Development of a PCR-based, genetic marker resource for the tomato-like nightshade relative, Solanum lycopersicoides using whole genome sequence analysis

Solanum lycopersicoides is a wild nightshade relative of tomato with known resistance to a wide range of pests and pathogens, as well as tolerance to cold, drought and salt stress. To effectively utilize S. lycopersicoides as a genetic resource in breeding for tomato improvement, the underlying basis of observable traits in the species needs to be understood. Molecular markers are important tools that can unlock the genetic underpinnings of phenotypic variation in wild crop relatives. Unfortunately, DNA markers that are specific to S. lycopersicoides are limited in number, distribution and polymorphism rate. In this study, we developed a suite of S. lycopersicoides-specific SSR and indel markers by sequencing, building and analyzing a draft assembly of the wild nightshade genome. Mapping of a total of 1.45 Gb of S. lycopersicoides contigs against the tomato reference genome assembled a moderate number of contiguous reads into longer scaffolds. Interrogation of the obtained draft yielded SSR information for more than 55,000 loci in S. lycopersicoides for which more than 35,000 primers pairs were designed. Additionally, indel markers were developed based on sequence alignments between S. lycopersicoides and tomato. Synthesis and experimental validation of 345 primer sets resulted in the amplification of single and multilocus targets in S. lycopersicoides and polymorphic loci between S. lycopersicoides and tomato. Cross-species amplification of the 345 markers in tomato, eggplant, silverleaf nightshade and pepper resulted in varying degrees of transferability that ranged from 55 to 83%. The markers reported in this study significantly expands the genetic marker resource for S. lycopersicoides, as well as for related Solanum spp. for applications in genetics and breeding studies.

Potato Germplasm Enhancement Enters the Genomics Era

The goal of germplasm enhancement is to introgress traits from wild crop relatives into cultivated material and eventually cultivars. It seeks to restore genetic diversity that has been lost over time or to augment cultivated material with novel alleles that improve parents in breeding programs. This paper discusses potato germplasm enhancement efforts in the past, focusing on effective examples such as disease resistance and processing quality. In addition, it outlines new strategies for enhancement efforts, shifting the focus from evaluating phenotypes to tracking and manipulating specific DNA sequences. In the genomics era, germplasm enhancement will increasingly be focused on identifying and introgressing alleles rather than traits. Alleles will come from a broad pool of genetic resources that include wild species relatives of potato, landraces, cultivated potato itself, and distantly-related species. Genomics tools will greatly increase the efficiency of introgressing multi-genic traits and will make it possible to identify rare alleles and utilize recessive alleles.

Manihot takape sp. nov. (Euphorbiaceae), a new tuberous subshrub from the Paraguayan Chaco

Manihottakape De Egea & Peña-Chocarro, sp. nov. is described and illustrated as a new species from the Paraguayan Chaco. It was collected while carrying out fieldwork related to the study of the most important Wild Crop Relatives of the country’s flora. Morphological characteristics that differentiate this species from closely related taxa, as well as its habitat, geographical distribution and conservation status are provided.

New distribution records of some wild crop relatives from India

Field surveys across various parts of the country coupled with an analysis of literature and examination of herbarium specimens revealed the natural distribution of six wild relatives of crop species in various states/union territories of India, viz., Cajanus scarabaeoides (from Lakshadweep), Cucumis javanicus (from Meghalaya), Hystrix duthiei (from Jammu & Kashmir), Luffa echinata (from Haryana) and Trichosanthes pilosa (from Andhra Pradesh), which have not been reported earlier from these states. Their descriptions, phenology, habitat and other field notes have been presented here.

Genetic diversity inOryza glumaepatulawild rice populations in Costa Rica and possible gene flow fromO. sativa

Wild crop relatives are an important source of genetic diversity for crop improvement. Diversity estimates are generally lacking for many wild crop relatives. The objective of the present study was to analyze how genetic diversity is distributed within and among populations of the wild rice speciesOryza glumaepatulain Costa Rica. We also evaluated the likelihood of gene flow between wild and commercial rice species because the latter is commonly sympatric with wild rice populations. Introgression may change wild species by incorporating alleles from domesticated species, increasing the risk of losing original variation. Specimens from all knownO. glumaepatulapopulations in Costa Rica were analyzed with 444 AFLP markers to characterize genetic diversity and structure. We also compared genetic diversity estimates betweenO. glumaepatulaspecimens andO. sativacommercial rice. Our results showed thatO. glumaepatulapopulations in Costa Rica have moderately high levels of genetic diversity, comparable to those found in South American populations. Despite the restricted distribution of this species in Costa Rica, populations are fairly large, reducing the effects of drift on genetic diversity. We found a dismissible but significant structure (θ= 0.02 ± 0.001) among populations. A Bayesian structure analysis suggested that some individuals share a significant proportion of their genomes withO. sativa. These results suggest that gene flow from cultivatedO. sativapopulations may have occurred in the recent past. These results expose an important biohazard: recurrent hybridization may reduce the genetic diversity of this wild rice species. Introgression may transfer commercial traits intoO. glumaepatula, which in turn could alter genetic diversity and increase the likelihood of local extinction. These results have important implications forin situconservation strategies of the only wild populations ofO. glumaepatulain Costa Rica.

Cultural Stewardship Accountability of Seed Bank Institutions for Indigenous Knowledge

A growing emphasis among seed banks in Australia and globally is the collection of seed and information associated with wild crop relatives of food and fodder crops. This is part of scientific efforts to store and document plant traits that may prove useful to deal with risks to food and bio security in the face of global climate changes. This has implications for indigenous communities because of the risk that indigenous knowledge may be collected and included as ‘data’ rather than as knowledge with significant cultural tethering. This articl provides a theoretical context for institutional seed banks to engage with indigenous people and specify indigenous knowledge stewardship accountability. This should help seed banks to operate with sensitivity to cultural wellbeing and minimise the risks from failure to satisfy accountability for indigenous knowledge stewardship. The article identifies four interrelated dimensions of indigenous knowledge stewardship, and identifies a tentative process for institutions to adapt this to indigenous knowledge stewardship strategy and practice. The process for realising indigenous knowledge stewardship accountability is the subject of further research.

Sequencing of wild crop relatives to support the conservation and utilization of plant genetic resources

The re-sequencing of the genomes of wild crop relatives is a rapid method to determine the likely utility of the germplasm in crop improvement. The conservation of genetic resources both in situ and ex situ can be guided by information on the novelty of specific populations at the whole-genome and specific allele levels. The analysis of Australian wild relatives of rice, coffee, Macadamia and Eucalypts is being used to support crop improvement and enhance food and energy security. Rice populations that are novel sources of diversity in the A genome of rice have been characterized at the whole-genome level. This has demonstrated the novelty of these species and will support taxonomic revisions of the Oryza species. Variation in the genomes of plants from diverse environments defines strategies that might be employed to develop climate-resilient crop varieties. Eucalypt sequencing aims to support the selection of species and genotypes for use as new energy crops.