Rapid genetic mapping of ESTs using SNP pyrosequencing and indel analysis

• Autorzy: Ching A , Rafalski A.
• Języki publikacji: EN

Abstrakty

EN

W describe an effective systematic approach to genetic mapping of cDNA clones, including those obtained from EST sequencing. The EST of interest is first partially sequenced from the 3'-end. PCR primers which bracket the 3'-UTR segment of the cDNA are designed. The corresponding gene segment is amplified from the parents of the mapping population, using primers equipped with 3'- and 5'-extensions to facilitate direct sequencing of PCR products. Comparison of the sequences obtained from the mapping parents frequently reveals single nucleotide polymorphisms or insertion / deletion polymorphisms, which can then be genotyped in a mapping population. The genotyping of SNPs is performed by pyrosequencing, a sequencing-by-synthesis method that has been used successfully in SNP diagnostics. SNP analysis of up to 96 samples, a number required to produce meaningful genetic segregation data, can be rapidly accomplished in parallel. The parental genotype of three loci, stearoyl-ACP desaturase, nucleoside-diphosphate kinase and sucrose synthetase-1 were determined by conventional sequencing, and the polymorphism so identified were scored by the pyrosequencing of 94 individuals of a maize recombinant-inbred population. These loci were successfully placed onto chromosomes 3, 7 and 9 respectively. This method is generally applicable to most plant species, which show sufficient sequence diversity in the 3'-UTR region of genes.

Słowa kluczowe

EN

cDNA clone; corn; DNA marker; single nucleotide polymorphism; plant genetics; mapping population; genetic mapping; maize

• Wydawca: -
• Czasopismo: Cellular and Molecular Biology Letters
• Rocznik: 2002
• Tom: 07
• Numer: 2B
• Opis fizyczny: p.803-810,fig.

Twórcy

autor

Ching A

• DuPont Crop Genetics, Molecular Genetics Group, 1, Innovation Way, Newark, DE 19711, USA

autor

Rafalski A.

Bibliografia

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