Sativa Accessions Research Articles

Differential Sources of Resistance from Lactuca serriola Against Three Races of Xanthomonas hortorum pathovar vitians (Brown, 1918) Morinière et al. 2020 Causing Bacterial Leaf Spot of Lettuce.

Bacterial leaf spot (BLS) of lettuce (Lactuca sativa L.) is caused by the bacterium Xanthomonas hortorum pv. vitians which is hypothesized to have at least three races of the pathogen present in North America as defined by their differential resistance phenotypes in lettuce cultivars/accessions. Though resistance to X. hortorum pv. vitians race 1 has been identified in cultivated lettuce, numerous other X. hortorum pv. vitians strains cause disease on cultivars carrying this resistance locus. Thus far, resistance to these 'additional' X. hortorum pv. vitians strains has not been adequately described in L. sativa or in any other wild Lactuca species sexually compatible with cultivated lettuce. We have performed an extensive screening of approximately 500 Lactuca accessions from L. sativa, L. serriola, L. saligna, L. virosa, L. aculeata, L. altaica, and L. perennis species to identify accessions resistant to these additional X. hortorum pv. vitians races. Following the initial screenings, greenhouse tests confirmed that X. hortorum pv. vitians race 2 and race 3 could be defined using Lactuca sativa accessions. Race 2 strain BS3217 had an incompatible response (hypersensitive response) on ten Lactuca serriola accessions including PI491114 and PI491108, while race 1 (BS0347) and race 3 (BS2861) strains of X. hortorum pv. vitians showed a compatible response (disease) on these genotypes. L. serriola accession ARM09-161 (and selections derived from it) was the only genotype resistant to the race 3 strain BS2861. L. serriola accessions identified in this study to be resistant to race 2 and race 3 of X. hortorum pv. vitians, together with race 1 resistant cultivars, can be used for pyramiding resistance loci against the three races of the BLS-causing pathogen.

HASCH - A high-throughput amplicon-based SNP-platform for medicinal cannabis and industrial hemp genotyping applications

BackgroundCannabis sativa is seeing a global resurgence as a food, fiber and medicinal crop for industrial hemp and medicinal Cannabis industries respectively. However, a widespread moratorium on the use and research of C. sativa throughout most of the 20th century has seen the development of improved cultivars for specific end uses lag behind that of conventional crops. While C. sativa research and development has seen significant investments in the recent past, resulting in a suite of publicly available genomic resources and tools, a versatile and cost-effective mid-density genotyping platform for applied purposes in breeding and pre-breeding is lacking. Here we report on a first mid-density fixed-target SNP platform for C. sativa.ResultsThe High-throughput Amplicon-based SNP-platform for medicinal Cannabis and industrial Hemp (HASCH) was designed using a combination of filtering and Integer Linear Programming on publicly available whole-genome sequencing and RNA sequencing data, supplemented with in-house generated genotyping-by-sequencing (GBS) data. HASCH contains 1,504 genome-wide targets of high call rate (97% mean) and even distribution across the genome, designed to be highly informative (> 0.3 minor allele frequency) across both medicinal cannabis and industrial hemp gene pools. Average numbers of mismatch SNP between any two accessions were 251 for medicinal cannabis (N = 116) and 272 for industrial hemp (N = 87). Comparing HASCH data with corresponding GBS data on a collection of diverse C. sativa accessions demonstrated high concordance and resulted in comparable phylogenies and genetic distance matrices. Using HASCH on a segregating F2 population derived from a cross between a tetrahydrocannabinol (THC)-dominant and a cannabidiol (CBD)-dominant accession resulted in a genetic map consisting of 310 markers, comprising 10 linkage groups and a total size of 582.7 cM. Quantitative Trait Locus (QTL) mapping identified a major QTL for CBD content on chromosome 7, consistent with previous findings.ConclusionHASCH constitutes a versatile, easy to use and cost-effective genotyping solution for the rapidly growing Cannabis research community. It provides consistent genetic fingerprints of 1504 SNPs with wide applicability genetic resource management, quantitative genetics and breeding.

