Identification, evaluation, and application of the genomic-SSR loci in ramie

Ming-Bao Luan,Jian-Hua Chen,Zhi-Min Sun,Ying Xu,Juan-Juan Zhu,Xiao-Fei Wang,Xin Deng,Ze-Mao Yang,Chen-Chen Liu

doi:10.5586/asbp.3510

Abstract

To provide a theoretical and practical foundation for ramie genetic analysis, simple sequence repeats (SSRs) were identified in the ramie genome and employed in this study. From the 115 369 sequences of a specific-locus amplified fragment library, a type of reduced representation library obtained by high-throughput sequencing, we identified 4774 sequences containing 5064 SSR motifs. SSRs of ramie included repeat motifs with lengths of 1 to 6 nucleotides, and the abundance of each motif type varied greatly. We found that mononucleotide, dinucleotide, and trinucleotide repeat motifs were the most prevalent (95.91%). A total of 98 distinct motif types were detected in the genomic-SSRs of ramie. Of them, The A/T mononucleotide motif was the most abundant, accounting for 41.45% of motifs, followed by AT/TA, accounting for 20.30%. The number of alleles per locus in 31 polymorphic microsatellite loci ranged from 2 to 7, and observed and expected heterozygosities ranged from 0.04 to 1.00 and 0.04 to 0.83, respectively. Furthermore, molecular identity cards (IDs) of the germplasms were constructed employing the ID Analysis 3.0 software. In the current study, the 26 germplasms of ramie can be distinguished by a combination of five SSR primers including Ibg5-5, Ibg3-210, Ibg1-11, Ibg6-468, and Ibg6-481. The allele polymorphisms produced by all SSR primers were used to analyze genetic relationships among the germplasms. The similarity coefficients ranged from 0.41 to 0.88. We found that these 26 germplasms were clustered into five categories using UPGMA, with poor correlation between germplasm and geographical distribution. Our study is the first large-scale SSR identification from ramie genomic sequences. We have further studied the SSR distribution pattern in the ramie genome, and proposed that it is possible to develop SSR loci from genomic data for population genetics studies, linkage mapping, quantitative trait locus mapping, cultivar fingerprinting, and as genetic diversity studies.

Highlights

Ramie [Boehmeria nivea (L.) Gaudich], known as Chinese grass, is a specialty fiber crop that provides raw material for the textile industry
Single nucleotide repeat motifs comprise the largest portion of ramie genomic-simple sequence repeat (SSR) loci, followed by dinucleotide and trinucleotide repeat motifs
This was significantly different from Caenorhabditis elegans [27], sorghum (Sorghum bicolor L.) [30], soybean rhizobia [31], Mesorhizobium loti [31], and Sinorhizobium meliloti [31], in which the genomic-SSR loci are comprised of nucleotide repeat units ranging from 4 bp to 6 bp in length

Summary

Introduction

Ramie [Boehmeria nivea (L.) Gaudich], known as Chinese grass, is a specialty fiber crop that provides raw material for the textile industry. It is known as the second most important fiber crop, after cotton, in China [1]. Luan et al / Genomic-SSR loci of ramie carotenoids, vitamin B2, and calcium, and have a high yield of approximately 7.5 t dry weight ha−1. It is the best concentrated feed for various ruminant animals and poultry in southern China [3]

Methods

Results

Conclusion