High density SNP mapping and QTL analysis for time of leaf budburst in Corylus avellana L.

Abstract

The growing area of European hazelnut (Corylus avellana L.) is increasing, as well as the number of producing countries, and there is a pressing need for new improved cultivars. Hazelnut conventional breeding process is slow, due to the length of juvenile phase and the high heterozygosity level. The development of genetic linkage maps and the identification of molecular markers tightly linked to QTL (quantitative trait loci) of agronomic interest are essential tools for speeding up the selection of seedlings carrying desired traits through marker-assisted selection. The objectives of this study were to enrich a previous linkage map and confirm QTL related to time of leaf budburst, using an F1 population obtained by crossing Tonda Gentile delle Langhe with Merveille de Bollwiller. Genotyping-by-Sequencing was used to identify a total of 9,999 single nucleotide polymorphism markers. Well saturated linkage maps were constructed for each parent using the double pseudo-testcross mapping strategy. A reciprocal translocation was detected in Tonda Gentile delle Langhe between two non-homologous chromosomes. Applying a bioinformatic approach, we were able to disentangle ‘pseudo-linkage’ between markers, removing markers around the translocation breakpoints and obtain a linear order of the markers for the two chromosomes arms, for each linkage group involved in the translocation. Twenty-nine QTL for time of leaf budburst were identified, including a stably expressed region on LG_02 of the Tonda Gentile delle Langhe map. The stability of these QTL and their coding sequence content indicates promise for the identification of specific chromosomal regions carrying key genes involved in leaf budburst.

Identification and Mapping of Eastern Filbert Blight Resistance Quantitative Trait Loci in European Hazelnut Using Double Digestion Restriction Site Associated DNA Sequencing

“…This high-throughput and lower cost methodology can then be used to quickly generate genetic linkage maps and identify marker trait associations to answer a broader range of research questions than have traditionally been investigated in the past. In this study, a SNP marker-based ddRADseq genetic linkage map of european hazelnut was created with relatively dense genome coverage similar to other recently developed SNP marker based linkage maps of european hazelnut (Rowley et al, 2018;Torello Marinoni et al, 2018), and then QTL experiments were conducted to specifically determine whether novel or previously known source(s) of EFB resistance QTL were associated with the disease resistance phenotype observed in an environment with high EFB disease pressure (New Jersey location). The putative 'Gasaway' R-gene (as well as resistance from 'Culpl a', 'Crvenje', 'Uebov', OSU 408.040, and OSU 495.072) was previously shown to reside on european hazelnut LG6 (Colburn et al, 2015(Colburn et al, , 2017G€ urcan and Mehlenbacher, 2010;Mehlenbacher et al, 2006;Sathuvalli and Mehlenbacher, 2013;Sathuvalli et al, 2012).…”

“…A total of 126 microsatellite or SSR markers from various sources (Akin et al, 2016;Bassil et al, 2005;Bhattarai and Mehlenbacher, 2018;Boccacci et al, 2005;Colburn et al, 2015Colburn et al, , 2017G€ urcan and Mehlenbacher, 2010;G€ urcan et al, 2010aIves et al, 2014;Mehlenbacher et al, 2006;Sathuvalli and Mehlenbacher, 2013;Sathuvalli et al, 2012) were genotyped as potential anchor markers for LG comparison between the current genetic linkage map and previous maps (Beltramo et al, 2016;Colburn et al, 2015Colburn et al, , 2017G€ urcan et al, 2010a;Ives et al, 2014;Mehlenbacher et al, 2006;Sathuvalli et al, 2011aSathuvalli et al, , 2011bSathuvalli et al, , 2012Torello Marinoni et al, 2018). A prefix indicated that LG was added to the SSR marker names.…”

“…MICROSATELLITE (SSR) GENOTYPING. Ninety SSR markers previously used for genotyping hazelnuts and linkage mapping (Beltramo et al, 2016;Colburn et al, 2015Colburn et al, , 2017G€ urcan et al, 2010a;Ives et al, 2014;Mehlenbacher et al, 2006;Sathuvalli et al, 2011aSathuvalli et al, , 2011bSathuvalli et al, , 2012Torello Marinoni et al, 2018) were found to be polymorphic between the two parents of the mapping population cross and are listed along with their motif type and primer sequence information (Supplemental Table 1). Six of the 90 SSR markers were removed from the final genetic linkage map because of greater than 4.2% missing data in the progeny population or suspect linkages.…”

“…The genetic distance of individual LGs ranged from a low of 70.5 cM (98 markers) for LG3, to a high of 196.0 cM (269 markers) for LG2. LG assignments were made via syntenic comparisons of SSR anchor markers to previous european hazelnut linkage maps (Beltramo et al, 2016;Colburn et al, 2015Colburn et al, , 2017G€ urcan and Mehlenbacher, 2010;G€ urcan et al, 2010a;Ives et al, 2014;Mehlenbacher et al, 2006;Sathuvalli and Mehlenbacher, 2013;Sathuvalli et al, 2011aSathuvalli et al, , 2011bSathuvalli et al, , 2012Torello Marinoni et al, 2018). Of the remaining 84 polymorphic SSR markers in the current linkage map, two SSR markers (B608 and B635) were not previously assigned to LGs on previous OSU european hazelnut linkage maps.…”

Discovery, Characterization, and Linkage Mapping of Simple Sequence Repeat Markers In Hazelnut

“…Although single nucleotide polymorphism (SNP) markers can be generated in large numbers by procedures including genotypingby-sequencing [GBS (Elshire et al, 2011)] and double digest RADseq (Peterson et al, 2012), SSR markers continue to have many research and breeding applications in plants. In hazelnut, for example, € Ozturk et al (2017) studied associations of SSR markers with nut and kernel traits in a Slovenian hazelnut collection, and Marinoni et al (2018) used SSR and SNP markers to identify QTL in a seedling population from 'Tonda Gentile delle Langhe' x 'Merveille de Bollwiller'.…”