Simple sequence repeats in Puccinia graminis: abundance, cross-formae speciales and intra-species utility, and development of novel markers
Simple sequence repeats in Puccinia graminis: abundance, cross-formae speciales and intra-species utility, and development of novel markers
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DOI：
10.1007/s13313-013-0199-x
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发表时间：
2013-01-01
影响因子：
1.4
通讯作者：
Park, Robert
中科院分区：
文献类型：
--
作者：
Karaoglu, Haydar;Lee, Crystal Man Ying;Park, Robert
我们评估了简单重复序列（SSR）的丰度和性质的小麦秆锈病的病原体，Puccinia graminis f。sp. triangulae的SSR标记，以鉴定和开发SSR标记。一种策略进行了测试，其中公开可用的基因组数据集提取的基因组序列的禾本科牧草f。sp. triangulae的丰度进行了搜索，并挖掘了候选的新的SSR标记，可以应用于广泛的柄锈菌物种。来自393个超重叠群的基因组分析总共产生了34，359个SSR重复基序。其中大部分（98%）是单核苷酸、二核苷酸和三核苷酸重复。AG/GA二核苷酸基序是最常见的，TTGTT基序是所有SSR中最长的。从设计的500对引物中，有460对产生了预期大小范围内的条带，最终开发了56个SSR标记。其中大部分是四核苷酸和五核苷酸基序，PIC值范围为0.40至0.91，平均PIC值为0.71。还研究了这些标记在代表5种柄锈菌和6种禾本科柄锈菌的11个分离物中的交叉扩增。冠状假单胞菌、条纹假单胞菌和小麦假单胞菌的PCR扩增频率较低，因此没有检测到显著的多态性。而在禾本科牧草中分别检测到10、10和11个多态性位点。sp. secalis、禾谷缢管蚜P. graminis f. sp. avenae和“Scabrum”锈病。这些SSR标记将有助于对小麦重要病原菌的遗传多样性进行分析。
We evaluated the abundance and nature of simple sequence repeats (SSRs) in the causal agent of stem rust of wheat, Puccinia graminis f. sp. tritici, in order to characterize and develop SSR markers. A strategy was tested in which publicly available genome datasets extracted from genome sequences of P. graminis f. sp. tritici were searched for abundance and mined for candidate novel SSR markers that could be applied to a wide range of Puccinia species. The genome analysis from 393 supercontigs yielded a total of 34,359 SSR repeat motifs. A majority of these (98 %) were mononucleotide, dinucleotide, and trinucleotide repeats. The AG/GA dinucleotide motifs were the most common, and a TTGTT motif was the longest of all SSRs. From a total of 500 primer pairs designed, 460 produced bands within the expected size range and 56 SSR markers were eventually developed. Most of these were tetranucleotide and pentanucleotide motifs with PIC values ranging from 0.40 to 0.91 with an average PIC value of 0.71. The cross amplification of these markers in 11 isolates representing five Puccinia species and six formae speciales of P. graminis was also investigated. The frequency of PCR amplifications was lower for the species P. coronata, P. striiformis and P. triticina, and consequently, no significant polymorphisms were detected. In contrast 10, 10, and 11 polymorphic SSR loci were identified in P. graminis f. sp. secalis, P. graminis f. sp. avenae, and the "Scabrum" rust, respectively. The SSR markers reported here will be useful to characterize and profile global diversity in the important pathogen P. graminis.