Scientia Agricultura Sinica ›› 2023, Vol. 56 ›› Issue (21): 4219-4233.doi: 10.3864/j.issn.0578-1752.2023.21.007

• PLANT PROTECTION • Previous Articles     Next Articles

Development and Application of Specific Molecular Markers for Six Homologous Rice Blast Resistance Genes in Pi9 Locus of Rice

YANG Hao1(), HUANG YanYan1(), YI ChunLin1, SHI Jun2, TAN ChuTian1, REN WenRui1, WANG WenMing1()   

  1. 1 State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130
    2 Institute of Rice Research, Mianyang Academy of Agricultural Sciences/Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Province, Mianyang 621023, Sichuan
  • Received:2023-07-23 Accepted:2023-09-06 Online:2023-11-01 Published:2023-11-06
  • Contact: WANG WenMing

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Abstract:

【Objective】The Pi9 resistance gene locus, conferring a broad-spectrum resistance against Magnaporthe oryzae, is consist by several tandem homologous genes. Over 10 resistance genes have been cloned from this gene locus. This study aims to clarify the R gene composition at Pi9 locus in rice resource materials and promote the application of those genes in rice resistance breeding.【Method】Comparing the DNA sequence of cloned R genes at Pi9 locus, the specific nucleotide polymorphism sites were screened as the candidate sites. Subsequently, each R gene was blasted with 155 rice genomes in the database of Rice Resource Center. The most specific nucleotide polymorphism sites were picked out from the candidate site in each gene to develop primer pair of molecular markers. The PCR product of primer pairs was used to mark indicated R gene in tested rice materials via parameter optimization. To verify the results, the R genes were cloned from indicated rice variety randomly and examined by Sanger sequencing, or analyzed the R genes from the genome database if the genome sequence of indicated rice variety exists in Rice Resource Center. The R genes in Pi9 locus have high homology, which cause same specific nucleotide polymorphism sites existing in different R genes. Therefore, some R genes are hardly identified by one molecular marker. For this case, several molecular markers were employed to identify the indicated R gene simultaneously. Moreover, some specific nucleotide polymorphism sites are single nucleotide polymorphism (SNP), in where the primers of molecular markers have a mismatched base. In order to improve the specificity of PCR amplification, the adjacent base of SNP was mutated to generate two mismatched bases at 3′ site of primer.【Result】Finally, the valid molecular markers were developed for each R gene and identified 32.09% tested materials containing R genes at Pi9 locus. Pi9, Pid4, PigmR, Piz-t, Pi2 and Pi9-type5 are present in 1, 7, 8, 14, 23 and 33 tested materials, respectively. The Pi9 only presents in monogenic line but not in rice parent lines. The other genes are usually present in two or more gene combinations in rice parent lines. The Pi9-type5 often presents in pair with Pi2 and Piz-t, and presents alone in three rice parents, Chenghui 993, HR2168 and Mianhui 365. Yuhui 38 contains the most R genes at Pi9 locus, including Pi2, Pi9-type5, PigmR and Pid4. Chuangu B, Chuannong 4B, Neixiang 6B and Shuang 1B contain Piz-t, PigmR and Pid4. Qianxiang 654B contains Piz-t and Pid4.【Conclusion】This study successfully developed specific molecular markers for six homologous rice blast resistance genes in Pi9 locus and identified the R gene composition in Pi9 locus for 110 rice parent lines that used in rice breeding in Sichuan basin. It also discovered different types of R genes combination at Pi9 locus and provided a clear reference for choosing the resistance source in rice breeding.

Key words: rice, rice blast, Pi9 locus, homologous gene, molecular marker

Table 1

The rice varieties used in this study"

