Sweetpotato [Ipomoea batatas (L.) Lam.] is a globally important staple food crop, especially for sub-Saharan Africa. Agronomic improvement of sweetpotato has lagged behind other major food crops due to a lack of genomic and genetic resources and inherent challenges in breeding a heterozygous, clonally propagated polyploid. Here, we report the genome sequences of its two diploid relatives, I. trifida and I. triloba, and show that these high-quality genome assemblies are robust references for hexaploid sweetpotato. Comparative and phylogenetic analyses reveal insights into the ancient whole-genome triplication history of Ipomoea and evolutionary relationships within the Batatas complex. Using resequencing data from 16 genotypes widely used in African breeding programs, genes and alleles associated with carotenoid biosynthesis in storage roots are identified, which may enable efficient breeding of varieties with high provitamin A content. These resources will facilitate genome-enabled breeding in this important food security crop.

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.

In plants, most disease resistance genes encode nucleotide binding Leu-rich repeat (NLR) proteins that trigger a rapid localized cell death called a hypersensitive response (HR) upon pathogen recognition. The maize (Zea mays) NLR protein Rp1-D21 derives from an intragenic recombination between two NLRs, Rp1-D and Rp1-dp2, and confers an autoactive HR in the absence of pathogen infection. From a previous quantitative trait loci and genome-wide association study, we identified a single-nucleotide polymorphism locus highly associated with variation in the severity of Rp1-D21-induced HR. Two maize genes encoding hydroxycinnamoyltransferase (HCT; a key enzyme involved in lignin biosynthesis) homologs, termed HCT1806 and HCT4918, were adjacent to this single-nucleotide polymorphism. Here, we show that both HCT1806 and HCT4918 physically interact with and suppress the HR conferred by Rp1-D21 but not other autoactive NLRs when transiently coexpressed in Nicotiana benthamiana. Other maize HCT homologs are unable to confer the same level of suppression on Rp1-D21-induced HR. The metabolic activity of HCT1806 and HCT4918 is unlikely to be necessary for their role in suppressing HR. We show that the lignin pathway is activated by Rp1-D21 at both the transcriptional and metabolic levels. We derive a model to explain the roles of HCT1806 and HCT4918 in Rp1-mediated disease resistance.

The process of evolution under domestication has been studied using phylogenetics, population genetics–genomics, quantitative trait locus (QTL) mapping, gene expression assays, and archaeology. Here, we apply an evolutionary quantitative genetic approach to understand the constraints imposed by the genetic architecture of trait variation in teosinte, the wild ancestor of maize, and the consequences of domestication on genetic architecture. Using modern teosinte and maize landrace populations as proxies for the ancestor and domesticate, respectively, we estimated heritabilities, additive and dominance genetic variances, genetic-by-environment variances, genetic correlations, and genetic covariances for 18 domestication-related traits using realized genomic relationships estimated from genome-wide markers. We found a reduction in heritabilities across most traits, and the reduction is stronger in reproductive traits (size and numbers of grains and ears) than vegetative traits. We observed larger depletion in additive genetic variance than dominance genetic variance. Selection intensities during domestication were weak for all traits, with reproductive traits showing the highest values. For 17 of 18 traits, neutral divergence is rejected, suggesting they were targets of selection during domestication. Yield (total grain weight) per plant is the sole trait that selection does not appear to have improved in maize relative to teosinte. From a multivariate evolution perspective, we identified a strong, nonneutral divergence between teosinte and maize landrace genetic variance–covariance matrices (G-matrices). While the structure of G-matrix in teosinte posed considerable genetic constraint on early domestication, the maize landrace G-matrix indicates that the degree of constraint is more unfavorable for further evolution along the same trajectory.