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Exploitation of Malus EST-SSRs and the utility in evaluation of genetic diversity in Malus and Pyrus

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Abstract

A total of 8117 suitable SSR-contaning ESTs were acquired by screening from a Malus EST database, among which dinudeotide SSRs were the most abundant repeat motif, within which, CT/TC followed by AG/GA were predominant. Based on the suitable sequences, we developed 147 SSR primer pairs, of which 94 pairs gave amplifications within the expected size range while 65 pairs were found to be polymorphic after a preliminary test. Eighteen primer pairs selected randomly were further used to assess genetic relationship among 20 Malus species or cultivars. As a result, these primers displayed high level of polymorphism with a mean of 6.94 alleles per locus and UPGMA cluster analysis grouped twenty Malus accessions into five groups at the similarity level of 0.6800 that were largely congruent to the traditional taxonomy. Subsequently, all of the 94 primer pairs were tested on four accessions of Pyrus to evaluate the transferability of the markers, and 40 of 72 functional SSRs produced polymorphic amplicons from which 8 SSR loci selected randomly were employed to analyze genetic diversity and relationship among a collection of Pyrus. The 8 primer pairs produced expected bands with the similar size in apples with an average of 7.375 alleles per locus. The observed heterozygosity of different loci ranged from 0.29 (MES96) to 0.83 (MES138), with a mean of 0.55 which is lower than 0.63 reported in genome-derived SSR marker analysis in Pyrus. The UPGMA dendrogram was similar to the previous results obtained by using RAPD and AFLP markers. Our results showed that these EST-SSR markers displayed reliable amplification and considerable polymorphism in both Malus and Pyrus, and will contribute to the knowledge of genetic study of Malus and genetically closed genera.

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Acknowledgments

We gratefully acknowledge Prof. David Spooner of Department of Horticulture, University of Wisconsin, for critical review of the manuscript. This research work was funded by the project (30871690) of the National Natural Science Foundation of China, project (R307605) from Natural Science Foundation of Zhejiang Province, China, the grant (2008C32011) from Science & Technology Department of Zhejiang Province and the earmarked fund for Modern Agro-industry Technology Research System of China.

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  1. Department of Horticulture, Zhejiang University, 310029, Hangzhou, China

    Lihua Yao, Xiaoyan Zheng, Danying Cai & Yuanwen Teng

  2. The State Agricultural Ministry Laboratory of Horticultural Plant Growth, Development & Quality Improvement, 310029, Hangzhou, China

    Lihua Yao, Xiaoyan Zheng, Danying Cai & Yuanwen Teng

  3. Research Institute of Pomology, Chinese Academy of Agricultural Sciences, 125100, Xingcheng, China

    Yuan Gao, Kun Wang & Yufen Cao

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  1. Lihua Yao
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Correspondence to Yuanwen Teng.

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Yao, L., Zheng, X., Cai, D. et al. Exploitation of Malus EST-SSRs and the utility in evaluation of genetic diversity in Malus and Pyrus . Genet Resour Crop Evol 57, 841–851 (2010). https://doi.org/10.1007/s10722-009-9524-1

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