Castanea sativa is an important multipurpose species in Europe for nut and timber production as well as for its role in the landscape and in the forest ecosystem. This species has low tolerance to chestnut gall wasp (Dryocosmus kuriphilus Yasumatsu), which is a pest that was accidentally introduced into Europe in early 2000 and devastated forest and orchard trees. Resistance to the gall wasp was found in the hybrid cultivar ‘Bouche de Bétizac’ (C. sativa × C. crenata) and studied by developing genetic linkage maps using a population derived from a cross between ‘Bouche de Bétizac’ and the susceptible cultivar ‘Madonna’ (C. sativa). The high-density genetic maps were constructed using double-digest restriction site-associated DNA-seq and simple sequence repeat markers. The map of ‘Bouche de Bétizac’ consisted of 1459 loci and spanned 809.6 cM; the map of ‘Madonna’ consisted of 1089 loci and spanned 753.3 cM. In both maps, 12 linkage groups were identified. A single major QTL was recognized on the ‘Bouche de Bétizac’ map, explaining up to 67–69% of the phenotypic variance of the resistance trait (Rdk1). The Rdk1 quantitative trait loci (QTL) region included 11 scaffolds and two candidate genes putatively involved in the resistance response were identified. This study will contribute to C. sativa breeding programs and to the study of Rdk1 genes.
Castanea
Quercus, Fagus,
Castanopsis.
Castanea:
C. sativa
C. crenata
C. mollissima
C. dentata
C. sativa
Phytophthora cinnamomi
Cryphonectria parasitica Murr.) [2]. In addition, most of the
C. sativa
Dryocosmus kuriphilus
C. sativa
C. crenata were carried out to introduce resistance genes to ink disease, canker blight, and chestnut gall wasp [2][3][4][5]. In the USA, backcross breeding was aimed at introducing blight resistance from
C. mollissima
C. dentata [6]. Moreover,
C. mollissima
C. crenata resistant cultivars, ‘Tanzawa’, ‘Tsukuba’, and ‘Ishizuchi’ were released by a public breeding program in 1959–1968. Initially, these cultivars showed total resistance to gall wasp. However, eventually, the presence of galls was found also in these cultivars, due to the appearance of new ecotypes of the insect [8]. In 1982, the parasitoid wasp
Torymus sinensis Kamijo (Hymenoptera: Torymidae) was released, and a rapid decrease of the infestation was obtained [9]. To date, the control of
D. kuriphilus
T. sinensis
The chestnut gall wasp was accidentally introduced into Italy and first reported in 2002. It quickly spread to all Italian regions and later into the surrounding countries [10], causing a remarkable decrease of production (−60% in 2014 in Italy). Studies on biological control aimed at introducing the parasitoid wasp
T. sinensis
C. sativa and hybrid cultivars [11]. Out of 62 cultivars, 2
C. sativa
C. crenata
C. sativa
C. crenata
2
2
Castanea
C. dentata
C. mollissima was first constructed using random amplified polymorphic DNAs (RAPDs) allowing the detection of molecular markers associated with blight resistance [13]. Subsequently,
C. sativa maps were built using intraspecific cross [14][15][16]. In 2013, the whole genome sequence of
C. mollissima was released [17], consisting of 724.0 Mb in 41,260 scaffolds (N50, 39.6 Kb) with 91.2% coverage of estimated genome size (794 Mb). In the same year, a highly informative genetic map of
C. mollissima was constructed, including 329 simple sequence repeats (SSRs) and 1064 single nucleotide polymorphisms (SNPs) markers using an expressed sequence tag database created by next-generation sequencing [18]. This consensus map consisted of 12 linkage groups ranging from 50.6 to 90.4 cM and encompassed 742.3 cM with an average distance of 0.64 cM between each pair of loci. More recent maps of
C. sativa
C. crenata were constructed and anchored to the consensus map by Kubisiak et al. [18] using SNPs and anchor SSRs [4][19].
Castanea
C. mollissima
C. dentata [13][18]. The molecular markers associated with ease of pellicle removal were developed and applied in
C. crenata breeding programs [19]. The quantitative trait loci (QTL) associated with agronomic traits including nut weight and pericarp splitting were identified from intraspecific crosses of
C. crenata [20]. QTLs for adaptive traits, such as time of budburst, growth, and carbon isotope discrimination were identified in
C. sativa [21]. In addition, QTLs for resistance to
P. cinnamomi
C. sativa
C. crenata
D. kuriphilus’
The genotyping by sequencing (GBS) method [22] has illustrated a cost-effective way to identify thousands of polymorphic markers. This method is based on the construction of a library based on reducing genome complexity using restriction enzymes, to ensure sufficient read depth for polymorphism discovery. Double-digest restriction site-associated DNA-Seq (ddRAD-Seq) is a modified GBS approach that involves a two-enzyme double digestion to reduce cost and time to prepare the sequencing libraries. After the double digestion, a precise size selection is applied to exclude too short and too long fragments, resulting in greater flexibility and robustness in region recovery [23]. In silico prediction prior to actual analysis contributes to optimization of the experimental conditions for ddRAD-Seq, e.g., choices of enzymes and plant materials [24]. As the cost of next-generation sequencing (NGS) has dramatically decreased [25], more and more genetic studies involved in genetic mapping, genome-wide association mapping, and population genetics have applied the ddRAD-Seq methods [24][26][27][28][29].
C. sativa
cultivars due to the lower quality of the Japanese chestnuts. Nevertheless,C. crenata
can be seen as a major source of genes of resistance or tolerance to pests and pathogens. Once these genes are known, the acquired knowledge can be used in breeding programs. A large effect QTL, expressed across two growing seasons, was mapped on the Bouche map linkage group K and explained up to 67–69% of the phenotypic variance of the response toD. kuriphilus
. A putative gene for a metacaspase-1b proteins was found in one of the scaffolds linked to theRdk1
QTL region. The high-density maps developed in this study support further genetic studies, and once a better reference genome will be available, it will allow a more in-depth exploration of the regions flanking the trait. In addition, the obtained BC1 progeny can be used to develop molecular markers for resistance to chestnut blight and ink disease as well as for other agronomic traits, including nut quality. Further analysis on progenies from different parental lines or genome-wide association (GWAS) approaches could contribute to finding more regions of interest as well as to confirm the newly identified one.