A transcriptome-based genetic map of Chinese chestnut (Castanea mollissima) and identification of regions of segmental homology with peach (Prunus persica)

Abstract

The Chinese chestnut (Castanea mollissima) carries resistance to Cryphonectria parasitica, the fungal pathogen inciting chestnut blight. The pathogen, introduced from Asia, devastated the American chestnut (Castanea dentata) throughout its native range early in the twentieth century. A highly informative genetic map of Chinese chestnut was constructed to extend genomic studies in the Fagaceae and to aid the introgression of Chinese chestnut blight resistance genes into American chestnut. Two mapping populations were established with three Chinese chestnut parents, 'Mahogany', 'Nanking', and 'Vanuxem', totaling 337 progeny. The transcriptome-based genetic map was created with 329 simple sequence repeat and 1,064 single nucleotide polymorphism markers all derived from expressed sequence tag sequences. Genetic maps for each parent were developed and combined to establish 12 consensus linkage groups spanning 742 cM, providing the the most comprehensive genetic map for a Fagaceae species to date. Over 75 % of the mapped markers from the Chinese chestnut consensus genetic map were placed on the physical map using overgo hybridization, providing a fully integrated genetic and physical map resource for Castanea spp. About half (57 %) of the Chinese chestnut genetic map could be assigned to regions of segmental homology with 58 % of the peach (Prunus persica) genome assembly. A three quantitative trait loci (QTL) model for blight resistance was verified using the new genetic markers and an existing interspecies (C. mollissima × C. dentata) F 2 mapping population. Two of the blight resistance QTLs in chestnut shared synteny with two QTLs for powdery mildew resistance in peach, indicating the potential conservation of disease resistance genes at these loci.

Identification of QTLs for Agronomic Traits in the Japanese Chestnut (<i>Castanea crenata</i> Sieb. et Zucc.) Breeding

“…On the other hand, in the Px43 population analysis, each of the parental maps and the integrated map had 10 or 11 linkage groups. Using 145 Chinese chestnut SSRs developed by Kubisiak et al (2013) as anchor markers, we found that each linkage group in the new maps showed a one-to-one correspondence with one of the groups in the Chinese chestnut consensus map (Fig. S2).…”

“…A regression mapping algorithm was used to build the linkage maps, and map distances were calculated according to the Kosambi mapping function (Kosambi, 1944). The linkage group names were assigned according to the Chinese chestnut genetic linkage maps (Kubisiak et al, 2013). The genetic maps were drawn using MapChart v. 2.2 software (Voorrips, 2002).…”

“…The six genetic maps were successfully aligned to the Chinese chestnut genetic map by using SSRs developed by Kubisiak et al (2013) as anchor markers. In total, 997 molecular markers (281 Japanese chestnut SSRs, 145 Chinese chestnut SSRs, 17 European chestnut SSRs, and 554 SNPs) were mapped on the six genetic maps ( Fig.…”

“…Subsequently, maps of the European chestnut were constructed using an intraspecific cross (Barreneche et al, 2004;Casasoli et al, 2001Casasoli et al, , 2006. Recently, a highly informative genetic map of the Chinese chestnut was constructed with 329 SSR markers and 1064 single-nucleotide polymorphism (SNP) markers using an expressed sequence tag (EST) database created by next-generation sequencing (Kubisiak et al, 2013). This consensus map consists of 12 linkage groups, each ranging from 50.6 to 90.4 cM, and encompasses 742.4 cM with an average distance of 0.64 cM between loci.…”

Development of genic and genomic microsatellites in Gleditsia triacanthos L. (Fabaceae) using Illumina sequencing

“…(Owusu et al 2013). The PCR mix (15 µl) consisted of 6μl double deionized water (Ultra Pure Water, Molecular Grade from Phenix Research Products), 5μl HotFIREPol (Oak Biotechnologies, containing 2mM dNTPs, 1U Taq polymerase, 10mM MgCl 2 ), 0.2μl of 5 μM forward primer with M13 tail (5'-CA-CGACGTTGTAAACGAC-3'), 1.5μl of 5μM 5' dye labelled (6-FAM) M13 primer, 0.5μl of 5 μM pig-tailed (5'-GTTTCTT-3') reverse primer (Sigma Aldrich Inc., St. Louis, MO) (Schuelke 2000, Kubisiak et al 2013) and 2μl DNA (~ 2ng). The PCR touchdown reaction was performed in an Applied Biosystems 2720 Thermal Cycler (Foster City, CA) with the following cycling conditions: initial denaturation at 95 ºC for 15 minutes, 10 touch-down cycles of 1 minute at 94 ºC, 1 minute at 60 ºC (decreasing 1 ºC each cycle), and 1 minute at 72 ºC, followed by 25 cycles of 1 minute denaturation at 94 ºC, a 1 minute annealing step at 50 ºC, 1 minute elongation at 72 ºC, and a final extension at 72 ºC for 20 minutes.…”