A high-density transcript linkage map of barley derived from a single population

Abstract

A high-resolution transcript linkage map of barley was created using a single doubled haploid (DH) mapping population, only 3 0 -end expressed sequence tags (ESTs) and only PCR-based assays. Cultivar 'Haruna Nijo' and an ancestral wild-form accession 'H602' were used as EST donors and crossing parents of the mapping population. Of the 10 366 primer sets developed from a non-redundant set of 3 0 EST sequences, 7700 sets generated useful amplicons and 3975 (52%) showed polymorphisms between the mapping parents. Of these, 2890 (28% of the total) were mapped by single nucleotide polymorphisms (1717), cleaved amplified polymorphic sequence (933) and INDELs (240). The present work involves an estimated 9% of the genes of barley. Of the mapped ESTs, 2689 (93%) are formatted in the Affymetrix Barley 1 GeneChip and full-length cDNA sequences are available for 1039 (36%). Mapped ESTs show highest similarity with sequences in the wheat gene index (93%) and moderate similarity with rice (50%). Comparison of mapped EST positions and the rice pseudomolecule indicated collinear regions between two species; these are particularly conserved for the entire barley chromosome 3H and rice chromosome 1. These mapped genes, together with a systematically developed set of genetic resources, will make it easier to directly clone genes showing simple inheritance and to determine the genetic basis of complex traits. The information will contribute to the development of a framework for the physical mapping of barley, which is necessary for genome sequencing.

Six-rowed spike4 ( Vrs4 ) controls spikelet determinacy and row-type in barley

“…For initial mapping, BOPA SNP markers (28) or SSR and EST based markers (SI Dataset S1B) were selected from the high-density transcript map of barley chromosome 3H (29). For further marker development in the defined vrs4 interval, we relied on the barley genome zipper (11).…”

Molecular mapping of SKr for crossability in common wheat

“…We are trying to saturate the map of chromosome 5B by using information on RFLP markers (Gale et al 1995), mapped EST of wheat (Linkiewicz et al 2004, Mochida et al 2009) and barley (Kota et al 2007, Sato et al 2009, and the colinearity of wheat to rice (Sorrells et al 2003) to identify the markers closely linked to the Kr1 locus as well as Skr.…”

A new genetic linkage map of barley (Hordeum vulgare L.) facilitates genetic dissection of height and spike length and angle

“…Over the last ten years, barley breeders have benefited from the availability of various genetic markers, including RFLP, AFLP, microsatellite, DArT, SNP, and STS (Kleinhofs et al, 1993;Rostoks et al, 2005;Wenzl et al, 2006;Hearnden et al, 2007;Marcel et al, 2007;Stein et al, 2007;Varshney et al, 2007;Potokina et al, 2008;Sato et al, 2009;Szűcs et al, 2009). These markers facilitated numerous mapping studies which led to marker assisted breeding applications.…”