<abstract xmlns="http://www.w3.org/1999/xhtml">

<p>Cross-amplification is a cost-effective method to extend the applicability of SSR markers to closely related taxa which lack their own sequence information. In the present study, 35 SSR markers developed in four oak species of Europe, North America and Asia were selected and screened in five species of the western Himalayas. Fifteen markers were successfully amplified in <italic>Quercus semecarpifolia</italic>, followed by 11 each in <italic>Q. floribunda</italic> and <italic>Q. leucotrichophora</italic>, 10 in <italic>Q. glauca</italic>, and 9 in <italic>Q. lana-ta</italic>. Except two primer pairs in <italic>Q. semecarpifolia</italic>, all were found to be polymorphic. Most of the positively cross-amplified SSRs were derived from the Asian oak, <italic>Q. mongolica</italic>. The genoty-ping of 10 individuals of each species with positively cross-amplified SSRs displayed varied levels of polymorphism in the five target oak species, viz., QmC00419 was most polymorphic in <italic>Q. floribunda</italic>, QmC00716 in <italic>Q. glauca</italic> and <italic>Q. lanata</italic>, QmC01368 in <italic>Q. leucotrichophora</italic>, and QmC02269 in <italic>Q. semecarpifolia</italic>. Among five oak species, the highest gene diversity was depicted in <italic>Q. lanata</italic> and <italic>Q. semecarpifolia</italic> with expected heterozygosity (He = 0.72), while the minimum was recorded for <italic>Q. leucotrichophora</italic> and <italic>Q. glauca</italic> (He = 0.65). The SSRs validated here provide a valuable resource to carry out further population genetic analysis in oaks of the western Himalayas.</p>
</abstract>

Cross-amplification is a cost-effective method to extend the applicability of SSR markers to closely related taxa which lack their own sequence information. In the present study, 35 SSR markers developed in four oak species of Europe, North America and Asia were selected and screened in five species of the western Himalayas. Fifteen markers were successfully amplified in Quercus semecarpifolia, followed by 11 each in Q. floribunda and Q. leucotrichophora, 10 in Q. glauca, and 9 in Q. lana-ta. Except two primer pairs in Q. semecarpifolia, all were found to be polymorphic. Most of the positively cross-amplified SSRs were derived from the Asian oak, Q. mongolica. The genoty-ping of 10 individuals of each species with positively cross-amplified SSRs displayed varied levels of polymorphism in the five target oak species, viz., QmC00419 was most polymorphic in Q. floribunda, QmC00716 in Q. glauca and Q. lanata, QmC01368 in Q. leucotrichophora, and QmC02269 in Q. semecarpifolia. Among five oak species, the highest gene diversity was depicted in Q. lanata and Q. semecarpifolia with expected heterozygosity (He = 0.72), while the minimum was recorded for Q. leucotrichophora and Q. glauca (He = 0.65). The SSRs validated here provide a valuable resource to carry out further population genetic analysis in oaks of the western Himalayas.

Cross-transferability-based identification and validation of simple sequence repeat (SSR) markers in oaks of western Himalayas

Silvae Genetica

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Cross-amplification is a cost-effective method to extend the applicability of SSR markers to closely related taxa which lack their own sequence information. In...

Cross-transferability-based identification and validation of simple sequence repeat (SSR) markers in oaks of western Himalayas

Published Online: Jun 20, 2021

Page range: 108 - 116

DOI: https://doi.org/10.2478/sg-2021-0009

Keywords
Cross-transferability, Genetic diversity, SSRs, Western Himalayan oaks, Quercus semecarpifolia, Quercus floribunda, Quercus leucotrichophora, Quercus glauca, Quercus lanata

© 2021 Chander Shekhar et al., published by Sciendo

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Cross-transferability-based identification and validation of simple sequence repeat (SSR) markers in oaks of western Himalayas

Published Online: Jun 20, 2021

Page range: 108 - 116

DOI: https://doi.org/10.2478/sg-2021-0009

KeywordsCross-transferability, Genetic diversity, SSRs, Western Himalayan oaks, Quercus semecarpifolia, Quercus floribunda, Quercus leucotrichophora, Quercus glauca, Quercus lanata

© 2021 Chander Shekhar et al., published by Sciendo

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Keywords
Cross-transferability, Genetic diversity, SSRs, Western Himalayan oaks, Quercus semecarpifolia, Quercus floribunda, Quercus leucotrichophora, Quercus glauca, Quercus lanata