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

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 . 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.

Investigation and genetic mapping of a Glomerella leaf spot resistance locus in apple

“…Approximately 163 426 SSR loci are distributed across 17 apple chromosomes (Guan et al. ). The release of the ‘Golden Delicious’ genome sequence (Velasco et al.…”

“…Furthermore, SSR markers are widely distributed throughout the apple genome. Approximately 163 426 SSR loci are distributed across 17 apple chromosomes (Guan et al 2011). The release of the 'Golden Delicious' genome sequence (Velasco et al 2010) has significantly simplified the search for SSR markers and the design of corresponding primers.…”

Draft genome sequence of ramie, Boehmeria nivea (L.) Gaudich

“…These studies demonstrated that the nutritive value of ramie is similar to that of alfalfa. Thus, ramie has become a new plant protein source for animal feed (Luan et al., ). In recent years, ramie has been frequently proposed as a potential phytoremediation crop due to its high heavy metal tolerance and absorption ability (Gong et al., ; Liu, Zhu, Tang, & Tang, ; Tang et al., ; Yang et al., , ).…”

Genetic Relationships of 118 Castanea Specific Germplasms and Construction of Their Molecular ID Based on Morphological Characteristics and SSR Markers

“…An important reason for the high heterozygosity of Chinese chestnuts is that they are cross-pollinated plants [ 17 ]. The SSR molecular markers developed and screened in this study were highly polymorphic, and the rich genetic diversity of the participating cultivars of Chinese chestnut can be explained by the fact that the SSR molecular markers were developed based on high-quality whole-genome sequence data from Chinese chestnut, and that the genomic SSRs exhibited higher genetic diversity [ 18 ]. Another possibility is that the involved Chinese chestnut species possessed more resources and complex genetic information.…”