Exploring Patterns of Sequence Variation in Regions Associated with Chestnut Blight Resistance Using Whole-Genome Resequencing of Chinese Chestnut (Castanea mollissima)

Chinese chestnut is the main donor of disease resistance in the blight resistance breeding program conducted by the American Chestnut Foundation (ACF), which aims to restore chestnut forests to eastern North America.  Chinese chestnuts show variability in susceptibility to blight, but the genetic basis of this variability and its potential impact on the American chestnut breeding program have not been extensively studied.  In particular, if differences in blight resistance correspond to high levels of allelic diversity at disease resistance loci in Chinese chestnut, reliance on a small number of resistance donor parents would be problematic for the long-term success of the breeding program.   The moderate size (~780-800 Mb) of the chestnut genome makes whole-genome resequencing a viable option for investigating functional genetic variation in Chinese chestnut.  We have currently sequenced the whole genomes (Illumina 100 bp paired-end reads: depth 10-25x) of 16 Chinese chestnuts and interspecific hybrids with variable blight resistance, utilizing the Chinese chestnut draft genome sequence and the sequence of three major blight resistance QTL regions for assembly.  We plan to sequence more individuals, and present preliminary analyses that have revealed patterns of sequence diversity across the three major blight resistance QTL and polymorphisms potentially associated with differences in blight resistance.