2017
DOI: 10.1073/pnas.1619268114
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Abstract: Comprehensive reverse genetic resources, which have been key to understanding gene function in diploid model organisms, are missing in many polyploid crops. Young polyploid species such as wheat, which was domesticated less than 10,000 y ago, have high levels of sequence identity among subgenomes that mask the effects of recessive alleles. Such redundancy reduces the probability of selection of favorable mutations during natural or human selection, but also allows wheat to tolerate high densities of induced mu… Show more

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Cited by 473 publications
(581 citation statements)
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“…This is particularly challenging in wheat because of the current unavailability of the complete genomic sequence. For the ones identified, the availability of sequenced mutant populations [104] alongside current genome editing tools like Clustered regularly interspaced short palindromic repeats-Cas9 technology will constitute an invaluable resource for their functional validation. In addition, a proper combination of omics approaches (such as RNA-seq), empowered with system biology tools, will help to construct regulatory pathways regulating Pi accumulation in wheat during its different developmental stages.…”
Section: Resultsmentioning
confidence: 99%
“…This is particularly challenging in wheat because of the current unavailability of the complete genomic sequence. For the ones identified, the availability of sequenced mutant populations [104] alongside current genome editing tools like Clustered regularly interspaced short palindromic repeats-Cas9 technology will constitute an invaluable resource for their functional validation. In addition, a proper combination of omics approaches (such as RNA-seq), empowered with system biology tools, will help to construct regulatory pathways regulating Pi accumulation in wheat during its different developmental stages.…”
Section: Resultsmentioning
confidence: 99%
“…We conclude with recommendations for how some of these challenges might be overcome using deep sequencing approaches. We reiterate the recommendation from others (Salmon et al, 2012;Jupe et al, 2013;Gardiner et al, 2016;Van Weymers et al, 2016;Krasileva et al, 2017) that non-amplicon based targeted sequence capture (e.g., whole genome exon capture or targeting of particular gene families) is the most promising method for tackling the full complexity of gene family evolution in complex genomes but suggest cautionary strategies that should be considered when interpreting evolutionary patterns.…”
Section: Introduction Background and Aimsmentioning
confidence: 84%
“…Fortunately, rapid advances in sequencing technology and bioinformatic processing mean that the toolbox available to resolve such challenges continues to improve. Targeted sequence capture, for example, has been used effectively to investigate genomic changes in polyploids (Salmon et al, 2012;Gardiner et al, 2016;Krasileva et al, 2017). However, even with these advances in technology there are important issues to consider when resolving and interpreting evolutionary dynamics of gene families, particularly for systems in which recent polyploidization and hybridization could complicate accurate assembly into orthologs and subsequent genotyping within and between copies.…”
Section: Introduction Background and Aimsmentioning
confidence: 99%
“…3b). In a genome-wide approach, tetraploid and hexaploid populations of wheat underwent exome sequencing to identify variation in more than 80% of protein-coding genes, which generated a unique and powerful resource for forward and reverse genetics 71 . In commercial breeding programmes, such mutant populations are coupled with genomics to identify genetic variation that is associated with important traits.…”
Section: Review Insightmentioning
confidence: 99%