ABSTRACT
The Polyploid Gene Assembler (PGA), developed and tested in this study, represents a new strategy to perform gene-space assembly from complex genomes using low coverage DNA sequencing. The pipeline integrates reference-assisted loci and de novo assembly strategies to construct high-quality sequences focused on gene content. Pipeline validation was conducted with wheat (Triticum aestivum), a hexaploid species, using barley (Hordeum vulgare) as reference, that resulted in the identification of more than 90% of genes and several new genes. Moreover, PGA was used to assemble gene content in Saccharum spontaneum species, a parental lineage for hybrid sugarcane cultivars. Saccharum spontaneum gene sequence obtained was used to reference-guided transcriptome analysis of six different tissues. A total of 39,234 genes were identified, 60.4% clustered into known grass gene families. Thirty-seven gene families were expanded when compared with other grasses, three of them highlighted by the number of gene copies potentially involved in initial development and stress response. In addition, 3,108 promoters (many showing tissue specificity) were identified in this work. In summary, PGA can reconstruct high-quality gene sequences from polyploid genomes, as shown for wheat and S. spontaneum species, and it is more efficient than conventional genome assemblers using low coverage DNA sequencing.
Subject(s)
Genome, Plant , Saccharum/genetics , Whole Genome Sequencing , Gene Expression Profiling , Gene Expression Regulation, Plant , Genes, Plant , Hordeum/genetics , Organ Specificity , Phylogeny , Sequence Analysis, RNA , Triticum/geneticsABSTRACT
A obtenção de cariopses de cana-de-açúcar por meio de cruzamento de parentais é de primordial importância para os programas de melhoramento de cultivares. Objetivou-se, neste trabalho comparar o ambiente de germinação de cariopses da casa de vegetação do Programa Cana IAC com um ambiente de condições controladas, a fim de avaliar sua eficiência, no período de 30/09 a 09/10/2004. Foram desenvolvidos dois experimentos, em delineamento experimental de blocos casualizados com quatro repetições, em Jaú, SP. Um deles foi montado sob condições de laboratório em câmara de germinação e outro em casa de vegetação em condições não controladas, sendo cada tratamento constituído por 100 cariopses por repetição, provenientes de seis cruzamentos. Foram realizadas avaliações do índice de velocidade de germinação (IVG), da porcentagem ( por centoG) e dos dias para emergência (DE), em intervalos de 24 horas, após a instalação dos testes. A massa de 100 sementes de cada cruzamento também foi avaliada com o propósito de verificar sua influência nos demais atributos da germinação. Os resultados foram submetidos à análise de variância e a comparação de médias foi feita pelo teste de Tukey, a 0,05 de significância. A massa de 100 sementes foi diferente entre os cruzamentos, e interferiu, de maneira geral, nos atributos IVG e por cento G. Concluiu-se que a casa de vegetação utilizada pelo Programa Cana IAC proporciona porcentagens de germinação semelhantes às da câmara de germinação, porém condições controladas favorecem o IVG e os DE.
The production of true seeds of sugarcane through parental crossing is primordial for the breeding programs of cultivars. With the objective of comparing the efficiency of the environment greenhouse used for seed germination in the IAC Sugarcane Program with an environment with controlled conditions (germination chamber), two experiments were carried out in a completely randomized block with four replicates of 100 seeds each, in Jaú (SP), from 09/30 to 10/09/2004. In both places the treatments were composed of seeds from six crossings. The evaluations accomplished were speed of germination index (SGI), germination percentage ( percent G) and days for emergence (DE) in 24 h intervals after set up treatments. The mass of 100 seeds of each crossing was also evaluated with the purpose of measuring its influence on other germination attributes. The data were submitted to the analysis of variance and averages were compared by the Tukey test at 0.005 significance. The weight of 100 seeds differed among the crossings, and, in general, it interfered with the attributes SGI and percent G. It was concluded that the greenhouse used by the IAC Sugarcane Program provides germination percentages similar to the germination chamber; however, controlled conditions improve SGI and DE.
