Identification of candidate genes for drought stress tolerance in rice by the integration of a genetic (QTL) map with the rice genome physical map

Wang, Xusheng; Zhu, Jun; Mansueto, Locedie; Bruskiewich, Richard

doi:10.1631/jzus.2005.b0382

Cited by 36 publications

(22 citation statements)

References 38 publications

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“…For the other sequences, we used BLAST (Altschul et al, 1997;Wang et al, 2005) to search all similar sequences related to an initial query with threshold E-value 10 −6 .…”

Section: Sequence Search Within Gismentioning

confidence: 99%

Analysis of the 3′ ends of tRNA as the cause of insertion sites of foreign DNA in Prochlorococcus

Liu

Zhu

2010

J. Zhejiang Univ. Sci. B

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Abstract:The purpose of this study was to investigate the characteristics of transfer RNA (tRNA) responsible for the association between tRNA genes and genes of apparently foreign origin (genomic islands) in five high-light adapted Prochlorococcus strains. Both bidirectional best BLASTP (basic local alignment search tool for proteins) search and the conservation of gene order against each other were utilized to identify genomic islands, and 7 genomic islands were found to be immediately adjacent to tRNAs in Prochlorococcus marinus AS9601, 11 in P. marinus MIT9515, 8 in P. marinus MED4, 6 in P. marinus MIT9301, and 6 in P. marinus MIT9312. Monte Carlo simulation showed that tRNA genes are hotspots for the integration of genomic islands in Prochlorococcus strains. The tRNA genes associated with genomic islands showed the following characteristics: (1) the association was biased towards a specific subset of all iso-accepting tRNA genes; (2) the codon usages of genes within genomic islands appear to be unrelated to the codons recognized by associated tRNAs; and, (3) the majority of the 3' ends of associated tRNAs lack CCA ends. These findings contradict previous hypotheses concerning the molecular basis for the frequent use of tRNA as the insertion site for foreign genetic materials. The analysis of a genomic island associated with a tRNA-Asn gene in P. marinus MIT9301 suggests that foreign genetic material is inserted into the host genomes by means of site-specific recombination, with the 3' end of the tRNA as the target, and during the process, a direct repeat of the 3' end sequence of a boundary tRNA (namely, a scar from the process of insertion) is formed elsewhere in the genomic island. Through the analysis of the sequences of these targets, it can be concluded that a region characterized by both high GC content and a palindromic structure is the preferred insertion site.

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“…For the other sequences, we used BLAST (Altschul et al, 1997;Wang et al, 2005) to search all similar sequences related to an initial query with threshold E-value 10 −6 .…”

Section: Sequence Search Within Gismentioning

confidence: 99%

Analysis of the 3′ ends of tRNA as the cause of insertion sites of foreign DNA in Prochlorococcus

Liu

Zhu

2010

J. Zhejiang Univ. Sci. B

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“…The stable expression of a QTL across a broad range of environmental conditions is a critical factor when breeding for wide adaptation and yield stability (Maccaferri et al 2008). Examples of such QTL have been reported in bread wheat (Quarrie et al 2006), rice (Wang et al 2005), pearl millet (Yadav et al 2002), and maize (Landi et al 2007).…”

Section: Introductionmentioning

confidence: 99%

Quantitative trait loci associated with drought tolerance in the model legume Medicago truncatula

