Courtois B.,UMR AGAP |
Frouin J.,UMR AGAP |
Greco R.,Parco Tecnologico Padano |
Bruschi G.,Italian Agricultural Research Council |
And 14 more authors.
Crop Science | Year: 2012
In southern Europe, rice (Oryza sativa L.) is grown as an irrigated crop in river deltas where it plays an important role in the agroecological equilibrium through soil desalinization. In these regions, rice is at the northern limit of its natural area of adaptation. Special cultivars are needed for these challenging conditions. Using modelbased and distance-based approaches, we analyzed the genetic structure of the European Rice Germplasm Collection (ERGC), which is composed of 425 accessions, using 25 simple sequence repeat (SSR) markers. We compared it with a reference set of 50 accessions that are representative of the diversity of O. sativa. Most of the ERGC accessions (89%) clustered with japonica types. The ERGC japonica accessions were classified into three groups: one group close to rice types of tropical origin that are found in the United States and Argentina and two groups of temperate origin showing less differentiation. The three japonica groups could be characterized according to their grain type and maturity class, which are the most strongly selected traits in European breeding programs. We extracted a core collection of 250 japonica accessions and characterized it using 70 single nucleotide polymorphisms (SNPs). The SSR and SNP dissimilarity matrices coincided reasonably well and for the best-supported structure, the percentages of admixture were highly correlated. The core collection can be used as an association panel to search for alleles of interest for temperate areas or as a training population for genomic selection. © Crop Science Society of America.
Garcia-Lor A.,Instituto Valenciano Of Investigaciones Agrarias Ivia |
Curk F.,Instituto Valenciano Of Investigaciones Agrarias Ivia |
Curk F.,French National Institute for Agricultural Research |
Snoussi-Trifa H.,Tunisian National Agronomic Research Institute INRAT |
And 5 more authors.
Annals of Botany | Year: 2013
Background and AimsDespite differences in morphology, the genera representing 'true citrus fruit trees' are sexually compatible, and their phylogenetic relationships remain unclear. Most of the important commercial 'species' of Citrus are believed to be of interspecific origin. By studying polymorphisms of 27 nuclear genes, the average molecular differentiation between species was estimated and some phylogenetic relationships between 'true citrus fruit trees' were clarified.MethodsSanger sequencing of PCR-amplified fragments from 18 genes involved in metabolite biosynthesis pathways and nine putative genes for salt tolerance was performed for 45 genotypes of Citrus and relatives of Citrus to mine single nucleotide polymorphisms (SNPs) and indel polymorphisms. Fifty nuclear simple sequence repeats (SSRs) were also analysed.Key ResultsA total of 16 238 kb of DNA was sequenced for each genotype, and 1097 single nucleotide polymorphisms (SNPs) and 50 indels were identified. These polymorphisms were more valuable than SSRs for inter-taxon differentiation. Nuclear phylogenetic analysis revealed that Citrus reticulata and Fortunella form a cluster that is differentiated from the clade that includes three other basic taxa of cultivated citrus (C. maxima, C. medica and C. micrantha). These results confirm the taxonomic subdivision between the subgenera Metacitrus and Archicitrus. A few genes displayed positive selection patterns within or between species, but most of them displayed neutral patterns. The phylogenetic inheritance patterns of the analysed genes were inferred for commercial Citrus spp.ConclusionsNumerous molecular polymorphisms (SNPs and indels), which are potentially useful for the analysis of interspecific genetic structures, have been identified. The nuclear phylogenetic network for Citrus and its sexually compatible relatives was consistent with the geographical origins of these genera. The positive selection observed for a few genes will help further works to analyse the molecular basis of the variability of the associated traits. This study presents new insights into the origin of C. sinensis. © 2012 The Author. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved.
Blomme G.,Commodity Systems and Genetic Resources Programme |
Ploetz R.,University of Florida |
Jones D.,Droitwich Spa |
De Langhe E.,Catholic University of Leuven |
And 9 more authors.
Annals of Applied Biology | Year: 2013
The genus Musa is not native to Africa. It evolved in tropical Asia, from southwest India eastward to the island of New Guinea. There is a growing circumstantial evidence which suggests that the East African Highland banana and the tropical lowland plantain were cultivated on the African continent since before 1 AD. It is also probable that ABB cooking and AB and AAB dessert cultivars were brought to the continent from India by Arabian traders from 600 AD, and that these were disseminated throughout East Africa. During the colonial era, the main centres of distribution for banana cultivars were botanical gardens, such as Zomba in Malawi, Entebbe in Uganda and Amani in Tanzania. It appears that the very early introductions of Highland banana and plantain arrived in Africa as a relatively clean material without the conspicuous pests and diseases that affect them in Asia. In contrast, several devastating problems now impact the crop in Africa, including nematodes, the borer weevil and diseases, most notably banana bunchy top, banana streak, Sigatoka leaf spots, Xanthomonas wilt and Fusarium wilt. We (a) provide chronological overviews of the first reports/observations of different Musa pests and pathogens/diseases in Africa, (b) highlight specific examples of when a pest or pathogen/disease was introduced via planting materials and (c) give recent examples of how the pests and pathogens spread to new regions via planting materials. In total, these production constraints threaten banana and plantain production throughout the continent and impact those who can ill afford lost production, the small-holder producer. Our intent in this review is to highlight the significance of these problems and the great importance that infested planting materials have played in their development. © 2012 Association of Applied Biologists.
