The soilborne oomycete Phytophthora cinnamomi—which causes root rot, trunk cankers, and stem lesions on an estimated 5,000 plant species worldwide—is a lethal pathogen of American chestnut (Castanea dentata) as well as many other woody plant species. P. cinnamomi is particularly damaging to chestnut and chinquapin trees (Castanea spp.) in the southern portion of its native range in the United States due to relatively mild climatic conditions that are conductive to disease development. Introduction of resistant genotypes is the most practical solution for disease management in forests because treatment with fungicides and eradication of the pathogen are neither practical nor economically feasible in natural ecosystems. Using backcross families derived from crosses of American chestnuts with two resistant Chinese chestnut cultivars Mahogany and Nanking, we constructed linkage maps and identified quantitative trait loci (QTLs) for resistance to P. cinnamomi that had been introgressed from these Chinese chestnut cultivars. In total, 957 plants representing five cohorts of three hybrid crosses were genotyped by sequencing and phenotyped by standardized inoculation and visual examination over a 6-year period from 2011 to 2016. Eight parental linkage maps comprising 7,715 markers were constructed, and 17 QTLs were identified on four linkage groups (LGs): LG_A, LG_C, LG_E, and LG_K. The most consistent QTLs were detected on LG_E in seedlings from crosses with both ‘Mahogany’ and ‘Nanking’ and LG_K in seedlings from ‘Mahogany’ crosses. Two consistent large and medium effect QTLs located ∼10 cM apart were present in the middle and at the lower end of LG_E; other QTLs were considered to have small effects. These results imply that the genetic architecture of resistance to P. cinnamomi in Chinese chestnut × American chestnut hybrid progeny may resemble the P. sojae–soybean pathosystem, with a few dominant QTLs along with quantitatively inherited partial resistance conferred by multiple small-effect QTLs.

Bacterial communities associated with seagrass bed sediments are not well studied. The work presented here investigated several factors and their impact on bacterial community diversity, including the presence or absence of vegetation, depth into sediment, and season. Double-gradient denaturing gradient gel electrophoresis (DG-DGGE) was used to generate banding patterns from the amplification products of 16S rRNA genes in 1-cm sediment depth fractions. Bioinformatics software and other statistical analyses were used to generate similarity scores between sections. Jackknife analyses of these similarity coefficients were used to group banding patterns by depth into sediment, presence or absence of vegetation, and by season. The effects of season and vegetation were strong and consistent, leading to correct grouping of banding patterns. The effects of depth were not consistent enough to correctly group banding patterns using this technique. While it is not argued that bacterial communities in sediment are not influenced by depth in sediment, this study suggests that the differences are too fine and inconsistent to be resolved using 1-cm depth fractions and DG-DGGE. The effects of vegetation and season on bacterial communities in sediment were more consistent than the effects of depth in sediment, suggesting they exert stronger controls on microbial community structure.

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Root rot (caused by Phytophthora cinnamomi) and chestnut blight (caused by Cryphonectria parasitica) are the two most destructive diseases affecting American chestnut, Castanea dentata. Therefore, breeding for resistance to both pathogens simultaneously is essential before the American chestnut can be restored to its full native range. Using combined genetic and genomic approaches, resistance to C. parasitica (Cp) has been mapped to three quantitative trait loci (QTLs) in chestnut. In addition, a marker set covering the chestnut genome has been generated for implementation in breeding for Cp resistance. Although P. cinnamomi was introduced to the USA far earlier than C. parasitica, an effort to breed for resistance to this pathogen has been initiated only recently. Selection of parental genotypes with a high inter-generational transmission rate of resistance to P. cinnamomi (Pc) allowed initiation of genetic studies. In pilot experiments with a limited number of progeny derived from AdairKY1 × GL158, a QTL for resistance (source Chinese chestnut, C. mollissima 'Nanking') to Pc was mapped to linkage group E (LG_E). Subsequently, three backcross families (HB1, HB2, and MK5) were selected from another source of resistance (C. mollissima 'Mahogany') for map construction and association analysis with 22 markers from LG_E. Our preliminary analyses confirmed the presence of a Pc resistance QTL on LG_E. In 2012, extended mapping populations (up to 200 individuals) representing the Mahogany and Nanking lineages of resistance were planted for phenotyping of Pc resistance and QTL mapping. Together, these materials and analyses should help resolve the location of Proc.

Restoration of American chestnut (Castanea dentata) depends on combining resistance to both the chestnut blight fungus (Cryphonectria parasitica) and Phytophthora cinnamomi, which causes Phytophthora root rot, in a diverse population of C. dentata. Over a 14-year period (2004 to 2017), survival and root health of American chestnut backcross seedlings after inoculation with P. cinnamomi were compared among 28 BC3, 66 BC4, and 389 BC3F3 families that descended from two BC1 trees (Clapper and Graves) with different Chinese chestnut grandparents. The 5% most resistant Graves BC3F3 families survived P. cinnamomi infection at rates of 75 to 100% but had mean root health scores that were intermediate between resistant Chinese chestnut and susceptible American chestnut families. Within Graves BC3F3 families, seedling survival was greater than survival of Graves BC3 and BC4 families and was not genetically correlated with chestnut blight canker severity. Only low to intermediate resistance to P. cinnamomi was detected among backcross descendants from the Clapper tree. Results suggest that major-effect resistance alleles were inherited by descendants from the Graves tree, that intercrossing backcross trees enhances progeny resistance to P. cinnamomi, and that alleles for resistance to P. cinnamomi and C. parasitica are not linked. To combine resistance to both C. parasitica and P. cinnamomi, a diverse Graves backcross population will be screened for resistance to P. cinnamomi, survivors bred with trees selected for resistance to C. parasitica, and progeny selected for resistance to both pathogens will be intercrossed.