Potential of SSR markers for plant breeding and variety identification in Australian barley germplasm

Abstract

SSR markers closely linked to 18 loci that control 16 important barley traits were assessed for their applicability in Australian barley breeding programs. A panel of 40 genotypes routinely used by the South Australian Barley Improvement Program (SABIP) was used to examine the usefulness of these SSR markers for marker assisted selection (MAS). The success of monitoring a trait locus from donor to recipient lines ranged from 10 to 98%, depending on the marker. SSRs with a high polymorphic information content (PIC) value were found to be the most useful for application in MAS. The assessment also indicated that SSRs derived from genomic sequences were more successful for MAS than those designed from expressed sequence tags. A total of 130 SSR markers were screened among 2 panels of Australian barley genotypes to determine which markers would be the most useful for discriminating Australian germplasm. PIC values generated by this screening were also compared with those generated using a panel of European barley genotypes. Using ordinary correlations (parametric), rank correlations (non-parametric), and partial correlations (multi-variate), a strong association was found between the 2 Australian panels, but no or weak correlation was observed between the 2 Australian panels and the European dataset. It can therefore be concluded that PIC values generated by SSR markers screened with European genotypes cannot be used to predict the usefulness of an SSR marker for discriminating Australian genotypes. From PIC values generated in this study, 36 SSR markers have been selected for the discrimination of Australian genotypes. These markers all show high and/or consistent PIC values among Australian and European barley genotypes.A R 0 2 1 7 8 S S R m a r k e r s f o r p l a n t b r e e d i n g i n b a r l e y A . K a r a k o u s i s e t a l .

Identification of informative SSR markers capable of distinguishing hybrid rice parental lines and their utilization in seed purity assessment

“…Furthermore, many of the modern high yielding varieties and hybrids are phenotypically less distinct making morphological evaluation more diYcult. Microsatellite markers have been used for genetic characterization of cultivars in wheat, maize, sunXower and tomato (Karkousis et al 2003;Wang et al 2002;Zhang et al 2005;Smith and Register 1998). The Biochemical and Molecular Techniques Group of the International Union for the Protection of New Varieties of Plants (UPOV) is evaluating diVerent DNA marker parameters prior to its routine use in establishing distinctness, uniformity and stability (DUS) of plant varieties (Bredemeijer et al 2002;UPOV-BMT 2002).…”

Genetic diversity of ICARDA’s worldwide barley landrace collection

“…Microsatellite primers and PCR multiplexing Twenty highly polymorphic SSR markers (Malysheva-Otto et al 2006;Hamza et al 2004;Matus and Hayes 2002;William et al 1997;Davila et al 1999;Saghai Maroof et al 1994;Karakousis et al 2003) covering the whole barley genome were used (Table 2). They included 17 genomic and 3 genic (HVCMA, HVLTPBB, HVWAXY) SSR markers.…”

Selection footprints in barley breeding lines detected by combining genotyping-by-sequencing with reference genome information

“…The authors hypothesized that it was the result of linkage of these markers to major loci for disease resistance or malting quality that were presumably under selection during the breeding process. Several authors have indicated changes in allelic frequencies, with a reduction in diversity for modern cultivars (Russell et al 2000;Karakousis et al 2003). Similarly, Fu and Somers (2009) using wheat microsatellites reported that allelic reduction occurred in every part of the wheat genome as a consequence of breeding.…”

“…The considerable differences between allelic frequencies at the F2 and F8 of the same cross are, most likely, the result of artificial selection. Karakousis et al (2003), using microsatellites, found that several SSRs assessed in F2 crosses showed distorted segregation, while others showed the expected 1:2:1 ratio. They explained this result as a consequence of preferential amplification of alleles, resulting in the inability to detect heterozygote's for some markers.…”