RESUMO
In quantitative trait locus (QTL) mapping studies, it is mandatory that the available financial resources are spent in such a way that the power for detection of QTL is maximized. The objective of this study was to optimize for three different fixed budgets the power of QTL detection 1 - beta* in recombinant inbred line (RIL) populations derived from a nested design by varying (1) the genetic complexity of the trait, (2) the costs for developing, genotyping, and phenotyping RILs, (3) the total number of RILs, and (4) the number of environments and replications per environment used for phenotyping. Our computer simulations were based on empirical data of 653 single nucleotide polymorphism markers of 26 diverse maize inbred lines which were selected on the basis of 100 simple sequence repeat markers out of a worldwide sample of 260 maize inbreds to capture the maximum genetic diversity. For the standard scenario of costs, the optimum number of test environments (E (opt)) ranged across the examined total budgets from 7 to 19 in the scenarios with 25 QTL. In comparison, the E (opt) values observed for the scenarios with 50 and 100 QTL were slightly higher. Our finding of differences in 1 - beta* estimates between experiments with optimally and sub-optimally allocated resources illustrated the potential to improve the power for QTL detection without increasing the total resources necessary for a QTL mapping experiment. Furthermore, the results of our study indicated that also in studies using the latest genomics tools to dissect quantitative traits, it is required to evaluate the individuals of the mapping population in a high number of environments with a high number of replications per environment.
Assuntos
Mapeamento Físico do Cromossomo/economia , Mapeamento Físico do Cromossomo/métodos , Locos de Características Quantitativas/genética , Alocação de Recursos , Zea mays/genética , Reprodutibilidade dos TestesAssuntos
Genoma Humano , Genômica/tendências , Haplótipos/genética , Mapeamento Físico do Cromossomo , Polimorfismo de Nucleotídeo Único/genética , Ásia/etnologia , Povo Asiático/genética , Pesquisa Biomédica/economia , População Negra/genética , Europa (Continente)/etnologia , Doenças Genéticas Inatas/genética , Predisposição Genética para Doença/genética , Genômica/economia , Humanos , Cooperação Internacional , Nigéria/etnologia , Patentes como Assunto/legislação & jurisprudência , Mapeamento Físico do Cromossomo/economia , População Branca/genéticaAssuntos
Biotecnologia/economia , Biotecnologia/legislação & jurisprudência , Genoma Humano , Genômica/economia , Genômica/legislação & jurisprudência , Haplótipos/genética , Variação Genética/genética , Humanos , Análise de Sequência com Séries de Oligonucleotídeos , Mapeamento Físico do Cromossomo/economia , Estados UnidosAssuntos
Genoma , Camundongos/genética , Mapeamento Físico do Cromossomo/métodos , Análise de Sequência de DNA/métodos , Animais , Genômica/economia , Genômica/métodos , Projeto Genoma Humano , Humanos , Mapeamento Físico do Cromossomo/economia , Análise de Sequência de DNA/economia , Sitios de Sequências RotuladasRESUMO
We have developed software that allows the prediction of the genomic location of a bacterial artificial chromosome (BAC) clone, or other large genomic clone, based on a simple restriction digest of the BAC. The mapping is performed by comparing the experimentally derived restriction digest of the BAC DNA with a virtual restriction digest of the whole genome sequence. Our trials indicate that this program identified the genomic regions represented by BAC clones with a degree of accuracy comparable to that of end-sequencing, but at considerably less cost. Although the program has been developed principally for use with Arabidopsis BACs, it should align large insert genomic clones to any fully sequenced genome.
Assuntos
Cromossomos Artificiais Bacterianos/genética , Impressões Digitais de DNA/métodos , Enzimas de Restrição do DNA/metabolismo , Genoma , Mapeamento Físico do Cromossomo/métodos , Software , Arabidopsis/genética , Pareamento Incorreto de Bases/genética , Clonagem Molecular , Mapeamento de Sequências Contíguas/métodos , Genoma de Planta , Biblioteca Genômica , Mapeamento Físico do Cromossomo/economia , Sensibilidade e EspecificidadeRESUMO
We describe here an efficient strategy for simultaneous genome mapping and sequencing. The approach is based on physically oriented, overlapping restriction fragment libraries called slalom libraries. Slalom libraries combine features of general genomic, jumping and linking libraries. Slalom libraries can be adapted to different applications and two main types of slalom libraries are described in detail. This approach was used to map and sequence (with approximately 46% coverage) two human P1-derived artificial chromosome (PAC) clones, each of approximately 100 kb. This model experiment demonstrates the feasibility of the approach and shows that the efficiency (cost-effectiveness and speed) of existing mapping/sequencing methods could be improved at least 5-10-fold. Furthermore, since the efficiency of contig assembly in the slalom approach is virtually independent of length of sequence reads, even short sequences produced by rapid, high throughput sequencing techniques would suffice to complete a physical map and a sequence scan of a small genome.
