Genetic diversity among air yam (dioscorea bulbifera) varieties based on single sequence repeat markers

Dioscorea is the largest genus in the Dioscoreaceae family, and includes a number of economically important species including the air yam, D. bulbifera L. This study aimed to develop new single sequence repeat primers and characterize the genetic diversity of local varieties that originated in several municipalities of Brazil. We developed an enriched genomic library for D. bulbifera resulting in seven primers, six of which were polymorphic, and added four polymorphic loci developed for other Dioscorea species. This resulted in 10 polymorphic primers to evaluate 42 air yam accessions. Thirty-three alleles (bands) were found, with an average of 3.3 alleles per locus. The discrimination power ranged from 0.113 to 0.834, with an average of 0.595. Both principal coordinate and cluster analyses (using the Jaccard Index) failed to clearly separate the accessions according to their origins. However, the 13 accessions from Conceição dos Ouros, Minas Gerais State were clustered above zero on the principal coordinate 2 axis, and were also clustered into one subgroup in the cluster analysis. Accessions from Ubatuba, São Paulo State were clustered below zero on the same principal coordinate 2 axis, except for one accession, although they were scattered in several subgroups in the cluster analysis. Therefore, we found little spatial structure in the accessions, although those from Conceição dos Ouros and Ubatuba exhibited some spatial structure, and that there is a considerable level of genetic diversity in D. bulbifera maintained by traditional farmers in Brazil152CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQFUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESPnão tem2007/04805-

Leaf-, Panel- And Latex-expressed Sequenced Tags From The Rubber Tree (hevea Brasiliensis) Under Cold-stressed And Suboptimal Growing Conditions: The Development Of Gene-targeted Functional Markers For Stress Response

Hevea brasiliensis is a native species of the Amazon Basin of South America and the primary source of natural rubber worldwide. Due to the occurrence of South American Leaf Blight disease in this area, rubber plantations have been extended to suboptimal regions. Rubber tree breeding is time-consuming and expensive, but molecular markers can serve as a tool for early evaluation, thus reducing time and costs. In this work, we constructed six different cDNA libraries with the aim of developing gene-targeted molecular markers for the rubber tree. A total of 8,263 reads were assembled, generating 5,025 unigenes that were analyzed; 912 expressed sequence tags (ESTs) represented new transcripts, and two sequences were highly up-regulated by cold stress. These unigenes were scanned for microsatellite (SSR) regions and single nucleotide polymorphisms (SNPs). In total, 169 novel EST-SSR markers were developed; 138 loci were polymorphic in the rubber tree, and 98 % presented transferability to six other Hevea species. Locus duplication was observed in H. brasiliensis and other species. Additionally, 43 SNP markers in 13 sequences that showed similarity to proteins involved in stress response, latex biosynthesis and developmental processes were characterized. cDNA libraries are a rich source of SSR and SNP markers and enable the identification of new transcripts. The new markers developed here will be a valuable resource for linkage mapping, QTL identification and other studies in the rubber tree and can also be used to evaluate the genetic variability of other Hevea species, which are valuable assets in rubber tree breeding. © 2014 The Author(s)

Microsatellite Marker Development For The Rubber Tree (hevea Brasiliensis): Characterization And Cross-amplification In Wild Hevea Species