Integration of machine learning models with microsatellite markers: New avenue in world grapevine germplasm characterization

Development of efficient analytical techniques is required for effective interpretation of biological data to take novel hypotheses and finding the critical predictive patterns. Machine Learning algorithms provide a novel opportunity for development of low-cost and practical solutions in biology. In this study, we proposed a new integrated analytical approach using supervised machine learning algorithms and microsatellites data of worldwide vitis populations. A total of 1378 wild (V. vinifera spp. sylvestris) and cultivated (V. vinifera spp. sativa) accessions of grapevine were investigated using 20 microsatellite markers. Data cleaning, feature selection, and supervised machine learning classification models vis, Naive Bayes, Support Vector Machine (SVM) and Tree Induction methods were implied to find most indicative and diagnostic alleles to represent wild/cultivated and originated geography of each population. Our combined approaches showed microsatellite markers with the highest differentiating capacity and proved efficiency for our pipeline of classification and prediction of vitis accessions. Moreover, our study proposed the best combination of markers for better distinguishing of populations, which can be exploited in future germplasm conservation and breeding programs.

Pan-Genome-Wide Identification and Transcriptome-Wide Analysis of ZIP Genes in Cucumber

The ZRT/IRT-like proteins (ZIPs) play critical roles in the absorption, transport, and intracellular balance of metal ions essential for various physiological processes in plants. However, little is known about the pan-genomic characteristics and properties of ZIP genes in cucumber (Cucumis sativus L.). In this study, we identified 10 CsZIP genes from the pan-genome of 13 C. sativus accessions. Among them, only CsZIP10 showed no variation in protein sequence length. We analyzed the gene structure, conserved domains, promoter cis-elements, and phylogenetic relationships of these 10 CsZIP genes derived from “9930”. Based on phylogenetic analysis, the CsZIP genes were classified into three branches. Amino acid sequence comparison revealed the presence of conserved histidine residues in the ZIP proteins. Analysis of promoter cis-elements showed that most promoters contained elements responsive to plant hormones. Expression profiling in different tissues showed that most CsZIP genes were expressed at relatively low levels in C. sativus leaves, stems, and tendrils, and CsZIP7 and CsZIP10 were specifically expressed in roots, indicating their potential involvement in the absorption and transport of metal ions. Transcriptomic data indicated that these 10 ZIP genes displayed responses to both downy mildew and powdery mildew, and CsZIP1 was significantly downregulated after both salt and heat treatments. In conclusion, this study deepens our understanding of the ZIP gene family and enhances our knowledge of the biological functions of CsZIP genes in C. sativus.

How crop breeding programs can improve plant factories' business and environmental sustainability: Insights from a farm level analysis

Plant factories, being more weather independent, can potentially contribute to global food security under climate change scenarios, but their profitability and environmental sustainability are debatable. This study quantitatively assessed the business sustainability and life-cycle-based carbon footprint of a hypothetical plant factory. A system dynamic model was constructed to simulate yearly profit and global warming potential (GWP) of a 2-ha hypothetical farm over 20 years using experimental data from growing 397 Brassica oleracea and 204 Eruca sativa accessions in a prototype plant factory in Singapore. Experimentally derived parameters include resource use data, maximum potential yield improvement, and the effect of increasing planting density on yield. Model simulations predicted that with accession-wide average yield (status quo), the hypothetical plant factory would meet 0.8 % of the leafy vegetable requirement of the population but earn negative profit. The estimated carbon footprint at the end of the simulation period was approximately 21 kg CO2-eq per kg of vegetables with lighting operations being the major contributor. A univariate-sensitivity analysis was conducted to understand how model parameters could affect the plant factory's profit represented by net present value (NPV) and environmental sustainability represented by GWP. Yield improvement was identified as the strongest influencer of NPV followed by price elasticity and annual fluctuations in vegetable price. Yield improvement was also the strongest influencer of GWP followed by planting density and unit light use. This study acknowledged the importance of crop breeding in plant factories' profit and environmental sustainability. The results indicated breeding high-quality unique varieties with improved yield and light use efficiency can potentially benefit plant factories' business and environmental sustainability.

