Study : Populus deltoides Raw sequence reads


Populus deltoides Raw sequence reads
Populus deltoides is one of the principal short rotation woody crop species for providing clean, renewable and sustainable fuels in North America, because of its fast perennial growth habit and wide natural distribution. While P. deltoides provides the benefits of an ideal bioenergy crop, the genes that regulate biomass productivity and carbon partitioning into lignicellulosics are largely unknown, despite their critical relevance for germplasm improvement. Recently, association genetics has become the primary approach for rapid identification of genes that regulate complex traits in humans, animals and agricultural/forestry crops. Poplars are particularly suited to unveil the molecular basis of biomass productivity and composition using this approach because of low domestication, large open-pollinated native populations, and high levels of genetic and phenotypic variation. However, with a few exceptions, association genetics studies in plants have been hampered by limited gene and polymorphism coverage, and restricted multiplex capacity of genotyping platforms. Here we propose a radically different approach for association mapping, which combines sequence-capture followed by high-throughput sequencing to genotype coding and regulatory sequences in the whole-genome of P. deltoides. To identify genetic polymorphisms that regulate biomass productivity and carbon partitioning in P. deltoides we will: (1) optimize sequence-capture for unbiased, high-throughput and low cost recovery of target coding and regulatory sequences in P. deltoides; (2) carry out whole-genome genotyping of a P. deltoides unstructured population for association mapping; and (3) identify significant SNP-trait associations with biomass growth and carbon partitioning to define genes and alleles that regulate trait variation. This proposal utilizes and advanced approach (association genetics) coupled to highly sophisticated genomic tools (sequence-capture and high-throughput sequencing) to uncover genes that regulate traits that determine biomass growth and composition that is unprecedented in tree crops. The research proposed is well aligned with aims of the Biological and Environmental Research Program to understand complex biological systems at the molecular and whole-plant level by exploring the DOE-derived genomic information and expanding its value for the scientific community.


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