Genomic insights into recent species divergence in Nicotiana benthamiana and natural variation in Rdr1 gene controlling viral susceptibility

Genetic diversity and population structure of Piper nigrum (black pepper) accessions based on next-generation SNP markers

Despite the economic importance of Piper nigrum (black pepper), a highly valued crop worldwide, development and utilization of genomic resources have remained limited, with diversity assessments often relying on only a few samples or DNA markers. Here we employed restriction-site associated DNA sequencing to analyze 175 P. nigrum accessions from eight main black pepper growing regions in Sri Lanka. The sequencing effort resulted in 1,976 million raw reads, averaging 11.3 million reads per accession, revealing 150,356 high-quality single nucleotide polymorphisms (SNPs) distributed across 26 chromosomes. Population structure analysis revealed two subpopulations (K = 2): a dominant group consisting of 152 accessions sourced from both home gardens and large-scale cultivations, and a smaller group comprising 23 accessions exclusively from native collections in home gardens. This clustering was further supported by principal component analysis, with the first two principal components explaining 35.2 and 12.1% of the total variation. Genetic diversity analysis indicated substantial gene flow (Nm = 342.21) and a low fixation index (FST = 0.00073) between the two subpopulations, with no clear genetic differentiation among accessions from different agro-climatic regions. These findings demonstrate that most current black pepper genotypes grown in Sri Lanka share a common genetic background, emphasizing the necessity to broaden the genetic base to enhance resilience to biotic and abiotic stresses. This study represents the first attempt at analyzing black pepper genetic diversity using high-resolution SNP markers, laying the foundation for future genome-wide association studies for SNP-based gene discovery and breeding.

The New Zealand perspective of an ecosystem biology response to grapevine leafroll disease

Grapevine leafroll-associated virus 3 (GLRaV-3) is a major pathogen of grapevines worldwide resulting in grapevine leafroll disease (GLD), reduced fruit yield, berry quality and vineyard profitability. Being graft transmissible, GLRaV-3 is also transmitted between grapevines by multiple hemipteran insects (mealybugs and soft scale insects). Over the past 20 years, New Zealand has developed and utilized integrated pest management (IPM) solutions that have slowly transitioned to an ecosystem-based biological response to GLD. These IPM solutions and combinations are based on a wealth of research within the temperate climates of New Zealand's nation-wide grape production. To provide context, the grapevine viruses present in the national vineyard estate and how these have been identified are described; the most pathogenic and destructive of these is GLRaV-3. We provide an overview of research on GLRaV-3 genotypes and biology within grapevines and describe the progressive development of GLRaV-3/GLD diagnostics based on molecular, serological, visual, and sensor-based technologies. Research on the ecology and control of the mealybugs Pseudococcus calceolariae and P. longispinus, the main insect vectors of GLRaV-3 in New Zealand, is described together with the implications of mealybug biological control agents and prospects to enhance their abundance and/or fitness in the vineyard. Virus transmission by mealybugs is described, with emphasis on understanding the interactions between GLRaV-3, vectors, and plants (grapevines, alternative hosts, or non-hosts of the virus). Disease management through grapevine removal and the economic influence of different removal strategies is detailed. Overall, the review summarizes research by an interdisciplinary team working in close association with the national industry body, New Zealand Winegrowers. Teamwork and communication across the whole industry has enabled implementation of research for the management of GLD.

Molecular perspectives on age-related resistance of plants to (viral) pathogens

Age-related resistance to microbe invasion is a commonly accepted concept in plant pathology. However, the impact of such age-dependent interactive phenomena is perhaps not yet sufficiently recognized by the broader plant science community. Toward cataloging an understanding of underlying mechanisms, this review explores recent molecular studies and their relevance to the concept. Examples describe differences in genetic background, transcriptomics, hormonal balances, protein-mediated events, and the contribution by short RNA-controlled gene silencing events. Throughout, recent findings with viral systems are highlighted as an illustration of the complexity of the interactions. It will become apparent that instead of uncovering a unifying explanation, we unveiled only trends. Nevertheless, with a degree of confidence, we propose that the process of plant age-related defenses is actively regulated at multiple levels. The overarching goal of this control for plants is to avoid a constitutive waste of resources, especially at crucial metabolically draining early developmental stages.

Polyploid Nicotiana section Suaveolentes originated by hybridization of two ancestral Nicotiana clades

Introduction

Nicotiana section Suaveolentes is an almost all-Australian clade of allopolyploid tobacco species that emerged through hybridization between diploid relatives of the genus. In this study, we aimed to assess the phylogenetic relationship of the Suaveolentes section with several Nicotiana diploid species based on both plastidial and nuclear genes.

Methods

The Nicotiana plastome-based phylogenetic analysis representing 47 newly re-built plastid genomes suggested that an ancestor of N. section Noctiflorae is the most likely maternal donor of the Suaveolentes clade. Nevertheless, we found clear evidence of plastid recombination with an ancestor from the Sylvestres clade. We analyzed 411 maximum likelihood-based phylogenetic trees from a set of conserved nuclear diploid single copy gene families following an approach that assessed the genomic origin of each homeolog.

Results

We found that Nicotiana section Suaveolentes is monophyletic with contributions from the sections Alatae, Sylvestres, Petunioides and Noctiflorae. The dating of the divergence between these sections indicates that the Suaveolentes hybridization predates the split between Alatae/Sylvestres, and Noctiflorae/Petunioides.

Discussion

We propose that Nicotiana section Suaveolentes arose from the hybridization of two ancestral species from which the Noctiflorae/Petunioides and Alatae/Sylvestres sections are derived, with Noctiflorae the maternal parent. This study is a good example in which the use of genome wide data provided additional evidence about the origin of a complex polyploid clade.