SSR analysis based on molecular characterisation of apple germplasm in Lithuania

Abstract

The survival of apple trees in old and abandoned orchards over 100 years indicates their adaptation to the local environment. These plants have passed an economic and ecological selection over the years. The structure of genetic diversity of apple germplasm in the old orchards of Lithuania is largely unknown. We applied a common set of 7 simple sequence repeat (SSR) markers to genotype 292 accessions across more than 50 geographic locations representing all Lithuanian geographic regions with the aim of analysing the distribution and structure of variation of the apple genetic resources. Eighty-one polymorphic alleles were identified. Of these, 5 alleles were unique, identified only in four individual genotypes. The COL locus was the most homozygous (44.7%) among the cultivars and clones of the apple; however, the part of the germplasm may be heterozygous for nullalleles and those individuals cannot be distinguished from the homozygous ones. The CH02c11 locus was the most heterozygous (90.0%) in the reference cultivars; meanwhile the CH04e05 locus was the most heterozygous (84.4%) among the analysed genotypes. Triploid genotypes constituted 12.5% among the analysed genotypes. A cluster analysis revealed 5 distinct clusters among the 182 diploid apple genotypes collected from the old orchards. According to molecular marker data, the names of 12 apple cultivars were attributed to 45 analysed unknown genotypes. It was found that traditional apple cultivars 'Popierinis', 'Paprastasis antaninis' and 'Pilkasis molinis' were the most prevalent cultivars in the old orchards. The apple genotypes that have survived in old orchards are valuable sources of traits for breeding as well as of high ecological, economic and heritage importance. Their use in breeding programs would significantly extend the diversity of adaptive genes of the domestic apple.

Assessing the Genetic Diversity of Daylily Germplasm Using SSR Markers: Implications for Daylily Breeding

“…The most reliable way to identify the cultivars' genetic diversity and origin is by using molecular markers [17][18][19]. The short sequence repeat (SSR) microsatellites are codominant markers suitable for pedigree studies [20][21][22] and breeding using marker-assisted selection [23][24][25]. SSR markers are even suitable on molecular evolutionary distant landrace studies [26,27].…”

Simple Sequence Repeat Characterisation of Traditional Apple Cultivars (Malus domestica Borkh.) Grown in the Region of Madrid (Central Spain)

“…SSRs are among the most widely used for cultivar identification because of their easy methodology, polymorphism, great discriminatory power, reproducibility and relatively low cost in comparison to other molecular techniques (Larsen et al 2018). In fact, SSRs are still the most common markers for diversity studies in woody species (Van Laere et al 2018), and, specifically, in apple characterisation used in many national germplasm banks, such as those of Lithuania (Mažeikienė et al 2019), Brazil (Mariano et al 2019), Greece (Ganopoulos et al 2018), Italy (Marconi et al 2018), Denmark (Larsen et al 2017), France (Lassois et al 2016), Portugal (Ferreira et al 2016, Turkey (Uzun et al 2016), Hungary (Király et al 2012), Iran (Gharghani et al 2009) and even used for comparisons at a pan-European level (Urrestarazu et al 2016).…”

Molecular, Physico-Chemical, and Sensory Characterization of the Traditional Spanish Apple Variety “Pero de Cehegín”

“…The molecular characterization of apple collections has been performed in the past using Simple Sequence Repeats (SSR). A high number of microsatellites have been described and used to identify different varieties [17][18][19][20] and to assess the genetic diversity in core collections [21][22][23][24]. In particular, there are several studies in Spanish germplasm collections [23] but to our knowledge, the "Pero de Cehegín" has not been included yet.…”