Genome-wide analysis of SSR and ILP markers in trees: diversity profiling, alternate distribution, and applications in duplication

Ya Lin Sang,Guanghua Qin,Xian Sheng Zhang,Lin Lin Luan,Li Fang Yu,Wan Chen Dong,Xinyao Xia,Yuling Qiao,Yumin Song,Zhi Wei Wang,Long Yang

doi:10.1038/s41598-017-17203-6

Abstract

Molecular markers are efficient tools for breeding and genetic studies. However, despite their ecological and economic importance, their development and application have long been hampered. In this study, we identified 524,170 simple sequence repeat (SSR), 267,636 intron length polymorphism (ILP), and 11,872 potential intron polymorphism (PIP) markers from 16 tree species based on recently available genome sequences. Larger motifs, including hexamers and heptamers, accounted for most of the seven different types of SSR loci. Within these loci, A/T bases comprised a significantly larger proportion of sequence than G/C. SSR and ILP markers exhibited an alternative distribution pattern. Most SSRs were monomorphic markers, and the proportions of polymorphic markers were positively correlated with genome size. By verifying with all 16 tree species, 54 SSR, 418 ILP, and four PIP universal markers were obtained, and their efficiency was examined by PCR. A combination of five SSR and six ILP markers were used for the phylogenetic analysis of 30 willow samples, revealing a positive correlation between genetic diversity and geographic distance. We also found that SSRs can be used as tools for duplication analysis. Our findings provide important foundations for the development of breeding and genetic studies in tree species.

Highlights

Perennial trees constitute more than 50% of the terrestrial biodiversity, act as large and persistent carbon sinks, and play important roles in climate regulation[1]
We performed a genome-wide identification of SSR, intron length polymorphism (ILP), and potential intron polymorphism (PIP) markers in 16 tree species whose genome sequences are currently available
Using the Perl pipeline, 67,259,820 SSR loci were identified from 16 tree species (Table 1), and genome size was found to be positively correlated with the number of identified SSR loci

Summary

Introduction

Perennial trees constitute more than 50% of the terrestrial biodiversity, act as large and persistent carbon sinks, and play important roles in climate regulation[1]. Hevea brasiliensis produces natural latex rubber which is a valuable material for medicine and industry[3], and Theobroma cacao supplies raw materials for the production of chocolate[4] Despite their great value, progress in breeding and molecular study has been hampered by their inherent long growth cycles, high levels of heterozygosis, and complex reproduction. We performed a genome-wide identification of SSR, ILP, and PIP markers in 16 tree species whose genome sequences are currently available. We used these markers to perform phylogenetic analysis in 30 willow samples, and duplication analysis in Populus trichocarpa and Elaeis guineensis. The results will be useful in modern molecular biology and genetic diversity studies

Methods

Results

Conclusion