编号
No.		 品种
Variety		 编号
No.		 品种
Variety		 编号
No.		 品种
Variety		 编号
No.		 品种
Variety
1 IRBLa-A (Pi-a) 35 绵恢146 Mianhui 146 69 泰恢808 Taihui 808 103 德香074B Dexiang 074B
2 IRBLi-F5 (Pi-i) 36 绵恢725 Mianhui 725 70 五山丝苗Wushansimiao 104 赣香B Ganxiang B
3 IRBLks-F5 (Pi-ks) 37 南恢558 Nanhui 558 71 西科恢768 Xikehui 768 105 广8B Guang 8B
4 IRBLk-Ka (Pi-k) 38 南恢968 Nanhui 968 72 雅禾Yahe 106 泸香618B Luxiang 618B
5 IRBLkp-K60 (Pi-kp) 39 蜀恢257 Shuhui 257 73 雅恢2115 Yahui 2115 107 绵5B Mian 5B
6 IRBLkh-K3 (Pi-kh) 40 蜀恢308 Shuhui 308 74 雅恢2116 Yahui 2116 108 忠香B Zhongxiang B
7 IRBLz-Fu (Pi-z) 41 蜀恢451 Shuhui 451 75 雅恢2117 Yahui 2117 109 内香6B Neixiang 6B
8 IRBLz5-CA (Pi-z5) 42 蜀恢498 Shuhui 498 76 雅恢2118 Yahui 2118 110 千乡654B Qianxiang 654B
9 IRBLzt-T (Pi-zt) 43 蜀恢505 Shuhui 505 77 雅恢2119 Yahui 2119 111 荃9311B Quan 9311B
10 IRBLta-K1 (Pi-ta) 44 蜀恢548 Shuhui 548 78 雅恢2199 Yahui 2199 112 蓉18B Rong 18B
11 IRBLb-B (Pi-b) 45 蜀恢573 Shuhui 573 79 雅恢2275 Yahui 2275 113 蓉7B Rong 7B
12 IRBLt-K59 (Pi-t) 46 蜀恢586 Shuhui 586 80 雅恢2348 Yahui 2348 114 双1B Shuang 1B
13 IRBLsh-B (Pi-sh) 47 蜀恢589 Shuhui 589 81 雅恢2816 Yahui 2816 115 泰丰B Taifeng B
14 IRBL1-CL (Pi-1) 48 猪毛糯Zhumaonuo 82 雅恢2918 Yahui 2918 116 武金4B Wujin 4B
15 IRBL3-CP4 (Pi-3) 49 HR2168 83 雅恢5049 Yahui 5049 117 武香B Wuxiang B
16 IRBL5-M (Pi-5) 50 R900 84 雅恢5217 Yahui 5217 118 雅1B Ya 1B
17 IRBL7-M (Pi-7) 51 R9311 85 雨恢38 Yuhui 38 119 雅3B Ya 3B
18 IRBL9-W (Pi-9) 52 成恢19 Chenghui 19 86 岳恢9113 Yuehui 9113 120 雅7B Ya 7B
19 IRBL12-M (Pi-12) 53 乐恢188 Lehui 188 87 粤农丝苗Yuenongsimiao 121 宜香1B Yixiang 1B
20 IRBL19-M (Pi-19) 54 乐恢584 Lehui 584 88 D297B 122 泰国香稻Thai fragrant rice
21 IRBLkm-Ts (Pi-km) 55 泸恢17 Luhui 17 89 D35B 123 楚粳28 Chugeng 28
22 IRBL20-IR24 (Pi-20) 56 泸恢8258 Luhui 8258 90 D62B 124 野香B Yexiang B
23 IRBLta2-Pi (Pi-ta2) 57 绵恢523 Mianhui 523 91 D79B 125 绵恢6139 Mianhui 6139
24 IRBL11-Zh (Pi-11) 58 绵恢528 Mianhui 528 92 F-32B 126 绵恢313 Mianhui 313
25 E33 59 绵恢662 Mianhui 662 93 F59B 127 绵恢357 Mianhui 357
26 成恢3203 Chenghui 3203 60 明恢63 Minghui 63 94 G46B 128 绵恢365 Mianhui 365
27 成恢727 Chenghui 727 61 明恢86 Minghui 86 95 川106B Chuan 106B 129 绵恢821 Mianhui 821
28 成恢993 Chenghui 993 62 内恢99-14 Neihui 99-14 96 川608B Chuan 608B 130 绵恢823 Mianhui 823
29 德恢6099 Dehui 6099 63 蜀恢137 Shuhui 137 97 川谷B Chuangu B 131 绵恢837 Mianhui 837
30 多恢1号 Duohui 1 64 蜀恢208 Shuhui 208 98 川华B Chuanhua B 132 绵恢857 Mianhui 857
31 航恢1179 Hanghui 1179 65 蜀恢527 Shuhui 527 99 川农1B Chuannong 1B 133 绵恢815 Mianhui 815
32 航恢570 Hanghui 570 66 蜀恢538 Shuhui 538 100 川农4B Chuannong 4B 134 地谷B Digu B
33 华占Huazhan 67 蜀恢569 Shuhui 569 101 川种3B Chuanzhong 3B
34 乐恢433 Lehui 433 68 蜀恢882 Shuhui 882 102 德66B De 66B

