Dissecting the telomere region of barley chromosome 5HL using rice genomic sequences as references: new markers for tracking a complex region in breeding

Zhang, Xiaoqi; Li, Chengdao; Panozzo, Joe; Westcott, Sharon; Zhang, Guoping; Tay, Amy; Appels, R.; Jones, Michael G. K.; Lance, Reg

doi:10.1007/s11032-010-9408-2

Cited by 16 publications

(5 citation statements)

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“…EST resources have proven to be excellent resources for gene discovery, molecular marker development, analysis of gene expression, and identification of candidate genes for phenotypes of interest in a number of species [21-23]. The EST approach is particularly useful for taxa whose genome sequence is presently unavailable or otherwise have limited sequence information.…”

Section: Introductionmentioning

confidence: 99%

“…Recently, ESTs have been used for identifying SNPs in many plant species such as rice, maize, barley, soybean, sugarcane, sugar beet and melon [ 24 - 30 ]. The abundance, ubiquity and interspersed nature of SNPs together with the potential of automatic high-throughput analysis make them ideal candidates as molecular markers for construction of high density genetic maps [ 30 ], association analysis of candidate genes with important agronomic traits [ 19 , 31 ], fine mapping of QTLs [ 32 ], genetic diversity assessment [ 33 , 34 ] and marker-assisted plant breeding [ 21 , 35 ]. In addition, SNPs located in known genes provide a fast alternative to analyse the fate of agronomically important alleles in breeding populations, thus providing functional markers.…”

Section: Introductionmentioning

confidence: 99%

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Integration of gene-based markers in a pearl millet genetic map for identification of candidate genes underlying drought tolerance quantitative trait loci

et al. 2012

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BackgroundIdentification of genes underlying drought tolerance (DT) quantitative trait loci (QTLs) will facilitate understanding of molecular mechanisms of drought tolerance, and also will accelerate genetic improvement of pearl millet through marker-assisted selection. We report a map based on genes with assigned functional roles in plant adaptation to drought and other abiotic stresses and demonstrate its use in identifying candidate genes underlying a major DT-QTL.ResultsSeventy five single nucleotide polymorphism (SNP) and conserved intron spanning primer (CISP) markers were developed from available expressed sequence tags (ESTs) using four genotypes, H 77/833-2, PRLT 2/89-33, ICMR 01029 and ICMR 01004, representing parents of two mapping populations. A total of 228 SNPs were obtained from 30.5 kb sequenced region resulting in a SNP frequency of 1/134 bp. The positions of major pearl millet linkage group (LG) 2 DT-QTLs (reported from crosses H 77/833-2 × PRLT 2/89-33 and 841B × 863B) were added to the present consensus function map which identified 18 genes, coding for PSI reaction center subunit III, PHYC, actin, alanine glyoxylate aminotransferase, uridylate kinase, acyl-CoA oxidase, dipeptidyl peptidase IV, MADS-box, serine/threonine protein kinase, ubiquitin conjugating enzyme, zinc finger C- × 8-C × 5-C × 3-H type, Hd3, acetyl CoA carboxylase, chlorophyll a/b binding protein, photolyase, protein phosphatase1 regulatory subunit SDS22 and two hypothetical proteins, co-mapping in this DT-QTL interval. Many of these candidate genes were found to have significant association with QTLs of grain yield, flowering time and leaf rolling under drought stress conditions.ConclusionsWe have exploited available pearl millet EST sequences to generate a mapped resource of seventy five new gene-based markers for pearl millet and demonstrated its use in identifying candidate genes underlying a major DT-QTL in this species. The reported gene-based markers represent an important resource for identification of candidate genes for other mapped abiotic stress QTLs in pearl millet. They also provide a resource for initiating association studies using candidate genes and also for comparing the structure and function of distantly related plant genomes such as other Poaceae members.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Integration of gene-based markers in a pearl millet genetic map for identification of candidate genes underlying drought tolerance quantitative trait loci

et al. 2012

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“…The area may include a cluster of genes involved in dormancy and various aspects of malt quality, such as endosperm modification and levels of starch-degrading enzymes (Li et al, 2003), or there could be a single gene with pleiotropic effects given the close correlation of many quality factors such as dormancy, hull thickness, a-amylase, and malt extract. Recent fine mapping of the area (Zhang et al, 2011) has identified several additional markers, but the mapping was unable to differentiate a cluster of genes from a single regulatory gene due to insufficient polymorphism among the samples tested. Recent fine mapping of the area (Zhang et al, 2011) has identified several additional markers, but the mapping was unable to differentiate a cluster of genes from a single regulatory gene due to insufficient polymorphism among the samples tested.…”

