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Crop wild relative populations of Beta vulgaris allow direct mapping of agronomically important genes.

ABSTRACT: Rapid identification of agronomically important genes is of pivotal interest for crop breeding. One source of such genes are crop wild relative (CWR) populations. Here we used a CWR population of <200 wild beets (B. vulgaris ssp. maritima), sampled in their natural habitat, to identify the sugar beet (Beta vulgaris ssp. vulgaris) resistance gene Rz2 with a modified version of mapping-by-sequencing (MBS). For that, we generated a draft genome sequence of the wild beet. Our results show the importance of preserving CWR in situ and demonstrate the great potential of CWR for rapid discovery of causal genes relevant for crop improvement. The candidate gene for Rz2 was identified by MBS and subsequently corroborated via RNA interference (RNAi). Rz2 encodes a CC-NB-LRR protein. Access to the DNA sequence of Rz2 opens the path to improvement of resistance towards rhizomania not only by marker-assisted breeding but also by genome editing.

SUBMITTER: Capistrano-Gossmann GG

PROVIDER: S-EPMC5467160 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature

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Crop wild relative populations of Beta vulgaris allow direct mapping of agronomically important genes.

Capistrano-Gossmann Gina G GG Ries D D Holtgräwe D D Minoche A A Kraft T T Frerichmann S L M SLM Rosleff Soerensen T T Dohm J C JC González I I Schilhabel M M Varrelmann M M Tschoep H H Uphoff H H Schütze K K Borchardt D D Toerjek O O Mechelke W W Lein J C JC Schechert A W AW Frese L L Himmelbauer H H Weisshaar B B Kopisch-Obuch F J FJ

Nature communications 20170606

Rapid identification of agronomically important genes is of pivotal interest for crop breeding. One source of such genes are crop wild relative (CWR) populations. Here we used a CWR population of <200 wild beets (B. vulgaris ssp. maritima), sampled in their natural habitat, to identify the sugar beet (Beta vulgaris ssp. vulgaris) resistance gene Rz2 with a modified version of mapping-by-sequencing (MBS). For that, we generated a draft genome sequence of the wild beet. Our results show the import ...[more]

PMID: 28585529

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Project description:Populations of widely distributed species often exhibit geographic variation in functional traits in response to environmental heterogeneity. Such trait variation may be the result of different adaptive mechanisms, including genetically based differentiation, phenotypic plasticity or a combination of both. Disentangling the genetic and environmental components of trait variation may be particularly interesting in crop wild relatives, since they may provide unique reservoirs of genetic diversity for crop improvement. In this study, we assessed ecotypic differentiation and patterns of plasticity to drought in populations of Lupinus angustifolius, a Mediterranean crop wild relative, from two climatically distinct regions in the Iberian Peninsula. Using an outdoor common garden, we compared phenotypic responses of inbred maternal families to two ecologically meaningful water availability treatments (drought and high-moisture). We measured 18 different functional traits related to growth, morphology, phenology and reproduction. Plants in the drought treatment grew less, had lower leaf chlorophyll content and photochemical efficiency, but also reproduced faster, produced larger seeds and altered leaflet morphology through increased leaflet thickness, higher leaflet dry matter content and lower specific leaf area. We also found significant differences between regions that likely reflect adaptation to climatically distinct environments, with populations from the south showing a faster onset of reproduction, higher leaf thickness and higher seed size, consistent with the drier conditions experienced in southern sites. Plasticity to drought was in most cases in the same direction as quantitative genetic differentiation (i.e. cogradient variation), providing evidence of the adaptive value of the plastic change. Our results show that both genetic differentiation and plasticity can generate adaptive phenotypic variation in L. angustifolius, and help to identify potentially valuable genetic resources to incorporate into breeding programmes.

Project description:BackgroundCrop wild relatives are wild species that are closely related to crops. They are valuable as potential gene donors for crop improvement and may help to ensure food security for the future. However, they are becoming increasingly threatened in the wild and are inadequately conserved, both in situ and ex situ. Information about the conservation status and utilisation potential of crop wild relatives is diverse and dispersed, and no single agreed standard exists for representing such information; yet, this information is vital to ensure these species are effectively conserved and utilised. The European Community-funded project, European Crop Wild Relative Diversity Assessment and Conservation Forum, determined the minimum information requirements for the conservation and utilisation of crop wild relatives and created the Crop Wild Relative Information System, incorporating an eXtensible Markup Language (XML) schema to aid data sharing and exchange.ResultsCrop Wild Relative Markup Language (CWRML) was developed to represent the data necessary for crop wild relative conservation and ensure that they can be effectively utilised for crop improvement. The schema partitions data into taxon-, site-, and population-specific elements, to allow for integration with other more general conservation biology schemata which may emerge as accepted standards in the future. These elements are composed of sub-elements, which are structured in order to facilitate the use of the schema in a variety of crop wild relative conservation and use contexts. Pre-existing standards for data representation in conservation biology were reviewed and incorporated into the schema as restrictions on element data contents, where appropriate.ConclusionCWRML provides a flexible data communication format for representing in situ and ex situ conservation status of individual taxa as well as their utilisation potential. The development of the schema highlights a number of instances where additional standards-development may be valuable, particularly with regard to the representation of population-specific data and utilisation potential. As crop wild relatives are intrinsically no different to other wild plant species there is potential for the inclusion of CWRML data elements in the emerging standards for representation of biodiversity data.

Project description:BACKGROUND: After crop-wild hybridization, some of the crop genomic segments may become established in wild populations through selfing of the hybrids or through backcrosses to the wild parent. This constitutes a possible route through which crop (trans)genes could become established in natural populations. The likelihood of introgression of transgenes will not only be determined by fitness effects from the transgene itself but also by the crop genes linked to it. Although lettuce is generally regarded as self-pollinating, outbreeding does occur at a low frequency. Backcrossing to wild lettuce is a likely pathway to introgression along with selfing, due to the high frequency of wild individuals relative to the rarely occurring crop-wild hybrids. To test the effect of backcrossing on the vigour of inter-specific hybrids, Lactuca serriola, the closest wild relative of cultivated lettuce, was crossed with L. sativa and the F(1) hybrid was backcrossed to L. serriola to generate BC(1) and BC(2) populations. Experiments were conducted on progeny from selfed plants of the backcrossing families (BC(1)S(1) and BC(2)S(1)). Plant vigour of these two backcrossing populations was determined in the greenhouse under non-stress and abiotic stress conditions (salinity, drought, and nutrient deficiency). RESULTS: Despite the decreasing contribution of crop genomic blocks in the backcross populations, the BC(1)S(1) and BC(2)S(1) hybrids were characterized by a substantial genetic variation under both non-stress and stress conditions. Hybrids were identified that performed equally or better than the wild genotypes, indicating that two backcrossing events did not eliminate the effect of the crop genomic segments that contributed to the vigour of the BC(1) and BC(2) hybrids. QTLs for plant vigour under non-stress and the various stress conditions were detected in the two populations with positive as well as negative effects from the crop. CONCLUSION: As it was shown that the crop contributed QTLs with either a positive or a negative effect on plant vigour, we hypothesize that genomic regions exist where transgenes could preferentially be located in order to mitigate their persistence in natural populations through genetic hitchhiking.

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Crop wild relative populations of Beta vulgaris allow direct mapping of agronomically important genes.

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Crop wild relative populations of Beta vulgaris allow direct mapping of agronomically important genes.

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