Sample sequence analysis uncovers recurrent horizontal transfers of transposable elements among grasses

Limited genome resources are a bottleneck in the study of horizontal transfer (HT) of DNA in plants. To solve this issue, we tested the usefulness of low-depth sequencing data generated from 19 previously uncharacterized panicoid grasses for HT investigation. We initially searched for horizontally transferred LTR-retrotransposons by comparing the 19 sample sequences to 115 angiosperm genome sequences. Frequent HTs of LTR-retrotransposons were identified solely between panicoids and rice (Oryza sativa). We consequently focused on additional Oryza species and conducted a non-targeted investigation of HT involving the panicoid genus Echinochloa, which showed the most HTs in the first set of analyses. The comparison of nine Echinochloa samples and ten Oryza species identified recurrent HTs of diverse transposable element (TE) types at different points in Oryza history, but no confirmed cases of HT for sequences other than TEs. One case of HT was observed from one Echinochloa species into one Oryza species with overlapping geographic distributions. Variation among species and datasets highlights difficulties in identifying all HT, but our investigations showed that sample sequence analyses can reveal the importance of HT for the diversification of the TE repertoire of plants

Tomato: a crop species amenable to improvement by cellular and molecular methods

Tomato is a crop plant with a relatively small DNA content per haploid genome and a well developed genetics. Plant regeneration from explants and protoplasts is feasable which led to the development of efficient transformation procedures. In view of the current data, the isolation of useful mutants at the cellular level probably will be of limited value in the genetic improvement of tomato. Protoplast fusion may lead to novel combinations of organelle and nuclear DNA (cybrids), whereas this technique also provides a means of introducing genetic information from alien species into tomato. Important developments have come from molecular approaches. Following the construction of an RFLP map, these RFLP markers can be used in tomato to tag quantitative traits bred in from related species. Both RFLP's and transposons are in the process of being used to clone desired genes for which no gene products are known. Cloned genes can be introduced and potentially improve specific properties of tomato especially those controlled by single genes. Recent results suggest that, in principle, phenotypic mutants can be created for cloned and characterized genes and will prove their value in further improving the cultivated tomato.

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

In Extended Data Fig. 1 of this Article, the labels ‘Market class’ and ‘Biological status’ were inadvertently swapped. In the corresponding figure legend, “Track 1: Biological status; Track 2: Market class;” should have been “Track 1: Market class; Track 2: Biological status;”. The original Article has been corrected online

Biotechnology for Sorghum Improvement

Modern molecular technologies will promote tremendous change in nature and efficiency of agricultural production. DNA markers can be used to enhance breeding programmes now, and genetic engineering will play an ever-more-important role. Different crops, and a single crop in different environments, will vary in the nature and degree to which these technologies can or should be utilized. Sorghum's strengths, particularly its high level of productivity under adverse conditions, make it a very important target for continued improvement. Molecular techniques will allow exceptional advances in the productivity of a crop species, in proportion to the effort applied to that species. Hence, sorghum will face more direct competition with other crops (e.g. maize and rice) than was previously possible. In order to continue its major contribution to world agriculture, sorghum must utilize its relative strengths and acquire new capacities. Fortunately, many of the tools developed in other grass species can be directly applied to sorghum improvement, partly due to the high degree of conservation in grass gene content and map colinearity. Appropriate applications of biotechnology will often be very different for different sorghum growers and users. However, with thoughtful selection and employment of pertinent biotechnology, sorghum production should be able to maintain or increase its agricultural significance.Les technologies moleculaires modernes vont entrainer des changements importants dans la nature et l'efficience de la production agricole. Les marqueurs DNA peuvent etre utilises pour accelerer les programmes d' amelioration tandis que le genie genetique pourra jouer un role pins que jamais important. Differentes plantes, aussi bien qu'une seule plante, cultivees dans differents environnements pourraient varier dans leur nature selon le degre avec lequel ces technologies pourraient etre utilisees. Les points forts du sorgho, particulierement son haut niveau de productivite sous des conditions adverses de production font de cette culture une cible importante pour une amelioration continue. Les techniques moleculaires permettront de faire des progres exceptionnels dans l'augmentation de la productivite des especes de cultures, selon les efforts qui seront mis sur ces especes. Ainsi, le sorgho fera face a la competition des nutres cultures comme le mais et le riz. Pour maintenir sa majeure contribution a l'agriculture mondiale, le sorgho doit utiliser ses points forts en vue d'acquerir des nouvelles capacites. Heureusement que pinsieurs outils developpes pour d'nutres graminees peuvent directement etre utilises pour l'amelioration du sorgho grace partiellement a son niveau eleve de conservation de genes et de colinearite. Les applications appropriees de biotechnologie seront souvent tres differentes pour differents producteurs ou utilisateurs de sorgho. Cependant, a l'aide d'une selection bien pensee et de l'usage pertinent de la biotechnologie, la production du sorgho pourrait maintenir et accroitre son importance agricole

5Gs for crop genetic improvement

Here we propose a 5G breeding approach for bringing much-needed disruptive changes to crop improvement. These 5Gs are Genome assembly, Germplasm characterization, Gene function identification, Genomic breeding (GB), and Gene editing (GE). In our view, it is important to have genome assemblies available for each crop and a deep collection of germplasm characterized at sequencing and agronomic levels for identification of marker-trait associations and superior haplotypes. Systems biology and sequencing-based mapping approaches can be used to identify genes involved in pathways leading to the expression of a trait, thereby providing diagnostic markers for target traits. These genes, markers, haplotypes, and genome-wide sequencing data may be utilized in GB and GE methodologies in combination with a rapid cycle breeding strategy

Paramutation: Heritable in trans effects

Paramutation is the heritable transfer of epigenetic information from one allele of a gene to another allele of the same gene. In general, the consequence of this trans-communication is a change in gene expression. Paramutation has been observed in plants, fungi and mammals, but is most extensively studied in maize thanks to the long-standing history of maize genetics. For decades, paramutation has been a mystery, but recent progress has shed light on the mechanisms underlying this phenomenon. The identification of MOP1 as an RNA-dependent RNA polymerase shows that RNA plays a crucial role in the trans-inactivation process. RNA however appears not the only player in the paramutation process. In this chapter, potential mechanisms will be discussed in light of characteristics that the various paramutation phenomena have in common