PubMed | UMR AGAP
Type: | Journal: Frontiers in plant science | Year: 2016
Tetraploidy modifies root anatomy which may lead to differentiated capacity to uptake and transport mineral elements. This work provides insights into physiological and molecular characters involved in boron (B) toxicity responses in diploid (2x) and tetraploid (4x) plants of Carrizo citrange (Citrus sinensis L. Osb. Poncirus trifoliata L. Raf.), a widely used citrus rootstock. With B excess, 2x plants accumulated more B in leaves than 4x plants, which accounted for their higher B uptake and root-to-shoot transport rates. Ploidy did not modify the expression of membrane transporters NIP5 and BOR1 in roots. The cellular allocation of B excess differed between ploidy levels in the soluble fraction, which was lower in 4x leaves, while cell wall-linked B was similar in 2x and 4x genotypes. This correlates with the increased damage and stunted growth recorded in the 2x plants. The 4x roots were found to have fewer root tips, shorter specific root length, longer diameter, thicker exodermis and earlier tissue maturation in root tips, where the Casparian strip was detected at a shorter distance from the root apex than in the 2x roots. The results presented herein suggest that the root anatomical characters of the 4x plants play a key role in their lower B uptake capacity and root-to-shoot transport.Tetraploidy enhances B excess tolerance in citrange CarrizoExpression of NIP5 and BOR1 transporters and cell wall-bounded B are similar between ploidiesB tolerance is attributed to root anatomical modifications induced by genome duplicationThe rootstock 4x citrange carrizo may prevent citrus trees from B excess.
Lachenaud P.,UPR 106 |
Fouet O.,UMR AGAP |
Couturier C.,British Petroleum |
Lanaud C.,UMR AGAP
Genetic Resources and Crop Evolution | Year: 2015
The wild cacao trees (Theobroma cacao L.) of French Guiana were investigated during several survey and collecting expeditions between 1985 and 1995. The many studies made of this material showed it to be highly original. New surveys were undertaken in May 2012 in south-eastern French Guiana, in the upper reaches of the Tanpok River and some of its tributaries, in order to enrich the cacao collection preserved at the Paracou-Combi site at Sinnamary (French Guiana). One of the aims of the expedition was to determine whether the populations from the upper-Tanpok were original and different from those already represented in the collection. From the 2012 mission four populations were identified. The material collected was described (location, tree and pod morphology). Genetic diversity of the collected genotypes and various controls was studied using SSR markers. The collected trees belonged to the “Guiana” group, but did not reveal any distinctive feature within the group. The genetic diversity encountered was low (He = 0.124). The outcome of these surveys is positive, since new populations were located. In order to preserve and carry out phenotypical studies (agro-morphology) on the new material collected, a plot was planted at Paracou-Combi in January 2013. © 2015 Springer Science+Business Media Dordrecht
Vandenbroucke H.,CIRAD - Agricultural Research for Development |
Mournet P.,CIRAD - Agricultural Research for Development |
Malapa R.,VARTC |
Glaszmann J.-C.,CIRAD - Agricultural Research for Development |
And 2 more authors.
Genome | Year: 2015
Kava (Piper methysticum) is a major cash crop in the Pacific. The aim of this study was to assess genetic variation among 103 accessions of kava using SSRs and DArTs. Genetic structure was determined using clustering analyses (WPGMA) and principal coordinate analyses (PCA). Thirteen SSR primers and 75 DArT markers were found polymorphic, and the two types of markers generated similar clustering patterns. Genetic distances ranged from 0 to 0.65 with an average of 0.24 using SSRs and from 0 to 0.64 with an average of 0.24 using DArT. Eleven genotypes were identified with SSR while 28 genotypes were identified with DArT markers. By combining the two sets of markers, a total of only 30 distinct genotypes were observed. In the Vanuatu archipelago, noble cultivars originating from different islands clustered together within a very narrow genetic base despite their diversity of morphotypes. SSR and DArT fingerprints allowed the identification of kava cultivars unsuitable for consumption, so called two-days, and clearly differentiated the wild types classified as P. methysticum var. wichmannii from the cultivars as var. methysticum. Molecular data reveals that all noble cultivars evolved by the predominance of clonal selection. Although they are represented by clearly distinct morphotypes, these cultivars are genetically vulnerable and their potential to adapt to forthcoming changes is limited. These newly developed markers provide high resolution and will be useful for kava diversity analyses and quality assessment. © 2015 Published by NRC Research Press.
Gwali S.,Makerere University |
Gwali S.,National Forestry Resources Research Institute NaFORRI |
Vaillant A.,UMR AGAP |
Nakabonge G.,Makerere University |
And 4 more authors.
