Application of Multi-Perspectives in Tea Breeding and the Main Directions

Tea plants are an economically important crop and conducting research on tea breeding contributes to enhancing the yield and quality of tea leaves as well as breeding traits that satisfy the requirements of the public. This study reviews the current status of tea plants germplasm resources and their utilization, which has provided genetic material for the application of multi-omics, including genomics and transcriptomics in breeding. Various molecular markers for breeding were designed based on multi-omics, and available approaches in the direction of high yield, quality and resistance in tea plants breeding are proposed. Additionally, future breeding of tea plants based on single-cellomics, pangenomics, plant-microbe interactions and epigenetics are proposed and provided as references. This study aims to provide inspiration and guidance for advancing the development of genetic breeding in tea plants, as well as providing implications for breeding research in other crops.

Germ Granule Evolution Provides Mechanistic Insight into Drosophila Germline Development

The copackaging of mRNAs into biomolecular condensates called germ granules is a conserved strategy to posttranscriptionally regulate germline mRNAs. In Drosophila melanogaster, mRNAs accumulate in germ granules by forming homotypic clusters, aggregates containing multiple transcripts from the same gene. Nucleated by Oskar (Osk), homotypic clusters are generated through a stochastic seeding and self-recruitment process that requires the 3' untranslated region (UTR) of germ granule mRNAs. Interestingly, the 3' UTR belonging to germ granule mRNAs, such as nanos (nos), have considerable sequence variations among Drosophila species and we hypothesized that this diversity influences homotypic clustering. To test our hypothesis, we investigated the homotypic clustering of nos and polar granule component (pgc) in four Drosophila species and concluded that clustering is a conserved process used to enrich germ granule mRNAs. However, we discovered germ granule phenotypes that included significant changes in the abundance of transcripts present in species' homotypic clusters, which also reflected diversity in the number of coalesced primordial germ cells within their embryonic gonads. By integrating biological data with computational modeling, we found that multiple mechanisms underlie naturally occurring germ granule diversity, including changes in nos, pgc, osk levels and/or homotypic clustering efficacy. Furthermore, we demonstrated how the nos 3' UTR from different species influences nos clustering, causing granules to have ∼70% less nos and increasing the presence of defective primordial germ cells. Our results highlight the impact that evolution has on germ granules, which should provide broader insight into processes that modify compositions and activities of other classes of biomolecular condensate.

Genetic resources and breeding approaches for improvement of amaranth (Amaranthus spp.) and quinoa (Chenopodium quinoa)

Nowadays, the human population is more concerned about their diet and very specific in choosing their food sources to ensure a healthy lifestyle and avoid diseases. So people are shifting to more smart nutritious food choices other than regular cereals and staple foods they have been eating for a long time. Pseudocereals, especially, amaranth and quinoa, are important alternatives to traditional cereals due to comparatively higher nutrition, essential minerals, amino acids, and zero gluten. Both Amaranchaceae crops are low-input demanding and hardy plants tolerant to stress, drought, and salinity conditions. Thus, these crops may benefit developing countries that follow subsistence agriculture and have limited farming resources. However, these are underutilized orphan crops, and the efforts to improve them by reducing their saponin content remain ignored for a long time. Furthermore, these crops have very rich variability, but the progress of their genetic gain for getting high-yielding genotypes is slow. Realizing problems in traditional cereals and opting for crop diversification to tackle climate change, research should be focused on the genetic improvement for low saponin, nutritionally rich, tolerant to biotic and abiotic stresses, location-specific photoperiod, and high yielding varietal development of amaranth and quinoa to expand their commercial cultivation. The latest technologies that can accelerate the breeding to improve yield and quality in these crops are much behind and slower than the already established major crops of the world. We could learn from past mistakes and utilize the latest trends such as CRISPR/Cas, TILLING, and RNA interference (RNAi) technology to improve these pseudocereals genetically. Hence, the study reviewed important nutrition quality traits, morphological descriptors, their breeding behavior, available genetic resources, and breeding approaches for these crops to shed light on future breeding strategies to develop superior genotypes.

