SnpHub

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About this dataset

This dataset contains 681 hexaploid wheat accessions published since 2019. The sequencing data were mapped to IWGSC RefSeq v1.0, and were annotated by IWGSC RefSeq v1.1 using SnpEff. For more details about the accessions, please check "SampleInfo" page.


Number of accessions Citation Corresponding author Institution of corresponding author
245 Weilong Guo, et al. Origin and adaptation to high altitude of Tibetan semi-wild wheat. Nature Communications, 2020, 11(1):5085. Qixin Sun
Zhongfu Ni
Huiru Peng
China Agricultural University
172 Yao Zhou, et al. Triticum population sequencing provides insights into wheat adaptation. Nature Genetics, 2020, 52(12):1412-1422. Fei Lu
Yuling Jiao
Institute of Genetics and Developmental Biology
Chinese Academy of Sciences
145 Chenyang Hao, et al. Resequencing of 145 Landmark Cultivars Reveals Asymmetric Sub-genome Selection and Strong Founder Genotype Effects on Wheat Breeding in China. Molecular Plant, 2020, 7;13(12):1733-1751. Xueyong Zhang
Hongfeng Lu
Institute of Crop Science
Chinese Academy of Agricultural Sciences
63 Hong Cheng, et al. Frequent intra- and inter-species introgression shapes the landscape of genetic variation in bread wheat. Genome Biology, 2019, 20(1):136. Yu Jiang
Qixin Sun
Weining Song
Northwest A&F University
26 Zhengzhao Yang, et al. ggComp enables dissection of germplasm resources and construction of a multiscale germplasm network in wheat. Plant Physiology, 2022, 28;188(4):1950-1965. Weilong Guo China Agricultural University
15 Sean Walkowiak, et al. Multiple wheat genomes reveal global variation in modern breeding. Nature, 2020, 588, 277-283. Curt A. McCartney
Manuel Spannagl
Thomas Wicker
Curtis J. Pozniak
University of Saskatchewan
10 Jing Liu, et al. Ectopic expression of VRT-A2 underlies the origin of Triticum polonicum and Triticum petropavlovskyi with long outer glumes and grains. Molecular Plant, 2021, 14(9), 1472-1488. Zhongfu Ni
Jie Liu
China Agricultural University
1 Yan Dong, et al. Fine mapping of QPm.caas-3BS, a stable QTL for adult-plant resistance to powdery mildew in wheat (Triticum aestivum L.). Theor Appl Genet, 135, 1083-1099 (2022). Xianchun Xia Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)
4 Unpublished Unpublished Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)
&
Crop Research Institute, Shandong Academy of Agricultural Sciences

Citation

1. About the dataset

The "SampleInfo" page shows the article source of each accessions.

2. About SnpHub

SnpHub is a Shiny-based server framework for retrieving, analyzing and visualizing the large genomic variations data in a lab.

Wenxi Wang, Zihao Wang, Xintong Li, Zhongfu Ni, Zhaorong Hu, Mingming Xin, Huiru Peng, Yingyin Yao, Qixin Sun, Weilong Guo. (2020). SnpHub: an easy-to-set-up web server framework for exploring large-scale genomic variation data in the post-genomic era with applications in wheat. GigaScience, 9(6), giaa060. https://doi.org/10.1093/gigascience/giaa060





Available samples


Available chromosomes


Pre-defined sample groups

Example: Sample1,#PredefinedGroup1,Sample2,Sample3 Use #ALL for all samples


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Results


            

            


            

            


            

            

Example: Sample1,#PredefinedGroup1,Sample2,Sample3 Use #ALL for all samples

            

            


            

            

Use #RAW for raw reference genome sequence. Example: Sample1,#PredefinedGroup1,Sample2,#RAW,Sample3
Download as fasta
Note: consensus sequences are generated by substituting variants based on the reference genome.

            

            

Consensus sequence(s)