Table 2

The primers of molecular markers and parameter setting of PCR amplification"

R基因
R gene		 引物名称
Primer name		 引物序列
Primer sequence		 产物长度
Product length (bp)		 退火温度
Annealing temperature (℃)		 延伸时间
Extension time (s)
Pi2 Pi2/z-t-F CTCTTCGTTGTATAGGACAGTTTCA 424 57 30
Pi2-R GTTCCACCATCTGAGATTCCTG
Pi9 Pi9-F CTCTTCGTTGTAGTAGAAAGTTTGT 788 45 50
Pi9-R TTCCAACCTGCAGCAAGAG
Pi9-type5 Pi9-type5F1 CTAAGAACAATAAGAAGGGCAG 454 62 30
Pi9-type5R1 CCTACTAGACGATTCCTTTGT
Pi9-type5F2 CGTTGTATAAGAGAGCTTGAATT 709 60 50
Pi9-type5R2 GCTGATCCAAATTGAAAATCAC
Pi9-type5F3 ATCTTTCCTGAGGATTTTGAAATAC 185 55 25
Pi9-type5mR CAAGTCTTAATTTTTCCTGCAG
Piz-t Pi2/z-t-F CTCTTCGTTGTATAGGACAGTTTCA 548 57 35
Piz-t-R3 GTAGATCTTCTTCAGGTGCA
Pi2/z-t-F CTCTTCGTTGTATAGGACAGTTTCA 502 59 30
Piz-t-R2 TCCTCAAGAATTCCATCCAACAC
Piz-t-F4 CAGAGAACGCCACCGAATT 169 59 20
Piz-t-R4 CACATTGCGAGCTGACTGATTA
Pi9-type9 Pi9-type9F2 AGAATGGGAGAAATTCTATGAAAAG 230 59 25
Pi9-type9R2 TAGTCATCATCCCAACCTGC
Pi9-type9F ACCTGAAGAAGATCTACTTATTGAA 305 59 25
Pi9-type9R AATCTCCTTGAGCTTTGGAT
Pi9-type9mF ACCTGAAGAAGATCTACTTATTGTA 305 59 25
Pi9-type9mR AATCTCCTTGAGCTTTGGTT
PigmR Pigm-F2 CACCTGAAGAAGTTCTACTTACG 111 59 20
Pigm-newmR1 ATAAGAATTATGATAAAGAGAAAGGTA
Pigm-newmF1 TCCTCCTCCCCTACTTAGT 180 59 20
Pigm-newmR1 ATAAGAATTATGATAAAGAGAAAGGTA
Pigm-mF4 GGAGAAGCTAGTATTCAAAAGG 297 59 20
Pigm-mR5 TGATACCTTCGGTCACTGAC
Pigm-mF6 GTATATGGATAGCAGAAGGGTAG 98 59 20
Pigm-mR7 CATACTTCGGTTGATTAGCTCAAA
Pid4 Pid4-mF GAATCTGTTTTTCCTGACTCTACA 797 59 50
Pid4-mR GGATTGTAAAAGAAACTTAATGAGT

Fig. 1

The position and application of molecular markers of Pi2 and Piz-t The nucleotide polymorphism analysis of primer pairs, Pi2/z-t-F and Piz-t-R2, Pi2/z-t-F and Piz-t-R3, Pi2/z-t-F4 and Piz-t-R4, for the molecular markers of Piz-t. The arrows indicate the site and direction of primers. The shaded lowercase letters indicate the polymorphic nucleotide sites in homologous genes"

Table 3

The rice materials containing Pi2"