Background: The rubber tree (Hevea brasiliensis) is native to the Amazon region and it is the major source of natural rubber in the world. Rubber tree breeding is time-consuming and expensive. However, molecular markers such as microsatellites can reduce the time required for these programs. This study reports new genomic microsatellite markers developed and characterized in H. brasiliensis and the evaluation of their transferability to other Hevea species. Findings: We constructed di- and trinucleotide-enriched libraries. From these two libraries, 153 primer pairs were designed and initially evaluated using 9 genotypes of H. brasiliensis. A total of 119 primer pairs had a good amplification product, 90 of which were polymorphic. We chose 46 of the polymorphic markers and characterized them in 36 genotypes of H. brasiliensis. The expected and observed heterozygosities ranged from 0.1387 to 0.8629 and 0.0909 to 0.9167, respectively. The polymorphism information content (PIC) values ranged from 0.097 to 0.8339, and the mean number of alleles was 6.4 (217). These 46 microsatellites were also tested in 6 other Hevea species. The percentage of transferability ranged from 82% to 87%. Locus duplication was found in H. brasiliensis and also in 5 of other species in which transferability was tested. Conclusions: This study reports new microsatellite markers for H. brasiliensis that can be used for genetic linkage mapping, quantitative trait loci identification and marker- assisted selection. The high percentage of transferability may be useful in the evaluations of genetic variability and to monitor introgression of genetic variability from different Hevea species into breeding programs. © 2012 Mantello et al.; licensee BioMed Central Ltd.5Pires, J.M., Secco, R.S., Gomes, J.I., (2002) Taxonomia e Fitogeografia das Seringueiras Hevea Spp, p. 103. , Belém: Embrapa Amazônia OrientalGonçalves, P., Cardoso, M., Ortolani, A.A., Origem, variabilidade e domesticação da HeveaUma revisão (1990) Pesquisa Agropecuária Brasileira, 25 (2), pp. 135-156. , 22950597Clément-Demange, A., Priyadarshan, P.M., Thuy Hoa, T.T., Venkatachalam, P., Hevea Rubber Breeding and Genetics (2007) Plant Breeding Reviews, pp. 3h. , New Jersey: John Wiley & Sons, Inc Janick J Volume 29 4Cornish, K., Similarities and differences in rubber biochemistry among plant species (2001) Phytochem, 57, pp. 1123-1134. , 10.1016/S0031-9422(01)00097-8Webster, C.C., Baulkwill, W.J., (1989) Rubber Longman Edn, , Longman Singapore Publishers LtdFeng, S.P., Li, W.G., Huang, H.S., Wang, J.Y., Wu, Y.T., Development, characterization and cross-species/genera transferability of EST-SSR markers for rubber tree (Hevea brasiliensis) (2009) Mol Breeding, 23, pp. 85-97. , 10.1007/s11032-008-9216-0Kalia, R.K., Rai, M.K., Kalia, S., Singh, R., Dhawan, A.K., Microsatellite markers: An overview of the recent progress in plants (2011) Euphytica, 177, pp. 309-334. , 10.1007/s10681-010-0286-9Chevallier, M.H., Genetic variability of Hevea brasiliensis germplasm using isozyme markers (1988) J Nat Rubber Res, 3, pp. 42-53Besse, P., Seguin, M., Lebrun, P., Chevallier, M.H., Nicolas, D., Lanaud, C., Genetic diversity among wild and cultivated populations of Hevea brasiliensis assessed by nuclear RFLP analysis (1994) Theor Appl Genet, 88, pp. 199-207Le Guen, V., Gay, C., Xiong, T.C., Souza, L.M., Rodier-Goud, M., Seguin, M., Development and characterization of 296 new polymorphic microsatellite markers for rubber tree (Hevea brasiliensis) (2011) Plant Breeding, 130, pp. 294-296. , 10.1111/j.1439-0523.2010.01774.xLespinasse, D., Rodier-Goud, M., Grivet, L., Leconte, A., Legnate, H., Seguin, M., A saturated genetic linkage map of rubber tree (Hevea spp.) based on RFLP, AFLP, microsatellite, and isozyme markers (2000) Theor Appl Genet, 100, pp. 127-138. , 10.1007/s001220050018Le Guen, V., Garcia, D., Mattos, C.R.R., Doaré, F., Lespinasse, D., Seguin, M., Bypassing of a polygenic Microcyclus ulei resistance