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Molecules 2016, 21(1), 66; doi:10.3390/molecules21010066

Genetic Diversity and Association of EST-SSR and SCoT Markers with Rust Traits in Orchardgrass (Dactylis glomerata L.)

1
Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu 611130, China
2
Institute of Agrifood Research and Technology (IRTA), Centre de Recerca en Agrigenòmica (CSIC-IRTA-UAB), Campus UAB–Edifici CRAG, Bellaterra, Cerdanyola del Vallès, Barcelona 08193, Spain
3
Department of Animal Science, Southwest University, Rongchang, Chongqing 402460, China
4
Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR 72704, USA
5
Department of Grassland Science, Sichuan Animal Science Academy, Chengdu 610066, China
6
Agricultural College, Sichuan Agricultural University, Chengdu 611130, China
These authors contributed equally to this work.
*
Authors to whom correspondence should be addressed.
Academic Editor: Derek J. McPhee
Received: 20 November 2015 / Revised: 24 December 2015 / Accepted: 29 December 2015 / Published: 8 January 2016
(This article belongs to the Section Molecular Diversity)
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Abstract

Orchardgrass (Dactylis glomerata L.), is a well-known perennial forage species; however, rust diseases have caused a noticeable reduction in the quality and production of orchardgrass. In this study, genetic diversity was assessed and the marker-trait associations for rust were examined using 18 EST-SSR and 21 SCoT markers in 75 orchardgrass accessions. A high level of genetic diversity was detected in orchardgrass with an average genetic diversity index of 0.369. For the EST-SSR and SCoT markers, 164 and 289 total bands were obtained, of which 148 (90.24%) and 272 (94.12%) were polymorphic, respectively. Results from an AMOVA analysis showed that more genetic variance existed within populations (87.57%) than among populations (12.43%). Using a parameter marker index, the efficiencies of the EST-SSR and SCoT markers were compared to show that SCoTs have higher marker efficiency (8.07) than EST-SSRs (4.82). The results of a UPGMA cluster analysis and a STRUCTURE analysis were both correlated with the geographic distribution of the orchardgrass accessions. Linkage disequilibrium analysis revealed an average r2 of 0.1627 across all band pairs, indicating a high extent of linkage disequilibrium in the material. An association analysis between the rust trait and 410 bands from the EST-SSR and SCoT markers using TASSEL software revealed 20 band panels were associated with the rust trait in both 2011 and 2012. The 20 bands obtained from association analysis could be used in breeding programs for lineage selection to prevent great losses of orchardgrass caused by rust, and provide valuable information for further association mapping using this collection of orchardgrass. View Full-Text
Keywords: association analysis; EST-SSR; genetic diversity; orchardgrass; rust; SCoT association analysis; EST-SSR; genetic diversity; orchardgrass; rust; SCoT
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Yan, H.; Zhang, Y.; Zeng, B.; Yin, G.; Zhang, X.; Ji, Y.; Huang, L.; Jiang, X.; Liu, X.; Peng, Y.; Ma, X.; Yan, Y. Genetic Diversity and Association of EST-SSR and SCoT Markers with Rust Traits in Orchardgrass (Dactylis glomerata L.). Molecules 2016, 21, 66.

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