Large-scale detection of rare variants via pooled multiplexed next-generation sequencing: towards next-generation Ecotilling.
Plant J
; 67(4): 736-45, 2011 Aug.
Article
em En
| MEDLINE
| ID: mdl-21554453
ABSTRACT
Common variants, such as those identified by genome-wide association scans, explain only a small proportion of trait variation. Growing evidence suggests that rare functional variants, which are usually missed by genome-wide association scans, play an important role in determining the phenotype. We used pooled multiplexed next-generation sequencing and a customized analysis workflow to detect mutations in five candidate genes for lignin biosynthesis in 768 pooled Populus nigra accessions. We identified a total of 36 non-synonymous single nucleotide polymorphisms, one of which causes a premature stop codon. The most common variant was estimated to be present in 672 of the 1536 tested chromosomes, while the rarest was estimated to occur only once in 1536 chromosomes. Comparison with individual Sanger sequencing in a selected sub-sample confirmed that variants are identified with high sensitivity and specificity, and that the variant frequency was estimated accurately. This proposed method for identification of rare polymorphisms allows accurate detection of variation in many individuals, and is cost-effective compared to individual sequencing.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Variação Genética
/
Mapeamento Cromossômico
/
Genoma de Planta
/
Populus
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Estudo de Associação Genômica Ampla
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Sequenciamento de Nucleotídeos em Larga Escala
Tipo de estudo:
Diagnostic_studies
Idioma:
En
Revista:
Plant J
Assunto da revista:
BIOLOGIA MOLECULAR
/
BOTANICA
Ano de publicação:
2011
Tipo de documento:
Article
País de afiliação:
Itália