Long-term human impacts on genetic structure of Italian walnut inferred by SSR markers

Abstract

Life history traits, historic factors, and human activities can all shape the genetic diversity of a species. In Italy, walnut (Juglans regia L.) has a long history of cultivation both for wood and edible nuts. To better understand the genetic variability of current Italian walnut resources, we analyzed the relationships among the genetic structure of local walnut populations (inferred by SSR markers) and human migrations along ancient routes, using the territory of Royal Tratturo Candela-Pescasseroli (RT) as a case study. Sixteen J. regia provenances were collected along RT and compared with 13 Italian provenances and the landrace Sorrento. Although the level of SSR polymorphism we observed was moderately high, AMOVA revealed that most of the diversity was located within individuals (92.58%), and geographical differentiation was low (D est = 0.076). Evidence for human-mediated domestication bottleneck events was detected in about 95% of walnut provenances. A Bayesian approach divided 456 walnut samples into three clusters: (1) Sorrento genotypes, (2) trees from the island of Sicily, and (3) the remaining germplasm. The UPGMA tree based on Nei's distances distinguished northeastern provenances and weakly grouped 12 of 16 provenances of RT. The observed genetic differences derived mainly from gradations in allele frequencies. Separation of the Sicilian provenance from the mainland may be explained in terms of founder effects and prolonged geographic isolation. Two contrasting forces, selection, and frequent inter-regional transfer of propagules, appear to drive the patterns of genetic variability for J. regia.

Optimizations of high throughput multiplex polymerase chain reaction with simple sequence repeat markers for genotyping of common walnut populations (<i>Juglans regia</i> L.)

“…The observed average number of alleles per locus is highly dependent on sample size. Accordingly, the average number of alleles of Croatian samples was lower compared with those in literature in which more individual trees were studied but the average number of effective alleles was consistent with the published data (Pollegioni et al 2009;Pollegioni et al 2011;Ruiz-Garcia et al 2011). The investigation of Croatian walnut population, which is small but complex population considering the mixing of different genotypes over the centuries, will provide insight into effects of traditional management on its population genetics.…”

“…A considerable number of authors reported their results after applying sets of those SSR markers on different walnut samples and species (Dangle et al 2005;Victory et al 2006;Ross-Davis et al 2008;Ardhya et al 2010). The same SSR markers were also used for genetic research of national common walnut populations and cultivars in Europe (Foroni et al 2005;Foroni et al 2006;Foroni et al 2007;Cabral et al 2008;Pollegioni et al 2011;Ruiz Garcia et al 2011) and in Asia (Ahmed et al 2012;Gunn et al 2010;Ibrahimov et al 2010;Karimi et al 2010;Kim et al 2012;Mahmoodi et al 2013;Pollegioni et al 2014;Vahdati et al 2015;Wang et al 2008).…”

Walnut: past and future of genetic improvement

“…The following sections depict an overview of these molecular studies and their application (Table 2). Woeste et al 2002;Dangl et al 2005;Hoban et al 2008;Zhang et al 2010;Qi et al 2011;Yi et al 2011;Wu et al 2012;Zhang et al 2013;Chen et al 2013;Najafi et al 2014;Topçu et al 2015;Ikhsan et al 2016;Dang et al 2015;Hu et al 2015;Dang et al 2016 Interspecific hybrids identification Pollegioni et al 2008Pollegioni et al , 2009 Genetic diversity/relationships determination Foroni et al 2005;Dangl et al 2005;Victory et al 2006;Robichaud et al 2006;Wang et al 2008;Aradhya et al 2009;Gunn et al 2010;Karimi et al 2010;Bai et al 2010;Mohsenipoor et al 2010;Ebrahimi et al 2011;Ruiz-Garcia et al 2011;Pollegioni et al 2011;Qi et al 2011;Grauke et al 2012;Mahmoodi et al 2013;Zhang et al 2013;Pop et al 2013;Najafi et al 2014;Dang et al 2015;Hu et al 2015;Han et al 2016;Noor Shah et al 2016;Ćelepirović et al 2016;Wang et al 2016;…”

“…Indeed, many accessions considered to be J. major were hybrids with J. microcarpa (Grauke et al 2012). In J. regia, the most important Italian landrace BSorrentoŵ as fingerprinted with SSR markers (Foroni et al 2005(Foroni et al , 2007, as well as other Italian walnut resources, to discover and characterize long-term human impacts and frequent human-mediated domestication events controlling genetic diversity (Pollegioni et al 2011). An analysis of the genetic structure in J. regia using SSRs revealed a high level of genetic diversity with five genetic groups linked to the centers of diversity of walnut in Eurasia (Aradhya et al 2009).…”

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

“…The same is true for most long-lived woody plants (Neale and Kremer 2011), although a few studies have targeted economically valuable species. Their conclusions ranged from a substantial human influence on the genetic structure of walnut (Juglans regia L.), irrespective of physical barriers (Pollegioni et al 2011), to much less significant effects in cork oak (Quercus súber L.) or Mediterranean cypress {Cupressus sempervirens L.), which appear to be more reliant on natural history than management (Magri et al 2007 andBagnoli et al 2009, respectively). Like the sweet chestnut, all these species are essentially wind pollinated.…”