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High-throughput single nucleotide polymorphism genotyping in wheat (Triticum spp.).

Aurélie Bérard¹, Marie Christine Le Paslier, Mireille Dardevet

¹INRA, UR1279 Etude du Polymorphisme des Génomes Végétaux, CEA-IG/Centre National de Génotypage, 2 rue Gaston Crémieux, CP5724, F-91057 Evry, France.

Plant Biotechnology Journal

|April 22, 2009

Summary

High-throughput genotyping technologies, like SNPlex, can successfully genotype polyploid wheat, enabling advancements in plant breeding. This study provides a core set of single nucleotide polymorphism (SNP) markers for polyploid wheat applications.

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Area of Science:

Genetics
Plant Breeding
Genomics

Background:

High-throughput single nucleotide polymorphism (SNP) genotyping technologies are advancing rapidly, primarily within the human genetics community.
These technologies are well-established for diploid species, but their applicability to polyploid plants, common in major crops, is less understood.

Purpose of the Study:

To evaluate the suitability of the SNPlex multiplex technology for genotyping polyploid wheat species.
To assess the performance of SNP genotyping in diverse Triticum taxa, including tetraploid and hexaploid species and their diploid relatives.

Main Methods:

The SNPlex technology was used to genotype 1314 wheat lines across four 384-well plates.
Genotyping data from 47 wheat SNPs were analyzed, with 40 markers yielding less than 20% missing data.
Validation of 11 markers was performed using Sanger sequencing and MassARRAY genotyping technology.

Main Results:

The SNPlex technology demonstrated successful genotyping in polyploid wheat species, with 40 markers performing well.
Genotype concordance between SNPlex and validation methods was high at 96%, with only one marker discarded.
A mapping study confirmed the expected genetic positions for six markers, and a core set of 39 SNPs was established.

Conclusions:

High-throughput genotyping technologies developed for diploid species are adaptable for use in polyploid plants like wheat, though manual verification may be necessary.
This research establishes a foundational set of SNP markers for polyploid wheat, paving the way for a more comprehensive SNPlex panel.