Genetic diversity in European chestnut populations by means of genomic and genic microsatellite markers

Abstract

Microsatellite or simple sequence repeats (SSRs) are one of the most used markers in population genetic studies. SSR markers developed from expressed sequence tags (EST) have proved useful to examine functional diversity in relation to adaptive variation. The information provided by both genomic and genic microsatellite markers could offer more accurate indication on the distribution of the genetic diversity among and within populations assuming different evolutionary drivers. This is the first study on chestnut (Castanea sativa Mill.) in which the genetic diversity was evaluated by means of genomic (SSRs) and genic (EST-SSRs) microsatellite markers. We genotyped nine natural European chestnut populations distributed throughout representative areas of contrasting climatic conditions in the Mediterranean basin. Genomic SSRs showed significantly higher levels of diversity in terms of number of alleles, effective number of alleles, expected heterozygosity and level of polymorphism. Furthermore, there were significant differences in the level of differentiation among populations. The UPGMA analysis revealed different clustering pattern between populations, being the grouping according to geographic distances in the case of genomic SSRs and two differentiated groups based on the northern-southern distribution of the populations for ESTSSRs. Furthermore, the EST-SSR transferability among related Castanea and Quercus species was stated. Our results confirm that combining genomic SSRs and ESTSSRs is a useful tool to give complementary information to explain the genetic and adaptive diversity in chestnut.

The assessment of genetic diversity of Castanea species by RAPD, AFLP, ISSR, and SSR markers

“…Although several molecular marker systems are currently available in the literature, most of the studies so far performed have employed only one marker system for the analysis and characterization of cultivated chestnuts. Recently, comparison between 2 marker methods on genetic diversity in chestnut is becoming common (Goulão et al, 2001;Martin et al, 2010). The dominant markers (RAPD, AFLP, and ISSR) used in this study provide a large number of polymorphic loci and were in general agreement with other studies of genetic diversity measurements.…”

Next-generation hybridization and introgression

“…Woodhead et al (2005) compared genetic diversity in the fern Athyrium distentifolium using EST-SSRs, genomic SSRs and AFLPs, and all marker types showed similar rank orders of population diversity and comparable F ST values, suggesting polymorphism in EST-SSRs can often be considered effectively neutral. In a comparison of EST-SSRs and genomic SSRs in Castanea, Martin et al (2010) found no significant differences in the F ST values calculated with the two marker types, suggesting no deviation from selective neutrality. However, genomic SSRs have higher relative diversities these systems, and a number of others (see references in Martin et al, 2010).…”

“…In a comparison of EST-SSRs and genomic SSRs in Castanea, Martin et al (2010) found no significant differences in the F ST values calculated with the two marker types, suggesting no deviation from selective neutrality. However, genomic SSRs have higher relative diversities these systems, and a number of others (see references in Martin et al, 2010). It should be remembered, however, that decreased variation at EST-SSR loci may be considered a benefit for interspecific studies, where homoplasy may be a problem.…”

Genetic characterization of chestnut (Castanea sativa Mill.) orchards and traditional nut varieties in El Bierzo, a glacial refuge and major cultivation site in northwestern Spain

“…Recent studies using molecular markers have confirmed that the genetic landscape of C. sativa is complex across its distribution area-from the Atlantic Ocean to the Caspian Sea-especially in traditional nut production areas, where both grafted material and wild populations have coexisted for long periods of time (Gobbin et al 2007;Lang et al 2007;Mattioni et al 2008Mattioni et al , 2013Martin et al 2010). The northwest region of the Iberian Peninsula is particularly interesting in this context because (i) it is located at one extreme of the distribution area and concentrates the most extensive sweet chestnut stands in Spain and Portugal, (ii) it has been one of the major focal points for the native species after the last glaciation, and (iii) it has a centenary tradition of chestnut cultivation and management Ramos-Cabrer and PereiraLorenzo 2005;Pereira-Lorenzo et al 2010aMartin et al 2012;Mattioni et al 2013).…”

“…Also known as simple sequence repeats (SSRs), these polymorphic markers have become widely used to study population genetic diversity, parental relationships, and patterns of gene flow, among other applications (Ellegren 2004). Whereas their development is still limited in forest trees (Neale and Kremer 2011), micro satellite loci have been successfully used in recent years to improve our overall understanding of the genetic landscape of sweet chestnut in Europe (e.g., Mattioni et al 2008;Martin et al 2010;and others). These markers have also been applied to genotype germplasm or differentiate chestnut cultivars, often at national or regional scales (e.g., Buck et al 2003;Marinoni et al 2003Marinoni et al , 2013Gobbin et al 2007;Martin et al 2009Martin et al , 2012.…”