Survey and analysis of simple sequence repeats in the Ustilaginoidea virens genome and the development of microsatellite markers

Publication date: 1 July 2016
Source:Gene, Volume 585, Issue 1
Author(s): Mina Yu, Junjie Yu, Huanhuan Li, Yahui Wang, Xiaole Yin, Huiwen Bo, Hui Ding, Yuxin Zhou, Yongfeng Liu
Ustilaginoidea virens is the causal agent of rice false smut, causing quantitative and qualitative losses in rice industry. However, the development and application of simple sequence repeat (SSR) markers for genetic diversity studies in U. virens were limited. This study is the first to perform large-scale development of SSR markers of this pathogen at the genome level, to (1) compare these SSR markers with those of other fungi, (2) analyze the pattern of the SSRs, and (3) obtain more informative genetic markers. U. virens is rich in SSRs, and 13,778 SSRs were identified with a relative abundance of 349.7SSRs/Mb. The most common motifs in the genome or in noncoding regions were mononucleotides, whereas trinucleotides in coding sequences. A total of 6 out of 127 primers were randomly selected to be used to analyze 115 isolates, and these 6 primers showed high polymorphism in U. virens. This study may serve as an important resource for molecular genetic studies in U. virens.



from #AlexandrosSfakianakis via Alexandros G.Sfakianakis on Inoreader http://ift.tt/1X3rhgY
via IFTTT