QTL mapping for Fusarium wilt resistance based on the whole-genome resequencing and their association with functional genes in Raphanus sativus

Abstract

Fusarium wilt is an important disease of radish, leading to severe decrease in yield and quality. In this study, we used 180 F 2 populations derived from a cross between radish inbred lines 'YR4' and 'YR18' to construct linkage group for the detecting quantitative trait locus (QTLs) related to Fusarium oxysporum resistance. Four QTLs related to Fusarium oxysporum resistance were detected on two linkage groups. Of the two major loci for FW resistance, FoRsR7.1 FOR59 was delimited to the 2.18-Mb physical interval on chromosome R07, with a high LOD value (5.17-12.84). Additionally, it explained 9.34%-27.97% of the phenotypic variation in three inoculation tests. The other major QTL, FoRsR9.3 FOR59 , was also detected in all inoculation tests, but it had a relatively low value (3.38-4.52) and explained 6.24%-8.82% of the phenotypic variation. On the basis of the re-sequencing data for the parental lines, we identi ed 5 Rrelated genes and 13 unknown genes with sequence variations at the gene and protein levels. A semiquantitative RT-PCR analysis revealed Rs382940 (TIR-NBS type) and Rs382200 (RLK type) were expressed only in 'YR4' from 0 to 6 days after the inoculation. Moreover, Rs382950 (TIR-NBS-LRR type) was more highly expressed in 'YR4' from 3 and 6 days after the inoculation. Therefore, these three genes are likely important for the FW resistance of radish. We identi ed several markers based on the potential candidate genes. These gene set might be useful for breeding system to introduce the Fusarium wilt resistance loci from 'YR4' to improve increasing tolerance to Fusarium oxysporum. Key MassageTwo major QTLs conferring resistance to Fusarium wilt were mapped using whole-genome resequencing.Sequence variations and gene expression level difference suggested that TIR-NBS and LRR-RLK were candidate genes. These genes were used for marker development for breeding in radish (Raphanus sativus).

Quantitative trait locus (QTL) analysis and fine-mapping for <i>Fusarium oxysporum</i> disease resistance in <i>Raphanus sativus</i> using GRAS-Di technology

“…In the later study, Yu et al (2020) fine-mapped the Fwr1 to a region of 139.8 kb between 2 DNA markers FM82 and FM87 and identified ORF4 as a YR candidate gene that encodes a serine/arginine-rich protein kinase. In another QTL analysis of radish, Ma et al (2021) detected 2 YR-QTLs, FoRsR7.1 and FoRsR9.3 on R7 and R9 chromosomes, respectively, and further argued five putative resistance-related genes in the region of FoRsR7.1. Lee et al (2021) reported that the genome-wide association study (GWAS) analysis using 225 radish accessions identified 44 single nucleotide polymorphisms (SNPs) and twenty candidate genes associated with YR.…”

“…At approximately 10 days after germination, each F 3 plant was genotyped using ForRs1-specific DNA markers and only those having homozygous recombinant chromosomes were used for the subsequent fine-mapping study. To compare our identified ForRs1 region with the location of the candidate genes identified by Ma et al (2021), the reference genome of R. sativus cv. WK10039, Rs2.0, was used (Cho et al 2022).…”

“…Positions and names of the DNA markers used in this study are indicated on RSAskr_r1.0, and the corresponding positions on the other 2 alleles were indicated with green dotted lines extending from them. Positions and the names of the genes associated with FoRsR7.1, that were identified by Ma et al (2021), are indicated on Rs2.0. When the allelic sequences of the FoRsR7.1 associated genes exist on RK15-1, their positions are indicated with dotted lines of blue and black extending from them as indicated on RS2.0.…”

“…Radish has a large production area worldwide, which makes it difficult to control FW with agrochemicals (Hida and Ashizawa 1985), and conventional farming methods are not very effective because the spores remain in the soil for a long period of time without a host (Gordon 2017). Therefore, the best method for its control is the use of Fusarium yellows resistance (YR) cultivars (Ma et al 2021, Pu et al 2012.…”

“…As mentioned above, one of the major YR-QTLs in radishes have been identified on the R7 chromosome (Kaneko et al 2007, Ma et al 2021, and several candidate genes have been proposed based on the co-localization of the identified QTLs. However, it is not known whether the QTLs detected in these different research groups are same or different from each other because of the lack of detailed molecular information of each locus, such as sequence information of the DNA markers that were used to define the loci.…”