Multiple methods for the identification of polymorphic simple sequence repeats (SSRs) in sorghum [Sorghum bicolor (L.) Moench]

Abstract

Simple sequence repeats (SSRs), also known as microsatellites, are highly variable DNA sequences that can be used as markers for the genetic analysis of plants. Three approaches were followed for the development of PCR primers for the amplification of DNA fragments containing SSRs from sorghum [Sorghum bicolor (L.) Moench]: a search for sorghum SSRs in public DNA databases; the use of SSR-specific primers developed in the Poaceae species maize (Zea mays L.) and seashore paspalum grass (Paspalum vaginatum Swartz); and the screening of sorghum genomic libraries by hybridization with SSR oligonucleotides. A total of 49 sorghum SSR-specific PCR primer pairs (two designed from GenBank SSR-containing sequences and 47 from the sequences of genomic clones) were screened on a panel of 17 sorghum and one maize accession. Ten primer pairs from paspalum and 90 from maize were also screened for polymorphism in sorghum. Length polymorphisms among amplification products were detected with 15 of these primer pairs, yielding diversity values ranging from 0.2 to 0.8 with an average diversity of 0.56. These primer pairs are now available for use as markers in crop improvement and conservation efforts.

DNA markers reveal genetic structure and localized diversity of Ethiopian sorghum landraces

“…The average number of alleles, 15.1 per locus, for the seven SSR loci was higher than values reported in other studies on sorghum (Brown et al, 1996;Taramino et al, 1997;Dean et al, 1999;Kong et al, 2000;Deu et al, 2010;Weerasooriya et al, 2016). We used a higher number of landraces than previous authors, and this may account for some of these differences.…”

“…Seven sorghum SSR markers (Brown et al, 1996;Taramino et al, 1997;Dean et al, 1999;Kong et al, 2000) were selected based on their polymorphism, amplified product size range and genome coverage. The M13 primer tailing system (Schuelke, 2000) was used to fluorescently label PCR products.…”

Genetic Diversity among Japanese Cultivated Sorghum Assessed with Simple Sequence Repeats Markers

“…Some amplifi cation products had a higher molecular weight (shadow, heteroduplex and faint minor band) than the SSR allele band. However, nine SSR markers produced all the expected SSR allele size reported (Brown, et al, 1996;Ghebru et al, 2002).…”

“…These oligonucleotide sequences were derived from SSR-containing clones of Sorghum bicolor cultivar RTx430 (Brown et al, 1996). The SSR markers used are distributed widely across the sorghum linkage groups (A-I), thus giving the comprehensive coverage of the sorghum genome.…”

“…the lane and band (the peaks region) and measure the fragment size. Only the reported allele size of loci (Brown, et al, 1996;Ghebru et al, 2002) as an amplifi cation product of SSR was used for genotyping ( Table 2). The size of the DNA fragments was determined relative to the size standard from the 1-kb size marker GIBCO/BRL.…”