Both of these maps provide detailed colinearity comparisons to rice at the whole genome level.ĭue to the remarkable colinearity among grass species, EST-derived markers can be used for saturation mapping of targeted genomic regions by using genomic information from other grass species including wheat ( Triticum aestivum L.), rice ( Oryza sativa L.), and Brachypodium. (2009) which contain 28 loci, respectively, derived from barley ESTs. More recently, two high density transcript linkage maps of barley were reported by Sato et al. (2007) made a systematic comparison to the rice genome providing extensive information on colinearity between barley and rice across the whole genome. With this high-density transcript map, Stein et al. (2007) using more than 1000 EST-derived markers (RFLPs, SSRs, and SNPs). The first comprehensive barley transcript map was recently developed by Stein et al. (2005) reported the first barley genetic linkage map that incorporated more than 300 SNP markers derived from barley ESTs. Barley ESTs have been used to develop simple sequence repeat (SSR) markers ( Thiel et al., 2003 Varshney et al., 2006), single nucleotide polymorphism (SNP) markers ( Kota et al., 2003 Rostoks et al., 2005 Stein et al., 2007 Sato et al., 2009 Close et al., 2009), sequence tagged site (STS) markers ( Mammadov et al., 2005 Marcel et al., 2007), and restriction fragment length polymorphism (RFLP) markers ( Stein et al., 2007). The large number of ESTs provides an excellent source for developing different types of DNA markers for genetic linkage mapping. 2007, from which 50,453 unigenes with 23,176 tentative consensus (TC) sequences and 27,094 singletons have been identified. (2008), a total of 437,713 barley ESTs generated from different cDNA libraries were deposited in GenBank at NCBI by 14 Sept. One of the most beneficial resources developed is a large collection of expressed sequence tags (ESTs). single stranded conformational polymorphismsĭ espite having a large genome with a large amount of repetitive DNA, barley has been the subject of intensive genomic studies.National Center for Biotechnology Information.This work refines the genetic and physical location of rpt.r and rpt.k and provides an initial step toward the map-based cloning of these two genes. Comparative analysis revealed that a 12.6-cM region containing the two resistance loci is colinear with a region of rice chromosome 2 between 23.7 and 29.9 Mb with only a few rearrangements, and nearly the same level of colinearity was observed between barley and Brachypodium in this region. Comparison of mapped ESTs along chromosome 6H to wheat bin-mapped ESTs suggests that rpt.r and rpt.k are most likely located on the long arm of chromosome 6H. The two resistance loci were delineated to a 1.6 cM genetic interval. Fifteen newly developed markers were added to the previous map, and most were distributed within a 27.0-cM interval spanning rpt.r and rpt.k. Additionally, we did a comparative analysis of this region to other grass species. In this study, we mined barley expressed sequence tag (EST) databases and developed EST-derived markers for further mapping of this region in a population derived from ‘Rika’ and ‘Kombar’. We previously identified a region near the centromere of barley ( Hordeum vulgare L.) chromosome 6H that harbors two closely linked net form net blotch resistance genes ( rpt.r and rpt.k).
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