Genome-wide mapping with biallelic markers in Arabidopsis thaliana

Abstract

Single-nucleotide polymorphisms, as well as small insertions and deletions (here referred to collectively as simple nucleotide polymorphisms, or SNPs), comprise the largest set of sequence variants in most organisms. Positional cloning based on SNPs may accelerate the identification of human disease traits and a range of biologically informative mutations. The recent application of high-density oligonucleotide arrays to allele identification has made it feasible to genotype thousands of biallelic SNPs in a single experiment. It has yet to be established, however, whether SNP detection using oligonucleotide arrays can be used to accelerate the mapping of traits in diploid genomes. The cruciferous weed Arabidopsis thaliana is an attractive model system for the construction and use of biallelic SNP maps. Although important biological processes ranging from fertilization and cell fate determination to disease resistance have been modelled in A. thaliana, identifying mutations in this organism has been impeded by the lack of a high-density genetic map consisting of easily genotyped DNA markers. We report here the construction of a biallelic genetic map in A. thaliana with a resolution of 3.5 cM and its use in mapping Eds16, a gene involved in the defence response to the fungal pathogen Erysiphe orontii. Mapping of this trait involved the high-throughput generation of meiotic maps of F2 individuals using high-density oligonucleotide probe array-based genotyping. We developed a software package called InterMap and used it to automatically delimit Eds16 to a 7-cM interval on chromosome 1. These results are the first demonstration of biallelic mapping in diploid genomes and establish means for generalizing SNP-based maps to virtually any genetic organism.

Identification and mapping of SNPs from ESTs in sunflower

“…Genome sequencing projects have shown that single base substitutions and/or small insertion-deletion polymorphisms (SNPs) are the most abundant type of DNA variation, e.g., occurring every 100-300 bases in the human genome. SNPs occur frequently in or near coding sequences (Cho et al 1999) and may be the causes of functional differences between alleles. Moreover, the development of EST sequencing projects now makes it possible to discover putative SNPs in silico with subsequent experimental verification.…”

Array-based high-throughput DNA markers for crop improvement

“…The utility of this technique described as tagged microarray marker approach has been demonstrated for humans and pea (Flavell et al, 2003;Ji et al, 2004). However, Affymetrix GeneChips can also be used for SNP genotyping of a number of samples for one or more genes of interest as done in Arabidopsis, where the array AT412 was used for the study of variation in several genes (for example, Eds16 (Cho et al, 1999), Rsf1 (Spiegelman et al, 2000) and FRI (Nordborg et al, 2002)). …”

New Arabidopsis Recombinant Inbred Line Populations Genotyped Using SNPWave and Their Use for Mapping Flowering-Time Quantitative Trait Loci

“…On the basis of available sequence data of Arabidopsis accessions, many SNP markers have been detected ; The Arabidopsis Information Resource (TAIR; http:/ /www.arabidopsis.org); Cereon database (http:/ /www.arabidopsis.org/Cereon/index.jsp); and (http:/ /walnut.usc.edu/2010.html). One of the various SNP detection systems (Cho et al 1999) is the recently described SNPWave method (van Eijk et al 2004).…”