Responses to water stress extremes in diverse red clover germplasm accessions

Red clover (Trifolium pratense L.), a key perennial pastoral species used globally, can strengthen pastural mixes to withstand increasingly disruptive weather patterns from climate change. Breeding selections can be refined for this purpose by obtaining an in-depth understanding of key functional traits. A replicated randomized complete block glasshouse pot trial was used to observe trait responses critical to plant performance under control (15% VMC), water deficit (5% VMC) and waterlogged conditions (50% VMC) in seven red clover populations and compared against white clover. Twelve morphological and physiological traits were identified as key contributors to the different plant coping mechanisms displayed. Under water deficit, the levels of all aboveground morphological traits decreased, highlighted by a 41% decrease in total dry matter and 50% decreases in both leaf number and leaf thickness compared to the control treatment. An increase in root to shoot ratio indicated a shift to prioritizing root maintenance by sacrificing shoot growth, a trait attributed to plant water deficit tolerance. Under waterlogging, a reduction in photosynthetic activity among red clover populations reduced several morphological traits including a 30% decrease in root dry mass and total dry matter, and a 34% decrease in leaf number. The importance of root morphology for waterlogging was highlighted with low performance of red clover: there was an 83% decrease in root dry mass compared to white clover which was able to maintain root dry mass and therefore plant performance. This study highlights the importance of germplasm evaluation across water stress extremes to identify traits for future breeding programs.

Genotyping of Jujube (Ziziphus spp.) Germplasm in New Mexico and Southwestern Texas

Since the early 19th century, a substantial amount of jujube (Ziziphus spp.) germplasm has been introduced from China and Europe into the United States. However, due to a lack of passport data, cultivar mislabeling is common and the genetic background of the introduced germplasm remains unknown. In the present study, a low-density SNP array was employed to genotype 204 jujube trees sampled from multiple locations in New Mexico, Texas, Missouri, and Kentucky. Multilocus matching of SNP profiles revealed a significant rate of genetic redundancy among these jujube samples. A total of 14 synonymous groups were detected, comprising 48 accessions. Bayesian clustering analysis and neighbor-joining tree partitioned the US jujube germplasm into two major clusters. The first cluster included cultivated genotypes (Ziziphus jujuba Mill.), whereas the other major cluster comprised the wild/sour jujube (Ziziphus spinosa Hu.). The results also revealed a unique jujube population at Fabens/Tornillo, Texas, and a semi-naturalized population at Tucumcari, NM. These findings will provide valuable guidance to jujube growers and researchers on the effective utilization of jujube germplasm in the horticultural industry.

Glucosinolate Diversity Analysis in Choy Sum (Brassica rapa subsp. chinensis var. parachinensis) Germplasms for Functional Food Breeding

The aim of this study was to analyze glucosinolates (GSLs) in germplasm that are currently conserved at the RDA-Genebank. The analysis focused on the glucosinolate diversity among the analyzed germplasms, with the goal of identifying those that would be most useful for future breeding efforts to produce nutritionally rich Choy sum plants. In total, 23 accessions of Choy sums that possessed ample background passport information were selected. On analyzing the glucosinolate content for 17 different glucosinolates, we observed aliphatic GSLs to be the most common (89.45%) and aromatic GSLs to be the least common (6.94%) of the total glucosinolates detected. Among the highly represented aliphatic GSLs, gluconapin and glucobrassicanapin were found to contribute the most (>20%), and sinalbin, glucoraphanin, glucoraphasatin, and glucoiberin were detected the least (less than 0.05%). We identified one of the accessions, IT228140, to synthesize high quantities of glucobrassicanapin and progoitrin, which have been reported to contain several therapeutic applications. These conserved germplasms are potential bioresources for breeders, and the availability of information, including therapeutically important glucosinolate content, can help produce plant varieties that can naturally impact public health.

Genetic diversity and population structure of bermudagrass (Cynodon spp.) revealed by genotyping-by-sequencing

Bermudagrass (Cynodon spp.) breeding and cultivar development is hampered by limited information regarding its genetic and phenotypic diversity. To explore diversity in bermudagrass, a total of 206 Cynodon accessions consisting of 193 common bermudagrass (C. dactylon var. dactylon) and 13 African bermudagrass (C. transvaalensis) accessions of worldwide origin were assembled for genetic characterization. Genotyping-by-sequencing (GBS) was employed for genetic marker development. With a minor allele frequency of 0.05 and a minimum call rate of 0.5, a total of 37,496 raw single nucleotide polymorphisms (SNPs) were called de novo and were used in the genetic diversity characterization. Population structure analysis using ADMIXTURE revealed four subpopulations in this germplasm panel, which was consistent with principal component analysis (PCA) and phylogenetic analysis results. The first three principal components explained 15.6%, 10.1%, and 3.8% of the variance in the germplasm panel, respectively. The first subpopulation consisted of C. dactylon accessions from various continents; the second subpopulation was comprised mainly of C. transvaalensis accessions; the third subpopulation contained C. dactylon accessions primarily of African origin; and the fourth subpopulation represented C. dactylon accessions obtained from the Oklahoma State University bermudagrass breeding program. Genetic diversity parameters including Nei's genetic distance, inbreeding coefficient, and Fst statistic revealed substantial genetic variation in the Cynodon accessions, demonstrating the potential of this germplasm panel for further genetic studies and cultivar development in breeding programs.

