Characterization and Development of Genomic SSRs in Pecan (Carya illinoinensis)
| Autor: | Xiaohua Yao, Qing Fang, Jun Wu, Chengcai Zhang, Chang Jun, Huadong Ren, Weizhong Shao |
|---|---|
| Rok vydání: | 2020 |
| Předmět: |
0106 biological sciences
Biology 01 natural sciences Genome 03 medical and health sciences food Genus pecan Genotype Cultivar DNA marker 030304 developmental biology Genetics 0303 health sciences Genetic diversity Carya Dendrogram food and beverages Forestry Carya illinoinensis lcsh:QK900-989 genetic diversity SSR food.food Genetic marker molecular marker assisted selection lcsh:Plant ecology 010606 plant biology & botany |
| Zdroj: | Forests Volume 11 Issue 1 Forests, Vol 11, Iss 1, p 61 (2020) |
| ISSN: | 1999-4907 |
| DOI: | 10.3390/f11010061 |
| Popis: | 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 &lsquo 87MX3-2&rsquo and &lsquo Pawnee&rsquo 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. |
| Databáze: | OpenAIRE |
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