseases were detected with accuracy up to 90%. The best machine learning algorithm was Bayesian additive regression trees (bartMachine method), while the best biomass yields prediction regressors were the days of year 150 and 165. These results were achieved at a Pilot level and the technologies showed industrial scale implementation potentials with tremendous benefits for the farmer, extension services, policy makers, and other parties at interest.

Sorghum crop is grown under tropical and temperate latitudes for several purposes including production of health promoting food from the kernel and forage and biofuels from aboveground biomass. One of the concerns of policy-makers and sorghum growers is to cost-effectively predict biomass yields early during the cropping season to improve biomass and biofuel management. The objective of this study was to investigate if Sentinel-2 satellite images could be used to predict within-season biomass sorghum yields in the Mediterranean region. Thirteen machine learning algorithms were tested on fortnightly Sentinel-2A and Sentinel-2B estimates of the fraction of Absorbed Photosynthetically Active Radiation (fAPAR) in combination with in situ aboveground biomass yields from demonstrative fields in Italy. A gradient boosting algorithm implementing the xgbtree method was the best predictive model as it was satisfactorily implemented anywhere from May to July. The best prediction time was the month of May followed by May–June and May–July. To the best of our knowledge, this work represents the first time Sentinel-2-derived fAPAR is used in sorghum biomass predictive modeling. The results from this study will help farmers improve their sorghum biomass business operations and policy-makers and extension services improve energy planning and avoid energy-related crises.

Apples (Males x domestica Borkh.) are one of the largest economically significant fruit crop worldwide. Due to the self-incompatibility of most Maim cultivars, the apple industry relies on insect pollinators to aid in cross-pollination to improve seed and fruit set. The introduction of crabapples as pollinizers has become a popular practice to promote cross-pollination in commercial apple orchards. Genetic compatibility with a desired apple cultivar is a critical feature of effective pollinizers, but the S-genotypes of many crabapple cultivars used for cross-pollination have not yet been reported. In this study, seven crabapple cultivars were genotyped, and the genomic DNA of one novel S-allele in 'Mt. Blanc' and three variants of previously discovered alleles in 'Manchurian', 'Snowdrift' and 'Indian Summer' were characterized. Genomic DNA sequences were submitted to National Center for Biotechnology Information (NCBI) GenBank, and PCR-based detection methods were developed. The methods and results of this study aim to enrich S-genotyping methodologies and inform pollinizer-cultivar compatibility in commercial orchards.

The main objective of this study was to evaluate the trustworthiness of seed image analysis as an approach to discriminate apple germplasm accessions. Digital images of seeds from 42 apple cultivars, acquired by a flatbed scanner, provided a phenotypic dataset with 106 morphometric variables. Stepwise Linear Discriminant Analysis (LDA) was used to examine this dataset, and the results were compared with available genetic data. The first comparison among cultivars provided a 38.8% cross-validation of correct identifications with a discriminant percentage ranging between 11.7 and 70%. In agreement with the genetic diversity analysis, the LDA could discriminate between the apples cultivars, identifying two main groups that could be further divided into additional subgroups. Based on our findings, we propose that seed image analysis is a valuable and affordable tool to investigate phenotypic diversity among a large number of apple cultivars.

Brown spot is one of the most serious fungal diseases that can affect pear fruits and leaves in the Po valley (Italy). Stemphylium vesicarium is the causal agent of this disease, and several antifungal treatments, repeated throughout the period between bloom and harvest, are needed to control its spread. Many of the most important pear cultivars (such as ‘Abbé Fétel’) are very susceptible to this fungus, while others (such as ‘Bartlett’ and its mutated sports) are known to be resistant. Our research aimed to develop molecular markers linked to this trait. To this end, 92 seedlings derived from an ‘Abbé Fétel’ × ‘Max Red Bartlett’ cross were evaluated for resistance to S. vesicarium for two consecutive years by artificial inoculation with conidia on detached leaves and fruits under controlled conditions in greenhouse. The extent of the lesions was recorded at different time points. A major QTL for susceptibility was located at the lower end of linkage group 15 of ‘Abbé Fétel’. This region was saturated with three SSR markers, and the putative position of a susceptibility gene was also estimated by the single gene mapping approach. This putative gene was located at 2 cM far from the lower end of the linkage group. Molecular markers tightly associated to this locus represent a first step towards the development of MAS (marker-assisted selection) to support the selection of new pear genotypes more resistant to brown spot.

Data obtained from Illumina resequencing of 63 apple cultivars were used to obtain full-length S-RNase sequences using a strategy based on both alignment and de novo assembly of reads. The reproductive biology of apple is regulated by the S-RNase-based gametophytic self-incompatibility system, that is genetically controlled by the single, multi-genic and multi-allelic S locus. Resequencing of apple cultivars provided a huge amount of genetic data, that can be aligned to the reference genome in order to characterize variation to a genome-wide level. However, this approach is not immediately adaptable to the S-locus, due to some peculiar features such as the high degree of polymorphism, lack of colinearity between haplotypes and extensive presence of repetitive elements. In this study we describe a dedicated procedure aimed at characterizing S-RNase alleles from resequenced cultivars. The S-genotype of 63 apple accessions is reported; the full length coding sequence was determined for the 25 S-RNase alleles present in the 63 resequenced cultivars; these included 10 previously incomplete sequences (S (5) , S (6a) , S (6b) , S (8) , S (11) , S (23) , S (39) , S (46) , S (50) and S (58) ). Moreover, sequence divergence clearly suggests that alleles S (6a) and S (6b) , proposed to be neutral variants of the same alleles, should be instead considered different specificities. The promoter sequences have also been analyzed, highlighting regions of homology conserved among all the alleles.

