A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica)

Jia, Guanqing; Huang, Xuehui; Zhi, Hui; Zhao, Yan; Zhao, Qiang; Li, Wenjun; Chai, Yimin; Yang, Lifang; Liu, Kunyan; Lu, Hengyun; Zhu, Chuanrang; Lu, Yiqi; Zhou, Congcong; Fan, Danlin; Weng, Qijun; Guo, Yunli; Huang, Tao; Zhang, Lei; Lu, Tingting; Feng, Qi; Hao, Haiyan; Liu, Hongkuan; Lü, Ping; Zhang, Ning; Li, Yuhui; Guo, Erhu; Wang, Shujun; Wang, Suying; Liu, Jinrong; Zhang, Wenfei; Chen, Guoqiu; Zhang, Baojin; Li, Wei; Wang, Yongfang; Li, Haiquan; Zhao, Bin; Li, Jiayang; Diao, Xianmin; Han, Bin

doi:10.1038/ng.2673

Cited by 406 publications

(379 citation statements)

References 38 publications

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“…Genome-wide association studies (GWAS), which seek to identify markers associated with a trait by large-scale genotyping of individuals differing for that trait, have recently been applied to cereal crop species with impressive results (Tian et al, 2011;Huang et al, 2012;Jia et al, 2013). GWAS may also be highly effective for the identification of brachypodium genes with roles in resistance to cereal disease.…”

Section: Future Prospects For Brachypodium As a Model For Cereal-pathmentioning

confidence: 99%

Brachypodium as an emerging model for cereal–pathogen interactions

et al. 2015

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Background Cereal diseases cause tens of billions of dollars of losses annually and have devastating humanitarian consequences in the developing world. Increased understanding of the molecular basis of cereal host-pathogen interactions should facilitate development of novel resistance strategies. However, achieving this in most cereals can be challenging due to large and complex genomes, long generation times and large plant size, as well as quarantine and intellectual property issues that may constrain the development and use of community resources. Brachypodium distachyon (brachypodium) with its small, diploid and sequenced genome, short generation time, high transformability and rapidly expanding community resources is emerging as a tractable cereal model.Scope Recent research reviewed here has demonstrated that brachypodium is either susceptible or partially susceptible to many of the major cereal pathogens. Thus, the study of brachypodium-pathogen interactions appears to hold great potential to improve understanding of cereal disease resistance, and to guide approaches to enhance this resistance. This paper reviews brachypodium experimental pathosystems for the study of fungal, bacterial and viral cereal pathogens; the current status of the use of brachypodium for functional analysis of cereal disease resistance; and comparative genomic approaches undertaken using brachypodium to assist characterization of cereal resistance genes. Additionally, it explores future prospects for brachypodium as a model to study cereal-pathogen interactions.Conclusions The study of brachypodium-pathogen interactions appears to be a productive strategy for understanding mechanisms of disease resistance in cereal species. Knowledge obtained from this model interaction has strong potential to be exploited for crop improvement.

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Section: Future Prospects For Brachypodium As a Model For Cereal-pathmentioning

confidence: 99%

Brachypodium as an emerging model for cereal–pathogen interactions

et al. 2015

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“…Genetic diversity and population structure studies in Chinese green foxtail [24] and domesticated landraces [25] revealed high level of genetic diversity, an average allele number per locus of 33.5 and 20.9, respectively. A high density haplotype map of 85 million single nucleotide polymorphism (SNP) markers was also constructed, which revealed genomic variation among 916 foxtail millet accessions collected from around the world [5]. All these analyses provide the genomic data for the development of the Setaria model system.…”

Section: Promoting Setaria As a Modelmentioning

confidence: 99%

“…Given their hybrid fecundity, foxtail millet and green foxtail could be viewed as a single species with two botanical names. With a high quality reference genome sequence [4] and a high-density haplotype map of genome variation [5] and other genomic data, the accumulated genomic information for foxtail millet and green foxtail has reached the level where this species pair can now truly be considered a novel model system. Several publications, foxtail millet: a sequencedriven grass model system by Doust et al [6], Setaria viridis: a model for C 4 photosynthesis by Brutnell et al [7], and two review papers of using foxtail millet and green foxtail as model [8,9] have helped foster enthusiasm and forward momentum that is leading to the development of Setaria as a model system.…”

Section: Initiation Of the Setaria Modelmentioning

confidence: 99%

“…Extensive progress has been made in characterizing different aspects of Setaria genetics. In addition to the two genome sequences of foxtail millet released in 2012 [4,20], a third genome sequence of foxtail millet (landrace Daqingjie) and a genome sequence of green foxtail (Accession N10) have also been released [5]. Re-sequencing of foxtail millet landrace Shilixiang was also carried out to identify useful markers for studies of agronomic characters [21].…”

Section: Promoting Setaria As a Modelmentioning

confidence: 99%

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Initiation of Setaria as a model plant

Diao¹,

Schnable²,

Bennetzen³

et al. 2014

Front. Agr. Sci. Eng.

101

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Model organisms such as Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) have proven essential for efficient scientific discovery and development of new methods. With the diversity of plant lineages, some important processes such as C 4 photosynthesis are not found in either Arabidopsis or rice, so new model species are needed. Due to their small diploid genomes, short life cycles, self-pollination, small adult statures and prolific seed production, domesticated foxtail millet (Setaria italica) and its wild ancestor, green foxtail (S. viridis), have recently been proposed as novel model species for functional genomics of the Panicoideae, especially for study of C 4 photosynthesis. This review outlines the development of these species as model organisms, and discusses current challenges and future potential of a Setaria model.

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“…Thirdly, compared to the limited magnitude in gene expression change that can be detected by microarray, the dynamic range of gene expression can be analyzed by RNA-seq is unprecedented [51]. Moreover, RNA-seq are used to characterize the single nucleotide variation (SNV) [52,53] and RNAediting activity in gene transcripts [54,55]. Notably, in regard to the non-model organisms that lack genome sequences, the RNA-seq technology is an extremely valuable tool.…”

Section: Second Generation Sequencing Versus Other Technologies In Trmentioning

confidence: 99%

De novo assembly of transcriptome from next‐generation sequencing data

Kong

Zhao

et al. 2016

Quant. Biol.

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Reconstruction of transcriptome by de novo assembly from next generation sequencing (NGS) short-sequence reads provides an essential mean to catalog expressed genes, identify splicing isoforms, and capture the expression detail of transcripts for organisms with no reference genome available. De novo transcriptome assembly faces many unique challenges, including alternative splicing, variable expression level covering a dynamic range of several orders of magnitude, artifacts introduced by reverse transcription, etc. In the current review, we illustrate the grand strategy in applying De Bruijn Graph (DBG) approach in de novo transcriptome assembly. We further analyze many parameters proven critical in transcriptome assembly using DBG. Among them, k-mer length, coverage depth of reads, genome complexity, performance of different programs are addressed in greater details. A multi-k-mer strategy balancing efficiency and sensitivity is discussed and highly recommended for de novo transcriptome assembly. Future direction points to the combination of NGS and third generation sequencing technology that would greatly enhance the power of de novo transcriptomics study.

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A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica)

Cited by 406 publications

References 38 publications

Brachypodium as an emerging model for cereal–pathogen interactions

Brachypodium as an emerging model for cereal–pathogen interactions

Initiation of Setaria as a model plant

De novo assembly of transcriptome from next‐generation sequencing data

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