'OutcrossSeq'  for identification of agronomically important genes in outcrossing crops
  ​Many important crops (e.g., tuber and tree crops) have the cross-pollination nature. In these crops, no inbred lines are available for genetic study and breeding due to self-incompatibility, clonal propagation way or long generation time, which makes the identifications of agronomically important genes relatively difficult, particularly in crops with complex autopolyploid genomes. Here we develop a method OutcrossSeq for mapping agronomically important loci in outcrossing crops based on whole-genome low-cost resequencing of genetic populations. We apply OutcrossSeq in tuber crop (sweet potato, autopolyploidy), tree crop (walnut tree, highly heterozygous diploidy) and hybrid crops (double-cross populations), and identify genomic loci underlying various agronomic traits with high mapping resolution. In several loci identified by OutcrossSeq, the causative genes or even the causative variants are identified and consistent with gene functional studies of previous reports. The results demonstrate that OutcrossSeq is robust to nearly all heterozygous species and will accelerate the genetic improvement of outcrossing crops.
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  ​The raw DNA sequencing data for individual samples of four populations (sweet potato, walnut tree, hybrid rice and hybrid maize) are deposited in the European Nucleotide Archive under accession numbers PRJEB36105, PRJEB36106, PRJEB36107 and PRJEB30877, and the VCF files for the four populations are deposited in the Genome Variation Map of in BIG Data Center under accession numbers PRJCA002429, PRJCA002430, PRJCA002431 and PRJCA002432.
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For Citation:
Chen M#, Fan W#, Ji F#, Hua H, Liu J, Yan M, Ma Q, Fan J, Wan Q, Zhang S, Liu G, Sun Z, Tian C, Zhao F, Zheng J, Zhang Q, Chen J, Qiu J, Wei X, Chen Z, Zhang P*，Pei D*, Yang J*, Huang X*. Genome-wide Identification of Agronomically Important Genes in Outcrossing Crops using OutcrossSeq. Mol. Plant. doi: 10.1016/j.molp.2021.01.003 (2021). [link]

Github site: https://github.com/xhhuanglab/OutcrossSeq
OutcrossSeq scripts
(including readme)
Example files for
software testing
Copyright © 2019 College of Life Sciences, Shanghai Normal University. 
Any questions or suggestions, please contact
Xuehui Huang Lab xhhuang@shnu.edu.cn
100 Guilin Road, Building #14, 907
Last update: 2020/12