Genetic Analysis and Fine Mapping of a Major QTL for the Resistance to Southern Rice Black-Streaked Dwarf Disease

doi:10.16819/j.1001-7216.2019.8057 135

Abstract

Abstract:

【Objective】Southern rice black-streaked dwarf virus(SRBSDV), which is transmitted by white-backed planthopper (Sogatella furcifera Horváth, WBPH), has caused severe yield loss in epidemic years in rice production. We analyzed the resistance mechanism of SRBSDV and identified the related gene locus by fine gene mapping to lay a scientific base for effective prevention and control of SRBSDV. 【Method】The resistance of rice material D4 against white-backed planthoppers were analyzed, and the genetic basis for the resistance to SRBSDV was analyzed by using F₂ population of Guanghui 998×D4. The major QTL for resistance to SRBSDV was identified using QTL-seq, and further verified by genetic linkage analysis. 【Result】D4 was resistant to SRBSDV but not to WBPH. Genetic analysis showed that the resistance of D4 was controlled by major gene and minor genes. QTL-seq and linkage analysis revealed that the major QTL for resistance to SRBSDV in rice was located within the 1.40 M region on chromosome 9, which was termed as qSRBSDV9. Then qSRBSDV9 was fine mapped on chromosome 9 with a 102.3 kb physical distance by substitution mapping. This region contained 21 predicted genes, nine of which were related to gibberellin signaling. 【Conclusion】The results reveals the characteristics and inheritance of resistance to SRBSDV in D4. The fine mapping of qSRBSDV9 lays a base for map-based cloning and utilization.

Key words: Southern rice black-streaked dwarf disease, white-backed planthopper, genetic analysis, QTL, fine mapping

摘要：

【目的】近年来由白背飞虱传播的南方水稻黑条矮缩病给水稻生产造成了巨大损失,开展该病的抗性遗传分析和基因精细定位,将为抗性育种提供材料和理论依据。【方法】分析了抗性材料D4对南方水稻黑条矮缩病的抗性特征,并通过广恢998/D4 F₂群体分析该病抗性的遗传规律,利用QTL-seq技术联合遗传连锁分析定位主效抗性QTL。【结果】D4对南方水稻黑条矮缩病的抗性表现为抗病毒性而非抗虫性,且受主效基因和微效基因共同控制。QTL-seq和连锁分析将南方水稻黑条矮缩病主效抗性QTL定位于第9染色体上,命名为qSRBSDV9。利用代换作图法进一步将qSRBSDV9定位在102.3 kb的区间内,该区间包含21个预测基因,其中9个基因与赤霉素信号传导相关。【结论】揭示了D4对南方水稻黑条矮缩病的抗性特征及遗传规律,精细定位了南方水稻黑条矮缩病主效抗性QTL qSRBSDV9。这为该QTL的图位克隆及育种利用奠定了基础。

关键词: 南方水稻黑条矮缩病, 白背飞虱, 遗传分析, QTL, 精细定位

CLC Number:

Baoxuan NONG, Bixia QIN, Xiuzhong XIA, Xinghai YANG, Zongqiong ZHANG, Yu ZENG, Guofu DENG, Jianhe CAI, Zhanbiao LI, Piqing LIU, Danting LI. Genetic Analysis and Fine Mapping of a Major QTL for the Resistance to Southern Rice Black-Streaked Dwarf Disease[J]. Chinese Journal OF Rice Science, 2019, 33(2): 135-143.

农保选, 秦碧霞, 夏秀忠, 杨行海, 张宗琼, 曾宇, 邓国富, 蔡健和, 李战彪, 刘丕庆, 李丹婷. 南方水稻黑条矮缩病抗性的遗传分析及主效QTL的精细定位[J]. 中国水稻科学, 2019, 33(2): 135-143.

Figures/Tables 7

References 46

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样品Sample	Clean数据 Clean data/bp	HQ clean数据 HQ clean data/bp	平均测序深度 Average depth/×	Read总数 Total reads	比对read数 Mapped reads	覆盖度 Coverage/%	GC含量 GC content/%	Q30含量 Q30 content/%
D4	22 783 003 500	21 308 456 571	55.88	142 913 376	138 406 793	92.66	44.78	84.36
GH998	30 069 649 500	29 089 431 251	76.28	195 193 248	189 390 713	93.26	43.45	94.56
R-pool	30 313 518 000	29 287 082 085	76.80	196 696 800	190 730 909	93.65	43.18	94.87
S-pool	27 220 437 600	26 367 983 261	69.14	177 553 354	171 577 580	93.35	45.11	95.02

样品Sample	Clean数据 Clean data/bp	HQ clean数据 HQ clean data/bp	平均测序深度 Average depth/×	Read总数 Total reads	比对read数 Mapped reads	覆盖度 Coverage/%	GC含量 GC content/%	Q30含量 Q30 content/%
D4	22 783 003 500	21 308 456 571	55.88	142 913 376	138 406 793	92.66	44.78	84.36
GH998	30 069 649 500	29 089 431 251	76.28	195 193 248	189 390 713	93.26	43.45	94.56
R-pool	30 313 518 000	29 287 082 085	76.80	196 696 800	190 730 909	93.65	43.18	94.87
S-pool	27 220 437 600	26 367 983 261	69.14	177 553 354	171 577 580	93.35	45.11	95.02

