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. 2021 Jan 6;21(1):3.
doi: 10.1186/s12870-020-02770-0.

Genomic survey sequencing, development and characterization of single- and multi-locus genomic SSR markers of Elymus sibiricus L

Yi Xiong  1 , Xiong Lei  1   2 , Shiqie Bai  2 , Yanli Xiong  1 , Wenhui Liu  3 , Wendan Wu  4 , Qingqing Yu  1 , Zhixiao Dong  1 , Jian Yang  1 , Xiao Ma  5
Affiliations

Genomic survey sequencing, development and characterization of single- and multi-locus genomic SSR markers of Elymus sibiricus L

Yi Xiong et al. BMC Plant Biol. .

Abstract

Background: Siberian wildrye (Elymus sibiricus L.) attracts considerable interest for grassland establishment and pasture recovery in the Qinghai-Tibet Plateau (QTP) due to its excellence in strong stress tolerance, high nutritional value and ease to cultivate. However, the lack of genomic information of E. sibiricus hampers its genetics study and breeding process.

Results: In this study, we performed a genome survey and developed a set of SSR markers for E. sibiricus based on Next-generation sequencing (NGS). We generated 469.17 Gb clean sequence which is 58.64× of the 6.86 Gb estimated genome size. We assembled a draft genome of 4.34 Gb which has 73.23% repetitive elements, a heterozygosity ratio of 0.01% and GC content of 45.68%. Based on the gnomic sequences we identified 67,833 SSR loci and from which four hundred were randomly selected to develop markers. Finally, 30 markers exhibited polymorphism between accessions and ten were identified as single-locus SSR. These newly developed markers along with previously reported 30 ones were applied to analyze genetic polymorphism among 27 wild E. sibiricus accessions. We found that single-locus SSRs are superior to multi-loci SSRs in effectiveness.

Conclusions: This study provided insights into further whole genome sequencing of E. sibiricus in strategy selection. The novel developed SSR markers will facilitate genetics study and breeding for Elymus species.

Keywords: Elymus sibiricus L.; Genetic diversity study; Genomic survey sequencing; Marker development; Single-locus SSR.

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Conflict of interest statement

The authors declare that they have no conflict of interest.

Figures

Fig. 1
Fig. 1
K-mer (k = 25) frequency distribution. The x-axis is depth and the y-axis represent the frequency at that depth. The genome size was calculated following ‘genome size = K-mer num/peak depth’. The two subpeaks were caused by certain repeats rate in the genome of E. sibiricus
Fig. 2
Fig. 2
Guanine plus cytosine (GC) content and depth correlation analysis. The x-axis represents the GC content and the y-axis is the sequence depth
Fig. 3
Fig. 3
The most abundant motifs (red portion) corresponding to mono- to hexa-nucleotide repeats
Fig. 4
Fig. 4
Motif frequency distributions of mono- to hexanucleotide motif types (y-axis) with different repeat numbers (from 5 to > 20, x-axis) in the de novo assembled genomic sequences of E. sibiricus. The z-axis represents the number of each type of motif
Fig. 5
Fig. 5
The UPGMA dendrogram and genetic structure of 27 studied E. sibiricus based on ESGA-SL markers. MGL, Mongolia; QTP, eastern Qinghai-Tibet Plateau; SI, Siberia
Fig. 6
Fig. 6
The PcoA analysis of 27 studied E. sibiricus based on ESGA-SL markers
See this image and copyright information in PMC

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