Origin, Distribution and Sequence Diversity of Rice Blast Resistance Locus LABR_64 in Rice

doi:10.16819/j.1001-7216.2019.8017

Abstract

Abstract:

【Objective】 A better understanding of the origin and distribution of disease resistance genes in rice germplasm is useful for breeding highly resistant varieties.【Method】We analyzed sequence diversity of the rice blast resistance locus LABR_64, which contains two homologous genes, LABR_64-1 and LABR_64-2, is located in the allelic region of Pi3/Pi5/Pii/Pi15 on rice chromosome 9. In addition, we analyzed the microsynteny of the LABR_64 orthologous region in different monocotyledons.【Result】The presence frequency (PF) of LABR_64 is 16%. All of the japonica rice cultivars carrying LABR_64 are highly resistant to rice blast and all of those without the locus are susceptible. In addition, the PF of LABR_64 in the indica subpopulation is lower than 5%. Although LABR_64 is correlated with the resistance to rice blast, many indica rice cultivars without LABR_64 are also resistant to rice blast. We also found that the LABR_64-2 sequence is much conserved. Moreover, the microsynteny analysis of the LABR_64 orthologous region in different monocotyledons indicated that LABR_64 originates after the separation of the monocotyledonous and dicotyledonous species, and at the early differentiation stage of monocotyledons.【Conclusion】The rice blast resistance phenotypes are closely correlated with the presence of the LABR_64 locus in japonica subpopulation, but not in indica, indicating that there are many other resistance loci in the indica subpopulation. The LABR_64-2 sequence can be used for developing molecular markers in marker-assisted rice blast resistance breeding. It also indicated that LABR_64 may play a role in disease resistance in different monocotyledons.

Key words: rice, rice blast resistance gene, sequence diversity, gene origin

摘要：

【目的】研究抗病基因在水稻种群中的分布特征是培育抗病品种的基础。【方法】以水稻第9染色体上与Pi3/Pi5/Pii/Pi15等位的抗病位点LABR_64为研究对象,结合稻瘟病抗性鉴定,对该位点中包含的两个抗病基因LABR_64-1和LABR_64-2在水稻群体中的分布特征进行了研究,并对其在单子叶植物中对应的直系同源序列进行了共线性分析。【结果】LABR_64位点在水稻中存在的频率约为16%,所有存在该位点的粳稻均表现高抗病性,缺失该位点的粳稻品种均表现出高感病性,而籼稻品种中LABR_64位点存在频率低于5%,虽然其存在情况下均表现出抗病性,但大部分缺失该位点品种也表现出抗性;存在LABR_64位点的品种中,LABR_64-2基因编码序列高度保守;LABR_64起源于单子叶与双子叶植物完全分离后及单子叶植物分化早期,其在不同的单子叶植物的分化过程中一直保持着良好的共线性。【结论】粳稻抗稻瘟病表型与LABR_64-1和LABR_64-2存在与否紧密关联,而籼稻的相关性不大,表明籼稻中其他抗性基因在稻瘟病抗性过程中起主导作用;鉴于LABR_64-2的高度保守性,可根据其编码序列设计分子标记,用于高效筛选抗稻瘟病粳稻品种;LABR_64可能在不同单子叶植物抗病过程中均具有重要作用。

关键词: 水稻, 抗稻瘟病基因, 序列多样性, 基因起源

CLC Number:

Yufei DENG, Minghao LIU, Dan WANG, Shimin ZUO, Houxiang KANG, Guoliang WANG. Origin, Distribution and Sequence Diversity of Rice Blast Resistance Locus LABR_64 in Rice[J]. Chinese Journal OF Rice Science, 2019, 33(1): 20-27.

邓雨飞, 刘明浩, 王丹, 左示敏, 康厚祥, 王国梁. 抗稻瘟病位点LABR_64的起源及其分布和序列多样性[J]. 中国水稻科学, 2019, 33(1): 20-27.

Figures/Tables 7

Table 1 Sequences of the primers used in this study.

引物名称 Primer name	目的基因 Target gene	正向引物 Forward sequence(5'-3')	反向引物 Backward sequence(5'-3')
引物1 Primer 1	LABR64-1	CGGAGAATAACTCCTTCGG	AAGGCTTGTCTTTCCAAAA
引物2 Primer 2	LABR64-2	CAAATGTTAGACACGGAAAT	CAACTTGTATGGTGGAACTG
引物3 Primer 3	LABR_64	CAGCCATGGCAGCCATATGACTG	CAGAGGAAGATCCTCCTCTCC
测序引物1 Sequencing primer 1	LABR64-1	GCCTGTAGGTTTTGGAAAG	GAGGGAGTGCTGTAATAGATAAA
测序引物2 Sequencing primer 2	LABR64-2	AGTTGAAGGAAATGTTGAGG	TTGGTAATGAAATCCGGTAA

Fig. 1. Blast resistance evaluation of the rice varieties which contain LABR_64 locus. M, 5000 bp marker; 1, Binulawan(indica, resistance level is 0); 2, IR36(indica, 0); 3, IR8(indica, 0); 4, Carolina Gold(japonica, 1); 5, Iguape Cateto(japonica, 1); N, Nipponbare.

Fig. 2. Distribution of LABR_64 in indica and japonica rice. A, Distribution of LABR_64-1(above), LABR_64-2(below) in resistant and susceptible indica rice. M, 5000 bp marker;Lanes 1-12, Susceptible cultivars; Lanes 13-24, Resistant cultivars. B, Distribution of LABR_64-1(above), LABR_64-2(below) in resistant and susceptible japonica rice. M, 5000 bp Marker;Lanes 1-12, Susceptible cultivars; Lanes 13-24, Resistant cultivars.

Fig. 3. Sequences diversity of rice blast resistance alleles of LABR_64-1.

Fig. 4. Sequences diversity of rice blast resistance alleles of LABR_64-2.

Fig. 5. Microsynteny of the LABR_64 orthologous regions in different monocotyledons. A, Nipponbare and 9311 (Nipponbare does not contain LABR_64, the triangles represent the LABR64-1 and LABR64-2 genes from the resistant japonica varieties). B, Nipponbare and Brachypodium distachyon; C, Nipponbare and Setaria viridis; D, Nipponbare and Sorghum bicolor; E, Nipponbare and Zea mays.

Fig. 6. Timeline of monocotyledon differentiation (Unit: million years).

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