SSR Development and Utilization with Rehmannia glutinosa Transcriptome

Abstract

Rehmannia glutinosa Libosch is a well-known medicinal plant in China. Despite its common use, very few molecular markers are available for this species, severely impeding any improvement of key agronomic traits. In this study, gene-based SSR (simple sequence repeat) markers were mined from the R. glutinosa transcriptome, assembled from leaf and root libraries, to obtain polymorphic information content (PIC). A total of 1,812 SSR (≥18 bp) loci were identified from 1,747 transcripts, in which 1,018 transcripts had significant homology to known proteins, and 35 transcripts were identified as non-coding RNA. Of all SSR loci, AG/GT was the most frequent SSRs repeat type, and bias of base composition presented SSRs loci from noncoding RNA. A set of 279 SSR primers (≥20 bp) were synthesized, of which 204 were successfully amplified in the Wen85-5 genome and 91 had a polymorphic information content between 0.33 and 0.90. Seven pairs of polymorphic SSR primers were selected to evaluate the genetic diversity of 36 R. glutinosa germplasms, and results demonstrated that cultivars are differ considerably from wild strains and that distinct genetic relationships exist among wild strains. The SSRs identified in this study provide critical information for future R. glutinosa breeding.

Whole Genomic EST-SSR Development Based on High-Throughput Transcript Sequencing in Proso Millet (Panicum miliaceum)

“…Simple sequence repeat (SSR) markers are highly reproducible, multi-allelic, co-dominant, ample and evenly distributed in the genome and considered as the most informative and useful marker (Powell et al, 1996;Gupta and Varshney, 2000;Li et al, 2016). From barley, wheat, rice and oat, Hu et al (2009) developed 46 SSRs markers for analyzing Proso millet genetic diversity.…”

Correlation Analysis of Yield and Photosynthetic Traits with Simple Repeat Sequence (SSR) Markers in Maize

“…To overcome these shortages of genetic linkage mapping, a correlation analysis method for genetic linkage and recombination was developed, a correlation analysis of LD (Linkage Disequilibrium) mapping for traits and specific alleles based on disequilibrium of genetic linkage (Gupta et al, 2005;Yang et al, 2007;Li et al, 2016). Compared to linkage mapping, the advantage of correlation analysis included that shorter term required to obtain population, requirement of fewer certain molecular markers, wider detection range, capability of scanning multiple specific alleles simultaneously, wider range for material selection (natural population was also acceptable), and higher detection accuracy (Miao et al, 2010).…”