C<scp>EREAL</scp> C<scp>HROMOSOME</scp> S<scp>TRUCTURE</scp>, E<scp>VOLUTION, AND</scp> P<scp>AIRING</scp>

Moore, Graham

doi:10.1146/annurev.arplant.51.1.195

Cited by 46 publications

(40 citation statements)

References 174 publications

(136 reference statements)

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“…Similar clustering in distal regions was also found in tetraploid wheat using PstI-based AFLP markers (Peng et al, 2000). The higher density of such clusters in distal regions could well be related to the trend of PstI-based markers to map in gene-rich, hypomethylated regions of the genome (Langridge and Chalmers, 1998;Moore, 2000). The results obtained from the present study indicate that DArT provides high quality markers that can be used to construct medium-density genetic linkage maps for plants even when no sequence information is available.…”

Section: Discussionsupporting

confidence: 57%

Development of a molecular linkage map of pearl millet integrating DArT and SSR markers

et al. 2011

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Pearl millet is an important component of food security in the semi-arid tropics and is assuming greater importance in the context of changing climate and increasing demand for highly nutritious food and feed. Molecular tools have been developed and applied for pearl millet on a limited scale. However, the existing tool kit needs to be strengthened further for its routine use in applied breeding programs. Here, we report enrichment of the pearl millet molecular linkage map by exploiting low-cost and high-

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Section: Discussionsupporting

confidence: 57%

Development of a molecular linkage map of pearl millet integrating DArT and SSR markers

et al. 2011

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“…Efforts to sequence other crop genomes, including maize, are underway (http://www.nsf.gov/bio/pubs/awards/genome02.htm) (Palmer et al, 2003;Whitelaw et al, 2003). The maize genome consists of about 2400 Mb, i.e., approximately 6-fold larger than that of rice (reviewed by Moore, 2000). It is estimated that the maize genome contains approximately 50,000 genes that account for only 10-15% of the genome (Bennetzen et al, 2001).…”

Section: Introductionmentioning

confidence: 99%

Evaluation of five ab initio gene prediction programs for the discovery of maize genes

Yao

Guo

et al. 2005

Plant Mol Biol

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Five ab initio programs (FGENESH, GeneMark.hmm, GENSCAN, GlimmerR and Grail) were evaluated for their accuracy in predicting maize genes. Two of these programs, GeneMark.hmm and GENSCAN had been trained for maize; FGENESH had been trained for monocots (including maize), and the others had been trained for rice or Arabidopsis. Initial evaluations were conducted using eight maize genes (gl8a, pdc2, pdc3, rf2c, rf2d, rf2e1, rth1, and rth3) of which the sequences were not released to the public prior to conducting this evaluation. The significant advantage of this data set for this evaluation is that these genes could not have been included in the training sets of the prediction programs. FGENESH yielded the most accurate and GeneMark.hmm the second most accurate predictions. The five programs were used in conjunction with RT-PCR to identify and establish the structures of two new genes in the a1-sh2 interval of the maize genome. FGENESH, GeneMark.hmm and GENSCAN were tested on a larger data set consisting of maize assembled genomic islands (MAGIs) that had been aligned to ESTs. FGENESH, GeneMark.hmm and GENSCAN correctly predicted gene models in 773, 625, and 371 MAGIs, respectively, out of the 1353 MAGIs that comprise data set 2.

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“…go.jp). In contrast, maize presents several challenges because of its relatively large ancient allotetraploid genome (Gaut et al, 2000;Moore, 2000), approximately six times larger than rice, and high levels of retrotransposons and segmental duplications. The sorghum (Sorghum bicolor) genome is approximately onethird the size of the genome of maize, 750 Mb and 2,400 Mb, respectively (Arumuganathan and Earle, 1991).…”

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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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CEREAL CHROMOSOME STRUCTURE, EVOLUTION, AND PAIRING

Cited by 46 publications

References 174 publications

Development of a molecular linkage map of pearl millet integrating DArT and SSR markers

Development of a molecular linkage map of pearl millet integrating DArT and SSR markers

Evaluation of five ab initio gene prediction programs for the discovery of maize genes

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

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