Variability of cell wall recalcitrance and composition in genotypes of Miscanthus from different genetic groups and geographical origin

Miscanthus is a promising crop for bioenergy and biorefining in Europe. The improvement of Miscanthus as a crop relies on the creation of new varieties through the hybridization of germplasm collected in the wild with genetic variation and suitable characteristics in terms of resilience, yield and quality of the biomass. Local adaptation has likely shaped genetic variation for these characteristics and is therefore important to quantify. A key biomass quality parameter for biorefining is the ease of conversion of cell wall polysaccharides to monomeric sugars. Thus far, the variability of cell wall related traits in Miscanthus has mostly been explored in accessions from limited genetic backgrounds. Here we analysed the soil and climatic conditions of the original collection sites of 592 Miscanthus genotypes, which form eight distinct genetic groups based on discriminant analysis of principal components of 25,014 single-nucleotide polymorphisms. Our results show that species of the genus Miscanthus grow naturally across a range of soil and climate conditions. Based on a detailed analysis of 49 representative genotypes, we report generally minor differences in cell wall characteristics between different genetic groups and high levels of genetic variation within groups, with less investigated species like M. floridulus showing lower recalcitrance compared to the other genetic groups. The results emphasize that both inter- and intra- specific variation in cell wall characteristics and biomass recalcitrance can be used effectively in Miscanthus breeding programmes, while also reinforcing the importance of considering biomass yield when quantifying overall conversion efficiency. Thus, in addition to reflecting the complexity of the interactions between compositional and structural cell wall features and cell wall recalcitrance to sugar release, our results point to traits that could potentially require attention in breeding programmes targeted at improving the Miscanthus biomass crop.

Evaluation of carboxylated poly l-lysine for cryopreservation of Labeo rohita sperm

Carboxylated poly l-lysine (CPLL) is an anti-freeze agent having pronounced non-permeating yet membrane stabilizing cryoprotective capabilities. The objective was to evaluate the CPLL supplementation in extender in terms of post thaw quality (sperm), total antioxidant activity (milt) and fertilization potential of cryopreserved Labeo rohita sperm. For this purpose, male brood fish reared at fish seed hatchery, Rawal Town Islamabad, Pakistan were captured from different rearing ponds and acclimatized in hatchery ponds for 6 hours. The brooder were injected with Ovaprim (0.2 ml/kg), milt was collected after 8 hours in cooled sterilized falcon tubes, maintained at 4°C and evaluated for sperm motility. The milt collected from three brooders (n=3) was diluted in extenders viz., modified Kurokura-2 extender having 10% methanol (control); experimental extenders with CPLL supplementation at the rate of 0.5%, 1% and 1.5%. Diluted milt was filled in 0.5ml straws, exposed to liquid nitrogen vapors and cryopreserved. Cryopreserved milt was thawed at 25⁰ C and assessed for post-thaw sperm quality. Sperm motility, motility duration, viability, total antioxidant capacity and DNA integrity was significantly higher (P<0.05) in extender having 1.5% CPLL than control. To evaluate the fertilization rates, male and female brooders were injected with Ovaprim at 0.2ml/Kg and 0.5ml/Kg body weight respectively. Fresh eggs and milt were collected through abdominal stripping. Batches of 10g of eggs from each female (n=2) were fertilized with one straw, each from frozen sperm with KE+methanol (control), KE+methanol+1.5% CPLL and 50 μl fresh milt (negative control). After 1.5 hours of fertilization, eggs were collected from all jars and a total of 200 eggs were counted. The fertilized eggs appeared clear and transparent while unfertilized eggs looked opaque with disintegrated nucleus. Sperm fertilization rate (%) was higher (P<0.05) in extender KE+methanol+1.5%CPLL (78.7±0.5) compared to control (KE+methanol) (52.0±0.4) however, it was lower compared to that of negative control, the fresh milt (85.2±0.6). In conclusion, supplementation of carboxylated poly l-lysine (1.5%) to modified Kurokura-2 extender having 10% methanol improves post thaw motility, motility duration, viability, DNA integrity, anti-oxidant capacity (milt) and fertilizing ability of cryopreserved L. rohita sperm.