Lathyrus diversity: resources with different origin with relevance to crop improvement

Lathyrus sativus L. is a legume crop, possessing high protein content, tolerant to drought, waterlogging and salinity. The main aim of the study was to evaluate the phenotypic diversity of the exchanged local Lathyrus accessions from Mediterranean region and south eastern Europe in order to review their potential for its ex situ conservation and sustainable use. The subject of the study were twenty four grass pea accessions with different origin, received on a project basis. The morphological, biological and economic characteristics were assessed on 10 pre-marked, normally developed plants from each accession using the International Classification of Species Lathyrus sp. and list of indicators. All exchanged accessions were registered in our national database and in European Search Catalogue for Plant Genetic Resources (EURISCO). Nine Lathyrus sativus accessions with Bulgarian origin were reproduced at the experimental field of IPGR, Sadovo and the seeds from them was included in AEGIS (A European Genebank Integrated System). Several accessions (C000095, C0000101, C0000100, BGR43334, BGR40415 and C00000103) were selected with promising results related to grain and forage yields. Cluster analysis classified the accessions into two distinct groups as accessions from Bulgaria, Romania and part of Serbia were grouped in the first cluster and all others in the second. As the best adapted accessions to Bulgarian environment condition were two accessions from Romania (C00096 and C00095), two from Serbia (C000100 and C000101) and two from Bosnia and Herzegovina (C00093 and C00094). They demonstrated good productivity and good adaptability. All exchanged accessions were registered in our National database and in EURISCO database.

Exploring the physiological efficiencies of promising rice (Oryza sativa) accessions for increasing grain yield

High grain yield in rice (Oryza sativa L.) is a cumulative contribution of different morphological and physiological traits. However, the selection of high-yielding genotypes based on physiological traits is difficult where a large set of genotypes is used. Therefore, a study was carried out during rainy (kharif) seasons of 2019 and 2020 at research farm of ICAR-National Rice Research Institute, Cuttack, Odisha to assess the physiological efficiency of 211 elite rice genotypes having varying yield potential. The elite genotypes were classified into high, medium, and low categories based on their field performance. The results revealed that 29, 41, 34, 31, 49, 35, 39, 29, and 30 genotypes showing high values for FLA (>51.51 cm2), TCC (>3.99 mg/g fresh weight), PN (>20.79), gs (>0.97), E (>9.03), TB (>15.95 t/ ha), GY (>6.27 t/ha), PR (>0.29 kg/cm), and CS (>42.12 g/stem) respectively. Among them, 3 genotypes i.e. IG-020, IG-211 and IG-010 were identified to be highly efficient in 4 traits, 2 genotypes i.e., IG-044 and IG-186 in 5 traits, and 2 genotypes; IG-008 and IG-161 were found to be superior in 7 traits along with high grain yield. The selection of these genotypes with superior morphological and physiological traits could be beneficial in the breeding programme in terms of increasing yield potential in rice.

Chitosan modulated antioxidant activity, inorganic ions homeostasis and endogenous melatonin to improve yield of Pisum sativum L. accessions under salt stress

Effects of NaCl stress and foliar treatment of chitosan (CTS) on growth, antioxidant activity, inorganic ions and yield attributes of two pea (Pisum sativum L.) accessions were analyzed in this study. Experimentation was done in total 36 pots with 2 accessions and in three way completely randomized design (CRD) with 3 replicates. P. sativum plants were supplied with three salt concentrations (0, 60 and 120 mM) and two concentrations of CTS (0 and 120 mg/L). Both P. sativum accessions performed notably different from each other under salt stress. On the basis of remarkable reduction in biomass and yield parameters of ccession 200–03 under NaCl stress, it is assumed that this accession might be sensitive against salt stress. Whereas accession 200–06 under NaCl stress showed non-significant reduction in yield and biomass indicating that this accession might be resistant against salt stress. Foliar treatment of CTS boosted antioxidant enzyme activities, enhanced secondary metabolites (leaf proline and total phenolics), lowered the level of H2O2 and improved the RMP and yield in both ccessions. Salt stress resulted in enhanced content of endogenous melatonin. Chitosan treatment further boosted melatonin synthesis. It is concluded that foliar treatment of CTS mitigated the deleterious effects of salt stress and modulated growth in P. sativum plants under salt stress. Therefore, it is recommended that chitosan induced growth modulation in plants may be exploited.

