GWAS: Linkage Analysis

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For many decades, linkage analysis has been well-established and shown to be an effective tool for studying the complex quantitative traits. Despite of its great successes, this approach has great weakness because it only captures limited allelic diversity existing in two parental lines and also limited in low genomic resolution (Borevitz and Nordborg 2003). To address this issue, GWAS utilizing diverse germplasm collections and recombination events that have been accumulated during the evolution and domestication has been proposed (Zhu et al. 2008). Without the involvements of costs and time for developing mapping populations, GWAS can investigate a set of genetically unstructured genotypes and generate more precise QTL positions if a sufficient …show more content…
Through GET, DNA can be altered in a very precise manner, often a single base (Huang et al. 2016). For targeted genome editing, two sequence-specific nucleases, zinc finger nucleases (ZFN) and transcription activator-like effector nucleases (TALEN), have been initially proposed to cut in the double-strand DNA in eukaryotic organisms (Ainley et al. 2013). More recently, clustered regular interspaced short palindromic repeats/CRISPR-associated nucleases (CRISPR/Cas) based on the bacterial and archaeal clustered regularly interspaced short palindromic repeats (CRISPR) adaptive immune system has become out as a potent and precise tool for genome editing (Cardi 2016; Sun et al. 2015). In principle, GET is based on the “break” in double-strand DNA by sequence-specific nucleases and then “repairs” through two different procedures; the non-homologous end-joining (NHEJ) or homology-directed repair (HDR) (Gaj et al. 2013, Puchta and Fauser 2014, Rinaldo and Ayliffe 2015, Voytas 2013). In soybean, mutations in targeted genes have been reported for unsaturation level of seed fatty acids by TALEN (Haun et al. 2014) and herbicide resistance by CRISPR/Cas9 (Li et al. 2015). Anyway, genome editing approach in soybean has not been associated with important agronomic traits (Curtin et al. 2011, Jacobs et al. 2015; Sun et al. 2015). The GET may provide an alternative to conventional breeding processes mainly rely on meiotic recombination events through artificial crossings between selected parent germplasm. However, the off-target effects are still the major issue of genome editing for functional genomics and plant breeding. Barabaschia et al. (2016) mentioned that very accurate and detailed bioinformatic analysis of target site is necessary for successful applications of GET, especially when the

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