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Mangin B.,French National Institute for Agricultural Research | Mangin B.,French National Center for Scientific Research | Sandron F.,French National Institute for Agricultural Research | Henry K.,S.A.S. Florimond Desprez Veuve and Fils | And 4 more authors.
Theoretical and Applied Genetics | Year: 2015

Key message: Genetic diversity in worldwide population of beets is strongly affected by the domestication history, and the comparison of linkage disequilibrium in worldwide and elite populations highlights strong selection pressure. Abstract: Genetic relationships and linkage disequilibrium (LD) were evaluated in a set of 2035 worldwide beet accessions and in another of 1338 elite sugar beet lines, using 320 and 769 single nucleotide polymorphisms, respectively. The structures of the populations were analyzed using four different approaches. Within the worldwide population, three of the methods gave a very coherent picture of the population structure. Fodder beet and sugar beet accessions were grouped together, separated from garden beets and sea beets, reflecting well the origins of beet domestication. The structure of the elite panel, however, was less stable between clustering methods, which was probably because of the high level of genetic mixing in breeding programs. For the linkage disequilibrium analysis, the usual measure (r2) was used, and compared with others that correct for population structure and relatedness (rS 2, rV 2, rVS 2). The LD as measured by r2 persisted beyond 10 cM within the elite panel and fell below 0.1 after less than 2 cM in the worldwide population, for almost all chromosomes. With correction for relatedness, LD decreased under 0.1 by 1 cM for almost all chromosomes in both populations, except for chromosomes 3 and 9 within the elite panel. In these regions, the larger extent of LD could be explained by strong selection pressure. © 2015, Springer-Verlag Berlin Heidelberg.


Klein E.,French National Center for Scientific Research | Brault V.,French National Institute for Agricultural Research | Klein D.,University of Strasbourg | Weyens G.,SESVanderHave | And 3 more authors.
Molecular Plant Pathology | Year: 2014

Plant infection by poleroviruses is restricted to phloem tissues, preventing any classical leaf rub inoculation with viral RNA or virions. Efficient virus inoculation to plants is achieved by viruliferous aphids that acquire the virus by feeding on infected plants. The use of promoter-driven infectious cDNA is an alternative means to infect plants and allows reverse genetic studies to be performed. Using Beet mild yellowing virus isolate 2ITB (BMYV-2ITB), we produced a full-length infectious cDNA clone of the virus (named BMYV-EK) placed under the control of the T7 RNA polymerase and the Cauliflower mosaic virus35S promoters. Infectivity of the engineered BMYV-EK virus was assayed in different plant species and compared with that of the original virus. We showed that invitro- or inplanta-derived transcripts were infectious in protoplasts and in whole plants. Importantly, the natural aphid vector Myzus persicae efficiently transmitted the viral progeny produced in infected plants. By comparing agroinoculation and aphid infection in a host range assay, we showed that the engineered BMYV-EK virus displayed a similar host range to BMYV-2ITB, except for Nicotiana benthamiana, which proved to be resistant to systemic infection with BMYV-EK. Finally, both the BMYV-EK P0 and the full-length clone were able to strongly interfere with post-transcriptional gene silencing. © 2013 BSPP AND JOHN WILEY & SONS LTD.


PubMed | S.A.S. Florimond Desprez Veuve and Fils, SESVanderHave and French National Institute for Agricultural Research
Type: Journal Article | Journal: TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik | Year: 2015

Genetic diversity in worldwide population of beets is strongly affected by the domestication history, and the comparison of linkage disequilibrium in worldwide and elite populations highlights strong selection pressure. Genetic relationships and linkage disequilibrium (LD) were evaluated in a set of 2035 worldwide beet accessions and in another of 1338 elite sugar beet lines, using 320 and 769 single nucleotide polymorphisms, respectively. The structures of the populations were analyzed using four different approaches. Within the worldwide population, three of the methods gave a very coherent picture of the population structure. Fodder beet and sugar beet accessions were grouped together, separated from garden beets and sea beets, reflecting well the origins of beet domestication. The structure of the elite panel, however, was less stable between clustering methods, which was probably because of the high level of genetic mixing in breeding programs. For the linkage disequilibrium analysis, the usual measure (r (2)) was used, and compared with others that correct for population structure and relatedness (r S (2) , r V (2) , r VS (2)). The LD as measured by r (2) persisted beyond 10 cM within the elite panel and fell below 0.1 after less than 2 cM in the worldwide population, for almost all chromosomes. With correction for relatedness, LD decreased under 0.1 by 1 cM for almost all chromosomes in both populations, except for chromosomes 3 and 9 within the elite panel. In these regions, the larger extent of LD could be explained by strong selection pressure.


