Homology of AFLP products in three mapping populations of barley

Waugh, Robbie; Bonar, N.; Baird, E.; Thomas, Bernhard; Graner, Andreas; Hayes, Patrick; Powell, W.

doi:10.1007/s004380050502

Cited by 144 publications

(58 citation statements)

References 21 publications

(40 reference statements)

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“…This occurred in cases where the AFLP marker was not linked to any of the SSR markers. Previous research has shown that homologous AFLP fragments map on the same chromosomes in different populations (Waugh et al 1997). The same conclusion was reached in our mapping of AFLP markers in different barley populations (data not shown).…”

Section: Discussionsupporting

confidence: 77%

Mapping and QTL analysis of the barley population Tallon × Kaputar

Çakır¹,

Poulsen²,

Galwey³

et al. 2003

Aust. J. Agric. Res.

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Abstract. A genetic map of barley with 224 AFLP and 39 simple sequence repeat (SSR) markers was constructed using a doubled haploid (DH) mapping population from a cross between the varieties Tallon and Kaputar. Linkage groups were assigned to individual barley chromosomes using the published map locations of the SSR markers as reference points. This genetic map was used to identify markers with linkage to agronomic, disease, and quality traits in barley. The population, which comprised 65 lines, was tested in a range of environments across Australia. Quantitative trait loci (QTLs) analyses were performed using software packages MapMaker, MapManager, and Qgene. Significant associations with markers were found for several traits. Grain yield showed significant association with regions on chromosomes 2H, 3H, and 5H over a range of sites throughout Australia. Regions on chromosomes 2H and 3H explained 30% and 26% of variation in lodging, respectively. Among quality traits, diastatic power was associated with regions on chromosomes 1H, 2H, and 5H (R 2 = 37%). Hot water extract was associated with a region on chromosome 6H and a marker not assigned to a chromosome (R 2 = 45%). There were also environment-specific QTLs for the traits analysed. The markers identified here present an opportunity for marker assisted selection of lines for these traits in barley breeding programs.

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Section: Discussionsupporting

confidence: 77%

Mapping and QTL analysis of the barley population Tallon × Kaputar

Çakır¹,

Poulsen²,

Galwey³

et al. 2003

Aust. J. Agric. Res.

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“…In the L94 · Vada RIL population of Qi et al (1998b), E38M54-294 was associated with RLP. In the RIL population, there is no doubt that the band on gel is from L94, but in the cultivar set the band could also originate from another part of the genome and co-migrate by identical mobility (Waugh et al 1997;Koopman and Gort 2004). However, the association between E38M54-294 and the Vada markers was just as high as the mutual correlation between the Vada markers in the Rphq2 region, indicating that no other band has been interfering.…”

Section: Rphq2mentioning

confidence: 85%

Linkage Disequilibrium Mapping of Morphological, Resistance, and Other Agronomically Relevant Traits in Modern Spring Barley Cultivars

et al. 2006

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A set of 148 modern spring barley cultivars was explored for the extent of linkage disequilibrium (LD) between genes governing traits and nearby marker alleles. Associations of agronomically relevant traits (days to heading, plant height), resistance traits (leaf rust, barley yellow dwarf virus (BYD)), and morphological traits (rachilla hair length, lodicule size) with AFLP markers and SSR markers were found. Known major genes and QTLs were confirmed, but also new putative QTLs were found. The LD mapping clearly indicated the common occurrence of Rph3, a gene for hypersensitivity resistance against Puccinia hordei, and also confirmed the QTL Rphq2 for prolonging latency period of P. hordei in seedlings. We also found strong indication for a hitherto not reported gene for resistance or tolerance to BYD on chromosome 2, linked to SSR marker HVM054. Our conclusion is that LD mapping is a valuable additional tool in the search for applicable marker associations with major genes and QTLs.

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“…Owing to their transferability across species, RFLPs were essential for the early synteny studies that identified evolutionary patterns and genome similarities among cereal crop species (Moore et al, 1995;Devos, 2005). Subsequently, amplified fragment length polymorphisms (AFLPs) were widely used for higher-density map development (Waugh et al, 1997;Hori et al, 2003;Takahashi et al, 2006), but this type of marker has issues with data quality. Sequence-based PCR markers-that is, sequence-tagged sites (STSs) (Mano et al, 1999) and simple sequence repeats (SSRs) (Ramsay et al, 2000)proved to be more reliable and informative and continue to serve as useful anchor loci for maps based on expressed sequence tags (ESTs).…”

Section: Introductionmentioning

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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Homology of AFLP products in three mapping populations of barley

Cited by 144 publications

References 21 publications

Mapping and QTL analysis of the barley population Tallon × Kaputar

Mapping and QTL analysis of the barley population Tallon × Kaputar

Linkage Disequilibrium Mapping of Morphological, Resistance, and Other Agronomically Relevant Traits in Modern Spring Barley Cultivars

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

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