Forests Trees and Livelihoods | Year: 2015
Shea trees (Vitellariaparadoxa C. F. Gaertn.) are classified locally into several folk or ethno-varieties by farmers in Uganda. It is, however, not clear whether this folk classification is supported by genetic differentiation between ethno-varieties. Genetically linked traits from folk classification are useful in conservation and breeding programmes. A total of 118 individual shea trees constituting 28 ethno-varieties sampled from three farming systems of Uganda were analysed using microsatellite markers. The number of alleles amplified per microsatellite locus ranged from 6 to 13 with an average of 9.5, with a total of 106 alleles identified. Observed (Ho) and expected heterozygosity (He) per locus ranged from 0.366 to 0.934 and 0.580 to 0.840, respectively. Mean Ho and He values for all loci across all ethno-varieties were 0.633 and 0.727, respectively. Analysis of molecular variance indicated that most of the variation (86.28%) occurred within individual trees; 11.25% was found among individual trees within ethno-varieties while 2.47% was found among ethno-varieties. The in-breeding index (f = 0.130), fixation index (θP = 0.025), gene flow value (Nm = 6.56) and cluster analysis show that all shea tree ethno-varieties were a single out-crossing population with very low genetic differentiation and high gene flow. The low differentiation in shea tree ethno-varieties was most likely due to the utilization of non-genetic traits in folk classification. However, while ethno-variety genetic structure was very weak, overall spatial population structure indicated the presence of three populations (West Nile, Northern and Teso). The West Nile population was more distantly related to the other two most likely due to isolation barriers such as the Rift Valley, Lake Albert and River Nile. © 2015 Taylor & Francis.
Cubry P.,CIRAD - Agricultural Research for Development |
Cubry P.,Michelin |
Pujade-Renaud V.,UMR AGAP |
Pujade-Renaud V.,University Blaise Pascal |
And 5 more authors.
Plant Breeding | Year: 2014
Despite its economic importance and recent genome release, the need for molecular tools for Hevea brasiliensis is high. In the frame of a disease resistance study, EST sequences were retrieved from public database or generated by sequencing SSH libraries. Sequences were trimmed and microsatellite motifs searched using an ad hoc bioinformatic pipeline, and pairs of primers for the amplification of candidate markers were generated. We found a total of 10 499 unigenes from both sources of sequences, and 673 microsatellites motifs were detected using the default parameters of the pipeline. Two hundred sixty-four primer pairs were tested and 226 (85.6%) successfully amplified. Out of the amplified candidate markers, 164 exhibited polymorphism. Relationships based on dendrograms using simple matching index and diversity statistics based on EST-SSRs were compared with Genomic SSRs, showing the potentialities of EST-derived microsatellites for resistance studies but also for population genetics approaches. © 2014 Blackwell Verlag GmbH.
Ruiz M.,Instituto Valenciano Of Investigaciones Agrarias |
Quinones A.,Instituto Valenciano Of Investigaciones Agrarias |
Martinez-Alcantara B.,Instituto Valenciano Of Investigaciones Agrarias |
Aleza P.,Instituto Valenciano Of Investigaciones Agrarias |
And 4 more authors.
Frontiers in Plant Science | Year: 2016
Tetraploidy modifies root anatomy which may lead to differentiated capacity to uptake and transport mineral elements. This work provides insights into physiological and molecular characters involved in boron (B) toxicity responses in diploid (2x) and tetraploid (4x) plants of Carrizo citrange (Citrus sinensis L. Osb. × Poncirus trifoliata L. Raf.), a widely used citrus rootstock. With B excess, 2x plants accumulated more B in leaves than 4x plants, which accounted for their higher B uptake and root-to-shoot transport rates. Ploidy did not modify the expression of membrane transporters NIP5 and BOR1 in roots. The cellular allocation of B excess differed between ploidy levels in the soluble fraction, which was lower in 4x leaves, while cell wall-linked B was similar in 2x and 4x genotypes. This correlates with the increased damage and stunted growth recorded in the 2x plants. The 4x roots were found to have fewer root tips, shorter specific root length, longer diameter, thicker exodermis and earlier tissue maturation in root tips, where the Casparian strip was detected at a shorter distance from the root apex than in the 2x roots. The results presented herein suggest that the root anatomical characters of the 4x plants play a key role in their lower B uptake capacity and root-to-shoot transport. Highlights Tetraploidy enhances B excess tolerance in citrange Carrizo Expression of NIP5 and BOR1 transporters and cell wall-bounded B are similar between loidies B tolerance is attributed to root anatomical modifications induced by genome duplication The rootstock 4x citrange carrizo may prevent citrus trees from B excess. © 2016 Ruiz, Quiñones, Martínez-Alcántara, Aleza, Morillon, Navarro, Primo-Millo and Martínez-Cuenca.
PubMed | Indian International Crops Research Institute for the Semi Arid Tropics, Center Detudes Regional Pour Iamelioration Of Iadaptation Secheressethies, University of Yaounde I, Center Detudes Regional Pour Iamelioration Of Iadaptation Secheresse Thies and 2 more.
Type: | Journal: Frontiers in plant science | Year: 2016
Cultivated peanut and synthetics are allotetraploids (2