Cosyn S.,SESVanderHave | Van Der Woude K.,SESVanderHave | Sauvenier X.,SESVanderHave | Evrard J.-N.,SESVanderHave
International Sugar Journal | Year: 2011

Twenty years ago, it would have been considered impossible growing sugar beet in tropical regions. The climate and the lack of know-how of local farmers were all limiting factors for the sugar beet crop. But times have changed, thanks to sugar beet seed breeders such as SESVanderHave. Significant efforts have been recently done to introduce sugar beet in regions where it has now a limited presence as a commercial crop. In field trials in India during 2007-2009 at ten sites beet yields of between 681 and 106 t/ha was achieved with sucrose content of 20% on average. However, perhaps the key obstacle to the rapid introduction to beet production and beet sugar processing in cane factories in tropics is the rather heavy capital investment to upgrade factories to allow them to process sugar beet. But the need to increase the sugar and ethanol production level for many developing countries, the need to diversify the crop portfolio to reduce production costs and to secure the supply in factories, as well as the extraordinary yield potential of sugar beet has increased the interest for the use of sugar beet in new markets. Therefore, SESVanderHave has invested heavily in the development of tropical sugar beet, especially in India, where the company has set up its own research programmes with local research institutes and farmers.


James L.C.,Brooms Barn | Bean K.M.R.,Brooms Barn | Grimmer M.K.,ADAS UK Ltd. | Barnes S.,SESVanderHave | And 2 more authors.
International Sugar Journal | Year: 2012

Sugar beet cultivars worldwide are susceptible to a wide range of pathogens and, with limited genetic host resistance available, the industry remains reliant on fungicide and insecticide treatments. Novel forms of genetic resistance to these pathogens are therefore highly sought. Our consortium has harnessed genetic diversity, from both wild and cultivated Beta germplasm, to identify novel genetic resistance to both viral and fungal pathogens. This study has employed a Quantitative Trait Locus (QTL) mapping approach to identify novel plant resistance (R) loci to foliar diseases such as Beet mild yellowing virus (BMYV), Erysiphe betae (powdery mildew) and Uromyces betae (rust) in a field environment. QTL mapping analysis identified that chromosome IV was of particular importance for conferring resistance to viral and fungal pathogens. Ultimately, this research aims to develop the genetic material and tools necessary to exploit natural 'broad spectrum' resistance of wild beets and enhance future elite sugar beet varieties suitable for UK conditions.


Adetunji I.,SESVanderHave
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik | Year: 2014

Linkage disequilibrium decay in sugar beet is strongly affected by the breeding history, and varies extensively between and along chromosomes, allowing identification of known and unknown signatures of selection. Genetic diversity and linkage disequilibrium (LD) patterns were investigated in 233 elite sugar beet breeding lines and 91 wild beet accessions, using 454 single nucleotide polymorphisms (SNPs) and 418 SNPs, respectively. Principal coordinate analysis suggested the existence of three groups of germplasm, corresponding to the wild beets, the seed parent and the pollen parent breeding pool. LD was investigated in each of these groups, with and without correction for genetic relatedness. Without correction for genetic relatedness, in the pollen as well as the seed parent pool, LD persisted beyond 50 centiMorgan (cM) on four (2, 3, 4 and 5) and three chromosomes (2, 4 and 6), respectively; after correction for genetic relatedness, LD decayed after <6 cM on all chromosomes in both pools. In the wild beet accessions, there was a strong LD decay: on average LD disappeared after 1 cM when LD was calculated with a correction for genetic relatedness. Persistence of LD was not only observed between distant SNPs on the same chromosome, but also between SNPs on different chromosomes. Regions on chromosomes 3 and 4 that harbor disease resistance and monogermy loci showed strong genetic differentiation between the pollen and seed parent pools. Other regions, on chromosomes 8 and 9, for which no a priori information was available with respect to their contribution to the phenotype, still contributed to clustering of lines in the elite breeding material.


PubMed | SESVanderHave
Type: Journal Article | Journal: TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik | Year: 2014

Linkage disequilibrium decay in sugar beet is strongly affected by the breeding history, and varies extensively between and along chromosomes, allowing identification of known and unknown signatures of selection. Genetic diversity and linkage disequilibrium (LD) patterns were investigated in 233 elite sugar beet breeding lines and 91 wild beet accessions, using 454 single nucleotide polymorphisms (SNPs) and 418 SNPs, respectively. Principal coordinate analysis suggested the existence of three groups of germplasm, corresponding to the wild beets, the seed parent and the pollen parent breeding pool. LD was investigated in each of these groups, with and without correction for genetic relatedness. Without correction for genetic relatedness, in the pollen as well as the seed parent pool, LD persisted beyond 50 centiMorgan (cM) on four (2, 3, 4 and 5) and three chromosomes (2, 4 and 6), respectively; after correction for genetic relatedness, LD decayed after <6 cM on all chromosomes in both pools. In the wild beet accessions, there was a strong LD decay: on average LD disappeared after 1 cM when LD was calculated with a correction for genetic relatedness. Persistence of LD was not only observed between distant SNPs on the same chromosome, but also between SNPs on different chromosomes. Regions on chromosomes 3 and 4 that harbor disease resistance and monogermy loci showed strong genetic differentiation between the pollen and seed parent pools. Other regions, on chromosomes 8 and 9, for which no a priori information was available with respect to their contribution to the phenotype, still contributed to clustering of lines in the elite breeding material.

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