Genome-Wide Association Mapping for Yield and Yield-Related Traits in Rice (Oryza Sativa L.) Using SNPs Markers

Rice (Oryza sativa L.) is a staple food for more than 50% of the world's population. Rice cultivar improvement is critical in order to feed the world's growing population. Improving yield is one of the main aims of rice breeders. However, yield is a complex quantitative trait controlled by many genes. The presence of genetic diversity is the key factor to improve the yield hence, the presence of diversity in any germplasm is important for yield improvement. In the current study, the rice germplasm was collected from Pakistan and the United States of America and a panel of 100 diverse genotypes was utilized to identify important yield and yield-related traits. For this, a genome-wide association study (GWAS) was performed to identify the genetic loci related to yield. The GWAS on the diverse germplasm will lead to the identification of new genes which can be utilized in the breeding program for improvement of yield. For this reason, firstly, the germplasm was phenotypically evaluated in two growing seasons for yield and yield-related traits. The analysis of variance results showed significant differences among traits which showed the presence of diversity in the current germplasm. Secondly, the germplasm was also genotypically evaluated using 10K SNP. Genetic structure analysis showed the presence of four groups which showed that enough genetic diversity was present in the rice germplasm to be used for association mapping analysis. The results of GWAS identified 201 significant marker trait associations (MTAs. 16 MTAs were identified for plant height, 49 for days to flowering, three for days to maturity, four for tillers per plant, four for panicle length, eight for grains per panicle, 20 unfilled grains per panicle, 81 for seed setting %, four for thousand-grain weight, five for yield per plot and seven for yield per hectare. Apart from this, some pleiotropic loci were also identified. The results showed that panicle length (PL) and thousand-grain weight (TGW) were controlled by a pleiotropic locus OsGRb23906 on chromosome 1 at 10,116,371 cM. The loci OsGRb25803 and OsGRb15974 on chromosomes 4 and 8 at the position of 14,321,111 cM and 6,205,816 cM respectively, showed pleiotropic effects for seed setting % (SS) and unfilled grain per panicle (UG/P). A locus OsGRb09180 on chromosome 4 at 19,850,601 cM was significantly linked with SS and yield/ha. Furthermore, gene annotation was performed, and results indicated that the 190 candidate genes or QTLs that closely linked with studied traits. These candidate genes and novel significant markers could be useful in marker-assisted gene selection and QTL pyramiding to improve rice yield and the selection of potential parents, recombinants and MTAs which could be used in rice breeding programs to develop high-yielding rice varieties for sustainable food security.

Comparative analysis of chloroplast genomes of 29 tomato germplasms: genome structures, phylogenetic relationships, and adaptive evolution

In order to compare and analyze the chloroplast (cp) genomes of tomato germplasms and understand their phylogenetic relationships, the cp genomes of 29 tomato germplasms were sequenced and analyzed in this study. The results showed highly conserved characteristics in structure, number of gene and intron, inverted repeat regions, and repeat sequences among the 29 cp genomes. Moreover, single-nucleotide polymorphism (SNP) loci with high polymorphism located at 17 fragments were selected as candidate SNP markers for future studies. In the phylogenetic tree, the cp genomes of tomatoes were clustered into two major clades, and the genetic relationship between S. pimpinellifolium and S. lycopersicum was very close. In addition, only rps15 showed the highest average K _A/K _S ratio in the analysis of adaptive evolution, which was strongly positively selected. It may be very important for the study of adaptive evolution and breeding of tomato. In general, this study provides valuable information for further study of phylogenetic relationships, evolution, germplasm identification, and molecular marker-assisted selection breeding of tomato.

Metabolic Composition and Quality Traits of Polygonatum cyrtonema Hua from Different Germplasms and Age Sections Based on Widely Targeted Metabolomics Analysis

