Towards a saturated sorghum map using RFLP and AFLP markers

Boivin, K.; Deu, Monique; Rami, Jean-François; Trouche, Gilles; Hamon, Perla

doi:10.1007/s001220051076

Cited by 100 publications

(68 citation statements)

References 21 publications

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“…The likely colinear relationship between large portions of the maize and sorghum genomes coupled with the smaller genome size of sorghum makes comparative map-based cloning studies especially attractive and feasible for this species. Dense genetic maps have been established for sorghum (Whitkus et al, 1992;Melake-Berhan et al, 1993;Chittenden et al, 1994;Dufour et al, 1997;Boivin et al, 1999;Peng et al, 1999;Bhattramakki et al, 2000;Menz et al, 2002). These sorghum maps contain DNA markers common to maize and other grass genetic maps, making crossreferencing between these species possible.…”

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Targeted Analysis of Orthologous Phytochrome A Regions of the Sorghum, Maize, and Rice Genomes using Comparative Gene-Island Sequencing

et al. 2002

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A "gene-island" sequencing strategy has been developed that expedites the targeted acquisition of orthologous gene sequences from related species for comparative genome analysis. A 152-kb bacterial artificial chromosome (BAC) clone from sorghum (Sorghum bicolor) encoding phytochrome A (PHYA) was fully sequenced, revealing 16 open reading frames with a gene density similar to many regions of the rice (Oryza sativa) genome. The sequences of genes in the orthologous region of the maize (Zea mays) and rice genomes were obtained using the gene-island sequencing method. BAC clones containing the orthologous maize and rice PHYA genes were identified, sheared, subcloned, and probed with the sorghum PHYAcontaining BAC DNA. Sequence analysis revealed that approximately 75% of the cross-hybridizing subclones contained sequences orthologous to those within the sorghum PHYA BAC and less than 25% contained repetitive and/or BAC vector DNA sequences. The complete sequence of four genes, including up to 1 kb of their promoter regions, was identified in the maize PHYA BAC. Nine orthologous gene sequences were identified in the rice PHYA BAC. Sequence comparison of the orthologous sorghum and maize genes aided in the identification of exons and conserved regulatory sequences flanking each open reading frame. Within genomic regions where micro-colinearity of genes is absolutely conserved, gene-island sequencing is a particularly useful tool for comparative analysis of genomes between related species.Many species within the grass family Poaceae provide staple grain and forage supplies for humans and animals and thus are of great economic and humanitarian importance. Members of the grass family are found in wide ranging areas of the world, demonstrating adaptability to diverse environmental conditions. Although genome sizes can vary greatly in the grasses (e.g. 420 Mb and 16,000 Mb for rice [Oryza sativa] and hexaploid wheat [Triticum aestivum], respectively [Arumuganathan and Earle, 1991]), recombinational mapping studies using common DNA markers indicate that gene order is generally conserved within long physical intervals between family members (Hulbert et al., 1990; Ahn and Tanksley, 1993;Van Deynze et al., 1998;Goff et al., 2002). This information has been used to construct comparative genetic maps among many grass species (for review, see Gale, 1997, 2000;Gale and Devos, 1998). The large variation in genome size observed in the grass family is attributable in part to differences in ploidy and to variation in the abundance of repetitive elements, primarily retrotransposons, located between low copy number genic regions in the genome (SanMiguel et al., 1996). In maize (Zea mays), retrotransposons are estimated to make up 50% to 80% of the genome (SanMiguel and Bennetzen, 1998). The repetitive sequences have little apparent sequence conservation among species (Hulbert et al., 1990; Bennetzen et al., 1994;Chen et al., 1998).Because of their widespread economic importance and genetic resources, rice and maize have been focal poin...

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Targeted Analysis of Orthologous Phytochrome A Regions of the Sorghum, Maize, and Rice Genomes using Comparative Gene-Island Sequencing

et al. 2002

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“…The two closest AFLP markers (aaccac6 and attcag) distally flanking Bru1 (Figure 2, step 1), from Asnaghi et al (2004), were cloned and analyzed by RFLP on our sorghum mapping population. The aaccac6 locus was mapped on LG4 (previously LG D; Boivin et al 1999) at 9.4 cM proximally from CDSR29. The attcag probe revealed no polymorphism in our sorghum mapping population.…”

Section: Resultsmentioning

confidence: 99%

“…We aligned our sorghum LG4 (previously LG D; Boivin et al 1999; our unpublished data) with LG4 (previously LG F) of the high-density RFLP map of Bowers et al (2003). Two common RFLP loci (CDSR29 and M738) allowed us to delimit the target region on the map of Bowers et al (2003) (Figure 2, step 1).…”

Section: Resultsmentioning

confidence: 99%

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Diploid/Polyploid Syntenic Shuttle Mapping and Haplotype-Specific Chromosome Walking Toward a Rust Resistance Gene (Bru1) in Highly Polyploid Sugarcane (2n ∼ 12x ∼ 115)

et al. 2008

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The genome of modern sugarcane cultivars is highly polyploid (12x), aneuploid, of interspecific origin, and contains 10 Gb of DNA. Its size and complexity represent a major challenge for the isolation of agronomically important genes. Here we report on the first attempt to isolate a gene from sugarcane by map-based cloning, targeting a durable major rust resistance gene (Bru1). We describe the genomic strategies that we have developed to overcome constraints associated with high polyploidy in the successive steps of map-based cloning approaches, including diploid/polyploid syntenic shuttle mapping with two model diploid species (sorghum and rice) and haplotype-specific chromosome walking. Their applications allowed us (i) to develop a high-resolution map including markers at 0.28 and 0.14 cM on both sides and 13 markers cosegregating with Bru1 and (ii) to develop a physical map of the target haplotype that still includes two gaps at this stage due to the discovery of an insertion specific to this haplotype. These approaches will pave the way for the development of future map-based cloning approaches for sugarcane and other complex polyploid species.

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“…Sorghum genome mapping based on DNA markers began in 1990s, and since then several maps have been published. Data from available relevant published maps of sorghum (Whitkus et al 1992;Chittenden et al 1994;Pereira et al 1994;Ragab et al 1994;Xu et al 1994;Dufour et al 1997;Ming et al 1998;Nagamura et al 1998;Tao et al 1998;Boivin et al 1999;Peng et al 1999) were assembled and entered into a relational database (SQL7.0 TM ). This curated data contain detailed information on the source including the material used, linkage group, distance, marker designation and alias marker designation in cases where the markers have been renamed by others.…”

Section: Consensus Map Of Sorghummentioning

confidence: 99%

Plant genomics and agriculture: From model organisms to crops, the role of data mining for gene discovery

Ortíz¹,

Mahalakshmi²

2001

Electron. J. Biotechnol.

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Towards a saturated sorghum map using RFLP and AFLP markers

Cited by 100 publications

References 21 publications

Targeted Analysis of Orthologous Phytochrome A Regions of the Sorghum, Maize, and Rice Genomes using Comparative Gene-Island Sequencing

Targeted Analysis of Orthologous Phytochrome A Regions of the Sorghum, Maize, and Rice Genomes using Comparative Gene-Island Sequencing

Diploid/Polyploid Syntenic Shuttle Mapping and Haplotype-Specific Chromosome Walking Toward a Rust Resistance Gene (Bru1) in Highly Polyploid Sugarcane (2n ∼ 12x ∼ 115)

Plant genomics and agriculture: From model organisms to crops, the role of data mining for gene discovery

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