in rubber tree, analyzed by QTL detection (2007) New Phytologist, 173, pp. 335-345. , 10.1111/j.1469-8137.2006.01911.x 17204080Le Guen, V., Lespinasse, D., Oliver, G., Rodier-Goud, M., Pinard, F., Seguin, M., Molecular mapping of genes conferring field resistance to South American Leaf Blight (Microcyclus ulei) in rubber tree (2003) Theor Appl Genet, 108, pp. 160-167. , 10.1007/s00122-003-1407-9 14504743Lespinasse, D., Grivet, L., Troispoux, V., Rodier-Goud, M., Pinard, F., Seguin, M., Identification of QTLs involved in the resistance to South American leaf blight (Microcyclus ulei) in the rubber tree (2000) Theor Appl Genet, 100, pp. 975-984. , 10.1007/s001220051379Souza, L.M., Mantello, C.C., Santos, M.O., Gonçalves, P.O., Souza, A.P., Microsatellites from rubber tree (Hevea brasiliensis) for genetic diversity analysis and cross amplification in six Hevea wild species (2009) Cons Genet Res, 1, pp. 75-79. , 10.1007/s12686-009-9018-7Yu, F., Wang, B.H., Feng, S.P., Wang, J.Y., Li, W.G., Wu, Y.T., Development, characterization, and cross-species/genera transferability of SSR markers for rubber tree (Hevea brasiliensis) (2010) Plant Cell Rep, 30, pp. 335-344. , 20960206Morgante, M., Hanafey, M., Powell, W., Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes (2002) Nat Genet, 30, pp. 194-200. , 10.1038/ng822 11799393Marconi, T.G., Costa, E.A., Miranda, H., Mancini, M.C., Cardoso-Silva, C.B., Oliveira, K.M., Pinto, L.R., Souza, A.P., Functional markers for gene mapping and gnetic diversity studies in sugarcane (2011) BMC Research Notes, 4, p. 264. , 10.1186/1756-0500-4-264 21798036Scott, K.D., Eggler, P., Seaton, G., Rossetto, M., Ablett, E.M., Lee, L.S., Henry, R.J., Analysis of SSRs derived from grape ESTs (2000) Theor Appl Genet, 100, pp. 723-726. , 10.1007/s001220051344Thiel, T., Michalek, W., Varshney, R.K., Graner, A., Exploiting EST databases for the development and characterization of genederived SSR-markers in barley (Hordeum vulgare L.) (2003) Theor Appl Genet, 106, pp. 411-422. , 12589540Han, Z., Wang, C., Song, X., Guo, W., Gou, J., Li, C., Chen, X., Zhang, T., Characteristics, development and mapping of Gossypium hirsutum derived EST-SSRs in allotetraploid cotton (2006) Theor Appl Genet, 112, pp. 430-439. , 10.1007/s00122-005-0142-9 16341684La Rota, M., Kantety, R.V., Yu, J.K., Sorrells, M.E., Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley (2005) BMC Genomics, 6, p. 2. , 10.1186/1471-2164-6-2 15631628Chen, C., Zhou, P., Choi, Y.A., Huang, S., Gmitter, F.G., Mining and characterizing microsatellites from citrus ESTs (2006) Theor Appl Genet, 112, pp. 1248-1257. , 10.1007/s00122-006-0226-1 16474971Fraser, L.G., Harvey, C.F., Crowhurst, R.N., De Silva, H.N., EST-derived microsatellites from Actinidia species and their potential for mapping (2004) Theor Appl Genet, 108, pp. 1010-1016. , 10.1007/s00122-003-1517-4 15067386Aggarwal, R.K., Hendre, P.S., Varshney, R.K., Bhat, P.R., Krishnakumar, V., Singh, L., Identification, characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species (2007) Theor Appl Genet, 114, pp. 359-372. , 10.1007/s00122-006-0440-x 17115127Jung, S., Albert, A., Jesudurai, C., Tomkins, J., Main, D., Frequency, type, distribution and annotation of simple sequence repeats in Rosaceae ESTs (2005) Funct Integr Genomics, 5, pp. 136-143. , 10.1007/s10142-005-0139-0 15761705Saha, T., Roy, C.B., Nazeer, M.A., Microsatellite variability and its use in the characterization of cultivated clones of Hevea brasiliensis (2005) Plant Breeding, 124, pp. 86-92. , 10.1111/j.1439-0523.2004.01053.xPerry, A.B., Chromosome Number and Phylogenetic Relationships in the Euphorbiaceae (1943) Am J Bot, 30, pp. 527-543. , 10.2307/2437291Leitch, A.R., Lim, K.Y., Leitch, I.J., Oneill, M., Chye, M., Low, F., Molecular cytogenetic studies in rubber, Hevea brasiliensis Muell. Arg. (Euphorbiaceae) (1998) Genome, 41, pp. 