The evolution of weedy plants

計畫名稱:The evolution of weedy plants

所屬單位:生演所

研究團隊:李承叡實驗室

計畫主持人:李承叡

資源需求:R

使用期間:2016/08~

研究主題:
The evolution of weedy plants

研究內容概述:
Weeds are plant species that are highly adapted to disturbed habitats such as farms and roadsides. While the ecology and traits making weeds weedy have been much studied (for example, drought tolerance, fast flowering, and tolerance to strong sunlight), the genetic and genomic architecture of weedy plant evolution remain obscure. Although the model plant Arabidopsis thaliana has long be regarded as a human-associated weed, our recent study discovered natural Arabidopsis accessions living in natural un-disturbed habitats. Those natural ice age “relicts” once occupied the whole Eurasia until later being rapidly replaced by the weedy “non-relict” population, likely facilitated by the expansion of agriculture. A. thaliana therefore represents a perfect model where different magnitude of “weediness” exist as within-species polymorphism, allowing detailed genetic investigation. We plan to use next generation sequencing to investigate natural DNA variation within this species and identify possible genomic regions controlling the evolution of weeds. Specifically, we will use the HPC system to map sequenced Illumina reads to reference genome and call single nucleotide polymorphism (SNP) with freely available third-party software. Population genomics analyses will be performed based on the SNP data, where we calculate allele frequency, population structure, and patterns of gene flow between natural relict versus weedy non-relict Arabidopsis thaliana. Combining with greenhouse and molecular biology experiments, we further plan to do genetic mapping for genes controlling weedy traits. Using phenotype and whole-genome data from at least 200 samples, we will perform quantitative trait loci mapping and genomewide association study.

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