The impact of genetic changes during crop domestication

Humans have domesticated hundreds of plant and animal species as sources of food, fiber, forage, and tools over the past 12,000 years, with manifold effects on both human society and the genetic structure of the domesticated species. The outcomes of crop domestication were shaped by selection driven by human preferences, cultivation practices, and agricultural environments, as well as other population genetic processes flowing from the ensuing reduction in effective population size. It is obvious that any selection imposes a reduction of diversity, favoring preferred genotypes, such as nonshattering seeds or increased palatability. Furthermore, agricultural practices greatly reduced effective population sizes of crops, allowing genetic drift to alter genotype frequencies. Current advances in molecular technologies, particularly of genome sequencing, provide evidence of human selection acting on numerous loci during and after crop domestication. Population-level molecular analyses also enable us to clarify the demographic histories of the domestication process itself, which, together with expanded archaeological studies, can illuminate the origins of crops. Domesticated plant species are found in 160 taxonomic families. Approximately 2500 species have undergone some degree of domestication, and 250 species are considered to be fully domesticated. The evolutionary trajectory from wild to crop species is a complex process. Archaeological records suggest that there was a period of predomestication cultivation while humans first began the deliberate planting of wild stands that had favorable traits. Later, crops likely diversified as they were grown in new areas, sometimes beyond the climatic niche of their wild relatives. However, the speed and level of human intentionality during domestication remains a topic of active discussion. These processes led to the so-called domestication syndrome, that is, a group of traits that can arise through human preferences for ease of harvest and growth advantages under human propagation. These traits included reduced dispersal ability of seeds and fruits, changes to plant structure, and changes to plant defensive characteristics and palatability. Domestication implies the action of selective sweeps on standing genetic variation, as well as new genetic variation introduced via mutation or introgression. Furthermore, genetic bottlenecks during domestication or during founding events as crops moved away from their centers of origin may have further altered gene pools. To date, a few hundred genes and loci have been identified by classical genetic and association mapping as targets of domestication and postdomestication divergence. However, only a few of these have been characterized, and for even fewer is the role of the wild-type allele in natural populations understood. After domestication, only favorable haplotypes are retained around selected genes, which creates a genetic valley with extremely low genetic diversity. These “selective sweeps” can allow mildly deleterious alleles to come to fixation and may create a genetic load in the cultivated gene pool. Although the population-wide genomic consequences of domestication offer several predictions for levels of the genetic diversity in crops, our understanding of how this diversity corresponds to nutritional aspects of crops is not well understood. Many studies have found that modern cultivars have lower levels of key micronutrients and vitamins. We suspect that selection for palatability and increased yield at domestication and during postdomestication divergence exacerbated the low nutrient levels of many crops, although relatively little work has examined this question. Lack of diversity in modern germplasm may further limit our capacity to breed for higher nutrient levels, although little effort has gone into this beyond a handful of staple crops. This is an area where an understanding of domestication across many crop taxa may provide the necessary insight for breeding more nutritious crops in a rapidly changing world

The impact of genetic changes during crop domestication on healthy food development

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Strengthening the impact of plant genetic resources through collaborative collection, conservation, characterisation, and evaluation: a tribute to the legacy of Dr Clive Francis

This paper is a tribute to the legacy of Dr Clive Francis, who directly and indirectly collected >14 000 accessions across 60 genera of pasture, forage, and crop species and their wild relatives around the Mediterranean basin, Eastern Africa, and Central and South Asia from 1973 to 2005. This was achieved by a collaborative approach that built strong interactions between disparate organisations (ICARDA, VIR, CLIMA, and Australian genebanks) based on germplasm exchange, conservation and documentation, capacity building, and joint collection. These activities greatly strengthened Australian pasture, forage, and crop genebanks, and led to widespread germplasm utilisation that has waned in the last 5 years, reflecting changing priorities among industry funding bodies and research providers. This situation must be reversed, given the pivotal role genetic resource collections must play to broaden the genetic and adaptive base of plant breeding, to meet the challenge of feeding an increasing population in a depleting resource base. Because the use of germplasm subsets that facilitate phenotyping will stimulate wider utilisation of genetic resources, we discuss the application of core collection and germplasm selection through habitat characterisation/filtering in Australian collections. Both are valid entry points into large collections, but the latter has the advantage of enabling both trait discovery and investigation of plant adaptation, and because it is based on a priori hypothesis testing, it increases understanding even when the trait of interest is not identified

Structural characterization of an ionic liquid in bulk and in nano-confined environment using data from MD simulations

This article contains data on structural characterization of the [C2Mim][NTf2] in bulk and in nano-confined environment obtained using MD simulations. These data supplement those presented in the paper “Insights from Molecular Dynamics Simulations on Structural Organization and Diffusive Dynamics of an Ionic Liquid at Solid and Vacuum Interfaces” [1], where force fields with three different charge methods and three charge scaling factors were used for the analysis of the IL in the bulk, at the interface with the vacuum and the IL film in the contact with a hydroxylated alumina surface. Here, we present details on the construction of the model systems in an extended detailed methods section. Furthermore, for best parametrization, structural and dynamic properties of IL in different environment are studied with certain features presented herein

The optical afterglow of the short gamma-ray burst GRB 050709

It has long been known that there are two classes of gamma-ray bursts (GRBs), mainly distinguished by their durations. The breakthrough in our understanding of long-duration GRBs (those lasting more than ~2 s), which ultimately linked them with energetic Type Ic supernovae, came from the discovery of their long-lived X-ray and optical afterglows, when precise and rapid localizations of the sources could finally be obtained. X-ray localizations have recently become available for short (duration <2 s) GRBs, which have evaded optical detection for more than 30 years. Here we report the first discovery of transient optical emission (R-band magnitude ~23) associated with a short burst; GRB 050709. The optical afterglow was localized with subarcsecond accuracy, and lies in the outskirts of a blue dwarf galaxy. The optical and X-ray afterglow properties 34 h after the GRB are reminiscent of the afterglows of long GRBs, which are attributable to synchrotron emission from ultrarelativistic ejecta. We did not, however, detect a supernova, as found in most nearby long GRB afterglows, which suggests a different origin for the short GRBs.Comment: 11 pages, 3 figures, press material at http://www.astro.ku.dk/dark

Computational Cancer Biology: An Evolutionary Perspective

ISSN:1553-734XISSN:1553-735