464-467Majumder, S.K., Chromosome studies of some species of Hevea (1964) J. Rubber Res. Inst. Malays, 18, pp. 269-273Ong, S.N., Chromosome morphology at pachytene stage in Hevea brasiliensis: A preliminary report (1975) Proceedings of the International Rubber Conference, pp. 3-12. , Kuala Lumpur: Rubber Research Institue of Malaysia Sripathi BBouharmont, J., Recherches taxonomiques et caryologiques chez quelques espèces du genre Hevea (1960) Série Scientifique, p. 64. , Volume 85 22953359Doyle, J.J., Doyle, J.L., A rapid DNA isolation procedure for small quantities of fresh leaf tissue (1987) Phytochem Bull, 19, pp. 11-15Billotte, N., Lagoda, P., Risterucci, A.M., Baurens, F.C., Microsatellite-enriched libraries: Applied methodology for the development of SSR markers in tropical crops (1999) Fruits, 54, pp. 277-288Temnykh, S., Declerck, G., Lukashova, A., Lipovich, L., Cartinhour, S., McCouch, S., 2001. Computational and experimental analysis of microsatellites in rice (Oryza sativaL.): Frequency, length variation, transposon associations, and genetic marker potential (2001) Genome Res, 11, pp. 1441-1452. , 10.1101/gr.184001 11483586Untergasser, A., Nijveen, H., Rao, X., Bisseling, T., Geurts, R., Leunissen, J.A.M., Primer3Plus, an enhanced web interface to Primer3 (2007) Nucleic Acids Res, 35, p. 23. , 71-W74Creste, S., Tulmann-Neto, A., Figueira, A., Detection of single repeat polymorphisms in denaturing polyacrilamide sequencing gels by silver staining (2001) Plant Mol Biol Rep, 19, pp. 229-306Miller, M.P., (1997) Tools for Population Genetic Analysis (TFPGA) 1.3: A Windows Program for the Analysis of Allozyme and Molecular Population Genetic Data, , Computer Software distributed by the autho

Microsatellites From Rubber Tree (hevea Brasiliensis) For Genetic Diversity Analysis And Cross-amplification In Six Hevea Wild Species

Hevea brasiliensis is native to the Amazonian rain forest and an important source of natural rubber. Twenty seven polymorphic microsatellite loci were isolated and characterized from a GA-CA enriched genomic library of H. brasiliensis. The number of alleles ranged from 2 to 20. The observed and expected heterozygosity ranged from 0.13 to 0.88 and from 0.00 to 0.89, respectively. Cross-species amplification of the markers developed for H. brasiliensis was successful in the wild Hevea species H. guianensis, H. rigidifolia, H. nitida, H. pauciflora, H. benthamiana and H. camargoana. The data indicated a high degree of sequence homology in the microsatellite flanking regions of these species. The developed SSR loci are a potential powerful tool for studies of population genetics, genetic diversity and gene flow among Hevea species. © Springer Science+Business Media B.V. 2009.117579Billotte, N., Lagoda, P.J.R., Risterucci, A.M., Baurens, F.C., Microsatellite-enriched libraries: Applied methodology for the development of SSR markers in tropical crops (1999) Fruits, 54, pp. 277-288Brondani, R.P.V., Brondani, C., Tarchini, R., Grattapaglia, D., Development, characterization and mapping of microsatellite markers in Eucalyptus grandis and E. urophylla (1998) Theor Appl Genet, 97, pp. 816-827Cataldo, F., Guayule rubber: A new possible world scenario for the production of natural rubber (2000) Prog Rubber Plast Technol, 16, pp. 31-59Choumane, W., Winter, P., Weigand, F., Kahl, G., Conservation and variability of sequence-tagged microsatellite sites (STMSs) from chickpea (Cicer aerietinum L.) within the genera Cicer (2000) Theor Appl Genet, 101, pp. 269-278Clement-Demange, A., Legnate, H., Seguin, M., Carron, M.P., Le Guen, V., Chapuset, T., Rubber tree (2000) Tropical Plant Breeding, pp. 455-480. , In: Charrier A, Jacquot M, Hamon S, Nicolas D et al (eds), Collection Reperes, CIRAD-ORSTOM, Montpellier, FranceCornish, K., Similarities and differences in rubber biochemistry among plant species (2001) Phytochem, 57, pp. 1123-1134Creste, S.A., Detection