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. 2021 May 27;10(6):1082.
doi: 10.3390/plants10061082.

Development of a New DNA Marker for Fusarium Yellows Resistance in Brassica rapa Vegetables

Naomi Miyaji  1   2 , Mst Arjina Akter  1   3 , Chizuko Suzukamo  4 , Hasan Mehraj  1 , Tomoe Shindo  5 , Takeru Itabashi  5 , Keiichi Okazaki  6 , Motoki Shimizu  2 , Makoto Kaji  4 , Masahiko Katsumata  4 , Elizabeth S Dennis  7   8 , Ryo Fujimoto  1
Affiliations

Development of a New DNA Marker for Fusarium Yellows Resistance in Brassica rapa Vegetables

Naomi Miyaji et al. Plants (Basel). .

Abstract

In vegetables of Brassica rapa L., Fusarium oxysporum f. sp. rapae (For) or F. oxysporum f. sp. conglutinans (Foc) cause Fusarium yellows. A resistance gene against Foc (FocBr1) has been identified, and deletion of this gene results in susceptibility (focbr1-1). In contrast, a resistance gene against For has not been identified. Inoculation tests showed that lines resistant to Foc were also resistant to For, and lines susceptible to Foc were susceptible to For. However, prediction of disease resistance by a dominant DNA marker on FocBr1 (Bra012688m) was not associated with disease resistance of For in some komatsuna lines using an inoculation test. QTL-seq using four F2 populations derived from For susceptible and resistant lines showed one causative locus on chromosome A03, which covers FocBr1. Comparison of the amino acid sequence of FocBr1 between susceptible and resistant alleles (FocBr1 and FocBo1) showed that six amino acid differences were specific to susceptible lines. The presence and absence of FocBr1 is consistent with For resistance in F2 populations. These results indicate that FocBr1 is essential for For resistance, and changed amino acid sequences result in susceptibility to For. This susceptible allele is termed focbr1-2, and a new DNA marker (focbr1-2m) for detection of the focbr1-2 allele was developed.

Keywords: Brassica rapa; DNA marker; Fusarium oxysporum f. sp. rapae; Fusarium yellows; QTL-seq; R gene; marker-assisted selection.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
QTL-seq results on chromosome A03. F2 populations derived from YBCG-11 × YBCG-12, YBCG-11 × YBCG-13, YBCG-11 × YBCG-14, and YBCG-08 × YBCG-09 hybrids were used. Blue dots indicate ∆SNP-index, and the red line indicates the sliding window average of ∆SNP-index. Light green lines represent p < 0.05. R and S represent resistant and susceptible, respectively. + and - represent the presence and absence of PCR amplification of Bra012688m marker, respectively.
Figure 2
Figure 2
Expression and genotype of FocBr1 in For resistant and susceptible lines. (a) Expression of FocBr1 and Bractin (control) was confirmed by RT-PCR. (b) DNA fragments of RT-PCR products digested by Hind III. YBCG-16 and YBCG-11 have FocBr1/FocBr1 homozygous or FocBr1/focbr1-1 heterozygous alleles. “Zaoh”, YBCG-12 and YBCG-15 have focbr1-2/focbr1-2 homozygous or focbr1-2/focbr1-1 heterozygous alleles, and YBCG-10 has focbr1-1/focbr1-1 homozygous allele.
Figure 3
Figure 3
Protein structure of FocBr1 in the resistant line of B. rapa. TIR (green box), NBS (blue box), and LRR region (orange box) were identified. Black lines represent the position of difference of amino acid sequences between resistant and susceptible lines in B. rapa, while amino acid sequences of FocBr1 in the susceptible lines were identical to the FocBo1 (Foc resistance gene in B. oleracea). Red lines represent the position of susceptible line-specific amino acid substitutions. Domains were predicted using HMMSCAN with Pfam database. (https://www.ebi.ac.uk/Tools/hmmer/, accessed on 1 April 2021) and NCBI conserved domain search (https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi, accessed on 1 April 2021).
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