QTL analysis to study the association between leaf size and abscisic acid accumulation in droughted rice leaves and comparisons across cereals

Quarrie, S. A.; Laurie, D. A.; Zhu, Jiahui; Lebreton, Claude; Semikhodskii, Andrei; Steed, Andrew; Witsenboer, H.; Calestani, Cristina

doi:10.1007/978-94-011-5794-0_15

Cited by 28 publications

(34 citation statements)

References 31 publications

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“…Additional mapping was carried out in a population of 155 F 2 progeny or their F 3 families from the cross IR20 (indica) ‫ן‬ 6383 (japonica) (Quarrie et al 1997). The A. thaliana ecotype Columbia was used for cross-hybridization experiments.…”

Section: Plant Materialsmentioning

confidence: 99%

Arabidopsis–Rice: Will Colinearity Allow Gene Prediction Across the Eudicot–Monocot Divide?

Devos

Beales²,

Nagamura³

et al. 1999

Genome Res.

106

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With the genomic sequencing of Arabidopsis nearing completion and rice sequencing very much in its infancy, a key question is whether we can exploit the Arabidopsis sequence to identify candidate genes for traits in cereal crops using a map-based approach. This requires the existence of colinearity between the Arabidopsis and cereal genomes, represented by rice, which is readily detectable using currently available resources, that is, Arabidopsis genomic sequence, rice ESTs, and genetic and physical maps. A detailed study of the colinearity remaining between two small regions of Arabidopsis chromosome 1 and rice suggests that at least in these regions of the Arabidopsis genome, conservation of gene orders with rice has been eroded to the point that it is no longer identifiable using comparative mapping. Although our analysis does not preclude that tracts of colinear gene orders may be identified using sequence comparisons or may exist in other regions of the rice and Arabidopsis genomes, it is unlikely that the extent of colinearity will be sufficient to allow map-based cross-species gene prediction and isolation. Our research also highlights the difficulties encountered in identifying orthologs using BLAST searches in incomplete sequence databases. This complicates the interpretation of comparative data among highly divergent species and limits the exploitation of Arabidopsis sequence in monocot studies.Comparative genome analyses have shown the existence of conserved gene orders (colinearity) in the genomes of different plant and mammal species. In plants, this is best documented in the grass family, where colinearity has been maintained over evolutionary periods as long as 60 million years (Devos and Gale 1997; Gale and Devos 1998). In mammals, the most comprehensive comparative maps are available for human and mouse, which diverged ∼70 million years ago (Carver and Stubbs 1997). Although short-range conserved synteny has been demonstrated between the genomes of human and chicken (Klein et al. 1996) and human and pufferfish (Elgar et al. 1996), which diverged some 300 and 400 million years ago, respectively, conserved synteny does not imply conservation of gene orders. Paterson et al. (1996) predicted that 43%-58% of chromosomal tracts Յ3 cM should have remained colinear over the evolutionary time period [130-240 million years (Wolfe et al. 1989;Crane et al. 1995)] separating the monocots and eudicots and provided some empirical mapping data to support this hypothesis. With a large part of the Arabidopsis sequence available, we aimed to investigate whether Arabidopsisrice colinearity can be identified and thus exploited using currently available data and tools. The key issue is not the existence of colinearity at the sequence level. It is clear that any colinearity that can be detected only when the genomic sequence is available for both rice and Arabidopsis will have limited applications. Once the rice sequence is available, the exploitation of rice, and not Arabidopsis, sequence will be the priority in cere...

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Section: Plant Materialsmentioning

confidence: 99%

Arabidopsis–Rice: Will Colinearity Allow Gene Prediction Across the Eudicot–Monocot Divide?

Devos

Beales²,

Nagamura³

et al. 1999

Genome Res.