of single sequence repeat polymorphism in denaturating polyacrylamide sequencing gels by silver staining (2001) Plant Mol Biol Rep, 19, pp. 299-306Decroocq, V., Fave, M.G., Hagen, L., Bordenave, L., Decroocq, S., Development and transferability of apricot and grape EST microsatellite markers across taxa (2003) Theor Appl Genet, 106, pp. 912-922Doyle, J.J., Doyle, J.L., A rapid DNA isolation procedure for small quantities of fresh leaf tissue (1987) Phytochem Bull, 19, pp. 11-15Lespinasse, D., Identification of QTLs involved in the resistance to South American Leaf Blight (Microcyclos ulei) in the rubber tree (2000) Theor Appl Genet, 100, pp. 975-984Lorieux, M., Ndjiondjop, M.-N., Ghesquière, A., A first interspecific Oryza sativa & Oryza glaberrima microsatellite-based genetic linkage map (2000) Theor Appl Genet, 100, pp. 593-601Miller, M.P., Tools for population genetic analysis (TFPGA) 1.3 (1997) A Windows Program for the Analysis of Allozyme and Molecular Population Genetic Data, , Computer software distributed by authorNodari, R.O., Ducroquet, J.P., Guerra, M.P., Meler, K., Genetic variability of Feijoa sellowiana germplasm (1997) Acta Hort, 452, pp. 41-46Pires, J.M., Secco, R.S., Gomes, J.I., (2002) Taxonomia E Fitogeografia Das Seringueiras Hevea Spp, p. 103. , Embrapa Amazônia Oriental, BelémSeguin, M., Hevea molecular genetics (1996) Plant Rech Dev, 3, pp. 77-88Yeh, F.C., Rong-Cai, Y., Boyle, T., (1998) POPGENE, , Edmonton. University of Alberta, Center for InternationalForestry Research, Alberta, CanadaZucchi, M.I., Brondani, R.P.V., Pinheiro, J.B., Chaves, L.J., Coelho, A.S.G., Vencovsky, R., Genetic structure and gene flow in Eugenia dysenterica DC in the Brazilian Cerrado utilizing SSR markers (2003) Genet Mol Biol, 26, pp. 449-45

Microsatellite In Aeschynomene Falcata (leguminosae): Diversity, Cross-amplification, And Chromosome Localization

Aeschynomene falcata is an important forage species; however, because of low seed production, it is underutilized as forage species. Aeschynomene is a polyphyletic genus with a challenging taxonomic position. Two subgenera have been proposed, and it is suggested that Aeschynomene can be split in 2 genera. Thus, new markers, such as microsatellite sequences, are desirable for improving breeding programs for A. falcata. Based on transferability and in situ localization, these microsatellite sequences can be applied as chromosome markers in the genus Aeschynomene and closely related genera. Here, we report the first microsatellite library developed for this genus; 11 microsatellites were characterized, with observed and expected heterozygosities ranging from 0.0000 to 0.7143 and from 0.1287 to 0.8360, respectively. Polymorphic information content varied from 0.1167 to 0.7786. The departure from Hardy-Weinberg equilibrium may have resulted from frequent autogamy, which is characteristic of A. falcata. Of the 11 microsatellites, 9 loci were cross-amplified in A. brevipes and A. paniculata and 7 in Dalbergia nigra and Machaerium vestitum. Five of these 7 cross-amplified microsatellites were applied as probes during the in situ hybridization assay and 2 showed clear signals on A. falcata chromosomes, ensuring their viability as chromosome markers.1341039010397Begum, R., Alam, S.S., Menzel, G., Schmidt, T., Comparative molecular cytogenetics of major repetitive sequence families of three Dendrobium species (Orchidaceae) from Bangladesh (2009) Ann. Bot, 104, pp. 863-872Billotte, N., Lagoda, P.J.R., Risterucci, A.M., Baurens, F.C., Microsatellite-enriched libraries: Applied methodology for the development of SSR markers in tropical crops (1999) Fruits, 54, pp. 277-288Cardoso, D., de Queiroz, L.P., Pennington, R.T., de Lima, H.C., Revisiting the phylogeny of papilionoid legumes: New insights from comprehensively sampled early-branching lineages (2012) Am. J. Bot, 99, pp. 1991-2013Creste, S., Tulmann