Chromosomal assignment and deletion mapping of barley EST markers

Nasuda, Shuhei; Kikkawa, Yukari; Ashida, Taizo; Islam, A. K. M. R.; Sato, Kazuhiro; Endo, Takashi R.

doi:10.1266/ggs.80.357

Cited by 62 publications

(68 citation statements)

References 40 publications

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“…Therefore, 24 out of 37 4HS markers (64.9%) and 39 out of 56 4HL markers (69.6%) were located in the distal regions accounting for no more than 25.6% of the 4HS arm and for no more than 43.1% of the 4HL arm, respectively. This fact suggests that EST markers or genes on chromosome 4H were more abundant in the distal region than in the proximal region, as observed for other barley chromosomes (Künzel et al, 2000;Nasuda et al, 2005;Ashida et al, 2007;Sakai et al, 2009). This trend was more obvious in the subtelomeric regions.…”

Section: Cytological Mapping Of Barley Est Markerssupporting

confidence: 59%

“…PCR analysis of the dissection lines First, we checked the PCR amplification of the 93 EST markers in the control lines to confirm that the markers are specific to chromosome 4H as reported by Nasuda et al (2005), and found that 37 were located on the 4HS arm and 56 on the 4HL arm. Then, we conducted PCR analysis for the 60 dissection and four control lines using the 93 EST markers ( Table 2).…”

Section: Pcr Analysismentioning

confidence: 99%

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Dissection of barley chromosome 4H in common wheat by the gametocidal system and cytological mapping of chromosome 4H with EST markers

2010

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We used two gametocidal (Gc) chromosomes 2C and 3CSAT to dissect barley chromosome 4H added to common wheat. The Gc chromosome induced chromosomal structural rearrangements in the progeny of the 4H addition line of common wheat carrying the monosomic Gc chromosome. We conducted in situ hybridization to select plants carrying rearranged 4H chromosomes and characterized the rearranged chromosomes by sequential C-banding and in situ hybridization. We established 60 dissection lines of common wheat carrying single rearranged 4H chromosomes. The rearranged 4H chromosomes had either a deletion or a translocation or a complicated structural change. The breakpoints were distributed in the short arm, centromere and the long arm at a rough ratio of 2:2:1. We conducted PCR analysis using the dissection lines and 93 EST markers specific to chromosome 4H. Based on the PCR result, we constructed a cytological map of chromosome 4H with 18 regions separated by the breakpoints of the rearranged chromosomes. Thirty-seven markers were present in the short arm and 56 in the long arm, and about 70% of the markers were present in no more than the distal 25.6% and 43.1% regions of the short and long arms, respectively. It is noteworthy that nine of the short-arm markers and 13 of the long-arm markers existed in the small subtelomeric regions at both ends characterized by the HvT01 sequences. We reconstructed a genetic map using 38 of the 93 markers that was used to construct the cytological map of chromosome 4H. The order of the markers on the genetic map was almost the same as that on the cytological map. On the genetic map, no markers were available in the pericentromeric region, but on the cytological map, 14 markers were present in the proximal region, and one of the markers was in the centromeric region of the short arm.

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Section: Cytological Mapping Of Barley Est Markerssupporting

confidence: 59%

Section: Pcr Analysismentioning

confidence: 99%

Dissection of barley chromosome 4H in common wheat by the gametocidal system and cytological mapping of chromosome 4H with EST markers

2010

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“…These 7H deletion and translocation lines were then used for the physical mapping of the 7H barley chromosome (Serizawa et al 2001). Nasuda et al (2005), Ashida et al (2007) and Sakai et al (2009) performed deletion mapping on barley chromosomes 7H, 5H and 3H using barley dissection lines and barley-specific EST Euphytica (2014) 195:315-329 321 markers. The barley dissection lines were produced from CS-Betzes addition lines, so they all carried chromosome segments from Betzes barley.…”

Section: Chromosome Pairing In Wheat 3 Barley Hybridsmentioning

confidence: 99%

Wheat–barley hybridization: the last 40 years

2013

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Several useful alien gene transfers have been reported from related species into wheat (Triticum aestivum), but very few publications have dealt with the development of wheat/barley (Hordeum vulgare) introgression lines. An overview is given here of wheat 9 barley hybridization over the last forty years, including the development of wheat 9 barley hybrids, and of addition and translocation lines with various barley cultivars. A short summary is also given of the wheat 9 barley hybrids produced with other Hordeum species. The meiotic pairing behaviour of wheat 9 barley hybrids is presented, with special regard to the detection of wheatbarley homoeologous pairing using the molecular cytogenetic technique GISH. The effect of in vitro multiplication on the genome composition of intergeneric hybrids is discussed, and the production and characterization of the latest wheat/barley translocation lines are presented. An overview of the agronomical traits (b-glucan content, earliness, salt tolerance, sprouting resistance, etc.) of the newly developed introgression lines is given. The exploitation and possible use of wheat/barley introgression lines for the most up-to-date molecular genetic studies (transcriptome analysis, sequencing of flow-sorted chromosomes) are also discussed.

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“…For example, Nasuda et al (2005) and Ashida et al (2007) mapped barley EST markers on the barley chromosome deletion stocks and estimated the physical location of these ESTs. Although the resolution in segmental allocation of markers was low in wheat deletion stock mapping (Sorrells et al, 2003), the approach is a useful first step in developing BAC contigs for genome sequencing.…”

Section: Snp Typing 17% Caps 9%mentioning

confidence: 99%

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

2009

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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.

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Chromosomal assignment and deletion mapping of barley EST markers

Cited by 62 publications

References 40 publications

Dissection of barley chromosome 4H in common wheat by the gametocidal system and cytological mapping of chromosome 4H with EST markers

Dissection of barley chromosome 4H in common wheat by the gametocidal system and cytological mapping of chromosome 4H with EST markers

Wheat–barley hybridization: the last 40 years

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

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