Integrated agricultural research and crop breeding: Allelopathic weed control in cereals and long-term productivity in perennial biomass crops

Future agricultural research will need to increasingly integrate ecological, physiological and molecular methods, in order to understand agricultural crops in situ and their interaction with the environment as well as organisms impacting on their long-term health and productivity ('agricultural eco-genomics'). The need for integration will increasingly implicate on crop breeding strategies for most agricultural systems. In this paper, implications are highlighted for two contrasting areas of agricultural research related to sustainable crop production: first, the possibilities to utilize crop allelopathic activity to suppress weeds as an alternative to chemical weed control; and second the increasing interest to environmentally friendly and sustainable produce perennial energy crops on agricultural land. 'Sustainability' in agriculture is difficult to define unequivocally, but frequently implies the increased utilization of ecological processes. Breeding strategies towards increased utilization of allelopathic crops require initially the integration and verification of allelopathic processes in various agricultural contexts, because there is currently great uncertainty about the predictable operation of allelopathic activity in different ecological contexts. Breeding programs for future biomass crops, most promising are perennials such as Salix, would greatly benefit from the integration of ecological information affecting long-term productivity, e.g., eco-physiological growth determinants at stand level and the biological control of pests. Agricultural eco-genomics could facilitate a compromise between intensive agriculture and the frequently expressed demand for greater sustainability in agriculture.

Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion

BACKGROUND: Sex chromosomes have evolved independently multiple times in eukaryotes and are therefore considered a prime example of convergent genome evolution. Sex chromosomes are known to emerge after recombination is halted between a homologous pair of chromosomes, and this leads to a range of non-adaptive modifications causing gradual degeneration and gene loss on the sex-limited chromosome. However, the proximal causes of recombination suppression and the pace at which degeneration subsequently occurs remain unclear. RESULTS: Here, we use long- and short-read single-molecule sequencing approaches to assemble and annotate a draft genome of the basket willow, Salix viminalis, a species with a female heterogametic system at the earliest stages of sex chromosome emergence. Our single-molecule approach allowed us to phase the emerging Z and W haplotypes in a female, and we detected very low levels of Z/W single-nucleotide divergence in the non-recombining region. Linked-read sequencing of the same female and an additional male (ZZ) revealed the presence of two evolutionary strata supported by both divergence between the Z and W haplotypes and by haplotype phylogenetic trees. Gene order is still largely conserved between the Z and W homologs, although the W-linked region contains genes involved in cytokinin signaling regulation that are not syntenic with the Z homolog. Furthermore, we find no support across multiple lines of evidence for inversions, which have long been assumed to halt recombination between the sex chromosomes. CONCLUSIONS: Our data suggest that selection against recombination is a more gradual process at the earliest stages of sex chromosome formation than would be expected from an inversion and may result instead from the accumulation of transposable elements. Our results present a cohesive understanding of the earliest genomic consequences of recombination suppression as well as valuable insights into the initial stages of sex chromosome formation and regulation of sex differentiation

The impact of global warming on plant diseases and insect vectors in Sweden

Cold winters and geographic isolation have hitherto protected the Nordic countries from many plant pathogens and insect pests, leading to a comparatively low input of pesticides. The changing climate is projected to lead to a greater rise in temperature in this region, compared to the global mean. In Scandinavia, a milder and more humid climate implies extended growing seasons and possibilities to introduce new crops, but also opportunities for crop pests and pathogens to thrive in the absence of long cold periods. Increased temperatures, changed precipitation patterns and new cultivation practices may lead to a dramatic change in crop health. Examples of diseases and insect pest problems predicted to increase in incidence and severity due to global warming are discussed