Neto, A., Figueira, A., Detection of single sequence repeat polymorphisms in denaturing polyacrylamide sequencing gels by silver staining (2001) Plant Mol. Biol. Rep, 19, pp. 299-306Ellis, J.R., Burke, J.M., EST-SSRs as a resource for population genetic analyses (2007) Heredity, 99, pp. 125-132Flajoulot, S., Ronfort, J., Baudouin, P., Barre, P., Genetic diversity among alfalfa (Medicago sativa) cultivars coming from a breeding program, using SSR markers (2005) Theor. Appl. Genet, 111, pp. 1420-1429Jones, R.M., McDonald, C.K., Clements, R.J., Bunch, G.A., Sown pastures in subcostal south-eastern Queensland: Pasture composition, legume persistence and cattle live weight gain over 10 years (2000) Trop. Grassl, 34, pp. 21-37Kalia, R.K., Rai, M.K., Kalia, S., Singh, R., Microsatellite markers: An overview of the recent progress in plants (2011) Euphytica, 177, pp. 309-334Kemp, S., (2002) PIC Calculator Extra, , http://www.genomics.liv.ac.uk/animal/pic.html, Accessed September 4, 2012Klitgaard, B.B., Lavin, M., Tribe Dalbergieae Sens. Lat (2005) Legumes of the World, pp. 307-335. , (Lewis GP, Schrire BD, MacKinder BA and Lock M, eds.). Royal Botanic Gardens, KewMiller, M.P., (1997) Tools for Populations Genetics Analyses V 1. 3. A Windows® program for the analysis of allozyme and molecular population genetic data, , http://www.ccg.unam.mx/~vinuesa/tlem09/docs/TFPGADOC.PDF, Accessed April 4, 2014Moraes, A.P., Leitch, I.J., Leitch, A.R., Chromosome studies in Orchidaceae: Karyotype divergence in Neotropical genera in subtribe Maxillariinae (2012) Bot. J. Linn. Soc, 170, pp. 29-39Pinheiro, F., Palma-Silva, C., de, B.F., Cozzolino, S., Cross-amplification and characterization of microsatellite loci for the Neotropical orchid genus Epidendrum (2009) Genet. Mol. Biol, 32, pp. 337-339Polido, C., (2013) Estudo Cromossômico da Tribo Dalbergieae Sensu Klitgaard & Lavin (2005), com Ênfase no Clado Dalbergia Sensu Stricto (Leguminosae, Papilionoideae), , Doctoral thesis, Universidade Estadual de Campinas, CampinasQueiroz, L., Cardoso, D.B.O.S., A new species of Aeschynomene L. (Leguminosae, Papilionoideae) from a continental sand dune area in north-eastern Brazil (2008) Bot. J. Linn. Soc, 157, pp. 749-753Ribeiro, R.A., Lavin, M., Lemos-Filho, J.P., Mendonça-Filho, C.V., The genus Machaerium (Leguminosae) is more closely related to Aeschynomene sect. Ochopodium than to Dalbergia: Inferences from combined sequence data (2007) Syst. Bot, 32, pp. 762-771Rousset, F., Genepop'007: A complete re-implementation of the genepop software for Windows and Linux (2008) Mol. Ecol. Resour, 8, pp. 103-106Ruiz, C., Asins, M.J., Comparison between Poncirus and Citrus genetic linkage maps (2003) Theor. Appl. Genet, 106, pp. 826-836Schwarzacher, T.P., Heslop-Harrison, P., (2000) Practical in Situ Hybridization, , 1st edn. Bios, OxfordTemnykh, S., DeClerck, G., Lukashova, A., Lipovich, L., Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): Frequency, length variation, transposon associations, and genetic marker potential (2001) Genome Res, 11, pp. 1441-1452Thiers, B., (2014) Index Herbariorum: A global Directory of Public Herbaria and Associated Staff, , http://sciweb.nybg.org/science2/IndexHerbariorum.asp, New York Botanical Garden's Virtual Herbarium. Available at. Accessed April 4, 201

De Novo Assembly And Transcriptome Analysis Of The Rubber Tree (hevea Brasiliensis) And Snp Markers Development For Rubber Biosynthesis Pathways

