Towards Better Grafting: SCoT and CDDP Analyses for Prediction of the Tomato Rootstocks Performance under Drought Stress

This study aims to predict the behavior of different tomato rootstocks under drought stress conditions. SCoT and CDDP analyses were employed to characterize the genetic relatedness among a commercial drought-sensitive tomato hybrid (cv. Bark) and four wild tomato accessions (LA2711, LA1995, LA3845, and LA4285) known for their tolerance to adverse conditions. The Bark plants were grafted onto the aforementioned wild accessions and self-grafted as control, and then the behavior of all graft unions was followed under normal and drought stress conditions. Our results showed a general genotype-dependent better growth and yield of heterografts than autografts under all growth conditions. Furthermore, clustering analysis based on growth, yield quantity and quality traits, and the leaf content of minerals, ABA, GA3, and proline, in addition to the activity of APX, POD, and DHAR reflected the same grouping pattern of the studied rootstocks exhibited by SCoT and CDDP. The identical grouping pattern supports the utilization of SCoT and CDDP as a robust screening tool helpful to predict the physiological and agronomical behavior of grafting on different tomato rootstocks. Furthermore, grafting could be a cost-efficient alternative method to improve drought tolerance in sensitive tomato genotypes.

Identification of elite germplasm of medicinally important Andrographis paniculata (Burm. f.) Nees with high content of four active diterpenoids in aerial parts from wild populations of eastern India

Andrographis paniculata is an Indian medicinal plant with tremendous therapeutic values due to the presence of active diterpenoids in its aerial parts. However, high domestic and export demand has led to overexploitation of wild populations of this species. With a view to bringing A. paniculata into cultivation and to reduce the pressure on wild populations, the present study was undertaken to identify elite germplasm from different locations of eastern India by analysing intraspecific variation in the content of four major active diterpenoids. A total of 166 wild accessions of A. paniculata analysed through high-performance liquid chromatography (HPLC) revealed remarkable variation in the sum of four active diterpenoids in the aerial parts, ranging from 0.41 to 8.55% on a dry weight basis. Three elite accessions (AP-6, AP-8, AP-46) having respectively 8.02, 8.36 & 8.55% of the sum of four major active diterpenoids were identified. These germplasm could be used for commercial cultivation and genetic improvement of A. paniculata.

Response of banana germplasms to banana bunchy top virus

Banana bunchy top virus (BBTV) is one of the important viruses causing disease in bananas and its infection has the potential to cause yield loss. This study was conducted to evaluate the response of several commercial cultivars (Cavendish, Bebek, Goroho, Tanduk, and Barangan Merah) and wild accessions (Klutuk NTT, Halabanensis, SPn 001, LNT 001, and Microcarpa) of banana to BBTV infection. Transmission of BBTV was carried out through banana aphid Pentalonia nigronervosa, using 20 adult aphids per plant with an acquisition feeding period of 24 hours on BBTV-infected plants and an inoculation feeding period on healthy test plants for 48 hours. Observation on plant growth and disease intensity was conducted for 8 weeks after inoculation. At the end of the observation period, only 5 cultivars, i.e. Cavendish, Bebek, Goroho, Barangan Merah, and Halabanensis showed typical symptoms of BBTV with disease incidence reached 80%, 60%, 20%, 20%, and 20% respectively. Significant inhibition of plant height and leaves width occurred in Cavendish, Bebek, and Goroho i.e. 44.60%, 36.31%; 12.62%, 41.08%; and 25%, 10.13%, respectively. This paper discusses the need for banana germplasm exploration to find sources of resistance to BBTV.

Dose-Response Study to Evaluate Dicamba Tolerance in Selected Wild Tomato Germplasm

A greenhouse dose-response study was conducted to determine the tolerance of three wild tomato accessions (TOM199, TOM198, TOM300) in comparison to a commercial cultivar (Better Boy) against the dicamba application at five rates (0, 70, 140, 210, and 280 g ae ha-1) at 14 and 28 days after treatment (DAT). Several physiological traits were evaluated at 0, 1, 3, 5, and 7 DAT. Wild accessions and cultivar were killed at all rates above 70 g ae ha-1 at 14 and 28 DAT, which is why differences between accessions and cultivar were only evident at 70 g ae ha-1. The GR50 (the herbicide rate that causes 50% reduction in dry weight) of Better Boy was 4.4 g ae ha-1 at 28 DAT, and this cultivar was approximately 11-fold more sensitive than wild accessions. At 7 DAT, the levels of H2O2 for wild accessions were lower than Better Boy up to 5 at 70 g ae ha-1 of dicamba. Furthermore, wild accessions showed lower herbicide absorption than Better Boy at all dicamba doses at 1, 3, and 7 DAT. All the three wild accessions expressed tolerance to the dicamba application at the dose of 70 g ae ha-1. At the same time, Better Boy and wild accessions were susceptible to dicamba application at rates of 140, 210, and 280 g ae ha-1.