2011

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Water shortage and heterogeneity in precipitation constitute the essential limiting factors for agricultural production in the Mediterranean basin. To understand the complex inheritance of tolerance to drought stress in Medicago truncatula, quantitative trait loci (QTLs) analysis was performed using a set of recombinant inbred lines (RILs) derived from a cross between the susceptible line Jemalong A17 and the tolerant line F83005.5. We conducted two experiments where the RILs and parental lines were grown in 0 mM and 75 mM of mannitol (D-) in tubes and in control and 33% of the field capacity (FC) in pots. In both experiments, line and line by water treatment interaction were significant. QTLs analysis showed that several putative genomic regions are involved in the variation of measured traits under the two water treatments in tubes and pots. A total of 21 QTLs on 8 linkage groups were detected for the measured traits in both experiments, 11 of them were in tubes conditions. Eight of these 11 QTLs were identified in control treatment and three in mannitol. While the number of QTLs identified in tubes under control conditions was more than under mannitol conditions, the highest number of QTLs was detected in water-stressed conditions in pots. The percentage of phenotypic variance explained by a single QTL (R 2 ) ranges from 11.7 to 26.3% in tubes and from 11.2 to 18.4% in pots depending on the trait, with 6 QTLs in each condition explaining \15% of the phenotypic variance. The number of common QTLs under two water treatments was one for length of stems (LS), number of internodes (NIN) and aerial dry weight (ADW) in tubes, and zero for NIN and one for LS and leaf area (LA) in pots. However, a few overlapping QTLs were found in tubes and pots on linkage groups 5 and 7 for LS and NIN.

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“…However, the role of PPO in the protection against drought‐induced damage in resurrection plants is unknown. Recent studies have indicated that phenol oxidizing enzymes may participate in the response to the defense reactions against various abiotic stresses including drought (Lee et al 2007, Sofo et al 2005, Wang et al 2005). However, the results concerning drought‐induced changes in PPO activity are ambiguous and varied among crop species and conditions (e.g.…”

Section: Introductionmentioning

confidence: 99%

Characterization of polyphenol oxidase changes induced by desiccation of Ramonda serbica leaves

Jovanović

Kukavica

Navari-Izzo

2008

Physiologia Plantarum

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Resurrection plants are able to dehydrate/rehydrate rapidly without cell damage by a mechanism, the understanding of which may be of ecological importance in the adaptation of crop plants to dry conditions. The o-diphenol oxidase in Ramonda serbica Pan. & Petrov, a rare resurrection plant of the Balkan Peninsula, was characterized in respect to different isoforms, preferable substrates and specific inhibitors. Two anionic isoforms with pI 4.6 and 4.7 were separated from turgid leaves. Three additional anionic isoforms (pI 5.1, 5.3 and 5.6) and three neutral isoforms (pI from 6.8 to 7.4) were induced in desiccated leaves. Based on apparent K(m) values, the affinity for reducing substrates decreased as follows: methyl catechol > chlorogenic acid > 3,4-dihydroxyphenylalanine > caffeic acid > pyrogallol. Polyphenol oxidase (PPO) activity was specifically sensitive to diethyldithiocarbamate and also inhibited by KCN, DTT and salicylic hydroxamic acid but with no inhibitory effect of Na3N. Plants were subjected to drought-to-near complete water loss (approximately 2% relative water content, RWC) and several fold higher PPO activity was detected in desiccated leaves. Ramonda leaves contain high levels of phenolics, which decreased during drought. Rehydration of dry leaves from 2% RWC to 95% RWC led to transient inhibition of PPO in the first few hours. Within a day, the levels completely recovered to those determined in desiccated leaves. The finding of desiccation-induced high activity of PPO and new isoforms, which were also present in rehydrated turgid leaves, indicates a substantial role for PPO in the adaptation mechanism of resurrection plants to desiccation and also to the oxidative stress during rehydration.

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Identification of candidate genes for drought stress tolerance in rice by the integration of a genetic (QTL) map with the rice genome physical map

Cited by 36 publications

References 38 publications

Analysis of the 3′ ends of tRNA as the cause of insertion sites of foreign DNA in Prochlorococcus

Analysis of the 3′ ends of tRNA as the cause of insertion sites of foreign DNA in Prochlorococcus

Quantitative trait loci associated with drought tolerance in the model legume Medicago truncatula

Characterization of polyphenol oxidase changes induced by desiccation of Ramonda serbica leaves

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