Hevea brasiliensis (Willd. Ex Adr. Juss.) Muell.-Arg. is the primary source of natural rubber that is native to the Amazon rainforest. The singular properties of natural rubber make it superior to and competitive with synthetic rubber for use in several applications. Here, we performed RNA sequencing (RNA-seq) of H. brasiliensis bark on the Illumina GAIIx platform, which generated 179,326,804 raw reads on the Illumina GAIIx platform. A total of 50,384 contigs that were over 400 bp in size were obtained and subjected to further analyses. A similarity search against the non-redundant (nr) protein database returned 32,018 (63%) positive BLASTx hits. The transcriptome analysis was annotated using the clusters of orthologous groups (COG), gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Pfam databases. A search for putative molecular marker was performed to identify simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs). In total, 17,927 SSRs and 404,114 SNPs were detected. Finally, we selected sequences that were identified as belonging to the mevalonate (MVA) and 2-C-methyl-D-erythritol 4-phosphate (MEP) pathways, which are involved in rubber biosynthesis, to validate the SNP markers. A total of 78 SNPs were validated in 36 genotypes of H. brasiliensis. This new dataset represents a powerful information source for rubber tree bark genes and will be an important tool for the development of microsatellites and SNP markers for use in future genetic analyses such as genetic linkage mapping, quantitative trait loci identification, investigations of linkage disequilibrium and marker-assisted selection. © 2014 Mantello et al.97Sakdapipanich, J.T., Structural characterization of natural rubber based on recent evidence from selective enzymatic treatments (2007) J Biosci Bioeng, 103, pp. 287-292. , doi:10.1263/jbb.103.287Cornish, K., Similarities and differences in rubber biochemistry among plant species (2001) Phytochemistry, 57, pp. 1123-1134Gronover, C.S., Wahler, D., Prüfer, D., (2005) Natural Rubber Biosynthesis and Physic- Chemical Studies on Plant Derived LatexSaha, T., Priyadarshan, P.M., (2012) Genomics of Tree Crops, , Schnell RJ, Priyadarshan PM, editors New York, NY: Springer New York. doi:10.1007/978-1-4614-0920-5Priyadarshan, P.M., Goncalves, P.D.S., (2003) Hevea Gene Pool for Breeding, pp. 101-114Leitch, A.R., Lim, K.Y., Leitch, I.J., Neill, M.O., Molecular cytogenetic studies in rubber (1998) Hevea, pp. 464-467Pires, J.M., Secco, R., Gomes, J.I., (2002) Taxonomia e Filogeografia Das Seringueiras (Hevea Spp) Belem: Embrapa Amazonia Oriental, p. 103Pushparajah, E., Natural rubber (2001) Tree Crop Ecosystems, , Last, F.T. 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Mitochondrial Atp-sensitive K+ Channels As Redox Signals To Liver Mitochondria In Response To Hypertriglyceridemia

We have recently demonstrated that hypertriglyceridemic (HTG) mice present both elevated body metabolic rates and mild mitochondrial uncoupling in the liver owing to stimulated activity of the ATP-sensitive potassium channel (mitoKATP). Because lipid excess normally leads to cell redox imbalance, we examined the hepatic oxidative status in this model. Cell redox imbalance was evidenced by increased total levels of carbonylated proteins, malondialdehydes, and GSSG/GSH ratios in HTG livers compared to wild type. In addition, the activities of the extramitochondrial enzymes NADPH oxidase and xanthine oxidase were elevated in HTG livers. In contrast, Mn-superoxide dismutase activity and content, a mitochondrial matrix marker, were significantly decreased in HTG livers. Isolated HTG liver mitochondria presented lower rates of H2O2 production, which were reversed by mitoKATP antagonists. In vivo antioxidant treatment with N-acetylcysteine decreased both mitoKATP activity and metabolic rates in HTG mice. These data indicate that high levels of triglycerides increase reactive oxygen generation by extramitochondrial enzymes that promote mitoKATP activation. The mild uncoupling mediated by mitoKATP increases metabolic rates and protects mitochondria against oxidative damage. Therefore, a biological role for mitoKATP as a redox sensor is shown here for the first time in an in vivo model of systemic and cellular lipid excess. © 2009 Elsevier Inc. 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