Artículos de revistas
Development Of Single Nucleotide Polymorphism Markers In The Large And Complex Rubber Tree Genome Using Next-generation Sequence Data
Registro en:
Molecular Breeding. Springer, v. 36, p. , 2016.
1380-3743
1572-9788
WOS:000382144700008
10.1007/s11032-016-0534-3
Autor
de Souza
Livia Moura; Toledo-Silva
Guilherme; Cardoso-Silva
Claudio Benicio; da Silva
Carla Cristina; de Araujo Andreotti
Isabela Aparecida; Oliveira Conson
Andre Ricardo; Mantello
Camila Campos; Le Guen
Vincent; de Souza
Anete Pereira
Institución
Resumen
Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) The development of single nucleotide polymorphism (SNP) markers provides the opportunity to improve many areas of plant breeding and population genetics. Unfortunately, for species such as the rubber tree (Hevea brasiliensis), the use of next-generation sequencing for genomic SNP discovery is very difficult because of the large genome size and the abundance of repeated sequences. Access to a set of validated SNP markers is a significant advantage for rubber researchers who wish to apply SNPs in scientific research. Here, we performed genomic sequencing of H. brasiliensis and generated 10,993,648 short reads, which were assembled into 10,071 contigs (N50 = 3078) by a de novo assembly strategy. A total of 2446 contigs presented no hits in the current H. brasiliensis genome assembly and may therefore be considered novel genomic sequences of rubber tree. A total of 143 putative polymorphic positions were selected, gene annotations were available for 58.7 % of the markers, and all of the sequences could be anchored to the released H. brasiliensis genome. These SNPs were validated in eight genotypes of H. brasiliensis and 15 F1 plants from a mapping population, resulting in 30 (20.9 %) positions correctly classified. The analysis revealed key candidate genes responsible for defence mechanisms and provided markers for further genetic improvement of Hevea in breeding programmes. 36 8 Fundacao de Amparo a Pesquisa do Estado de Sao Paulo Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES, Computational Biology Program and Agropolis Program) Conselho Nacional de Desenvolvimento Cientifico e Tecnologico Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)