Development of SSR markers from transcriptome data for the pear rust pathogenGymnosporangium asiaticum

Abstract

The pear‐cypress rust Gymnosporangium asiaticum is one of the most significant causal agents of pear rust in Asian pear, severely affecting the pear industry. Research on the genetic diversity of this widespread pathogen has been hampered due to the absence of molecular markers. In the current study, we developed 16 novel microsatellite markers for G. asiaticum from transcriptome data by combining next‐generation sequencing and PCR screening. These polymorphic markers were tested on 96 individuals from nine provinces in China. The number of alleles for these markers ranged from two to nine, with an average of five at each locus. The polymorphic information content ranged from 0.0411 to 0.7666, with an average of 0.4417. In addition, the observed (HO) and expected (HE) heterozygosities were 0.0312–0.6941 and 0.0417–0.8000, respectively. We also observed low‐to‐moderate levels of genetic differentiation and extremely significant gene flow between the nine provinces. Of these 16 developed simple sequence repeat loci, 11 were transferable to other Gymnosporangium species. These new microsatellite markers can be used in future large‐scale studies of the genetic structure and diversity of G. asiaticum.

Development of EST-SSR primers and genetic diversity analysis of the southern blight pathogen Sclerotium rolfsii using transcriptome data

“…Currently, RNA-seq has been used in the SSR development of G. yamadae and G. asiaticum ( Tao et al, 2018 ). EST-SSR can detect numerous alleles, with high repeatability and inter-species transferability due to the presence of microsatellites regions throughout the transcriptome ( Weng et al, 2020 ). In addition, EST-SSR can display the functional information of the sample genome, and the sequences identified in the homologous genes are more conserved, so it has the characteristics of large amount of information, good universality and simple development ( Wu et al, 2014 ).…”

“…Transcriptomic SSR locus analysis revealed that tri-nucleotide repeats had the highest occurrence frequency, accounting for 52.53% of the repeats, which aligns with the results of previous reports on other fungi ( Qian et al, 2013 ). However, tetra-nucleotide repeats tend to stutter less than tri-nucleotide and di-nucleotide repeats and are markedly more accurate and reliable ( Weng et al, 2020 ). Therefore, one of the principles in selecting EST-SSR primers of S. rolfsii involved the selection of a sequence with a repeat unit of di- to penta-nucleotides to increase diversification.…”

“… Jebaraj et al (2017) also showed that the nature and type of host may influence genetic variation between the isolates using nuclear (RAPD & ISSR) markers. Of note, all diversity indices are affected by sample size ( Barrantes and Sandoval, 2009 ; Weng et al, 2020 ). Thus, the above results will be affected by the low sample size of each group.…”