Polygonatum rhizomes are rich in various compounds with many biological activities and are widely used in functional foods and pharmaceutical products. In order to screen for superior Polygonatum cyrtonema Hua (P. cyrtonema) germplasm and also to elucidate the nutritional and medicinal values of rhizomes, the metabolic composition and quality traits of rhizomes from different germplasms and age sections of P. cyrtonema were analysed by widely targeted metabolomics, and the molecular mechanism of triacylglycerol synthesis was explored. The results showed that the different germplasms and age sections of P. cyrtonema were rich in different nutritional and medicinal components. Of these, the broad-leaved green stem (GK) germplasm is rich in polysaccharides, alkaloids, and lipids; the pointed-leaved green stem (JL) germplasm is rich in flavonoids, steroids, and amino acids, while the pointed-leaved purple stem (JZ) germplasm contains more phenolic acids. The one-year (AT) age section is rich in polysaccharides, steroids, organic acids, and lipids; the three years (CT) age section contains more flavonoids, alkaloids, and amino acid metabolites. Lipids were significantly enriched in the broad-leaved green stem germplasm and the one-year age section. Interestingly, the highest accumulation of triacylglycerols, an important component of lipids, was also found in the GK germplasm and the AT age section. Nineteen, 14, and 13 members of the glycerol-3-phosphate acyltransferase (GPAT), lysophosphatidic acid acyltransferase (LPAT), and diacylglycerol acyltransferase (DGAT) gene families, respectively, involved in triacylglycerol synthesis were also identified. The quantitative real-time PCR (qRT-PCR) results further suggested that the differentially expressed PcDGAT1, PcDGAT2.4, PcGPAT9.1, PcLPAT2.9, and PcLPAT4.3 genes may play important roles in triacylglycerol synthesis in P. cyrtonema. Therefore, this study provides a new theoretical reference for product development and the breeding of new varieties of Polygonatum species.

Characterization of the USDA Cucurbita pepo, C. moschata, and C. maxima germplasm collections

The Cucurbita genus is home to a number of economically and culturally important species. We present the analysis of genotype data generated through genotyping-by-sequencing of the USDA germplasm collections of Cucurbita pepo, C. moschata, and C. maxima. These collections include a mixture of wild, landrace, and cultivated specimens from all over the world. Roughly 1,500 - 32,000 high-quality single nucleotide polymorphisms (SNPs) were called in each of the collections, which ranged in size from 314 to 829 accessions. Genomic analyses were conducted to characterize the diversity in each of the species. Analysis revealed extensive structure corresponding to a combination of geographical origin and morphotype/market class. Genome-wide associate studies (GWAS) were conducted using both historical and contemporary data. Signals were observed for several traits, but the strongest was for the bush (Bu) gene in C. pepo. Analysis of genomic heritability, together with population structure and GWAS results, was used to demonstrate a close alignment of seed size in C. pepo, maturity in C. moschata, and plant habit in C. maxima with genetic subgroups. These data represent a large, valuable collection of sequenced Cucurbita that can be used to direct the maintenance of genetic diversity, for developing breeding resources, and to help prioritize whole-genome re-sequencing.

Autochthonous Apple Cultivars from the Campania Region (Southern Italy): Bio-Agronomic and Qualitative Traits

Apple (Malus × domestica Borkh.) is an important fruit crop widely spread in the cold and mild climates of temperate regions in the world, with more than 93 million tons harvested worldwide in 2021. The object of this work was to analyze thirty-one local apple cultivars of the Campania region (Southern Italy) using agronomic, morphological (UPOV descriptors) and physicochemical (solid soluble content, texture, pH and titratable acidity, skin color, Young's modulus and browning index) traits. UPOV descriptors highlighted similarities and differences among apple cultivars with a depth phenotypic characterization. Apple cultivars showed significant differences in fruit weight (31.3-236.02 g) and physicochemical trait ranging from 8.0 to 14.64° Brix for solid soluble content, 2.34-10.38 g malic acid L^-1 for titratable acidity, and 15-40% for browning index. Furthermore, different percentages in apple shape and skin color have been detected. Similarities among the cultivars based on their bio-agronomic and qualitative traits have been evaluated by cluster analyses and principal component analyses. This apple germplasm collection represents an irreplaceable genetic resource with considerable morphological and pomological variabilities among several cultivars. Nowadays, some local cultivars, widespread only in restricted geographical areas, could be reintroduced in cultivation contribution to improving the diversity of our diets and contemporary to preserve knowledge on traditional agricultural systems.