Deciphering phylogenetic relationships and genetic diversity of Moroccan saffron (Crocus sativus L.) using SSRg markers and chloroplast DNA SNP markers

The molecular characterization of C. sativus accessions is of great interest for clonal selection and preservation of valuable resources with the best productive traits and specific patterns related to local products. To analyze the genetic diversity of Moroccan saffron, fourteen new saffron accessions were evaluated, twelve of which were from Morocco and two from Kozani in Greece, and the Quercy region of France. These accessions differ by their geographical distribution and altitudes. Seven specific C. sativus Simple-sequence repeats (SSRs) primers were considered. Their combinations generated 13 monomorphic alleles across all studied accessions with an average of 1.85 allele/locus. Additionally, fourteen unique ABRII/Cs30 SSR locus sequences were obtained and registered in the NCBI database (MZ868510-MZ868523). Single nucleotide polymorphism (SNP) was also assessed considering the ABRII/Cs30 locus. By excluding gaps and missing data from the sequence alignment, 161 sites were produced. The DnaSP analysis of all accessions revealed 40 polymorphic sites, including thirty-two among the Moroccan accessions. Nucleotide diversity (PiT) was 0.03896, while the average nucleotide difference was 6.27273. The haplotype diversity (HD) of Moroccan and all accessions was 0.848 and 0.875, respectively, demonstrating a strong capacity of the ABRII/Cs30 locus to distinguish saffron accessions. The Tazenakht (TK) population was the most polymorphic, while the Low land (TB) population was monomorphic. Sequence-based genetic relationships imply that Moroccan saffron likely originated from Greece. Our results show that the SNPs approach is a powerful tool to evaluate genetic diversity among C. sativus accessions. The present molecular analysis indicates that Moroccan saffron is not a single clone. This outcome constitutes a sound basis for developing a core collection representative of the biodiversity of Moroccan saffron to conserve and enhance this critical commodity.

Morphological characterization and in vitro digestibility of seven Lathyrus sativus (grass pea) accessions originating from Eurasia, Africa, and Canada

Lathyrus sativus is considered as an important economical source of high-quality proteins and adaptability to global climate change. To detect accessions useful for future breeding strategies, the genetic variability among and within seven Lathyrus sativus accessions was assessed by morphological characters and the in vitro digestibility study. An important genetic diversity was found using various morphological traits. The significant heterogeneity revealed by variance analysis (ANOVA) and correlation test could be elucidated by the different geographical origins of the studied accessions and the natural selection of grass pea. The Principal Component Analysis (PCA) and Hierarchical Cluster Analysis (HCA) exhibited the accumulation of several genotypes in the same cluster which confirm that these genotypes are not dispersed according to their origin. Whereas, the individuals of grass pea from Ethiopia were collected in distinct group indicating that these samples are close each other’s and are different from the other accessions. In the same aim, the in vitro digestion model showed that most of the proteins were digested after 60-min incubation except the β-lathyrin protein. The different digestion kinetics found could be used as a method to distinguish different crop accessions. In fact, the densitometry analysis of β-lathyrin protein band showed that grass pea from Ethiopia, Germany, Bangladesh, and Morocco were more digested than grass pea from Canada, Afghanistan, and Greece in gastric phase, and Grass pea from Afghanistan and Germany were more digested than the rest of the samples in duodenal phase.

Monoecious Cannabis sativa L. discloses the organ-specific variation in glandular trichomes, cannabinoids content and antioxidant potential

Cannabis sativa L., an industrially important plant, is a source of medicinally important cannabidiol (CBD) and Δ9-tetrahydrocannabinol (D9-THC). C. sativa is mainly a dioecious plant. However, rarely monoecious plants with hermaphrodite inflorescence were also reported naturally. The monoecious C. sativa plant research is still inadequate compared to dioecious plants. The present study aims to evaluate four monoecious C. sativa accessions (CH-1, CH-2, CH-3 and CH-4) for organ-specific (leaves, male flowers, and female flowers) distribution of trichomes, histochemical localization phytocannabinoids in trichomes, and phytocannabinoids content and antioxidant potential. Results showed that morphological traits differed in all the accessions (p < 0.05). The phytocannabinoids are produced in capitate sessile and capitate stalked glands. The highest density of phytocannabinoids synthesizing glands was found in female flowers (46.67–57.01 mm-2), followed by male flowers (30.73–33.98 mm-2) and leaves (12.37–23.64 mm-2) in different monoecious accessions. The female flower produces the maximum content of total phytocannabinoids. In the same way, the female flower shows the highest free radical scavenging activity and total antioxidant capacity compared to other studied plant parts. In conclusion, the CH-1 accession is superior to the other in terms of morphological characters, phytocannabinoids synthesizing glands and cannabinoids content. Moreover, the levels of phytocannabinoids are higher in female flowers than the male flowers and leaves. The approach towards monoecious accession with higher cannabinoid content has enormous potential for industrial applications.

