title: Genetic Diversity and Association of EST-SSR and SCoT Markers with Rust Traits in Orchardgrass (Dactylis glomerata L.).
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.
authors.affiliation: Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu 611130, China. yanhaidong1991@163.com.
authors.forename: Haidong
authors.initials: H
authors.lastname: Yan
authors.affiliation: 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. zhang.yu@cragenomica.es.
authors.forename: Yu
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Department of Animal Science, Southwest University, Rongchang, Chongqing 402460, China. zbin78@163.com.
authors.forename: Bing
authors.initials: B
authors.lastname: Zeng
authors.affiliation: Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR 72704, USA. guohuayin1997@gmail.com.
authors.forename: Guohua
authors.initials: G
authors.lastname: Yin
authors.affiliation: Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu 611130, China. zhangxq@sicau.edu.cn.
authors.forename: Xinquan
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Department of Grassland Science, Sichuan Animal Science Academy, Chengdu 610066, China. jiyang221@163.com.
authors.forename: Yang
authors.initials: Y
authors.lastname: Ji
authors.affiliation: Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu 611130, China. huanglinkai@sicau.edu.cn.
authors.forename: Linkai
authors.initials: L
authors.lastname: Huang
authors.affiliation: Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu 611130, China. jiangxiaomei830@163.com.
authors.forename: Xiaomei
authors.initials: X
authors.lastname: Jiang
authors.affiliation: Agricultural College, Sichuan Agricultural University, Chengdu 611130, China. ku0082005@126.com.
authors.forename: Xinchun
authors.initials: X
authors.lastname: Liu
authors.affiliation: Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu 611130, China. pengyanlee@163.com.
authors.forename: Yan
authors.initials: Y
authors.lastname: Peng
authors.affiliation: Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu 611130, China. maroar@126.com.
authors.forename: Xiao
authors.initials: X
authors.lastname: Ma
authors.affiliation: Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu 611130, China. yanyanhong3588284@126.com.
authors.forename: Yanhong
authors.initials: Y
authors.lastname: Yan
mesh_terms: D016000:Cluster Analysis; D031745:Dactylis / Q000235:genetics* / Q000382:microbiology; D020224:Expressed Sequence Tags; D005819:Genetic Markers; D018745:Genome, Plant; D015810:Linkage Disequilibrium; D018895:Microsatellite Repeats; D005810:Multigene Family; D010641:Phenotype; D010935:Plant Diseases / Q000235:genetics* / Q000382:microbiology; D011110:Polymorphism, Genetic; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable
chemical_list: D005819:Genetic Markers
keywords: EST-SSR; SCoT; association analysis; genetic diversity; orchardgrass; rust