Genome-wide development of miRNA-based SSR markers in Cleistogenes songorica and analysis of their transferability to Gr
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PLANT GENETICS • ORIGINAL PAPER
Genome-wide development of miRNA-based SSR markers in Cleistogenes songorica and analysis of their transferability to Gramineae/non-Gramineae species Gisele Kanzana 1 & Yufei Zhang 1 & Tiantian Ma 1 & Wenxian Liu 1 & Fan Wu 1 & Qi Yan 1 & Xueyang Min 1 & Zhuanzhuan Yan 1 & Blaise Pascal Muvunyi 1 & Jie Li 1 & Zhengshe Zhang 1 & Yufeng Zhao 1 & Jiyu Zhang 1 Received: 27 October 2019 / Revised: 28 April 2020 / Accepted: 7 May 2020 # Institute of Plant Genetics, Polish Academy of Sciences, Poznan 2020
Abstract Simple sequence repeat (SSR) markers are commonly used for many genetic applications, such as map construction, fingerprinting, and genetic diversity analyses, due to their high reproducibility, polymorphism, and abundance. Endogenous miRNAs play essential roles in plant development and gene expression under diverse biotic and abiotic stress conditions. In the present study, we predicted 110 miRNA-SSR primer pairs from 287 precursor miRNAs. Among 110 primer pairs, 85 were successfully amplified and examined for transferability to other Gramineae and non-Gramineae species. The results showed that all 82 primer pairs yielded unambiguous and strong amplification, and across the 23 studied Cleistogenes accessions, a total of 385 alleles were polymorphic. The number of alleles produced per primer varied from 3 to 11, with an average of 4.69 per locus. The expected heterozygosity (He) ranged from 0.44 to 0.88, with an average of 0.74 per locus, and the PIC (Polymorphism Information Content) values ranged from 0.34 to 0.87, with an average of 0.69 per locus. Furthermore, 1422 miRNA target genes were predicted and analyzed using the GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases. In conclusion, the results showed that an miRNA-based microsatellite marker system can be applicable for genetic diversity and marker-assisted breeding studies. Keywords Cleistogenes songorica . MicroRNA . Simple sequence repeat . Genetic diversity . Transferability . Target genes Communicated by: Izabela Pawłowicz Electronic supplementary material The online version of this article (https://doi.org/10.1007/s13353-020-00561-9) contains supplementary material, which is available to authorized users. * Jiyu Zhang [email protected]
Zhuanzhuan Yan [email protected]
Gisele Kanzana [email protected]
Blaise Pascal Muvunyi [email protected]
Yufei Zhang [email protected]
Jie Li [email protected]
Tiantian Ma [email protected]
Zhengshe Zhang [email protected]
Wenxian Liu [email protected] Fan Wu [email protected] Qi Yan [email protected] Xueyang Min [email protected]; [email protected]
Yufeng Zhao [email protected] 1
State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, People’s Republic of China
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