Genetic variation and population structure of Oryza sativa accessions in the AfricaRice collection and development of the AfricaRice O. sativa Core Collection

AbstractGenetic diversity studies provide an increased understanding of genebank collections and enhance their use for improving global food security. This study explores the genetic variation and population structure of 5738 rice (Oryza sativa L.) accessions representing 39.6% of the O. sativa collection conserved in the AfricaRice genebank of which 74.0% originated from African countries. These accessions were genotyped with 25,904 polymorphic DArTseq‐based single nucleotide polymorphisms (SNPs). Genetic distances between pairs of accessions indicate high variability, with 21.0% of pairs being moderately distant and 78.2% highly distant from each other. The genotyped accessions are traditionally grown in six different agro‐ecologies from 73 countries. Using neighbor‐joining tree, principal component, and model‐based population structure analyses, the accessions were divided into four genotypic groups representing the two O. sativa subspecies, Japonica (787 accessions) and Indica, which were further divided into landraces (1879 accessions), and improved cultivars (3027 accessions), and a fourth small group of admixed accessions. Subclusters identifying a specific agro‐ecology (upland, lowland, and mangrove swamp) or originating country were noted. Using the maximum length sub‐tree method, we selected 10% of the total accessions to form the “AfricaRice O. sativa Core Collection” (AROSCC). The subset of 600 O. sativa accessions captures more than 95% of the SNP polymorphisms in the entire collection. The AROSCC is an important resource to support pre‐breeding and rice improvement programs around the world.

Field Pea (Pisum sativum) Germplasm Screening for Seedling Ascochyta Blight Resistance and Genome-Wide Association Studies Reveal Loci Associated with Resistance to Peyronellaea pinodes and Ascochyta koolunga.

Ascochyta blight is a damaging disease that affects the stems, leaves, and pods of field pea (Pisum sativum) and impacts yield and grain quality. In Australia, field pea Ascochyta blight is primarily caused by the necrotrophic fungal species Peyronellaea pinodes and Ascochyta koolunga. In this study, we screened 1,276 Pisum spp. germplasm accessions in seedling disease assays with a mix of three isolates of P. pinodes and 641 accessions with three mixed isolates of A. koolunga (513 accessions were screened with both species). A selection of three P. sativum accessions with low disease scores for either pathogen, or in some cases both, were crossed with Australian field pea varieties PBA Gunyah and PBA Oura, and recombinant inbred line populations were made. Populations at the F3:4 and F4:5 generation were phenotyped for their disease response to P. pinodes and A. koolunga, and genotypes were determined using the diversity arrays technology genotyping method. Marker-trait associations were identified using a genome-wide association study approach. Trait-associated loci were mapped to the published P. sativum genome assembly, and candidate resistance gene analogues were identified in the corresponding genomic regions. One locus on chromosome 2 (LG1) was associated with resistance to P. pinodes, and the 8 Mb genomic region contains 156 genes, two of which are serine/threonine protein kinases, putatively contributing to the resistance trait. A second locus on chromosome 5 (LG3) was associated with resistance to A. koolunga, and the 35 Mb region contains 488 genes, of which five are potential candidate resistance genes, including protein kinases, a mitogen-activated protein kinase, and an ethylene-responsive protein kinase homolog.

Agronomic performance of the Camelina sativa accession and its biogas production

This research was set up in 2013 in agroecological conditions of continental Croatia (3 different locations). The extperiment was set as a split-plot design in four replicates, with three levels of the main treatments of soil tillage (CT - plowing; MD - reduced multiple disk harrowing; SD - reduced single disk harrowing) and levels of subtreatment fertilization (F0 - control; F1 - standard KAN fertilization; F2 - fertilization with 5% urea solution; F3 - Profert Mara; F4 - Profert NGT; F5 - Thiofer; F6 - EM Aktiv). The highest camelina grain and biomass yield was achieved in the subtreatment F6 when using microbiological fertilizer EM Aktiv, regardless of the applied agrotechnics. After the harvest experiment, anaerobic batch co-digestion of camelina and cow manure was conducted under thermophilic conditions to determine camelina's potential for biogas production. The biogas potential of camelina was expressed as biogas and methane yields which ranged from 382.00 and 246.04 cm3 g-1 VS, respectively. If compared to maize which is often used as a standard for comparison of methane yields, maize methane yields are higher by 21 to 40%

Assessment of Wild Rocket (Diplotaxis tenuifolia (L.) DC.) Germplasm Accessions by NGS Identified SSR and SNP Markers.

