Large‐scale detection of rare variants via pooled multiplexed next‐generation sequencing: towards next‐generation Ecotilling

• Published in: The Plant journal : for cell and molecular biology 2011-08, Vol.67 (4), p.736-745
• Main Authors: Marroni, Fabio, Pinosio, Sara, Di Centa, Eleonora, Jurman, Irena, Boerjan, Wout, Felice, Nicoletta, Cattonaro, Federica, Morgante, Michele
• Format: Article
• Language: English
• Subjects: Alleles; Base Sequence; Biological and medical sciences; Biosynthesis; Chromosome Mapping - economics; Chromosome Mapping - methods; Chromosomes, Plant - genetics; Fundamental and applied biological sciences. Psychology; Genetic Variation - genetics; Genome, Plant - genetics; Genome-Wide Association Study - economics; Genome-Wide Association Study - methods; Genomics; Genotype; High-Throughput Nucleotide Sequencing - methods; Lignin - biosynthesis; Mutation; next‐generation sequencing; Phenotype; Plant biology; Plant physiology and development; Plant Proteins - genetics; Polymorphism; Polymorphism, Single Nucleotide - genetics; pooled multiplexed sequencing; Populus - genetics; populus nigra; rare variants; Sensitivity and Specificity; Sequence Analysis, DNA; SNP
• ISSN: 0960-7412; 1365-313X
• DOI: 10.1111/j.1365-313X.2011.04627.x

Summary 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.