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Open AccessArticle

Characterization and Development of Genomic SSRs in Pecan (Carya illinoinensis)

Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang District, Hangzhou 311400, China
Jiande Forestry Bureau, Jiande, Hangzhou 311600, China
Forestry Center of Jiande, Jiande, Hangzhou 311600, China
Author to whom correspondence should be addressed.
Forests 2020, 11(1), 61;
Received: 4 December 2019 / Revised: 18 December 2019 / Accepted: 2 January 2020 / Published: 4 January 2020
(This article belongs to the Section Forest Ecophysiology and Biology)
Research Highlights: The distribution of simple sequence repeat (SSR) motifs in two draft genomes of pecan was evaluated. Sixty-six SSR loci were validated by PCR amplification in pecan. Twenty-two new development markers can be used for genetic study in genus Carya. Background and Objectives: Pecan has good nutritional and health benefits and is an important crop worldwide. However, the genetic research in this species is insufficient. One of the main reasons for this is the lack of enough accurate, convenient, and economical molecular markers. Among different marker types, SSR loci are enormously useful in genetic studies. However, the number of SSRs in C. illinoinensis (Wangenh.) K. Koch is limited. Materials and Methods: The distribution of SSR motifs in the pecan genome was analyzed. Then, the primers for each SSR were designed. To evaluate their availability, 74 SSR loci were randomly selected and amplified in pecan. Finally, 22 new SSRs and eight former ones were picked to evaluate the genetic diversity in 60 pecan genotypes and to determine their transferability in other Carya species. Results: 145,714 and 143,041 SSR motifs were obtained from two draft genomes of ‘87MX3-2’ and ‘Pawnee’, respectively. In total, 9145 candidate primers were obtained. Sixty-six (89.19%) primers amplified the target products. Among the 30 SSRs, 29 loci showed polymorphism in 60 pecan genotypes. The polymorphic information content (PIC) values ranged from 0.012 to 0.906. In total, 26, 25, and 22 SSRs can be used in C. cathayensis Sarg., C. dabieshanensis W. C. Cheng & R. H. Chang, and C. hunanensis W.C. Liu, respectively. Finally, the dendrogram of all individuals was constructed. The results agree with the geographic origin of the four species and the pedigree relationships between different pecan cultivars. Conclusions: The characterization of SSRs in the pecan genome and the new SSRs will promote the progress of genetic study and breeding in pecan, as well as other species of genus Carya. View Full-Text
Keywords: pecan; Carya; SSR; genetic diversity; DNA marker; molecular marker assisted selection pecan; Carya; SSR; genetic diversity; DNA marker; molecular marker assisted selection
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Zhang, C.; Yao, X.; Ren, H.; Chang, J.; Wu, J.; Shao, W.; Fang, Q. Characterization and Development of Genomic SSRs in Pecan (Carya illinoinensis). Forests 2020, 11, 61.

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