Dinucleotide microsatellites fromEucalyptus sieberi: inheritance, diversity, and improved scoring of single-base differences

Abstract

Eight dinucleotide microsatellites were developed in Eucalyptus sieberi L. Johnson (silvertop ash), a member of the subgenus Eucalyptus. Transfer of six of these to the subgenus Symphyomyrtus and their Mendelian inheritance are demonstrated using a full-sib cross in Eucalyptus nitens. Genetic diversity parameters are presented for the eight loci based on a sample of 100 old-growth E. sieberi trees from a single natural stand. One locus, Es266, had an atypically high fixation index, and significantly deviated from Hardy-Weinberg equilibrium genotypic proportions, indicating the likely presence of null alleles. Two of the loci, Es076 and Es140, had many alleles that differed in size by only a single base pair, possibly because of short poly(A) or poly(T) stretches in their flanking regions. These two loci were by far the most polymorphic, but were difficult to score reliably on a capillary DNA sequencer. Reliability of scoring of these two one-base microsatellite loci was markedly improved by the incorporation of internal reference alleles into each sample analysed.

Marker-Based Quantitative Genetics in the Wild?: The Heritability and Genetic Correlation of Chemical Defenses in Eucalyptus

“…We tested a panel of 30 loci developed in E. globulus (G. Moran, personal communication; Steane et al 2001), E. nitens (Byrne et al 1996), E. sieberi (Glaubitz et al 2001), and E. leucoxylon (Ottewell et al 2005) on up to 95 randomly chosen E. melliodora samples.…”

Progress in Myrtaceae genetics and genomics: Eucalyptus as the pivotal genus

“…More informative, codominant markers such as isozymes, RFLPs, and ESTs were indeed successfully used to map eucalypt genomes (Byrne et al 1995;Gion et al 2000;Thamarus et al 2002) but did not provide the levels of polymorphism and throughput required for routine mapping in multiple pedigrees. It was only with the more recent development of large numbers of highly polymorphic microsatellite (or SSR) markers for Eucalyptus (Brondani et al 1998(Brondani et al , 2006Glaubitz et al 2001;Ottewell et al 2005;Steane et al 2001) that comparative mapping could be performed and linkage map synteny established across multiple pedigrees (Brondani et al 2006;Freeman et al 2006;Marques et al 2002;Hudson et al 2011;Kullan et al 2012). …”

Population genetic analysis and phylogeny reconstruction in Eucalyptus (Myrtaceae) using high-throughput, genome-wide genotyping

“…The development of microsatellite primers for eucalypt taxa (Brondani et al 1998(Brondani et al , 2006Byrne et al 1996;Glaubitz et al 2001;Jones et al 2001;Ottewell et al 2005;Shepherd et al 2006;Steane et al 2001;Thamarus et al 2002) opened the door for reliable genome-wide genotyping of a relatively large number of samples. Microsatellite markers gave researchers the power to examine genetic relationships within and among populations of one (e.g., Butcher et al 2009;Elliott and Byrne 2003;Jones et al 2007;Payn et al 2008;Rathbone et al 2007;Walker et al 2009; see also Byrne 2008 and references therein) or a few closely related species (e.g., Holman et al 2003, Le et al 2009, Shepherd et al 2008.…”