Development and characterization of a new set of 164 polymorphic EST-SSR markers for diversity and breeding studies in rubber tree (Hevea brasiliensis Mull. Arg.)

Plant Breed.ISI Document Delivery No.: AJ4WPTimes Cited: 0Cited Reference Count: 31Cited References: Argout X, 2008, BMC GENOMICS, V9, DOI 10.1186/1471-2164-9-512 BESSE P, 1994, THEOR APPL GENET, V88, P199, DOI 10.1007/BF00225898 Conesa A, 2005, BIOINFORMATICS, V21, P3674, DOI 10.1093/bioinformatics/bti610 Cubry P, 2013, BMC GENOMICS, V14, DOI 10.1186/1471-2164-14-10 Ellis JR, 2007, HEREDITY, V99, P125, DOI 10.1038/sj.hdy.6801001 Feng SP, 2009, MOL BREEDING, V23, P85, DOI 10.1007/s11032-008-9216-0 Garcia D, 2011, PHYSIOL MOL PLANT P, V76, P126, DOI 10.1016/j.pmpp.2011.07.006 Gupta PK, 2005, PLANT MOL BIOL, V57, P461, DOI 10.1007/s11103-005-0257-z Gupta S, 2013, PLANT BREEDING, V132, P367, DOI 10.1111/pbr.12070 Kumar Yadav H., 2010, TREE GENET GENOMES, V7, P207 Le Guen V., 2008, EXPLORATION DIVERSIT Le Guen V, 2011, PLANT BREEDING, V130, P294, DOI 10.1111/j.1439-0523.2010.01774.x Le Guen V, 2009, TREE GENET GENOMES, V5, P673, DOI 10.1007/s11295-009-0218-9 Lespinasse D, 2000, THEOR APPL GENET, V100, P127, DOI 10.1007/s001220050018 Li DJ, 2012, BMC GENOMICS, V13, DOI 10.1186/1471-2164-13-192 Liu KJ, 2005, BIOINFORMATICS, V21, P2128, DOI 10.1093/bioinformatics/bti282 Ohyama A, 2009, MOL BREEDING, V23, P685, DOI 10.1007/s11032-009-9265-z Perovic D, 2009, MOL BREEDING, V23, P641, DOI 10.1007/s11032-009-9262-2 Perrier Xavier, 2003, P31 Perrier X., 2006, DARWIN SOFTWARE Pootakham W, 2012, PLANT BREEDING, V131, P555, DOI 10.1111/j.1439-0523.2012.01982.x Rafalski JA, 2010, CURR OPIN PLANT BIOL, V13, P174, DOI 10.1016/j.pbi.2009.12.004 Rozen S, 2000, Methods Mol Biol, V132, P365 SAITOU N, 1987, MOL BIOL EVOL, V4, P406 Seguin Marc, 2003, P277 Souza LM, 2009, CONSERV GENET RESOUR, V1, P75, DOI 10.1007/s12686-009-9018-7 Triwitayakorn K, 2011, DNA RES, V18, P471, DOI 10.1093/dnares/dsr034 Tyrka M, 2008, J APPL GENET, V49, P127, DOI 10.1007/BF03195605 Varshney RK, 2005, TRENDS BIOTECHNOL, V23, P48, DOI 10.1016/j.tibtech.2004.11.005 Vigouroux Y, 2005, GENETICS, V169, P1617, DOI 10.1534/genetics.104.032086 Wen Mingfu, 2010, BMC Res Notes, V3, P42, DOI 10.1186/1756-0500-3-42Cubry, Philippe Pujade-Renaud, Valerie Garcia, Dominique Espeout, Sandra Le Guen, Vincent Granet, Francoise Seguin, MarcFrench National Research Agency (Agence Nationale pour la Recherche; contrat ANR/Genoplante) [GPLA07017C]This work was performed as part of the CIRAD - Michelin collaborative project 'Genesalb' supported by a grant from the French National Research Agency (Agence Nationale pour la Recherche; contrat ANR/Genoplante no GPLA07017C). We thank the Montpellier Languedoc-Roussillon Grand plateau technique regional for hosting the SSR genotyping activities. ESTtik database was made available by the SouthGreen bioinformatics platform at http://southgreen.cirad.fr/. We thank Ronan Rivallan for technical help, Xavier Argout for computational procedures and data retrieving, Gerald Oliver for keeping some vegetal material in a greenhouse in Montpellier, Jean-Marc Thevenin and Fabien Doare for providing us with some fresh material from CIRAD's Pointe Combi Centre (French Guyana) collection.Wiley-blackwellHobokenDespite 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 10499 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

