Genetic mapping and characterization of sorghum and related crops by means of maize DNA probes.

Hulbert, Scot H.; Richter, Todd; Axtell, John D.; Bennetzen, Jeffrey L.

doi:10.1073/pnas.87.11.4251

Cited by 265 publications

(124 citation statements)

References 25 publications

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“…In previous work, it was noted that at least some of the highly repeated sequences of maize hybridize to only a few fragments in sorghum DNA (Hulbert et al, 1990). These observations suggest that the repetitive sequences of maize may have evolved at a higher rate than low-copy-number genomic sequences or that they have a different evolutionary origin.…”

Section: The Sh2-7527 Insertion Is Not a Repetitive Sequence In Closementioning

confidence: 96%

The Maize Genome Contains a Helitron Insertion

et al. 2003

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The maize mutation sh2-7527 was isolated in a conventional maize breeding program in the 1970s. Although the mutant contains foreign sequences within the gene, the mutation is not attributable to an interchromosomal exchange or to a chromosomal inversion. Hence, the mutation was caused by an insertion. Sequences at the two Sh2 borders have not been scrambled or mutated, suggesting that the insertion is not caused by a catastrophic reshuffling of the maize genome. The insertion is large, at least 12 kb, and is highly repetitive in maize. As judged by hybridization, sorghum contains only one or a few copies of the element, whereas no hybridization was seen to the Arabidopsis genome. The insertion acts from a distance to alter the splicing of the sh2 pre-mRNA. Three distinct intron-bearing maize genes were found in the insertion. Of most significance, the insertion bears striking similarity to the recently described DNA helicase-bearing transposable elements termed Helitrons . Like Helitrons , the inserted sequence of sh2-7527 is large, lacks terminal repeats, does not duplicate host sequences, and was inserted between a host dinucleotide AT. Like Helitrons , the maize element contains 5 TC and 3 CTRR termini as well as two short palindromic sequences near the 3 terminus that potentially can form a 20-bp hairpin. Although the maize element lacks sequence information for a DNA helicase, it does contain four exons with similarity to a plant DEAD box RNA helicase. A second Helitron insertion was found in the maize genomic database. These data strongly suggest an active Helitron in the present-day maize genome.

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Section: The Sh2-7527 Insertion Is Not a Repetitive Sequence In Closementioning

confidence: 96%

The Maize Genome Contains a Helitron Insertion

et al. 2003

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“…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 points for studies of genome organization and evolution in the Poaceae (Gaut et al, 2000;Isawa and Shimamoto, 1996). The small size of the rice genome makes it a particularly attractive target for large-scale sequencing projects (Goff et al, 2002;Yu et al, 2002) and physical mapping studies (http://rgp.dna.affrc.…”

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confidence: 99%

“…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).…”

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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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“…Isozyme loci initially shown to be syntenic in Triticum aestivum (Hart and Langston 1977) are also syntenic in many relatives of wheat (Hart 1979). DNA markers have demonstrated a nearly perfect retention of linkage alignment in tomato and potato (Bonierbale et al 1988), and linkage conservation has been found among sorghum and its relatives (Hulbert et al 1990). Comparisons of more divergent taxa, such as tomato and pepper , have detected few conserved linkages.…”

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confidence: 99%