引物 Primer	正向引物序列 Forward primer (5'-3')	反向引物序列 Reverse primer (5'-3')
Indel 4	TGAAACTGGACAAATTACCC	AGGAGTACATGACAAGTGGG
Indel 5	AAAATGAAACCCAACATGAC	CTTTATTTGCTTGCTCGATT
Indel 6	AACCAGATATCTTGACCCCT	GAACGAAGACTCGGTCAATA
Indel 7	AATTACGTTGTGGCAATACA	CGTAGCGATAAGAATGTGTG
Indel 18	AGTCCCATCCAAACATAGTG	CAGAGCAGGTTGTCAACAG
Indel 22	CTGTCAGACACGATCAGAGA	CATGCATGTCCTCTTGCT
Indel 23	TTCTGCACACAATCTTTTTG	AGCCATGCTAGCTAGTTCAC
Indel 29	ATCCTTTGCCATATCATCAG	AACGGTTGTACGAGTGAGAT
Indel 40	AAATCCACGCAGTTCAAG	ACTAGGACCTGATTCCCATT
Indel 43	AACCACTTGTCTTAGTCAAAAA	CACTGTTTGATCATTCGTCT
M1	CAAAATAAGTTGGTTTTGGC	GTGTTTCTCCTTAATCTGCG
M2	CTTCTCCGTCCAAACTACC	CCCCAGTAGAAGGTCATGT
M3	TAATTAGTGTGTTGCACCGA	AAGCTAAACAGCACCATCAT
M4	TGTGGGGTATCCACTAGTTC	AAGACGAGTGGTCAAACATT
M5	GATAGATATAACGCGAGGCA	ATATTCCCCTATTCCACACC
M6	AGCCAAAAACAACCTTACAA	AGCTCTCTGTCACTAGCTGC
M7	TACGGTTTTGTAAACCTGCT	TCGGATCTAACAGGTGGTAA
M8	AATGAATCAGCAGAAGGAAA	GGTAGTTGTGTCAAGGGCT
M9	ACATGTTACTGGGCCTAAAA	CCCTTGAAAATGACGATAAG
M10	ACTCTGGGAGTGGAGGAT	ACCTCACCTGTTCTGTGTTC
M11	CCGTTTTTCTTATTCCTACG	GAACATATGATTGGGTTGGT
M12	GAATCATCCACACACACAGA	GTTCACCTGCAGACTCTCTC
M13	TAACGGCTGTTTCTTTCTTC	TATCTACAGTTTCCCGCTGT
M14	TCTTTCCCTTCCTCTCTCTC	AAATATGCCACTCCAGAAAA
M15	GTCGGTGCTGGAGGAACT	CCGCCTTCTTCCTCGTTAT

引物 Primer	正向引物序列 Forward primer (5'-3')	反向引物序列 Reverse primer (5'-3')
Indel 4	TGAAACTGGACAAATTACCC	AGGAGTACATGACAAGTGGG
Indel 5	AAAATGAAACCCAACATGAC	CTTTATTTGCTTGCTCGATT
Indel 6	AACCAGATATCTTGACCCCT	GAACGAAGACTCGGTCAATA
Indel 7	AATTACGTTGTGGCAATACA	CGTAGCGATAAGAATGTGTG
Indel 18	AGTCCCATCCAAACATAGTG	CAGAGCAGGTTGTCAACAG
Indel 22	CTGTCAGACACGATCAGAGA	CATGCATGTCCTCTTGCT
Indel 23	TTCTGCACACAATCTTTTTG	AGCCATGCTAGCTAGTTCAC
Indel 29	ATCCTTTGCCATATCATCAG	AACGGTTGTACGAGTGAGAT
Indel 40	AAATCCACGCAGTTCAAG	ACTAGGACCTGATTCCCATT
Indel 43	AACCACTTGTCTTAGTCAAAAA	CACTGTTTGATCATTCGTCT
M1	CAAAATAAGTTGGTTTTGGC	GTGTTTCTCCTTAATCTGCG
M2	CTTCTCCGTCCAAACTACC	CCCCAGTAGAAGGTCATGT
M3	TAATTAGTGTGTTGCACCGA	AAGCTAAACAGCACCATCAT
M4	TGTGGGGTATCCACTAGTTC	AAGACGAGTGGTCAAACATT
M5	GATAGATATAACGCGAGGCA	ATATTCCCCTATTCCACACC
M6	AGCCAAAAACAACCTTACAA	AGCTCTCTGTCACTAGCTGC
M7	TACGGTTTTGTAAACCTGCT	TCGGATCTAACAGGTGGTAA
M8	AATGAATCAGCAGAAGGAAA	GGTAGTTGTGTCAAGGGCT
M9	ACATGTTACTGGGCCTAAAA	CCCTTGAAAATGACGATAAG
M10	ACTCTGGGAGTGGAGGAT	ACCTCACCTGTTCTGTGTTC
M11	CCGTTTTTCTTATTCCTACG	GAACATATGATTGGGTTGGT
M12	GAATCATCCACACACACAGA	GTTCACCTGCAGACTCTCTC
M13	TAACGGCTGTTTCTTTCTTC	TATCTACAGTTTCCCGCTGT
M14	TCTTTCCCTTCCTCTCTCTC	AAATATGCCACTCCAGAAAA
M15	GTCGGTGCTGGAGGAACT	CCGCCTTCTTCCTCGTTAT