Apple (Malus × domestica Borkh.) is a species possessing S-RNase-based self-incompatibility. Knowledge of the S-genotype of cultivars is very important both for breeders and growers, in order to plan compatible crosses and cultivar combinations. Here we report a revision of the S-genotype of the cultivar Murray which is in disagreement with previous reports, and the characterization of the newly identified S-RNase allele. Moreover, Murray carries the Rvi5 gene for apple scab resistance, which was mapped at the bottom of linkage group 17, in a position close to that of the S-locus. To evaluate whether the segregation of S-alleles can influence that of Rvi5, we analyzed the linkage between the two loci in 215 progeny individuals from the cross Galaxy × Murray. Our results suggest that the S-genotype of cultivars used as parents can dramatically influence the frequency of seedlings inheriting the resistance gene, and this aspect can be exploited to increase the efficiency of breeding programs aimed at pyramiding scab resistance genes.

Apple germplasm collections are increasingly appreciated as a repository for the genetic improvement of species, and their evaluation is an essential prerequisite for their utilization in apple breeding. A set of 418 apple genotypes, including 383 accessions from the Italian germplasm and 35 International cultivars as reference, was analyzed using 15 SSRs with the aim of assessing the genetic diversity within this panel of varieties, evaluating relationships among them and determining their genetic structure. Genetic analyses performed by Bayesian model-based clustering revealed a clear differentiation of two major groups (G1 and G2). Local Italian accessions were grouped mainly in G2 while all except one of the reference cultivars were found in G1. Each of these two clusters has been further divided into two subgroups by a nested approach. These results were confirmed by factorial correspondence (FCA) and molecular variance (AMOVA) analyses. A core collection of 55 accessions, representative of the Italian apple germplasm and capable of retaining all the 238 SSR alleles detected on 192 unique genotypes, was established by the M-strategy method. The Italian apple germplasm represents an important source of genetic diversity which can be used, in addition to other characterized European germplasm collections, to optimize the efficiency of genome-wide association studies aimed at identifying the genomic regions controlling major horticultural traits.

The Pyrus species exhibit the gametophytic self -incompatibility which is considered to be the most widespread self-incompatibility system among flowering plants. This system prevents self-fertilization through a specific pollen-pistil recognition mechanism. The S-allele diversity in the Iranian genotypes indicates that the pear germplasm of Iran can be an excellent source of variability for breeding programs. In this study, the S-RNases of 64 pear cultivars and wild genotypes of Pyrus species of Iran and Europe including Pyrus communis, Pyrus salicifolia, Pyrus syriaca and Pyrus ussuriensis were amplified using consensus and allele-specific primers by PCR-based method. This method was used for the detection of product size characteristics of the 23 S-RNases (S101-S125) and revealed the existence of one new allele named S127 and the footprint of S8 of P. pyrifolia syn. P. serotina in Iranian genotypes. Interestingly, in 6 specimens allele PcS127 is coupled with PpS8, suggesting that these plants might come from subgroups or populations where the contribution of P. Pyrifolia syn. P. serotina is more consistent. The pool of S-RNases found in the Iranian germplasm had a different composition from the European cultivars, and showed traces of significant genetic contribution from other species. Also, application of this approach in 21 European cultivars allowed re-evaluation of alleles of Veerdi (S101/S104) and Conseiller a la Coeur (S103/S123/S105).

Brown spot (Stemphylium vesicarium) is one of the most serious fungal disease that affects the pear tree orchards in the Po valley. In this region, which produces 90% of the pears in Italy, several antifungal treatments must be repeated along the period between flowering and harvest. In addition, many of the most widely grown varieties of pear (e.g., ‘Abbe Fetel’) are very susceptible to this fungus, while others, such as William and his mutated sports are substantially resistant. With the aim to develop molecular markers linked with brown spot resistance, plants derived from the cross ‘Abbe Fetel’ × ‘Max Red Bartlett’ were challenged for two consecutive years with a suspension of conidia both on leaves and fruits of each seedling. As a control, both the parents of the progeny and the varieties ‘Conference’ and ‘William’ were inoculated. On the genetic maps of the two parents QTL analysis revealed the presence of two QTLs, one for resistance to brown spot in ‘Max Red Bartlett’ and another for the susceptibility in ‘Abbe Fetel’. The availability of molecular markers in the regions of QTLs is an important step forward towards the selection of new pear genotypes resistant to brown spot by Marker-Assisted Selection (MAS).