Prevalence of Ineffective Haplotypes at the Rice Blast Resistance (R) Gene Loci in Chinese Elite Hybrid Rice Varieties Revealed by Sequence-Based Molecular Diagnosis
Prevalence of Ineffective Haplotypes at the Rice Blast Resistance (R) Gene Loci in Chinese Elite Hybrid Rice Varieties Revealed by Sequence-Based Molecular Diagnosis
复制标题
基于序列的分子诊断揭示中国杂交水稻优良品种稻瘟病抗性（R）基因座无效单倍型的流行
作者：
肖贵;杨健源;朱小源;吴俊;周波
同一个稻胚R基因位点上的多个单倍型具有极高的序列相似性，这使得利用分子标记进行基因诊断的方法在彼此区分上不太有效。水稻优良品种中R基因/单倍型的组成和分布模式尚未得到广泛的分析。本研究采用PCR扩增和测序的方法，对54个中国优良水稻品种的R基因单倍型进行了诊断。4个靶主R基因座的不同数量的功能性和非功能性单倍型，即，参考已知R基因的参考序列，推导出Pi 2/9、Pi 5、Pik和Pib。功能单倍型在Pi 2/9（15%）和Pik（9%）基因座中的频率相对较低，而在Pi 5（50%）和Pib（54%）基因座中的频率相对较高。有趣的是，在Pi 2/9、Pik和Pibloci的非功能性单倍型的显著频率分别为33%、39%和46%，可追溯的原始供体被鉴定，这表明它们最有可能是通过在各种育种计划中使用不需要的供体而无意传播的。在Pi 5基因座的情况下，只有一个单倍型，即，Pi 5已被识别。对54个水稻品种对鉴别菌株的反应进行了评价，结果表明，鉴别菌株的反应与其同源无毒基因（Avr）频率或单倍型频率有很好的相关性。FourRgenes，即，Pi_2、Piz-t、Pi_50和Pikm对水稻品种的抗病性有显著影响。另外两个尚未在水稻品种中利用的基因Pi 9和Pikh，由于其对当代稻瘟病群体的高抗性频率，在持久抗性育种中显示出很好的应用价值。基于序列分析的分子诊断技术为鉴定和验证水稻抗稻瘟病基因位点的单倍型和有效抗稻瘟病基因提供了一条新的途径。
Multiple haplotypes at the same rice blastR-gene locus share extremely high sequence similarity, which makes the gene diagnostic method using molecular markers less effective in differentiation from one another. The composition and distribution pattern of deployedRgenes/haplotypes in elite rice varieties has not been extensively analyzed. In this study, we employed PCR amplification and sequencing approach for the diagnosis ofR-gene haplotypes in 54 Chinese elite rice varieties. A varied number of functional and nonfunctional haplotypes of 4 target majorR-gene loci, i.e.,Pi2/9,Pi5,Pik, andPib, were deduced by referring to the reference sequences of knownRgenes. Functional haplotypes accounted for relatively low frequencies for thePi2/9(15%) andPik(9%) loci but for relatively high frequencies for thePi5(50%) andPib(54%) loci. Intriguingly, significant frequencies of 33%, 39%, 46% of non-functional haplotypes at thePi2/9,Pik, andPibloci, respectively, with traceable original donors were identified, suggesting that they were most likely unintentionally spread by using undesirable donors in various breeding programs. In the case ofPi5locus, only a single haplotype, i.e.,Pi5was identified. The reactions of 54 rice varieties to the differential isolates were evaluated, which showed a good correlation to the frequency of cognate avirulence (Avr) genes or haplotypes in the differential isolates. FourRgenes, i.e.,Pi2,Piz-t,Pi50, andPikmwere found to contribute significantly to the resistance of the elite rice varieties. Other two genes,Pi9andPikh, which were not utilized in rice varieties, showed promising values in breeding durable resistance due to their high resistance frequencies to the contemporary rice blast population. The sequence-based molecular diagnosis provided a promising approach for the identification and verification of haplotypes in differentR-gene loci and effectiveRgenes valuable for breeding durable rice resistance to rice blast.
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DOI：
10.1186/s12284-018-0203-8
发表时间：
2018-02-17
期刊：
Rice (New York, N.Y.)
影响因子：
--
作者：
Mi J;Yang D;Chen Y;Jiang J;Mou H;Huang J;Ouyang Y;Mou T
通讯作者：
Mou T
影响因子：
5.3
作者：
通讯作者：
--
影响因子：
5.3
作者：
Takahashi A;Hayashi N;Miyao A;Hirochika H
通讯作者：
Hirochika H
影响因子：
5.5
作者：
Pertoldi C;Tokarska M;Wójcik JM;Demontis D;Loeschcke V;Gregersen VR;Coltman D;Wilson GA;Randi E;Hansen MM;Bendixen C
通讯作者：
Bendixen C
DOI：
10.1186/s12284-017-0176-z
发表时间：
2017-12
期刊：
Rice (New York, N.Y.)
影响因子：
--
作者：
Xiao G;Borja FN;Mauleon R;Padilla J;Telebanco-Yanoria MJ;Yang J;Lu G;Dionisio-Sese M;Zhou B
通讯作者：
Zhou B