编号
No.		 材料
Material		 编号
No.		 材料
Material		 编号
No.		 材料
Material
8 IRBLz5-CA 46 蜀恢586 Shuhui 586 82 雅恢2918 Yahui 2918
25 E33 50 R900 83 雅恢5049 Yahui 5049
29 德恢6099 Dehui 6099 70 五山丝苗Wushansimiao 84 雅恢5217 Yahui 5217
31 航恢1179 Hanghui 1179 72 雅禾Yahe 85 雨恢38 Yuhui 38
33 华占Huazhan 73 雅恢2115 Yahui 2115 87 粤农丝苗Yuenongsimiao
40 蜀恢308 Shuhui 308 74 雅恢2116 Yahui 2116 118 雅1B Ya 1B
43 蜀恢505 Shuhui 505 77 雅恢2119 Yahui 2119 133 绵恢815 Mianhui 815
44 蜀恢548 Shuhui 548 79 雅恢2275 Yahui 2275

Table 4

The rice materials containing Piz-t"

编号
No.		 材料
Material		 引物Primer
Pi2/z-t-F Piz-t-R2 Pi2/z-t-F Piz-t-R3 Piz-t-F4 Piz-t-R4
9 IRBLzt-T √ √ √
42 蜀恢498 Shuhui 498 √ √ √
52 成恢19 Chenghui 19 √ √ √
56 泸恢8258 Luhui 8258 √ √ √
61 明恢86 Minghui 86 √ √ √
63 蜀恢137 Shuhui 137 √ √ √
64 蜀恢208 Shuhui 208 √ √ √
78 雅恢2199 Yahui 2199 √ √ √
97 川谷B Chuangu B √ √ √
100 川农4B Chuannong 4B √ √ √
109 内香6B Neixiang 6B √ √ √
110 千乡654B Qianxiang 654B √ √ √
113 蓉7B Rong 7B √ √ √
114 双1B Shuang 1B √ √ √
阳性对照Positive control 中花11 ZH11 √ √ √

Fig. 2

The nucleotide polymorphism analysis of primer pairs for the molecular markers of Pi9 and Pi9-type5 The nucleotide polymorphism analysis of primer pairs, Pi9-type5F1 and Pi9-type5R1, Pi9-type5F2 and Pi9-type5R2, Pi9-type5F3 and Pi9-type5mR, for the molecular markers of Pi9-type5. The arrows indicate the site and direction of primers. * indicates artificial mutated base in primer for improving specificity of PCR amplification. The shaded lowercase letters indicate the polymorphic nucleotide sites in homologous genes. The shaded uppercase letters indicate the primer mismatched site generated by artificial mutated base in homologous genes"

Table 5

The rice materials containing Pi9-type5"

编号
No.		 材料
Material		 引物Primer
Pi9-type5-F1 Pi9-type5-R1 Pi9-type5-F2 Pi9-type5-R2 Pi9-type5-F3 Pi9-type5-mR
8 IRBLz5-CA √ √ √
9 IRBLzt-T √ √ √
25 E33 √ √ √
28 成恢993 Chenghui 993 √ √ √
29 德恢6099 Dehui 6099 √ √ √
31 航恢1179 Hanghui 1179 √ √ √
33 华占Huazhan √ √ √
40 蜀恢308 Shuhui 308 √ √ √
42 蜀恢498 Shuhui 498 √ √ √
43 蜀恢505 Shuhui 505 √ √ √
44 蜀恢548 Shuhui 548 √ √ √
46 蜀恢586 Shuhui 586 √ √ √
50 R900 √ √ √
52 成恢19 Chenghui 19 √ √ √
56 泸恢8258 Luhui 8258 √ √ √
61 明恢86 Minghui 86 √ √ √
63 蜀恢137 Shuhui 137 √ √ √
64 蜀恢208 Shuhui 208 √ √ √
70 五山丝苗Wushansimiao √ √ √
72 雅禾Yahe √ √ √
73 雅恢2115 Yahui 2115 √ √ √
74 雅恢2116 Yahui 2116 √ √ √
77 雅恢2119 Yahui 2119 √ √ √
78 雅恢2199 Yahui 2199 √ √ √
79 雅恢2275 Yahui 2275 √ √ √
82 雅恢2918 Yahui 2918 √ √ √
83 雅恢5049 Yahui 5049 √ √ √
84 雅恢5217 Yahui 5217 √ √ √
85 雨恢38 Yuhui 38 √ √ √
87 粤农丝苗Yuenongsimiao √ √ √
118 雅1B Ya 1B √ √ √
128 绵恢365 Mianhui 365 √ √ √
133 绵恢815 Mianhui 815 √ √ √

