Genome-wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress

Abstract

More than 2,000 genome-wide barley single nucleotide polymorphisms (SNPs) were developed by resequencing unigene fragments from eight diverse accessions. The average genome-wide SNP frequency observed in 877 unigenes was 1 SNP per 200 bp. However, SNP frequency was highly variable with the least number of SNP and SNP haplotypes observed within European cultivated germplasm reflecting effects of breeding history on genetic diversity. More than 300 SNP loci were mapped genetically in three experimental mapping populations which allowed the construction of an integrated SNP map incorporating a large number of RFLP, AFLP and SSR markers (1,237 loci in total). The genes used for SNP discovery were selected based on their transcriptional response to a variety of abiotic stresses. A set of known barley abiotic stress QTL was positioned on the linkage map, while the available sequence and gene expression information facilitated the identification of genes potentially associated with these traits. Comparison of the sequenced SNP loci to the rice genome sequence identified several regions of highly conserved gene order providing a framework for marker saturation in barley genomic regions of interest. The integration of genome-wide SNP and expression data with available genetic and phenotypic information will facilitate the identification of gene function in barley and other non-model organisms.

A high density barley microsatellite consensus map with 775 SSR loci

“…The consensus map integrates already published (Saghai Maroof et al 1994;Becker and Heun 1995;Liu et al 1996;Struss and Plieske 1998;Ramsay et al 2000;Li et al 2003;Thiel et al 2003) and very recently developed (mainly GBM and scssr; Rostoks et al 2005;Varshney et al 2006a;Marcel et al 2007) barley SSR markers.…”

“…Most of the markers mapped in the OWB population are AFLP markers, but the segregation data for 230 microsatellite loci could also be obtained (Table 1). Within the latter set of 230 microsatellite loci, 34 are new scssr (SCRI-SSR) loci recently integrated into a SNP map of barley (Rostoks et al 2005) and provided by Joanne Russell. Finally, the segregation data of 418 Liu et al (1996) Theor Appl Genet (2007) …”

“…Therefore, they represent a functional class of molecular markers (Andersen and Lü bberstedt 2003). The functional SSR markers include earlier published genic SSR markers (Saghai Maroof et al 1994;Becker and Heun 1995;Pillen et al 2000) and recently developed EST-derived SSR markers (Thiel et al 2003;Rostoks et al 2005;Varshney et al 2006a;Marcel et al 2007). In total, 44% of the SSR marker loci (339) placed on the consensus map are genic/functional-SSR loci.…”

Integration of the barley genetic and seed proteome maps for chromosome 1H, 2H, 3H, 5H and 7H

“…In three cases, the chromosome location of the corresponding gene was known, providing a means to validate the spot segregation data. Thus, the gene encoding serpin Z7 is located on chromosome 5H (von WettsteinKnowles 1993), the gene encoding the α-amylase/trypsin inhibitor BMAI-1 is located on chromosome 2H (Mena et al 1992), and the barley grain peroxidase-encoding gene is found on chromosome 7H (Rostoks et al 2005). The known chromosome locations corresponded to group A (containing serpin Z7 spots), C (containing BMAI-1), B and M (containing barley grain peroxidase), respectively (Table 1, Supplementary Fig.…”

“…In addition, this type of analysis can identify chromosome locations of transacting regulators of the proteins observed, as well as structural genes encoding the proteins themselves (Consoli et al 2002). Expression of the peroxidase gene on chromosome 7H was reported to be affected by abiotic stress (Rostoks et al 2005), and therefore, the presence or absence of the protein in different cultivars might be an indicator of stress tolerance.…”