Onaga Geoffrey, Wydra Kerstin, Koopmann Birger, Séré Yakouba, von Tiedemann Andreas
First, third, and fifth authors: Division of Plant Pathology and Crop Protection, Department of Crop Sciences, and second author: CLB-Tropical and Subtropical Agriculture and Forestry, Georg-August-University Göttingen, Germany; and fourth author: Africa Rice Center, P.O. Box 33581, Dar es Salaam, Tanzania.
Phytopathology. 2015 Aug;105(8):1137-45. doi: 10.1094/PHYTO-10-14-0281-R. Epub 2015 Aug 10.
Rice blast, caused by Magnaporthe oryzae, is one of the emergent threats to rice production in East Africa (EA), where little is known about the population genetics and pathogenicity of this pathogen. We investigated the genetic diversity and mating type (MAT) distribution of 88 isolates of M. oryzae from EA and representative isolates from West Africa (WA) and the Philippines (Asia) using amplified fragment length polymorphism markers and mating-type-specific primer sets. In addition, the aggressiveness of each isolate was evaluated by inoculating on the susceptible Oryza sativa indica 'Co39', scoring the disease severity and calculating the disease progress. Hierarchical analysis of molecular variance revealed a low level of genetic differentiation at two levels (FST 0.12 and FCT 0.11). No evidence of population structure was found among the 65 isolates from EA, and gene flow among EA populations was high. Moreover, pairwise population differentiation (GST) in EA populations ranged from 0.03 to 0.04, suggesting that >96% of genetic variation is derived from within populations. However, the populations from Asia and WA were moderately differentiated from EA ones. The spatial analysis of principal coordinates and STRUCTURE revealed overlapping between individual M. oryzae isolates from EA, with limited distinctness according to the geographic origin. All the populations were clonal, given the positive and significant index of association (IA) and standardized index of association (rd), which indicates a significant (P<0.001) departure from panmixia (IA and rd=0). Both MAT1-1 and MAT1-2 were detected. However, MAT1-1 was more prevalent than MAT1-2. Pathogenicity analysis revealed variability in aggressiveness, suggesting a potential existence of different races. Our data suggest that either M. oryzae populations from EA could be distributed as a single genetic population or gene flow is exerting a significant influence, effectively swamping the action of selection. This is the first study of genetic differentiation of rice-infecting M. oryzae strains from EA, and may guide further studies on the pathogen as well as resistance breeding efforts.
稻瘟病由稻瘟病菌引起，是东非水稻生产面临的新威胁之一，而关于该病原菌的群体遗传学和致病性，人们所知甚少。我们使用扩增片段长度多态性标记和交配型特异性引物组，研究了来自东非的88株稻瘟病菌分离株以及来自西非和菲律宾（亚洲）的代表性分离株的遗传多样性和交配型（MAT）分布。此外，通过接种易感的籼稻品种‘Co39’，评估每个分离株的致病力，对病害严重程度进行评分并计算病害进展。分子方差的层次分析显示，在两个水平上遗传分化程度较低（FST为0.12，FCT为0.11）。在来自东非的65个分离株中未发现群体结构的证据，且东非群体间的基因流较高。此外，东非群体间的成对群体分化（GST）范围为0.03至0.04，这表明>96%的遗传变异源自群体内部。然而，来自亚洲和西非的群体与东非的群体有中等程度的分化。主坐标空间分析和STRUCTURE分析表明，来自东非的稻瘟病菌分离株个体之间存在重叠，根据地理来源的差异有限。鉴于关联指数（IA）和标准化关联指数（rd）为正且显著，所有群体均为克隆性群体，这表明与随机交配（IA和rd = 0）存在显著差异（P<0.001）。检测到了MAT1-1和MAT1-2两种交配型。然而，MAT1-1比MAT1-2更普遍。致病性分析揭示了致病力的变异性，表明可能存在不同的生理小种。我们的数据表明，要么来自东非的稻瘟病菌群体以单一遗传群体的形式分布，要么基因流正在发挥重大影响，有效地掩盖了选择的作用。这是对来自东非的感染水稻的稻瘟病菌株遗传分化的首次研究，可能会为该病原菌的进一步研究以及抗病育种工作提供指导。