A chickpea genetic variation map based on the sequencing of 3,366 genomes

Zero hunger and good health could be realized by 2030 through effective conservation, characterization and utilization of germplasm resources1. So far, few chickpea (Cicerarietinum) germplasm accessions have been characterized at the genome sequence level2. Here we present a detailed map of variation in 3,171 cultivated and 195 wild accessions to provide publicly available resources for chickpea genomics research and breeding. We constructed a chickpea pan-genome to describe genomic diversity across cultivated chickpea and its wild progenitor accessions. A divergence tree using genes present in around 80% of individuals in one species allowed us to estimate the divergence of Cicer over the last 21 million years. Our analysis found chromosomal segments and genes that show signatures of selection during domestication, migration and improvement. The chromosomal locations of deleterious mutations responsible for limited genetic diversity and decreased fitness were identified in elite germplasm. We identified superior haplotypes for improvement-related traits in landraces that can be introgressed into elite breeding lines through haplotype-based breeding, and found targets for purging deleterious alleles through genomics-assisted breeding and/or gene editing. Finally, we propose three crop breeding strategies based on genomic prediction to enhance crop productivity for 16 traits while avoiding the erosion of genetic diversity through optimal contribution selection (OCS)-based pre-breeding. The predicted performance for 100-seed weight, an important yield-related trait, increased by up to 23% and 12% with OCS- and haplotype-based genomic approaches, respectively.

Flowering Times of Wild Arabidopsis Accessions From Across Norway Correlate With Expression Levels of FT, CO, and FLC Genes

Temperate species often require or flower most rapidly in the long daylengths, or photoperiods, experienced in summer or after prolonged periods of cold temperatures, referred to as vernalization. Yet, even within species, plants vary in the degree of responsiveness to these cues. In Arabidopsis thaliana, CONSTANS (CO) and FLOWERING LOCUS C (FLC) genes are key to photoperiod and vernalization perception and antagonistically regulate FLOWERING LOCUS T (FT) to influence the flowering time of the plants. However, it is still an open question as to how these genes vary in their interactions among wild accessions with different flowering behaviors and adapted to different microclimates, yet this knowledge could improve our ability to predict plant responses in variable natural conditions. To assess the relationships among these genes and to flowering time, we exposed 10 winter-annual Arabidopsis accessions from throughout Norway, ranging from early to late flowering, along with two summer-annual accessions to 14 weeks of vernalization and either 8- or 19-h photoperiods to mimic Norwegian climate conditions, then assessed gene expression levels 3-, 5-, and 8-days post vernalization. CO and FLC explained both FT levels and flowering time (days) but not rosette leaf number at flowering. The correlation between FT and flowering time increased over time. Although vernalization suppresses FLC, FLC was high in the late-flowering accessions. Across accessions, FT was expressed only at low FLC levels and did not respond to CO in the late-flowering accessions. We proposed that FT may only be expressed below a threshold value of FLC and demonstrated that these three genes correlated to flowering times across genetically distinct accessions of Arabidopsis.

Genetic diversity and volatile oil components variation in Achillea fragrantissima wild accessions and their regenerated genotypes

