Molecular characterisation of indigenous Swedish apple cultivars based on SSR and S-allele analysis

Abstract

Trees of 68 apple cultivars, aimed for preservation by the 'National Program for diversity of cultivated plants' as mandate cultivars, were analysed using a set of 10 SSR (simple sequence repeat) primer pairs and the self-incompatibility (S-)locus to evaluate genetic diversity and reveal inter-cultivar relationships. The 12 polymorphic SSR loci exhibited 2 to 15 alleles, with expected heterozygozity (H(e)) ranging from 0.36 to 0.88 and a mean of 0.74. Numerous alleles were classified as rare or unique (35% and 18% respectively). For the S-locus, a total of 14 alleles were identified in this study. Five alleles, S1-S3, S5 and S7 had frequencies ranging from 11 to 18%, whereas the remaining 9 alleles were below 6%. All sexually obtained cultivars could be distinguished with the set of SSR loci. Sports were identical with their progenitors in two cases, but differed in one SSR allele in a third case. An SSR-based dendrogram, based on Roger's genetic distances, did not reveal any clear pattern of clustering. The genetic distances were, however, correlated with a corresponding matrix obtained in a previously conducted RAPD-based study of the same cultivars. Non-mandate parents of Swedish mandate cultivars together with some other reference cultivars were included in this study to check the accuracy of allele scoring, verify parentage and compare the results of this study with those presented in previously published studies. Some discrepancies in allele sizing were revealed and the possibilities of avoiding this problem are discussed.

Genetic Diversity, Population Structure, Parentage Analysis, and Construction of Core Collections in the French Apple Germplasm Based on SSR Markers

“…Numerous diversity studies have been performed on apple germplasm (Garkava-Gustavsson et al 2008;Gasi et al 2010;Gross et al 2014;Hokanson et al 2001;Liang et al 2015;Moriya et al 2011;Pereira-Lorenzo et al 2008;Song et al 2006;Urrestarazu et al 2012;van Treuren et al 2010) but as far as we know, the present study is the largest one to be performed so far at a national level with such a large number of SSR markers. Apple genetic resources are conserved by many very active structures in France (Fig.…”

“…(Zhen et al 2004). These markers have proved advantageous for diversity studies on apple (Garkava-Gustavsson et al 2008;Gasi et al 2010;Gross et al 2014;Hokanson et al 2001;Liang et al 2015;Moriya et al 2011;Pereira-Lorenzo et al 2008;Song et al 2006;Urrestarazu et al 2012;van Treuren et al 2010), and several hundred SSR markers have been developed and genetically mapped across the 17 linkage groups of the apple genome (Gianfranceschi et al 1998;Liebhard et al 2002;Silfverberg-Dilworth et al 2006).…”

Genetic analysis of Anatolian apples (Malus sp.) by simple sequence repeats

“…Similarly in this study, CH01d08, CH02d11, CH04e03, and CH04g10 produced high number of alleles (16–20). In addition, as suggested by the ECPGR (the European Cooperative Programme for Plant Genetic Resources), CH01f02, CH01h01, and CH02c06 appear to be useful to optimize fingerprinting protocols and enable reliable comparisons to be made between different germplasm collections reported in different studies (Galli et al, ; Ramos‐Cabrer et al, ; Cavanna et al, ; Garkava‐Gustavsson et al, ; Evans et al, ; Gasi et al, ; Gross et al, ; Potts et al, ; Urrestarazu et al, ).…”

“…Of the four European accession groups used in comparisons, the Italian accession group, which contains 22 apple accessions (Cavanna et al, ), was compared with Anatolian accessions at two shared loci (CH01f02 and CH01d08). Spanish (Ramos‐Cabrer et al, ), Swedish (Garkava‐Gustavsson et al, ), and Bosnia and Herzegovina (BH) (Gasi et al, ) accession groups, with 55, 60, and 19 accessions, respectively, were compared with Anatolian accession groups. CH02d11, CH03g07, and COL were used in comparisons with Spanish accessions while CH02c06, CH02b10, and COL and CH01h01, CH01h10, and CH02c06 were used in comparisons with Swedish and Bosnia and Herzegovina accessions, respectively.…”

Identification of marker alleles linked to fire blight resistance QTLs in apple genotypes

“…PCR amplification conditions were as follows: 94°C 2 min 30 s, followed by 35 cycles of 94°C 30 s, 58°C 1 min, 72°C 1 min, ended with a 5 min extension at 72°C (Garkava‐Gustavsson et al. ), except for ChFbE06, which were as follows: 5 min at 94°C, then 30 cycles of 30 s at 94°C, 45 s at 56°C and 45 s at 72°C, followed by eight cycles of 30 s at 94°C, 45 s at 53°C and 45 s at 72°C, with a final elongation step of 10 min at 72°C (Paraviccini et al., ). Amplification of the products identified by specific SCAR primers was resolved via electrophoresis in horizontal 1.5% agarose gels in a 1× TAE buffer.…”