Solanum malmeanum, a promising wild relative for potato breeding

Crop wild relatives are gaining increasing attention. Their use in plant breeding is essential to broaden the genetic basis of crops as well as to meet industrial demands, for global food security and sustainable production. Solanum malmeanum (Solanum sect. Petota, Solanaceae) is a wild relative of potatoes (S. tuberosum) from Southern South America, occurring in Argentina, Brazil, Paraguay and Uruguay. This wild potato has been largely mistaken for or historically considered as conspecific with S. commersonii. Recently, it was reinstated at the species level. Retrieving information on its traits and applied uses is challenging, because the species name has not always been applied correctly and also because species circumscriptions and morphological criteria applied to recognize it have not been consistent. To overcome these difficulties, we performed a thorough literature reference survey, herbaria specimens' identification revision and genebank database queries to review and update the information available on this potato wild relative, contributing to an increase in research on it to fully understand and explore its potential for potato breeding. Scarce studies have been carried out concerning its reproductive biology, resistance against pests and diseases as well as tolerance to abiotic stresses and evaluation of quality traits. The scattered information available makes it less represented in genebanks and genetic studies are missing. We compile, update and present available information for S. malmeanum on taxonomy, geographical distribution, ecology, reproductive biology, relationship with its closest relatives, biotic and abiotic stresses resistance and quality traits and discuss ways to overcome sexual barriers of hybridization and future perspectives for its use in potato breeding. As a final remark, we highlight that this species' potential uses have been neglected and must be unlocked. Thus, further studies on morphological and genetic variability with molecular tools are fundamental for an efficient conservation and applied use of this promising genetic resource.

Genetic Diversity and Population Structure of a Wide Pisum spp. Core Collection

Peas (Pisum sativum) are the fourth most cultivated pulses worldwide and a critical source of protein in animal feed and human food. Developing pea core collections improves our understanding of pea evolution and may ease the exploitation of their genetic diversity in breeding programs. We carefully selected a highly diverse pea core collection of 325 accessions and established their genetic diversity and population structure. DArTSeq genotyping provided 35,790 polymorphic DArTseq markers, of which 24,279 were SilicoDArT and 11,511 SNP markers. More than 90% of these markers mapped onto the pea reference genome, with an average of 2787 SilicoDArT and 1644 SNP markers per chromosome, and an average LD50 distance of 0.48 and 1.38 Mbp, respectively. The pea core collection clustered in three or six subpopulations depending on the pea subspecies. Many admixed accessions were also detected, confirming the frequent genetic exchange between populations. Our results support the classification of Pisum genus into two species, P. fulvum and P. sativum (including subsp. sativum, arvense, elatius, humile, jomardii and abyssinicum). In addition, the study showed that wild alleles were incorporated into the cultivated pea through the intermediate P. sativum subsp. jomardii and P. sativum subsp. arvense during pea domestication, which have important implications for breeding programs. The high genetic diversity found in the collection and the high marker coverage are also expected to improve trait discovery and the efficient implementation of advanced breeding approaches.

Capturing Genetic Diversity in Seed Collections: An Empirical Study of Two Congeners with Contrasting Mating Systems

Plant mating systems shape patterns of genetic diversity and impact the long-term success of populations. As such, they are relevant to the design of seed collections aiming to maximise genetic diversity (e.g., germplasm conservation, ecological restoration). However, for most species, little is known empirically about how variation in mating systems and genetic diversity is distributed. We investigated the relationship between genetic diversity and mating systems in two functionally similar, co-occurring species of Hakea (Proteaceae), and evaluated the extent to which genetic diversity was captured in seeds. We genotyped hundreds of seedlings and mother plants via DArTseq, and developed novel implementations of two approaches to inferring the mating system from SNP data. A striking contrast in patterns of genetic diversity between H. sericea and H. teretifolia was revealed, consistent with a contrast in their mating systems. While both species had mixed mating systems, H. sericea was found to be habitually selfing, while H. teretifolia more evenly employed both selfing and outcrossing. In both species, seed collection schemes maximised genetic diversity by increasing the number of maternal lines and sites sampled, but twice as many sites were needed for the selfing species to capture equivalent levels of genetic variation at a regional scale.

Identification and Characterization of New Seedborne Pathogens in Phaseolus vulgaris Landraces of Southern Italy

The diagnostic survey of seedborne fungal pathogens is fundamental for symptomless material stored in gene banks to avoid the diffusion of pathogens by germplasm distribution and propagation. In this work, seeds of Southern Italian landraces of the common bean (Phaseolus vulgaris L.) belonging to the gene bank at CREA (Italy) were inspected to assess their phytosanitary status. The phytopathological analysis revealed the presence of the most common pathogens associated with common bean seeds such as Fusarium spp., Macrophomina phaseolina, Rhizoctonia solani, Colletotrichum lindemuthianum and Diaporthe/Phomopsis complex. However, new fungi able to completely inhibit seed germination were also observed. The most aggressive were isolated, and the morpho-pathological characterization, DNA sequencing and phylogenetic analysis allowed us to define the strains as Botryosphaeria dothidea CREA OF 360.4 and Diplodia mutila CREA OF 420.36. These two plant pathogens are generally associated with grapevines and other fruit trees. Pathogenicity tests were carried out along with a transmissibility test in which the transmission of the pathogens to the seedlings was proven. Host range experiments revealed the ability of these pathogens to infect crops such as pepper and melon. To our knowledge, this is the first time that B. dothidea and D. mutila were detected on the common bean.

