High-throughput genotyping by whole-genome resequencing.

By Xuehui Huang, Qi Feng, Q. Qian, Qiang Zhao, Lu Wang, Ahong Wang, Jianping Guan, Danlin Fan, Qijun Weng, Tao Huang and 3 more. Genome Research, 2009

856 citations recorded by the source corpus.

The next-generation sequencing technology coupled with the growing number of genome sequences opens the opportunity to redesign genotyping strategies for more effective genetic mapping and genome analysis. We have developed a high-throughput method for genotyping recombinant populations utilizing whole-genome resequencing data generated by the Illumina Genome Analyzer. A sliding window approach is designed to collectively examine genome-wide single nucleotide polymorphisms for genotype calling and recombination breakpoint determination. Using this method, we constructed a genetic map for 150 rice recombinant inbred lines with an expected genotype calling accuracy of 99.94% and a resolution of recombination breakpoints within an average of 40 kb. In comparison to the genetic map constructed with 287 PCR-based markers for the rice population, the sequencing-based method was approximately 20x faster in data collection and 35x more precise in recombination breakpoint determination. Using the sequencing-based genetic map, we located a quantitative trait locus of large effect on plant height in a 100-kb region containing the rice "green revolution" gene. Through computer simulation, we demonstrate that the method is robust for different types of mapping populations derived from organisms with variable quality of genome sequences and is feasible for organisms with large genome sizes and low polymorphisms. With continuous advances in sequencing technologies, this genome-based method may replace the conventional marker-based genotyping approach to provide a powerful tool for large-scale gene discovery and for addressing a wide range of biological questions.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/59d10aa27664579481fc7882c6cd681b4add7ed7

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Citations in the corpus

Genotyping-By-Sequencing for Plant Genetic Diversity Analysis: A Lab Guide for SNP Genotyping (2014, background): “It was inspired by the whole genome sequence effort in rice [2] and builds upon the protocol of restriction site-associated DNA (RAD) tags [12].”
Comprehending crystalline β-carotene accumulation by comparing engineered cell models and the natural carotenoid-rich system of citrus (2011, positive): “…and drives AhNRAMP1 cDNA under the control of the –272/–131 region of the barley IDS2 gene containing Fe-deﬁciency-responsive element 1 (IDE1) and IDE2, ﬂanked by the –90/+8 region of the CaMV35S X tobacco ( Nicotiana tabacum L. cv. Petit-Havana SR1) according to the method of Helmer et al. (1984).”
A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species (2011, methodology): “and has been used to rapidly determine the complete chloroplast genome sequences of spruce and several pine species [15] and for discovery and mapping of genomic SNPs in rice [16,17].”
Genome-wide genetic marker discovery and genotyping using next-generation sequencing (2011, methodology): “This approach has been used to construct genetic maps for rice based on low-coverage whole-genome resequencing of hundreds of recombinant inbred lines (RILs”
Utilization of next-generation sequencing platforms in plant genomics and genetic variant discovery (2010, methodology): “An important application of second-generation sequencing technologies has been the identification of sequencing variants, by aligning short DNA or cDNA reads to the sequence of a DNA molecule from another individual, another strain or another species (Barbazuk et al. 2007; Hillier et al. 2008; Ossow”
Development of genome-wide SNP assays for rice (2010, methodology): “…2010) With rapid changes in technology and computational resources, the two-step paradigm of SNP-discovery followed by SNP-detection is rapidly merging into a single, sequencebased process of simultaneous SNP discovery and detection (Craig et al. 2008, Cronn et al. 2008, Huang et al. 2009, 2010).”
Gene Pyramiding for Sustainable Crop Improvement against Biotic and Abiotic Stresses (2020, methodology): “Sequencing of each line within a recombinant inbred line (RIL) population has been used to easily and reliably classify recombinant breakpoints [108].”
Genomic Selection in Plant Breeding (2011, background): “As the cost continues to drop for whole-genome sequencing (Podolak, 2010), genetic mapping and genotyping by resequencing are now possible for plants with complete genomic sequences (Huang et al., 2009).”
Natural variations and genome-wide association studies in crop plants. (2014, methodology): “For genotyping of recombinant populations, a method that utilizes low-coverage whole-genome resequencing data was developed (38, 137).”
Genotyping‐by‐Sequencing for Plant Breeding and Genetics (2012, methodology): “Whole-genome resequencing has been applied in Arabidopsis thaliana (L.) Heynh., 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…”
High-Throughput SNP Genotyping to Accelerate Crop Improvement (2014, background): “13X sequence coverage for mapping populations and approximately 1X sequence coverage for diverse germplasm (Huang et al. 2009; Huang et al. 2010; Xu et al. 2010; Huang et al. 2012).”
The genetics of inbreeding depression (2009, background): “New DNA sequencing technologies may greatly lower the costs and time required to genotype mapping population”