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Sciences in Cold and Arid Regions ›› 2020, Vol. 12 ›› Issue (3): 180-188.doi: 10.3724/SP.J.1226.2020.00180

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Fast genetic mapping in barley: case studies of cuticle mutants using RNA-sequencing

XiaoFeng Li1,2,Chao Li3,Qin Zhou4,GuoXiong Chen1,PengShan Zhao1()   

  1. 1.Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu 730000, China
    2.University of Chinese Academy of Sciences, Beijing 100049, China
    3.Shanghai Center for Plant Stress Biology, Centre for Excellence in Molecular Plant Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China
    4.Gaolan Station of Agricultural and Ecological Experiment, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu 730000, China
  • Received:2019-12-06 Accepted:2020-04-01 Online:2020-06-30 Published:2020-06-29
  • Contact: GuoXiong Chen,PengShan Zhao E-mail:guoxiong@lzb.ac.cn

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Abstract:

Barley (Hordeum vulgare L.) is one of the earliest domesticated crop species and ranked as the fourth largest cereal production worldwide. Forward genetic studies in barley have greatly advanced plant genetics during the last century; however, most genes are identified by the conventional mapping method. Array genotyping and exome-capture sequencing have also been successfully used to target the causal mutation in barley populations, but these techniques are not widely adopted because of associated costs and partly due to the huge genome size of barley. This review summarizes three mapping cases of barley cuticle mutants in our laboratory with the help of RNA-sequencing. The causal mutations have been successfully identified for two of them and the target genes are located in the pericentromeric regions. Detailed information on the mapping-by-sequencing, mapping-and-sequencing, and RNA-sequencing assisted linkage mapping are presented and some limitations and challenges on the mapping assisted by RNA sequencing are also discussed. The alternative and elegant methods presented in this review may greatly accelerate forward genetics of barley mapping, especially for laboratories without large funding.

Key words: barley, mapping-by-sequencing, RNA-sequencing, cuticle, point mutations

Figure 1

Phenotype comparisons of three cuticle mutants with wild type plants. (a) detached leaves of eibi1.b and wild type after 1 h at room temperature, (b) phenotypes of Foma and cer-zv.342 plants, scale bars in both are 10 cm, (c) adult plants of Bowman and cer-b.2, scale bar is 10 cm"

Figure 2

Conventional mapping and mapping-by-sequencing of eibi1. (a) segregation analyses, (b) chromosome location, (c) rough and fine mapping results, (d) flowchart of mapping-by-sequencing of eibi1. The data in (a), (b), and (c) are from previous publications (Chen et al., 2004, 2009a, 2009b, 2011), while the data in d are from Zhou et al. (2017a). Markers in red color denote the cosegregation with the eibi1 locus"

Figure 3

Mapping-and-sequencing of cer-zv, cer-ym, and cer-yl. (a) segregation analyses, (b) chromosome location, (c) rough and fine mapping results of cer-zv.268, (d) mapping results of cer-ym.753, (e) mapping results of cer-yl.187, (f) flowchart of mapping-and-sequencing and validation of cer-zv, cer-ym, and cer-yl. The data in a-e are from previous publications (Li et al., 2013, 2015, 2017), while data in (f) are from Li et al. (2017). Markers in red color denote the cosegregation with the cer-zv.268 locus"

Figure 4

RNA-seq assisted linkage mapping of cer-b.2 BW-NIL. (a) segregation analyses, (b) rough mapping results of cer-b.2 BW107/BW-NIL, (c) polymorphic markers are developed by the comparison of 23-19 and cer-b.2 BW-NIL transcripts located in the candidate interval on the genome zipper chromosome 3H (Mayer et al., 2011) and the region surrounding MLOC_69561 from the barley physical map (Mayer et al., 2012), (d) rough and fine mapping results of cer-b.2 BW-NIL, CAPSs markers used for mapping are from the description in (c). The data in (a), (c), and (d), are from Zhou et al. (2017b), while data in (b) are from Druka et al. (2011). Markers in red color denote the cosegregation with the cer-b.2 BW-NIL locus. To be noted, the unigene dataset of 23-19 is from Zhou et al. (2017a)"

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