Volatilomics of raspberry fruit germplasm by combining chromatographic and direct-injection mass spectrometric techniques

The application of direct-injection mass spectrometric (DI-MS) techniques, like Proton Transfer Reaction Time of Flight Mass Spectrometry (PTR-ToF-MS) has been suggested as a reliable phenotyping tool for fruit volatilome assessment in both genetic and quality-related studies. In this study the complexity of raspberry aroma was investigated by a comprehensive untargeted VOC analysis, done by combining SPME-GC-MS and PTR-ToF-MS assessments with multi-block discriminant analysis using the DIABLO mixOmics framework. The aim was to acquire an exhaustive characterization of the raspberry volatilome according to different fruit ripening stages (pink, ripe, and overripe) and genetic variances (50 accessions), as well as to investigate the potential of PTR-ToF-MS as a rapid and high throughput VOC phenotyping tool to address issues related to raspberry fruit quality. Results of this study demonstrated the complementarity between SPME-GC-MS and PTR-ToF-MS techniques to evaluate the raspberry aroma composition. PTR-ToF-MS generates reliable raspberry VOC fingerprints mainly due to a reduced compound fragmentation and precise content estimation. In addition, the high collinearity between isomers of monoterpenes and norisoprenoids, discovered by GC analysis, reduces the main analytic limitation of PTR-ToF-MS of not being able to separate isomeric molecules. The high similarity between the VOC matrices obtained by applying PTR-ToF-MS and SPME-GC-MS confirmed the possibility of using PTR-ToF-MS as a reliable high throughput phenotyping tool for raspberry volatiolome assessment. In addition, results provided by the germplasm collection investigation enabled to distinguish the best performing accessions, based on VOCs composition, to be used as superior parental lines for future breeding programs.

Unlocking the genetic diversity of Indian turmeric (Curcuma longa L.) germplasm based on rhizome yield traits and curcuminoids

Turmeric is an important commercial crop widely grown in Asia due to its pharmacological and nutritional value. India is the centre of turmeric diversity and many turmeric accessions have good rhizome yield, varying curcuminoids content and are well-adapted to various agro-climatic zones. In the present study, we unravel the diversity among 200 Indian turmeric accessions based on rhizome yield traits and curcuminoids content. Clustering and correlation studies were also performed to group the turmeric accessions and to observe the relationship between the traits. Results revealed the presence of large variability among turmeric accessions including the major traits such as yield (24.77 g p^-1 to 667.63 g p^-1), dry recovery percentage (13.42% to 29.18%), curcumin (0.41% to 2.17%), demethoxycurcumin (0.38% to 1.45%), bisdemethoxycurcumin (0.37% to 1.24%) and total curcuminoid content (1.26% to 4.55%). The superior germplasm identified for curcuminoids content were as follows; curcumin (CL 157 - 2.17% and CL 272 - 2.13%), demethoxycurcumin (CL 253 - 1.45% and CL 157 - 1.31%), bisdemethoxycurcumin (CL 216 - 1.24% and CL 57 - 1.11%) and total curcuminoid content (CL 157 - 4.55% and CL 272 - 4.37%). Clustering based on dendrogram, grouped 200 accessions into seven clusters. Among seven clusters, the maximum number of accessions were grouped into cluster II while cluster VII showed maximum mean value for majority of the traits. Correlation analysis revealed a significant relationship between the traits where the total curcuminoid content is significantly and positively correlated with the primary rhizome core diameter and length of the secondary rhizome. The selection of these particular traits may result in the identification of germplasm with high total curcuminoid content. Taken together, it is the first report on the large screening of turmeric accessions for variation in the rhizome yield traits and curcuminoids content. The genetic diversity revealed in this study could be useful for further crop improvement programs in turmeric to develop new varieties with high rhizome yield coupled with high curcuminoids content.

Morphological, Biochemical, and Molecular Diversity of an Indian Ex Situ Collection of Pomegranate (Punica granatum L.)

