High-throughput genotyping by whole-genome resequencing

Huang, Xuehui; Feng, Qi; Qian, Qian; Zhao, Qiang; Wang, Lu; Wang, Ahong; Guan, Jianping; Fan, Danlin; Weng, Qijun; Huang, Tao; Dong, Guojun; Su, Tao; Han, Bin

doi:10.1101/gr.089516.108

Cited by 805 publications

(748 citation statements)

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“…Using a sequencing-based genotyping method 41 , we sequenced 271 lines in the population with 0.53 coverage for each, and constructed an ultra-dense genotype map. A total of 15 domestication-related traits were phenotyped, with 58 QTLs detected using a composite interval mapping method ( Supplementary Fig.…”

Section: Article Researchmentioning

confidence: 99%

A map of rice genome variation reveals the origin of cultivated rice

Huang

Kurata

Wei

et al. 2012

Nature

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1,407

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Crop domestications are long-term selection experiments that have greatly advanced human civilization. The domestication of cultivated rice (Oryza sativa L.) ranks as one of the most important developments in history. However, its origins and domestication processes are controversial and have long been debated. Here we generate genome sequences from 446 geographically diverse accessions of the wild rice species Oryza rufipogon, the immediate ancestral progenitor of cultivated rice, and from 1,083 cultivated indica and japonica varieties to construct a comprehensive map of rice genome variation. In the search for signatures of selection, we identify 55 selective sweeps that have occurred during domestication. In-depth analyses of the domestication sweeps and genome-wide patterns reveal that Oryza sativa japonica rice was first domesticated from a specific population of O. rufipogon around the middle area of the Pearl River in southern China, and that Oryza sativa indica rice was subsequently developed from crosses between japonica rice and local wild rice as the initial cultivars spread into South East and South Asia. The domestication-associated traits are analysed through high-resolution genetic mapping. This study provides an important resource for rice breeding and an effective genomics approach for crop domestication research.Cultivated rice (Oryza sativa L.), which is grown worldwide and is one of the most important cereals for human nutrition, is considered to have been domesticated from wild rice (Oryza rufipogon) thousands of years ago 1-4 . The differences between O. sativa and O. rufipogon are reflected in a wide range of morphological and physiological traits [5][6][7][8][9] . Despite the fact that rice is a major cereal and a model system for plant biology, the evolutionary origins and domestication processes of cultivated rice have long been debated. The puzzles about rice domestication include: (1) where the geographic origin of cultivated rice was, (2) which types of O. rufipogon served as its direct wild progenitor, and (3) whether the two subspecies of cultivated rice, indica and japonica, are derived from a single or multiple domestications.A wide range of genetic and archaeological studies have been carried out to examine the phylogenetic relationships of rice, and investigate the demographic history of rice domestication [10][11][12][13][14][15][16][17][18][19] . Molecular phylogenetic analyses indicated that indica and japonica originated independently 3,10,20 . However, the well-characterized domestication genes in rice were found to be fixed in both subspecies with the same alleles, thus supporting a single domestication origin [6][7][8][9]16 . Recently, a demographic analysis of single-nucleotide polymorphisms (SNPs) detected from 630 gene fragments suggested a single domestication origin of rice 17 . Meanwhile, population genetics analyses of genome-wide data of cultivated and wild rice have tended to suggest that indica and japonica genomes generally appear to be of independent origin 1...

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Section: Article Researchmentioning

confidence: 99%

A map of rice genome variation reveals the origin of cultivated rice

Huang

Kurata

Wei

et al. 2012

Nature

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1,407

109

1,518

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“…japonica cv. Nipponbare (Huang et al 2009). The population has been expanded, and a total of 270 individuals were sequenced and used in this study.…”

Section: Generation Of Example Data Of An Experimental Resultsmentioning

confidence: 99%

“…Single nucleotide polymorphisms identification between parents by low-coverage sequencing Recently, we developed a strategy for high-throughput genotyping of recombinant inbred lines (RILs) derived from a cross between two sequenced rice accessions (Nipponbare and 93-11) (IRGSP 2005;Yu et al 2002) by bar-coded resequencing with ∼0.02-fold coverage of rice genome for each line (Huang et al 2009). The applicability in genotyping the mapping population still relies on high-quality sequences of the parents to identify SNPs (Nipponbare and 93-11 had BAC-based sequences and whole-genome shotgun sequences, respectively).…”