Fig. 3

The nucleotide polymorphism analysis of primer pairs for the molecular markers of PigmR The arrows indicate the site and direction of primers. * indicates artificial mutated base in primer for improving specificity of amplification. The shaded lowercase letters indicate the polymorphic nucleotide sites in homologous genes. The shaded uppercase letters indicate the primer mismatched sites generated by artificial mutated base in homologous genes"

Table 6

The rice varieties containing PigmR"

编号
No.		 材料
Material		 引物Primer
Pigm-F2+
Pigm-newmR1		 Pigm-newmF1+
Pigm-newmR1		 Pigm-mF4+
Pigm-mR5		 Pigm-mF6+
Pigm-mR7
85 雨恢38 Yuhui 38 √ √ √ √
97 川谷B Chuangu B √ √ √ √
100 川农4B Chuannong 4B √ √ √ √
109 内香6B Neixiang 6B √ √ √ √
112 蓉18B Rong 18 B √ √ √ √
113 蓉7B Rong 7B √ √ √ √
114 双1B Shuang 1B √ √ √ √
134 地谷B Digu B √ √ √ √
阳性对照Positive control 谷梅4号Gumei 4 √ √ √ √

Fig. 4

The position and application of molecular marker of Pid4"

Table 7

The rice varieties containing Pid4"

编号
No.		 材料
Material
85 雨恢38 Yuhui 38
97 川谷B Chuangu B
100 川农4B Chuannong 4B
109 内香6B Neixiang 6B
110 千乡654B Qianxiang 654B
113 蓉7B Rong 7B
114 双1B Shuang 1B
阳性对照Positive control 地谷B Digu B

Table 8

Blast resistance gene composition at Pi9 locus in the rice parent varieties"

编号
No.		 材料
Material		 抗性基因Resistance gene
Pi2 Piz-t Pi9 Pi9-type5 PigmR Pid4
18 IRBL9-W √
8 IRBLz5-CA √ √
25 E33 √ √
29 德恢6099 Dehui 6099 √ √
31 航恢1179 Hanghui 1179 √ √
33 华占Huazhan √ √
40 蜀恢308 Shuhui 308 √ √
43 蜀恢505 Shuhui 505 √ √
44 蜀恢548 Shuhui 548 √ √
46 蜀恢586 Shuhui 586 √ √
50 R900 √ √
70 五山丝苗Wushansimiao √ √
72 雅禾Yahe √ √
73 雅恢2115 Yahui 2115 √ √
74 雅恢2116 Yahui 2116 √ √
77 雅恢2119 Yahui 2119 √ √
79 雅恢2275 Yahui 2275 √ √
82 雅恢2918 Yahui 2918 √ √
83 雅恢5049 Yahui 5049 √ √
84 雅恢5217 Yahui 5217 √ √
85 雨恢38 Yuhui 38 √ √ √ √
87 粤农丝苗Yuenongsimiao √ √
118 雅1B Ya 1B √ √
133 绵恢815 Mianhui 815 √ √
9 IRBLzt-T √ √
42 蜀恢498 Shuhui 498 √ √
52 成恢19 Chenghui 19 √ √
56 泸恢8258 Luhui 8258 √ √
61 明恢86 Minghui 86 √ √
63 蜀恢137 Shuhui 137 √ √
64 蜀恢208 Shuhui 208 √ √
78 雅恢2199 Yahui 2199 √ √
97 川谷B Chuangu B √ √ √
100 川农4B Chuannong 4B √ √ √
109 内香6B Neixiang 6B √ √ √
113 蓉7B Rong 7B √ √ √
114 双1B Shuang 1B √ √ √
110 千乡654B Qianxiang 654B √ √
28 成恢993 Chenghui 993 √
49 HR2168 √
128 绵恢365 Mianhui 365 √
134 地谷B Digu B √ √
112 蓉18B Rong 18B √
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