106

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show abstract

“…The recent development of high-density linkage maps has provided the tools for dissecting the genetic basis underlying complex traits, such as drought resistance, into individual components. Quantitative trait locus (QTL) mapping has been carried out in an attempt to determine the genetic basis of several traits that may be related to drought resistance, including OA (Lilley et al 1996;Zhang et al 1999Zhang et al , 2001Robin et al 2003), cellmembrane stability (Tripathy et al 2000), abscisic acid (ABA) content (Quarrie et al 1994(Quarrie et al , 1997, stomatal regulation , leaf water status, and root morphology (Champoux et al 1995;Ray et al 1996;Yadav et al 1997;Ali et al 2000;Courtois et al 2000;Zheng et al 2000;Zhang et al 2001;Kamoshita et al 2002;Price et al 2002). However, it is not clear how these attributes are related to the performance of the genotypes at the whole-plant level, and how they function to reduce the drought damage to fitness-and productivity-related traits.…”

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confidence: 99%

Genetic Basis of Drought Resistance at Reproductive Stage in Rice: Separation of Drought Tolerance From Drought Avoidance

et al. 2006

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Drought tolerance (DT) and drought avoidance (DA) are two major mechanisms in drought resistance of higher plants. In this study, the genetic bases of DTand DA at reproductive stage in rice were analyzed using a recombinant inbred line population from a cross between an indica lowland and a tropical japonica upland cultivar. The plants were grown individually in PVC pipes and two cycles of drought stress were applied to individual plants with unstressed plants as the control. A total of 21 traits measuring fitness, yield, and the root system were investigated. Little correlation of relative yield traits with potential yield, plant size, and root traits was detected, suggesting that DTand DA were well separated in the experiment. A genetic linkage map consisting of 245 SSR markers was constructed for mapping QTL for these traits. A total of 27 QTL were resolved for 7 traits of relative performance of fitness and yield, 36 QTL for 5 root traits under control, and 38 for 7 root traits under drought stress conditions, suggesting the complexity of the genetic bases of both DT and DA. Only a small portion of QTL for fitness-and yield-related traits overlapped with QTL for root traits, indicating that DT and DA had distinct genetic bases.

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“…In many studies, markers such as RFLP (restriction fragment length polymorphism), CAPS (cleaved amplified polymorphic sequence), microsatellites or genes are used together with AFLP markers. They can provide clues about the chromosome assignment of linkage groups or links to existing maps [2,31], but they can also give a framework to which AFLP markers are added [4]. Here, the markers are presented in their most likely order.…”

Section: Discussionmentioning

confidence: 99%

AFLP linkage map of the Japanese quail Coturnix japonica

et al. 2003

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-The quail is a valuable farm and laboratory animal. Yet molecular information about this species remains scarce. We present here the first genetic linkage map of the Japanese quail. This comprehensive map is based solely on amplified fragment length polymorphism (AFLP) markers. These markers were developed and genotyped in an F2 progeny from a cross between two lines of quail differing in stress reactivity. A total of 432 polymorphic AFLP markers were detected with 24 TaqI/EcoRI primer combinations. On average, 18 markers were produced per primer combination. Two hundred and fifty eight of the polymorphic markers were assigned to 39 autosomal linkage groups plus the ZW sex chromosome linkage groups. The linkage groups range from 2 to 28 markers and from 0.0 to 195.5 cM. The AFLP map covers a total length of 1516 cM, with an average genetic distance between two consecutive markers of 7.6 cM. This AFLP map can be enriched with other marker types, especially mapped chicken genes that will enable to link the maps of both species and make use of the powerful comparative mapping approach. This AFLP map of the Japanese quail already provides an efficient tool for quantitative trait loci (QTL) mapping. Japanese quail / AFLP / genetic map / linkage groups / chromosomes

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QTL analysis to study the association between leaf size and abscisic acid accumulation in droughted rice leaves and comparisons across cereals

Cited by 28 publications

References 31 publications

Arabidopsis–Rice: Will Colinearity Allow Gene Prediction Across the Eudicot–Monocot Divide?

Arabidopsis–Rice: Will Colinearity Allow Gene Prediction Across the Eudicot–Monocot Divide?

Genetic Basis of Drought Resistance at Reproductive Stage in Rice: Separation of Drought Tolerance From Drought Avoidance

AFLP linkage map of the Japanese quail Coturnix japonica

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