Pomegranate (Punica granatum, L.) is a fruit tree that is increasingly popular worldwide due to the health-related properties of the fruit juice. While several studies highlighted the rich phytochemical diversity, few efforts have been devoted to an integrative understanding of the level of diversity of this species. This study investigated the diversity of 40 pomegranate accessions in an Indian ex situ collection by using twenty-nine morphological traits, six biochemical parameters, and twenty-nine Simple Sequence Repeats (SSR) markers. Among the evaluated traits, fruit volume (23.34% CV), fruit weight (21.12% CV), and fruit color (*a) (22.69 % CV) largely contributed to the morphological classification. Based on Mahalanobis D2 distance and Tocher's clustering, the 40 pomegranate accessions were grouped into eight clusters, partly consistent with their origin. Specifically, cultivars introduced from foreign countries were present in distinct clusters. The SSR marker analysis generated 66 alleles. The observed heterozygosity values ranged from 0.05 to 0.63, with a mean value of 0.30. Maximum molecular genetic dissimilarity was observed between 'IC-318720' and 'Gul-e-Shah Red' (0.30). The neighbor-joining dendrogram separated wild accessions from cultivated varieties. The combination of morphological, biochemical, and molecular characterization allowed for comprehensively characterizing the pomegranate diversity and provided information on the relationships between the different aspects of the diversity. This work also suggests that the origin of the accessions is an important factor of discrimination and that the level of admixture between local and foreign material is currently limited.

Genetic Diversity of Viral Populations Associated with Ananas Germplasm and Improvement of Virus Diagnostic Protocols

Pineapple (Ananas comosus L. [Merr.]) accessions from the U.S. Tropical Plant Genetic Resources and Disease Research (TPGRDR) in Hilo, Hawaii were subjected to RNA-sequencing to study the occurrence of viral populations associated with this vegetatively propagated crop. Analysis of high-throughput sequencing data obtained from 24 germplasm accessions and public domain transcriptome shotgun assembly (TSA) data identified two novel sadwaviruses, putatively named "pineapple secovirus C" (PSV-C) and "pineapple secovirus D" (PSV-D). They shared low amino acid sequence identity (from 34.8 to 41.3%) compared with their homologs in the Pro-pol region of the previously reported PSV-A and PSV-B. The complete genome (7485 bp) corresponding to a previously reported partial sequence of the badnavirus, pineapple bacilliform ER virus (PBERV), was retrieved from one of the datasets. Overall, we discovered a total of 69 viral sequences representing ten members within the Ampelovirus, Sadwavirus, and Badnavirus genera. Genetic diversity and recombination events were found in members of the pineapple mealybug wilt-associated virus (PMWaV) complex as well as PSVs. PMWaV-1, -3, and -6 presented recombination events across the quintuple gene block, while no recombination events were found for PMWaV-2. High recombination frequency of the RNA1 and RNA2 molecules from PSV-A and PSV-B were congruent with the diversity found by phylogenetic analyses. Here, we also report the development and improvement of RT-PCR diagnostic protocols for the specific identification and detection of viruses infecting pineapple based on the diverse viral populations characterized in this study. Given the high occurrence of recombination events, diversity, and discovery of viruses found in Ananas germplasm, the reported and validated RT-PCR assays represent an important advance for surveillance of viral infections of pineapple.

A CRISPR-based lateral flow assay for plant genotyping and pathogen diagnostics

Efficient pathogen diagnostics and genotyping methods enable effective disease management and breeding, improve crop productivity and ensure food security. However, current germplasm selection and pathogen detection techniques are laborious, time-consuming, expensive and not easy to mass-scale application in the field. Here, we optimized a field-deployable lateral flow assay, Bio-SCAN, as a highly sensitive tool to precisely identify elite germplasm and detect mutations, transgenes and phytopathogens in <1 h, starting from sample isolation to result output using lateral flow strips. As a proof of concept, we genotyped various wheat germplasms for the Lr34 and Lr67 alleles conferring broad-spectrum resistance to stripe rust, confirmed the presence of synthetically produced herbicide-resistant alleles in the rice genome and screened for the presence of transgenic elements in the genome of transgenic tobacco and rice plants with 100% specificity. We also successfully applied this new assay to the detection of phytopathogens, including viruses and bacterial pathogens in Nicotiana benthamiana, and two destructive fungal pathogens (Puccinia striiformis f. sp. tritici and Magnaporthe oryzae Triticum) in wheat. Our results illustrate the power of Bio-SCAN in crop breeding, genetic engineering and pathogen diagnostics to enhance food security. The high sensitivity, simplicity, versatility and in-field deployability make the Bio-SCAN as an attractive molecular diagnostic tool for diverse applications in agriculture.