Rocket is the common designation for two baby-leaf salad crops of the Brassicaceae family: Eruca sativa (L.) Cav., usually referred to as annual garden rocket, and Diplotaxis&amp;nbsp;tenuifolia (L.) DC. commonly named to as perennial wild rocket. E. sativa is used for human consumption since antiquity. However, the growing consumer preference for D. tenuifolia is being accompanied by the fast increase in its production area and commercialization of new cultivars. Nevertheless, the worldwide number of wild rocket accessions maintained in germplasm collections is very reduced, the solution for which situation the project "REMIRucula" intends to contribute, establishing a germplasm collection at the INIAV, Oeiras, Portugal. Herein, we report on the establishment via next generation sequencing (NGS) of the first genome assembly of D. tenuifolia and the identification of specific single sequence repeat (SSR) and single nucleotide polymorphisms (SNP) loci for the establishment of specific DNA-markers for this species. A representative set of 87 D. tenuifolia and 3 E. sativa accessions were assessed by 5 SSR and 9 SNP-CAPS markers, allowing a drastic discrimination between both species and the establishment of unequivocal molecular fingerprints for the analyzed accessions. The non-discrimination within six pairs and one trio of D. tenuifolia accessions is discussed.

Genetic variation and structural diversity in major seed proteins among and within Camelina species

Main conclusionGenetic variation in seed protein composition, seed protein gene expression and predictions of seed protein physiochemical properties were documented in C. sativa and other Camelina species.Seed protein diversity was examined in six Camelina species (C. hispida, C. laxa, C. microcarpa, C. neglecta, C. rumelica and C. sativa). Differences were observed in seed protein electrophoretic profiles, total seed protein content and amino acid composition between the species. Genes encoding major seed proteins (cruciferins, napins, oleosins and vicilins) were catalogued for C. sativa and RNA-Seq analysis established the expression patterns of these and other genes in developing seed from anthesis through to maturation. Examination of 187 C. sativa accessions revealed limited variation in seed protein electrophoretic profiles, though sufficient to group the majority into classes based on high MW protein profiles corresponding to the cruciferin region. C. sativa possessed four distinct types of cruciferins, named CsCRA, CsCRB, CsCRC and CsCRD, which corresponded to orthologues in Arabidopsis thaliana with members of each type encoded by homeologous genes on the three C. sativa sub-genomes. Total protein content and amino acid composition varied only slightly; however, RNA-Seq analysis revealed that CsCRA and CsCRB genes contributed > 95% of the cruciferin transcripts in most lines, whereas CsCRC genes were the most highly expressed cruciferin genes in others, including the type cultivar DH55. This was confirmed by proteomics analyses. Cruciferin is the most abundant seed protein and contributes the most to functionality. Modelling of the C. sativa cruciferins indicated that each type possesses different physiochemical attributes that were predicted to impart unique functional properties. As such, opportunities exist to create C. sativa cultivars with seed protein profiles tailored to specific technical applications.

Integrative Analyses of Transcriptomes and Metabolomes Reveal Associated Genes and Metabolites with Flowering Regulation in Common Vetch (Vicia sativa L.)

As an important source of protein for livestock and human consumption, Vicia sativa is cultivated worldwide, but its seed production is hampered at high altitudes because of the short frost-free period. Flowering represents the transition from a vegetative to a reproductive period, and early flowering benefits plant seed production at high altitudes. However, the molecular mechanisms of flowering regulation in V. sativa remain elusive. In the present study, two V. sativa accessions with different flowering characteristics were used: Lan3 (early-flowering) was cultivated by our laboratory, and 503 (late-flowering) was selected from 222 V. sativa accessions after three years of field experiments. The shoot samples (shoot tip length = 10 cm) of these two accessions were collected 63, 70, and 77 days after sowing, and the molecular regulatory mechanism of the flowering process was identified by integrative analyses of the transcriptomes and metabolomes. Kyoto Encyclopedia of Genes and Genomes enrichment showed that the synthesis and signal transduction of plant hormone pathways were the most enriched pathways in 4274 differentially expressed genes (DEGs) and in 259 differential metabolites between Lan3 and 503. Moreover, the contents of three metabolites related to salicylic acid biosynthesis and the transcription levels of two DEGs related to salicylic acid signal transduction in Lan3 were higher than those in 503. Further verification in various accessions indicated that salicylic acid metabolism may be involved in the flowering regulation process of V. sativa. These findings provide valuable information for understanding the flowering mechanism and for promoting breeding research in V. sativa.

