Nuclear and chloroplast microsatellite markers to assess genetic diversity and evolution in hazelnut species, hybrids and cultivars

Abstract

The U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon, preserves more than 800 accessions of hazelnut (Corylus) including C. avellana cultivars and representatives of 10 other recognized shrub and tree species. Characterization and study of genetic diversity in this collection requires cross-transferable markers such as trinucleotide microsatellite or simple sequence repeat (SSR) markers and universal chloroplast SSR markers. We developed new SSR markers, and evaluated 114Corylus accessions representing 11 species and 44 interspecific hybrids. Eight of 23 SSRs generated easy-to-score alleles in all species and seven were highly polymorphic. For the seven, the average heterozygosity was moderate at 0.49 while allele number, genetic diversity and PIC were high at 11.71, 0.79 and 0.76, respectively. The three most polymorphic SSRs were CaC-C008, CaC-C040 and CaC-C118. Neighbor joining (NJ) clustering and structure analysis agreed with taxonomic analysis and supported inclusion of C. maxima in the large polymorphic species C. avellana. Analysis also indicated that C. californica is a distinct species rather than a botanical variety of C. cornuta. Six universal cpSSRs were polymorphic in Corylus and generated an average of 3 alleles per locus and 21 chlorotypes. Diversity at these cpSSRs was high and ranged from 0.33 to 0.64, with an average of 0.69. Incongruence in NJ topologies between the nuclear and chloroplast markers could be attributed to chloroplast capture during the ancestral diversification of the genus, or homoplasy. The phylogeographical relationships among the 21 chlorotypes in the 11 Corylus species support Asia as a refugium where several hazelnut lineages survived during glaciation and from which they reappeared only later after the dispersal event from Asia through the Mediterranean to Europe, and across the Atlantic to North America.

Resolving the Speciation Patterns and Evolutionary History of the Intercontinental Disjunct Genus Corylus (Betulaceae) Using Genome-Wide SNPs

“… Ancestral area reconstructions based on the BBM method in RASP. The insert map shows the geographical distribution of Corylus species, overlaid on major floristic divisions (A–H) according to Zhang et al (2005) and Bassil et al (2013) . Letters and colors in the legend refer to extant and possible ancestral areas, and combinations of these.…”

“…C. mandshurica ( Ohwi, 1965 ) and C. cornuta subsp. californica ( Furlow, 1997 ) by some taxonomists, but as distinct species by others ( Bassil et al, 2013 ). In view of the significant geographical isolation and covering more taxa, we treat them as four distinct species so as to conduct a comprehensive species analysis.…”

“…To reconstruct the broad-scale biogeographical history of Corylus , we coded the distribution of each extant species as a character with eight states according to floristic division proposed by Zhang et al (2005) and Bassil et al (2013) : A, Northeast Asia; B, Qinling Mountains and Central Plains of China; C, Central and East China; D, southwestern China; E, the Himalayas; F, European-Mediterranean Area; G, eastern NA; H, western NA. Ancestral area reconstruction and the estimation of the spatial patterns of geographic diversification within Corylus were inferred using the Bayesian Binary MCMC (BBM) method, as implemented in RASP 4.0 ( Yu et al, 2015 ).…”

“…The species within each complex have been variously lumped and split. Over the past decades, several molecular studies have provided important insights into the phylogeny and taxonomy of Corylus ( Erdogan and Mehlenbacher, 2000 ; Whitcher and Wen, 2001 ; Bassil et al, 2013 ). However, these above studies are still failed to reach an ideal result partly because of the incomplete taxa sampling and partly due to the low resolution in species delimitation.…”

Characterization of the complete chloroplast genome of the Chinese endemic tree Corylus heterophylla var. sutchuenensis

“…sutchuenensis is a separate species (Hu X 1955) or just a C. heterophylla variant (Zhang et al 2005). Although several chloroplast (cp) DNA markers have previously been used for the phylogenetic analysis of Corylus (Erdogan and Mehlenbacher 2000;Palme and Vendramin 2002;Boccacci and Botta 2009;Bassil et al 2013;Martins et al 2013), except for Corylus chinensis (GenBank accession number KX814336) (Hu et al 2017), little is known about the cp genome in this genus. In the present study, we report the first complete cp genome sequence of C. heterophylla var.…”