Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

By Xun Xu, Xin Liu, Song Ge, J. Jensen, F. Hu, Xin Li, Yang Dong, Ryan N. Gutenkunst, L. Fang, Lei Huang and 15 more. Nature Biotechnology, 2011

799 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/5445d2999223edc295190dbff723bb91e969d5af

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Citations in the corpus

SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data (2014, background): “A variety of studies have begun to utilize and illustrate how to deal with extensive SNP data [5-10].”
Heterosis: Many Genes, Many Mechanisms—End the Search for an Undiscovered Unifying Theory (2012, background): “This concept is consistent with extensive single-nucleotide polymorphism (SNP), indel, and transposon variation found within and near genes when comparing individual genomes within species [60–65].”
Past and Future Use of Wild Relatives in Crop Breeding (2017, background): “Abbreviations: CSSL, chromosome segment substitution line; CWR, crop wild relative; MAS, marker-assisted selection; QTL, quantitative trait locus; SNP, single-nucleotide polymorphism; WGS, wholegenome shotgun sequence.”
SNP-Based Genetic Linkage Map of Soybean Using the SoySNP6K Illumina Infinium BeadChip Genotyping Array (2013, background): “Millions of SNPs were generated in Soybean (Lam et al., 2010), Arabidopsis (Zhang et al., 2009), Rice (Subbaiyan et al., 2012; Xu et al., 2012), and other crops (Sim et al., 2012a,b; Sharpe et al., 2013; Delourme et al., 2013).”
Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data (2013, background): “Since the polymorphism differences between rice cultivars are limited, a high quality reference genome sequence is essential for the comparison of closely related rice cultivars (Zhang et al. 2010; Lu et al. 2010; Huang et al. 2012; Xu et al. 2012; Yang et al. 2012) so that errors can be minimized.”
Natural variations and genome-wide association studies in crop plants. (2014, methodology): “Owing to significant decreases in sequencing cost, this strategy has been successfully applied in several crops (34, 39, 43, 60, 123, 127).”
The Sequence of 1504 Mutants in the Model Rice Variety Kitaake Facilitates Rapid Functional Genomic Studies (2017, methodology): “High-quality genomic DNA was isolated from young leaves using the cetyltrimethyl ammonium bromide (CTAB) method (Xu et al., 2012).”
Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array (2014, background): “Advances in next-generation sequencing have significantly facilitated the discovery of SNPs by whole genome (Berkman et al., 2012; Chia et al., 2012; Xu et al., 2012), transcriptome (Allen et al., 2011; Cavanagh et al., 2013; Oliver et al., 2013) or reduced-representation sequencing in diverse…”
Genotyping‐by‐Sequencing for Plant Breeding and Genetics (2012, background): “…rice (Oryza sativa L.), and maize (Zea mays L.) (Huang et al., 2009; Ashelford et al., 2011; Gan et al., 2011; Chia et al., 2012; Jiao et al., 2012; Xu et al., 2012), although it quickly becomes less manageable with larger, more complex genomes that lack a solid reference genome (Morrell et al.,…”
COLD1 confers chilling tolerance in rice. (2015, positive): “Several developmental trait-related genes, such as SH4 and PROG1, with signatures of domestication in cultivated rice have been identified using genetic mapping for quantitative trait loci (QTLs) and genome-wide association studies (GWAS) (Huang et al., 2012; Xu et al., 2012).”