Tolerance against brown planthopper (Nilaparvata lugens) in wild rice (Oryza sativa) accessions

Brown planthopper, Nilaparvata lugens (Stål), is a major insect pest of rice in all the rice growing areas of the world. In the present study, the tolerance mechanism of resistance in wild rice accessions belonging to different Oryza species such as O. nivara (IRGC104646, CR100204), O. australiensis (IRGC105275, IRGC105270), O. punctata (IRGC99577) along with resistant check, Ptb33 and susceptible check, TN1 has been studied. The experiments were carried out on 30-days old plants under glasshouse conditions during kharif 2017 and 2018. IRGC99577 (22.80 and 24.00) took maximum days to hopper burn condition during both seasons. Functional plant loss index (%) was minimum in IRGC99577 (18.10%) followed by Ptb33 (20.96%) and IRGC104646 (29.47%). Least plant dry weight loss index (mg) was observed in Ptb33 and highest in TN1 during both the seasons. Overall, results indicated that rice accessions, IRGC99577 and IRGC104646 showed high levels of tolerance as compared to other wild rice accessions that were tested. The identified accessions thus could serve as potential sources of resistance in breeding BPH resistant varieties.

Can biochemical traits bridge the gap between genomics and plant performance? A study in rice under drought.

The possibility of introducing metabolic/biochemical phenotyping to complement genomics-based predictions in breeding pipelines has been considered for years. Here we examine to what extent and under what environmental conditions metabolic/biochemical traits can effectively contribute to understanding and predicting plant performance. In this study, multivariable statistical models based on flag leaf central metabolism and oxidative stress status were used to predict grain yield (GY) performance for 271 indica rice (Oryza sativa) accessions grown in the field under well-watered and reproductive stage drought conditions. The resulting models displayed significantly higher predictability than multivariable models based on genomic data for the prediction of GY under drought (Q2 = 0.54–0.56 versus 0.35) and for stress-induced GY loss (Q2 = 0.59–0.64 versus 0.03–0.06). Models based on the combined datasets showed predictabilities similar to metabolic/biochemical-based models alone. In contrast to genetic markers, models with enzyme activities and metabolite values also quantitatively integrated the effect of physiological differences such as plant height on GY. The models highlighted antioxidant enzymes of the ascorbate–glutathione cycle and a lipid oxidation stress marker as important predictors of rice GY stability under drought at the reproductive stage, and these stress-related variables were more predictive than leaf central metabolites. These findings provide evidence that metabolic/biochemical traits can integrate dynamic cellular and physiological responses to the environment and can help bridge the gap between the genome and the phenome of crops as predictors of GY performance under drought.

KASP Markers Reveal Established and Novel Sources of Resistance to Pea Seedborne Mosaic Virus in Pea Genetic Resources.

Pea seed-borne mosaic virus (PSbMV) is both seedborne and aphid-transmitted and can cause economic losses for pea (Pisum sativum L.) production by reducing yield through decreased seed weight and number. The P1 pathotype is especially virulent, affecting this important vegetable crop across the United States and internationally in regions of West Asia, North Africa, Europe, and Australia. Previously, two kompetitive allele-specific PCR (KASP) genotyping markers (eIF4E resistant 1 and 2) were developed and validated on P. sativum accessions identifying two PSbMV pathotype P1 resistance alleles in the eukaryotic translation initiation factor gene, eIF4E. The current study utilized these novel markers to rapidly evaluate 318 genetic resource accessions maintained as part of the United States Department of Agriculture National Plant Germplasm System's Pea Single Plant Collection (PSPC). The evaluations also included 58 commercial and other plant introduction (PI) lines that were assessed for the two eIF4E resistance alleles. All genotyping results were validated in greenhouse assays by confirmation of observable disease symptoms after inoculations and by enzyme-linked immunosorbent assays. The eIF4E resistant 1 and 2 alleles were found in 18 accessions from the PSPC, five commercial lines, and 14 other PI accessions. A single PSPC accession showed resistance to PSbMV pathotype P1 that is believed to be a novel source of resistance based on sequencing analysis of eIF4E. Sources of resistance were identified in the PSPC and in commercial cultivars that can be introgressed into breeding lines using traditional techniques to reduce the time and cost required to generate germplasm with superior disease-resistant traits.