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Acta Agronomica Sinica ›› 2019, Vol. 45 ›› Issue (11): 1664-1671.doi: 10.3724/SP.J.1006.2019.92003


Mapping of QTLs for resistance to rice black-streaked dwarf disease

LIU Jiang-Ning1,2,WANG Chu-Xin1,2,ZHANG Hong-GEN1,2,*(),MIAO Yi-Xu1,2,GAO Hai-Lin1,2,XU Zuo-Peng1,2,LIU Qiao-Quan1,2,TANG Shu-Zhu1,2   

  1. 1 Jiangsu Key Laboratory of Crop Genetics and Physiology / Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, Jiangsu, China
    2 Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, Jiangsu, China
  • Received:2019-01-11 Accepted:2019-06-12 Online:2019-11-12 Published:2019-07-09
  • Contact: Hong-GEN ZHANG E-mail:zhg@yzu.edu.cn
  • Supported by:
    This study was supported by the National Major Project for Developing New GM Crops(2016ZX08001002-003);the National Natural Science Foundation of China(31771743);the Project Funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD)


Rice black-streaked dwarf virus disease (RBSDV) may cause great loss of rice production, and breeding resistant varieties is an effective method to control RBSDV. To develop resistant varieties, it is important to screen germplasm that shows RBSDV resistance and to identify the genes/quantitative trait loci (QTLs) contained. In the present study, a set of 222 recombinant inbred lines (RILs) derived from the cross between L5494 (a susceptible japonica variety) and IR36 (a resistant indica variety) were constructed for RBSDV-resistant QTL mapping. With natural infection test, the RBSDV incidences of L5494 and IR36 were 84.26% and 28.70%, respectively, and the disease incidence of RILs was ranged from 11.21% to 89.81%. Using 134 polymorphic molecular markers, a linkage genetic map was constructed. The map covered a total length of 1475.97 cM with an average interval of 11. 1 cM between adjacent markers. Four RBSDV-resistant QTLs were discovered using QTL IciMapping 4.0 Software, of which, qRBSDV-1, qRBSDV-2, and qRBSDV-9 were from the resistant parent IR36, and qRBSDV-6 from the susceptible parent L5494. QTLs qRBSDV-1, qRBSDV-2, qRBSDV-6, and qRBSDV-9 were located on chromosomes 1, 2, 6, and 9, respectively, which explained 12.64%, 16.00%, 10.82%, and 8.43% of the phenotypic variations. Moreover, a RBSDV-resistant QTL from 93-11 (O. sativa spp. indica) at the qRBSDV-1 locus was confirmed by a near isogenic line that harbors qRBSDV-1 derived from 93-11 with the Nipponbare (O. sativa spp. japonica) genetic background. Our findings will be benefit for the marker assisted breeding of RBSDV-resistant varieties.

Key words: rice black-streaked dwarf viral disease, recombinant inbred line, QTL mapping

Fig. 1

Incidence of black-streaked dwarf disease in IR36, L5494 and a susceptible line from RIL population A: parent IR36; B: parent L5494; C: a susceptible line from RIL population."

Fig. 2

Frequency distribution of rice black-streaked dwarf virus disease resistance based on the disease percentage in RIL population"

Fig. 3

A molecular linkage map of rice based on L5494/IR36 RIL population"

Fig. 4

Locations of QTL for resistance to rice black-streaked dwarf virus disease on chromosomes"

Table 1

Parameters associated with QTL for rice black-streaked dwarf virus disease resistance identified in L5494/IR36 RIL population"

Left marker
Right marker
PVE (%)
qRBSDV-1 2015 Chr.1 AP-39.6 RM104 2.96 6.19 4.39
2016 Chr.1 AP-39.6 RM104 4.44 12.64 7.16
qRBSDV-2 2016 Chr.2 CHR2-4 RM341 6.89 16.00 7.61
qRBSDV-6 2013 Chr.6 RM19234 CHR-6-1 4.68 13.33 -2.61
2014 Chr.6 RM19234 CHR-6-1 2.91 11.00 -2.11
2016 Chr.6 RM19234 CHR-6-1 5.45 10.82 -6.20
qRBSDV-9 2013 Chr.9 RM242 RM160 3.30 8.71 2.10
2014 Chr.9 RM242 RM160 4.56 12.27 2.11
2015 Chr.9 RM242 RM160 3.48 6.62 4.31
2016 Chr.9 RM242 RM160 3.94 8.43 5.48

Fig. 5

Re-sequencing map for chromosome segment substitution line N9 Each blue line and red line represent single nucleotide polymorphisms of ‘Nipponbare’ and ‘93-11’, respectively. The red box in Chr.1 indicates a substituted fragment derived from 93-11."

Table 2

Incidence of rice black-streaked dwarf virus disease in Nipponbare, 93-11, and N9 (%)"

Repeat 1
Repeat 2
Repeat 3
2017 日本晴Nipponbare 31.20 32.73 29.63 31.19
93-11 18.33 10.19 18.35 15.62**
N9 25.65 29.17 24.32 26.38*
2018 日本晴Nipponbare 8.00 18.00 13.00 10.33
93-11 0 3.00 3.00 2.00*
N9 4.00 1.00 1.02 2.01*

Fig. 6

Incidence of rice black-streaked dwarf virus disease in Nipponbare and N9 in 2017 A: Nipponbare; B: N9."

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