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3 Biotech (2018) 8:255
https://doi.org/10.1007/s13205-018-1279-y
ORIGINAL ARTICLE
Isolation and characterization of fusarium wilt resistance gene analogs
in radish
Xiaona Yu
1
· Dong Hyun Kang
1
· Su Ryun Choi
1
· Yinbo Ma
1
· Lu Lu
1
· Sang Heon Oh
1
· Sushil Satish Chhapekar
1
·
Yong Pyo Lim
1
Received: 28 November 2017 / Accepted: 6 May 2018 / Published online: 14 May 2018
© Springer-Verlag GmbH Germany, part of Springer Nature 2018
Abstract
The resistance gene analog (RGA)-based marker strategy is an effective supplement for current marker reservoir of radish
disease-resistance breeding. In this study, we identified RGAs based on the conserved nucleotide-binding site (NBS) and
S-receptor-like kinase (SRLK) domains. A total of 68 NBS-RGAs and 46 SRLK-RGAs were isolated from two FW-resistant
radish inbred lines, B2 and YR31, and one susceptible line, YR15. A BLASTx search revealed that the NBS-RGAs contained
six conserved motifs (i.e., P loop, RNBS-A, Kinase-2, RNBS-B, RNBS-C, and GLPL) and the SRLK-RGAs, contained two
conserved motifs (i.e., G-type lectin and PAN-AP). A phylogenetic analysis indicated that the NBS-RGAs could be separated
into two classes (i.e., toll/interleukin receptor and coiled-coil types), with six subgroups, and the SRLK-RGAs were divided
into three subgroups. Moreover, we designed RGA-specific markers from data-mining approach in radish databases. Based
on marker analysis, 24 radish inbred lines were clustered into five main groups with a similarity index of 0.44 and showing
genetic diversity with resistance variation in those radish inbred lines. The development of RGA-specific primers would be
valuable for marker-assisted selection during the breeding of disease-resistant radish cultivars.
Keywords Resistance gene analogs (RGA) · Fusarium wilt · Nucleotide-binding site (NBS) · S-receptor-like kinase
(SRLK)
Introduction
Fusarium wilt (FW) widely recognized as one of the most
destructive fungal disease influencing radish (Raphanus
sativus L.; 2n = 18) yield and quality, which is caused by
Fusarium oxysporum. Currently used chemical treatments to
control this disease are harmful to the environment. During
the last two decades, several quantitative trait loci (QTLs)
and genes conferring FW resistance have been mapped and
isolated in diverse plants, including Arabidopsis thaliana
(Cole and Diener 2013; Diener and Ausubel 2005; Shen
and Diener 2013), Chinese cabbage (Shimizu et al. 2014),
cabbage (Shimizu et al. 2014; Lv et al. 2014), tomato (Cat-
anzariti et al. 2015; Gonzalez-Cendales et al. 2016; Simons
et al. 1998; Wei et al. 2014) as well as radish (Yu et al.
2013). However, until now, the underlying genetic basis of
the disease-resistance mechanisms in radish has not been
fully characterized, especially the disease-resistance genes
(R genes). Most R genes have similar structures and encode
conserved motifs, including the nucleotide-binding site
(NBS), Toll/interleukin-1 receptor (TIR), coiled-coil (CC),
and protein receptor-like kinase (RLK) (Ellis et al. 2000;
Jones and Jones 1997; McHale et al. 2006). The conserved
regions of different R genes may be useful for developing
degenerate marker-based strategies to isolate and map R
genes or their analogs.
Molecular technologies in modern breeding have acceler-
ated the breeding of disease-resistant plants. For example,
FW-resistance genes have been cloned in tomato, includ-
ing I-2, which encodes a CC–NBS–leucine-rich repeat
(LRR) protein (Simons et al. 1998; Wei et al. 2014), I-3,
Xiaona Yu and Dong Hyun Kang contributed equally to this work.
Electronic supplementary material The online version of this
article (https ://doi.org/10.1007/s1320 5-018-1279-y) contains
supplementary material, which is available to authorized users.
* Yong Pyo Lim
yplim@cnu.ac.kr
1
Molecular Genetics and Genomics Laboratory, Department
of Horticulture, Chungnam National University,
Daejeon 34134, South Korea
@Phil_Robichaud
@deepthiw
@JoseServera