Pearl millet genomic vulnerability to climate change in West Africa highlights the need for regional collaboration

Climate change is already affecting agro-ecosystems and threatening food security by reducing crop productivity and increasing harvest uncertainty. Mobilizing crop diversity could be an efficient way to mitigate its impact. We test this hypothesis in pearl millet, a nutritious staple cereal cultivated in arid and low-fertility soils in sub-Saharan Africa. We analyze the genomic diversity of 173 landraces collected in West Africa together with an extensive climate dataset composed of metrics of agronomic importance. Mapping the pearl millet genomic vulnerability at the 2050 horizon based on the current genomic-climate relationships, we identify the northern edge of the current areas of cultivation of both early and late flowering varieties as being the most vulnerable to climate change. We predict that the most vulnerable areas will benefit from using landraces that already grow in equivalent climate conditions today. However, such seed-exchange scenarios will require long distance and trans-frontier assisted migrations. Leveraging genetic diversity as a climate mitigation strategy in West Africa will thus require regional collaboration

Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments

Pearl millet [Pennisetum glaucum (L.) R. Br., syn. Cenchrus americanus (L.) Morrone], is a staple food for over 90 million poor farmers in arid and semi-arid regions of sub-Saharan Africa and South Asia. We report the ~1.79 Gb genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. Resequencing analysis of 994 (963 inbreds of the highly cross-pollinated cultigen, and 31 wild accessions) provides insights into population structure, genetic diversity, evolution and domestication history. In addition we demonstrated the use of re-sequence data for establishing marker trait associations, genomic selection and prediction of hybrid performance and defining heterotic pools. The genome wide variations and abiotic stress proteome data are useful resources for pearl millet improvement through deploying modern breeding tools for accelerating genetic gains in pearl millet.publishersversionPeer reviewe

Structuration de la diversité génétique et analyse des patrons de déséquilibre de liaison de l'espèce Coffea canephora Pierre ex. Froehner

The search for associations between molecular markers and variation of traits with agronomic importance is a main goal of Marker-Assisted Selection development, especially for perennials species. Knowledge of genetic diversity and structure is a prerequisite for such studies. In the same way, knowledge of structure and extant of Linkage Disequilibrium in populations is an important task. We strengthen and fine-tuned previously described genetic structure and diversity of Coffea canephora Pierre in order to assess the capabilities of association mapping based approaches for this species. We laid the basis for rapid characterization of genetic resources with the help of microsatellite markers and clarify the genetic origin of a previously nonstudied population. Future development of core-collections will benefit from these results. Structure and extent of Linkage Disequilibrium was determined at different scales and for different populations or genetic groups, with the help of 108 genome wide markers, giving the opportunities to identify suitable populations for the 2 assocation mapping categories, genome-wide scan and candidate region. A first try of association mapping confirms the important capabilities of such approaches for our species. Implications of genetic diversity and structure as well as Linkage Disequilibrium structure for future breeding purposes are discussedLa recherche d'associations entre marqueurs moléculaires et les variations de caractères d'intérêt agronomique est un enjeu majeur du développement de la sélection assistée par marqueurs, notamment pour des espèces pérennes. La connaissance de la diversité génétique et de la structure de celle-ci est un préalable indispensable à la mise en place de telles études. Au même titre, la connaissance de l'étendue et de l'intensité du déséquilibre de liaison au sein des populations considérées est également nécessaire. Nous avons donc entrepris de confirmer et de préciser la diversité et la structure génétique de Coffea canephora Pierre afin d'évaluer les potentialités d'études d'association sur cette espèce. Nous avons posé les bases d'une caractérisation rapide des collections de ressources génétiques de cette espèce à l'aide de marqueurs microsatellites et précisé l'origine génétique d'une population jusqu'à présent non étudiée. Cette base pourra également servir au développement de futures cores-collections. L'évaluation de la structure et de l'étendue du déséquilibre de liaison à différentes échelles et au niveau de différentes populations ou groupes de diversité à l'aide de 108 marqueurs répartis sur l'ensemble du génome nous a permis de proposer des populations utilisables pour les 2 types d'approches de génétique d'associations, scan génome entier ou région candidate. Un premier essai d'étude d'association a montré les potentialités importantes de ces approches pour notre espèce. Les implications de l'importance de la diversité génétique et de sa structure ainsi que de la structure du déséquilibre de liaison au sein de nos populations pour l'amélioration sont discutées