mentioning

confidence: 99%

“…Coventry et al (2003) suggested it could be a regulatory gene. Recent fine mapping of the area (Zhang et al, 2011) has identified several additional markers, but the mapping was unable to differentiate a cluster of genes from a single regulatory gene due to insufficient polymorphism among the samples tested. Australian barley breeders generally prefer the SD2 QTL for dormancy because of the potential for severe PHS in Australia and a strong requirement for dormancy.…”

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confidence: 99%

Identification of Barley Breeding Lines Combining Preharvest Sprouting Resistance with “Canadian‐type” Malting Quality

Edney¹,

Legge

Izydorczyk³

et al. 2013

Crop Science

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1447ReseaRch T wo-rowed cultivars of Canadian malting barley (Hordeum vulgare L.) are known to produce excellent quality malt. High levels of starch-degrading enzymes and free amino nitrogen (FAN) combined with good extract levels result in a malt quality profile that has strong market demand, especially among high-adjunct brewers. These desirable qualities in Canadian malt originate from the absence of dormancy and a rapid onset of germination in barley, which allows good enzyme development and adequate endosperm breakdown. However, the tendency for rapid germination predisposes the Canadian barley to preharvest sprouting (PHS), a phenomenon whereby barley germinates in the field under extended moist conditions at or near harvest time. Sprouting in malting barley is undesirable as it leads to reduction of germinative energy during storage, which consequently results in poor-quality malt (Briggs et al., 1981) with high levels of wort b-glucan and low extract. Good-quality malt can be made from slightly sprouted barley (Sole, 1994) but only if dry barley has ABSTRACT Rapid onset of germination in Canadian malting barley (Hordeum vulgare L.) facilitates production of good quality malt but predisposes barley to preharvest sprouting (PHS). Dormancy can be bred into barley to avoid PHS but some dormancy genes negate the potential for the "Canadian-type" malt quality associated with a rapid start to germination. The microsatellite marker, GMS001, identified lines with PHS resistance and "Canadian-type" malt quality in a cross between an Australian cultivar, Baudin, with PHS resistance, and a Canadian malt barley breeding line, TR253, without PHS resistance. The resulting population was grown at three sites over 2 yr with select site/years malted and analyzed for quality. Rapid visco analysis indicated PHS in some barley lines with as little as 11 mm of rain near harvest. The rapid visco analysis results substantiated the importance of the marker on chromosome 5H as breeding lines with the Baudin allele were less susceptible to sprouting, although they exhibited variable malt quality. Lines with the TR253 allele were PHS susceptible but had better and more consistent malt quality. Among the lines with the Baudin allele, five with PHS resistance and consistently good malt quality were identified. Among the lines with the TR253 allele, one showed good PHS resistance and the desirable "Canadiantype" malt quality. These lines could serve as potential parents of future genotypes combining PHS resistance with good "Canadian-type" malting potential.

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“…region will provide a tool to further dissect the chromosomal region (Zhang et al, 2010). These QTL regions were also reported to control other hydrolytic enzyme activity and malting quality (Li et al, 2009).…”

Section: Discussionmentioning

confidence: 99%

QTLs for malting flavour component associated with pre-harvest sprouting susceptibility in barley (Hordeum vulgare L.)

Jin

Harasymow

Bonnardeaux

et al. 2011

Journal of Cereal Science

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Dissecting the telomere region of barley chromosome 5HL using rice genomic sequences as references: new markers for tracking a complex region in breeding

Cited by 16 publications

References 24 publications

Integration of gene-based markers in a pearl millet genetic map for identification of candidate genes underlying drought tolerance quantitative trait loci

Integration of gene-based markers in a pearl millet genetic map for identification of candidate genes underlying drought tolerance quantitative trait loci

Identification of Barley Breeding Lines Combining Preharvest Sprouting Resistance with “Canadian‐type” Malting Quality

QTLs for malting flavour component associated with pre-harvest sprouting susceptibility in barley (Hordeum vulgare L.)

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