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, 122 (8), 1591-604

Fine Mapping of qSTV11(KAS), a Major QTL for Rice Stripe Disease Resistance

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Fine Mapping of qSTV11(KAS), a Major QTL for Rice Stripe Disease Resistance

Ying-Xin Zhang et al. Theor Appl Genet.

Abstract

Rice stripe disease, caused by rice stripe virus (RSV), is one of the most serious diseases in temperate rice-growing areas. In the present study, we performed quantitative trait locus (QTL) analysis for RSV resistance using 98 backcross inbred lines derived from the cross between the highly resistant variety, Kasalath, and the highly susceptible variety, Nipponbare. Under artificial inoculation in the greenhouse, two QTLs for RSV resistance, designated qSTV7 and qSTV11(KAS), were detected on chromosomes 7 and 11 respectively, whereas only one QTL was detected in the same location of chromosome 11 under natural inoculation in the field. The stability of qSTV11(KAS) was validated using 39 established chromosome segment substitution lines. Fine mapping of qSTV11(KAS) was carried out using 372 BC(3)F(2:3) recombinants and 399 BC(3)F(3:4) lines selected from 7,018 BC(3)F(2) plants of the cross SL-234/Koshihikari. The qSTV11(KAS) was localized to a 39.2 kb region containing seven annotated genes. The most likely candidate gene, LOC_Os11g30910, is predicted to encode a sulfotransferase domain-containing protein. The predicted protein encoded by the Kasalath allele differs from Nipponbare by a single amino acid substitution and the deletion of two amino acids within the sulfotransferase domain. Marker-resistance association analysis revealed that the markers L104-155 bp and R48-194 bp were highly correlated with RSV resistance in the 148 landrace varieties. These results provide a basis for the cloning of qSTV11(KAS), and the markers may be used for molecular breeding of RSV resistant rice varieties.

Figures

Fig. 1
Fig. 1
Development of genetic populations for rough and fine mapping of qSTV11KAS. MAS marker-assisted selection
Fig. 2
Fig. 2
Frequency distribution of resistance to RSV based on the relative disease-rating index (RDRI) of the backcross inbred lines (BILs) a Natural field infection; b Artificial inoculation
Fig. 3
Fig. 3
QTLs identified for resistance to RSV in Nipponbare/Kasalath//Nipponbare backcross inbred line (BIL) population. Hollow boxes denote QTLs for resistance to RSV identified by artificial inoculation, and solid box denotes QTL identified by natural field infection
Fig. 4
Fig. 4
The ratio for the relative disease-rating index (RDRI) of chromosome segment substitution lines (CSSLs) and their parents. In each line, bars denote the mean value with standard deviation (n = 4). Shaded bars represent the susceptible (RDRIs ranged from 40 to 69) and highly susceptible (RDRIs over 70.0) lines; hatched bars indicate the highly resistant (RDRIs less than 29.0) lines; dotted bar indicates the recipient parent, Koshihikari; black bar indicate donor parent, Kasalath
Fig. 5
Fig. 5
The identification of qSTV11KAS using chromosome segment substitution lines (CSSLs). The stripe-resistance phenotypes and the graphical genotypes of three CSSLs harboring qSTV11KAS locus. The dashed lines represent the positions of RFLP markers. Black and white bars indicate chromosome regions derived from donor parent (Kasalath) and background parent (Koshihikari), respectively. The RDRI of each line was denoted as mean and standard derivation (n = 4). **Indicates significant difference (P < 0.001) between CSSLs and Koshihikari (Student’s t test). HS highly susceptible, HR highly resistant
Fig. 6
Fig. 6
Genetic and physical maps of the qSTV11KAS gene and candidate gene analysis. a Linkage map of chromosome 11 constructed using 286 BC3F2 plants. The qSTV11KAS locus was mapped between markers L104 and R48. Numbers show genetic distance between adjacent markers. The location of Stvb-i between two RFLP markers XNpb220 and XNpb254 (underlined) is shown with diagonally hatched box. b Fine mapping of qSTV11KAS. The locus was mapped between markers R15 and R53. The number of recombinants between the markers and qSTV11KAS is indicated under the map. c High-resolution genetic map of qSTV11KAS. The locus was narrowed down to a 39.2 kb region on the BAC clone OSJNBa0025K21 (GenBank no. AC136009) between the markers C1 and R53. d Rice gene models from Release 6.1 of the MSU Rice Genome Annotation Project (http://rice/plantbiology.msu.edu/)
Fig. 7
Fig. 7
Frequency distribution of F2:3 lines (n = 168) with different ratio for the relative disease rating index (RDRI), derived from the cross Aichi97/Kasalath. Means and ranges of the parents and the highly susceptible check Wuyujing #3 (n = 4) are indicated as black dots with short bars
Fig. 8
Fig. 8
cDNA and predicted amino acid sequence of LOC_Os11g30910 protein from the Kasalath and Nipponbare alleles. a Alignment of the cDNA sequence of LOC_Os11g30910 from the Kasalath and Nipponbare. Asterisks indicate single-base substitutions between the Kasalath and Nipponbare. Ellipsoid represents deletion in Kasalath. b Predicted amino acid sequence of LOC_Os11g30910 protein. Small rectangular boxes indicate amino acid substitution or deletions between the Kasalath and Nipponbare. Dashed line indicates sulfotransferase domain-containing region of LOC_Os11g30910 protein

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