“Spot-On” SNP Genotyping: Figure 1.

Ellis, Michael C.

doi:10.1101/gr.10.7.895

“…mate because of the technical problem of resolving more than one chiasma per chromosome arm at this meiotic stage. Thus, we expect that genetic maps of B. distachyon could be quickly generated given its high crossover frequency and given the development of high-throughput markers such as single nucleotide repeats (Ellis, 2000). In diploid B. distachyon ecotypes, the five pairs of chromosomes are sufficiently dissimilar to enable positive identification in routine squash preparations of somatic tissue.…”

Section: Analysis Of the B Distachyon Genome Will Provide A Valuablementioning

confidence: 99%

Brachypodium distachyon. A New Model System for Functional Genomics in Grasses

Draper¹

2001

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A new model for grass functional genomics is described based on Brachypodium distachyon, which in the evolution of the Pooideae diverged just prior to the clade of "core pooid" genera that contain the majority of important temperate cereals and forage grasses. Diploid ecotypes of B. distachyon (2n = 10) have five easily distinguishable chromosomes that display high levels of chiasma formation at meiosis. The B. distachyon nuclear genome was indistinguishable in size from that of Arabidopsis, making it the simplest genome described in grasses to date. B. distachyon is a self-fertile, inbreeding annual with a life cycle of less than 4 months. These features, coupled with its small size (approximately 20 cm at maturity), lack of seed-head shatter, and undemanding growth requirements should make it amenable to high-throughput genetics and mutant screens. Immature embryos exhibited a high capacity for plant regeneration via somatic embryogenesis. Regenerated plants display very low levels of albinism and have normal fertility. A simple transformation system has been developed based on microprojectile bombardment of embryogenic callus and hygromycin selection. Selected B. distachyon ecotypes were resistant to all tested cereal-adapted Blumeria graminis species and cereal brown rusts (Puccinia reconditia). In contrast, different ecotypes displayed resistance or disease symptoms following challenge with the rice blast pathogen (Magnaporthe grisea) and wheat/barley yellow stripe rusts (Puccinia striformis). Despite its small stature, B. distachyon has large seeds that should prove useful for studies on grain filling. Such biological characteristics represent important traits for study in temperate cereals.

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“…Thus, we expect that genetic maps of B. distachyon could be quickly generated given its high crossover frequency and given the development of high-throughput markers such as single nucleotide repeats (Ellis, 2000). In diploid B. distachyon ecotypes, the five pairs of chromosomes are sufficiently dissimilar to enable positive identification in routine squash preparations of somatic tissue.…”

Section: Analysis Of the B Distachyon Genome Will Provide A Valuablementioning

confidence: 99%

Brachypodium distachyon. A New Model System for Functional Genomics in Grasses

Draper

¹

,

Mur

²

,

Jenkins

³

et al. 2001

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A new model for grass functional genomics is described based on Brachypodium distachyon, which in the evolution of the Pooideae diverged just prior to the clade of "core pooid" genera that contain the majority of important temperate cereals and forage grasses. Diploid ecotypes of B. distachyon (2n ϭ 10) have five easily distinguishable chromosomes that display high levels of chiasma formation at meiosis. The B. distachyon nuclear genome was indistinguishable in size from that of Arabidopsis, making it the simplest genome described in grasses to date. B. distachyon is a self-fertile, inbreeding annual with a life cycle of less than 4 months. These features, coupled with its small size (approximately 20 cm at maturity), lack of seed-head shatter, and undemanding growth requirements should make it amenable to high-throughput genetics and mutant screens. Immature embryos exhibited a high capacity for plant regeneration via somatic embryogenesis. Regenerated plants display very low levels of albinism and have normal fertility. A simple transformation system has been developed based on microprojectile bombardment of embryogenic callus and hygromycin selection. Selected B. distachyon ecotypes were resistant to all tested cereal-adapted Blumeria graminis species and cereal brown rusts (Puccinia reconditia). In contrast, different ecotypes displayed resistance or disease symptoms following challenge with the rice blast pathogen (Magnaporthe grisea) and wheat/barley yellow stripe rusts (Puccinia striformis). Despite its small stature, B. distachyon has large seeds that should prove useful for studies on grain filling. Such biological characteristics represent important traits for study in temperate cereals.The past two decades have witnessed an explosion in the use of model eukaryotic organisms to aid studies on species of significant commercial or biological interest. Historically, specific eukaryotes (e.g. Saccharomyces cerevisiae and Caenorhabditis elegans) have attained the status of "models" because they reflect the individual characteristics of species of medical, industrial, or agricultural interest and are often small, easy to work with in large numbers, and cheap to maintain. More recently, the power of model species has been augmented by the development of whole genome sequencing programs. The new field of "functional genomics" provides further challenges for model organisms in the drive to understand the function of each gene in any genome. This requires a plethora of tools to allow an integrative examination of complex biological problems and relate phenotype to genotype. There are two distinct categories of technology that need to be in place to exploit fully any proposed model organism in a functional genomics program (Table I). The technology associated with "physical genomics" is often standardized, generally organism independent, and can be developed theoretically for any species, given sufficient investment of time and resources. In contrast, the "biological genomics" capability associated with any parti...

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“…Recently, numerous methods have been developed for direct genotyping of SNPs (reviewed in: Ellis, 2000; Gut, 2001; Kwok, 2000; Kwok, 2001; Shi, 2001; Syvänen, 2001; Twyman and Primrose, 2003) and SNPs have therefore become increasingly popular markers, particularly in population genetics and evolutionary studies (Syvänen, 2001). Markers in close vicinity of the genes underlying a trait may be in linkage disequilibrium (LD) (Johnson and Todd, 2000) and this makes SNPs especially attractive for the identification of such genes via association and linkage studies (Spiegelman et al ., 2000).…”

Section: Introductionmentioning

confidence: 99%