Section: Resultsmentioning

confidence: 99%

“…And newly available sequencing platforms with up to 10 Gb output per lane and techniques for higher multiplex levels will make this method even faster and more cost-effective. Through this approach, a high-resolution map can be constructed and nearly all recombination events in one population can be identified (Huang et al 2009;Xie et al 2010). Then traits are able to be associated with the individuals of the population efficiently (Rounsley and Last 2010).…”

Section: Discussionmentioning

confidence: 99%

“…A sequencing-based method was recently developed to genotype recombinant populations, where all the individuals in the population were sequenced with low genome coverage (Huang et al 2009). Moreover, through large-scale genome sequencing of hundreds of landraces, a high-density haplotype map containing~3.6 million SNPs was constructed in rice (http://www.ncgr.ac.cn/RiceHapMap).…”

Section: Introductionmentioning

confidence: 99%

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SEG-Map: A Novel Software for Genotype Calling and Genetic Map Construction from Next-generation Sequencing

Zhao

Huang

Lin

et al. 2010

Rice

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The advent of next-generation sequencing technologies opens a new era for discovering genome diversity and genetic mapping. A sequencing-based method was recently developed to genotype recombinant populations with considerably improved resolution and reduced time and cost. To effectively implement this method, here we report the development of an analytic pipeline, sequencing enabled genotyping for mapping recombination populations (SEG-Map), for genotype calling and constructing genetic maps from next-generation sequencing data. SEG-Map was designed to interface with the commonly used tools for mapping next-generation short reads. The output data of SEG-Map would then allow constructing genetic maps and subsequent quantitative trait loci analyses directly. The package is available at http://www.ncgr.ac.cn/software/ SEG. Moreover, directly sequencing over 500 rice landraces enabled a construction of a high-density rice haplotype map. This data set with an average of 2-3 SNPs per kilobyte between indica and japonica could be effectively used in the sequencing-based genotyping of their recombinant mapping populations.

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Unravelling the Mystery of Sudden Cardiac Death Through Genetic Approaches

Koo

Chui

et al. 2011

Encyclopedia of Life Sciences

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The sudden unexplained death syndrome is a tragic and distressing event, which may arise due to an underlying fatal cardiac arrhythmia, which may be associated with a defective ion channel. These electrical abnormalities of the heart do not present with gross structural changes, rendering it a challenging task to the forensic pathologist in ascertaining the cause of death during autopsies. The attempts to identify genetic variations in the key ion channels known to cause arrhythmias have only been able to reveal the presence of putative mutations in a small percentage of the cases. It is thus imperative to look beyond the discovery of single‐nucleotide polymorphisms to other forms of genetic variations (such as copy number variations and structural rearrangements), as well as alternative mechanisms that may underlie the molecular pathogenesis of arrhythmias and electrocardiographic abnormalities causing sudden death. Additionally, the various technological platforms for genetic analysis are also described in this article. Key Concepts: Sudden unexplained death syndrome is an important clinical problem. Sudden death may be the result of a fatal cardiac arrhythmia. Arrhythmias are associated with genetic mutations in ion channel genes. Genetic mutations often exhibit incomplete penetrance. Genetic mutations may have functional impact on the ion channel. Single‐nucleotide polymorphisms only account for a fraction of the cases. Copy number variations and chromosomal aberrations may play a role in sudden death pathology. The role of alternative mechanisms such as epigenetics in arrhythmias/sudden death remains to be ascertained. The technology for identifying genetic variations is advancing rapidly. Genome‐wide sequencing is expected to become increasingly feasible.

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High-throughput genotyping by whole-genome resequencing

Cited by 805 publications

References 19 publications

A map of rice genome variation reveals the origin of cultivated rice

A map of rice genome variation reveals the origin of cultivated rice

SEG-Map: A Novel Software for Genotype Calling and Genetic Map Construction from Next-generation Sequencing

Unravelling the Mystery of Sudden Cardiac Death Through Genetic Approaches

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