Background Wild medicinal plants are suffering natural environmental stresses and habitat destruction. The genetic diversity evaluation of wild accessions and their in vitro raised genotypes using molecular markers, as well as the estimation of substances of pharmaceutical value in wild plants and their regenerated genotypes are convenient approaches to test the genetic fidelity of regenerated plants as a source of substances of pharmaceutical value. In this study, the genetic diversity of 12 accessions of the medicinal plant Achillea fragrantissima, representing five sites in the mountains of South Sinai, Egypt, were estimated by the inter simple sequence repeats (ISSR) fingerprinting and their volatile oil components were identified using gas chromatography-mass spectrometry (GC-MS) analysis. The same accessions were regenerated in vitro and the genetic diversity and volatile oil components of propagated genotypes were determined and compared to their wild parents. Results Clustering and principal component analyses indicated that the wild accessions and their regenerated genotypes were genetically differentiated, but the regenerated plants are relatively more diverse compared to their wild parents. However, genetic variation between wild accessions is inherited to their in vitro propagated genotypes indicating genotypic differentiation of the examined accessions. The number of volatile oil compounds in the wild A. fragrantissima accessions was 31 compounds while in the in vitro propagated plants only 24 compounds were detected. Four major compounds are common to both wild and regenerated plants; these are artemisia ketone, alpha-thujone, dodecane, and piperitone. Conclusions Genome profiling and essential oil components analysis showed variations in A. fragrantissima accessions from different populations. Genetic differences between wild and regenerated genotypes were analyzed and validated with the final conclusion that in vitro conditions elicited higher genetic variation that is associated with reduced amount and diversity in the essential oil components.

Genetic resources of narrow-leaved lupine (Lupinus angustifolius L.) and their role in its domestication and breeding

Narrow-leaved lupine (Lupinus angustifolius L.) is a cultivated multipurpose species with a very short history of domestication. It is used as a green manure, and for feed and food. This crop shows good prospects for use in pharmacology and as a source of fish feeds in aquaculture. However, its genetic potential for the development of productive and adaptable cultivars is far from being realized. For crop species, the genetic base of the cultivated gene pool has repeatedly been shown as being much narrower than that of the wild gene pool. Therefore, efficient utilization of a species’ genetic resources is important for the crop’s further improvement. Analyzing the information on the germplasm collections preserved in national gene banks can help perceive the worldwide diversity of L. angustifolius genetic resources and understand how they are studied and used. In this context, the data on the narrow-leaved lupine collection held by VIR are presented: its size and composition, the breeding status of accessions, methods of studying and disclosing intraspecific differentiation, the classifications used, and the comparison of this information with available data on other collections. It appeared that VIR’s collection of narrow-leaved lupine, ranking as the world’s second largest, differed significantly from others by the prevalence of advanced cultivars and breeding material in it, while wild accessions prevailed in most collections. The importance of the wild gene pool for the narrow-leaved lupine breeding in Australia, the world leader in lupine production, is highlighted. The need to get an insight into the species’ ecogeographic diversity in order to develop cultivars adaptable to certain cultivation conditions is shown. The data on the testing of VIR’s collection for main crop characters valuable for breeders are presented. Special attention is paid to the study of accessions with limited branching as a promising gene pool for cultivation in relatively northern regions of Russia. They demonstrate lower but more stable productivity, and suitability for cultivation in planting patterns, which has a number of agronomic advantages. Analyzing the work with narrow-leaved lupine genetic resources in different national gene banks over the world helps shape the prospects of further activities with VIR’s collection as the only source of promising material for domestic breeding.

Haplotype mapping uncovers unexplored variation in wild and domesticated soybean at the major protein locus cqProt-003

Here, we present association and linkage analysis of 985 wild, landrace and cultivar soybean accessions in a pan genomic dataset to characterize the major high-protein/low-oil associated locus cqProt-003 located on chromosome 20. A significant trait associated region within a 173 kb linkage block was identified and variants in the region were characterised, identifying 34 high confidence SNPs, 4 insertions, 1 deletion and a larger 304 bp structural variant in the high-protein haplotype. Trinucleotide tandem repeats of variable length present in the third exon of gene 20G085100 are strongly correlated with the high-protein phenotype and likely represent causal variation. Structural variation has previously been found in the same gene, for which we report the global distribution of the 304bp deletion and have identified additional nested variation present in high-protein individuals. Mapping variation at the cqProt-003 locus across demographic groups suggests that the high-protein haplotype is common in wild accessions (94.7%), rare in landraces (10.6%) and near absent in cultivated breeding pools (4.1%), suggesting its decrease in frequency primarily correlates with domestication and continued during subsequent improvement. However, the variation that has persisted in under-utilized wild and landrace populations holds high breeding potential for breeders willing to forego seed oil to maximise protein content. The results of this study include the identification of distinct haplotype structures within the high-protein population, and a broad characterization of the genomic context and linkage patterns of cqProt-003 across global populations, supporting future functional characterisation and modification.