BackgroundWeedy rice (red rice), a conspecific weed of cultivated rice (Oryza sativa L.), is a significant problem throughout the world and an emerging threat in regions where it was previously absent. Despite belonging to the same species complex as domesticated rice and its wild relatives, the evolutionary origins of weedy rice remain unclear. We use genome-wide patterns of single nucleotide polymorphism (SNP) variation in a broad geographic sample of weedy, domesticated, and wild Oryza samples to infer the origin and demographic processes influencing U.S. weedy rice evolution.ResultsWe find greater population structure than has been previously reported for U.S. weedy rice, and that the multiple, genetically divergent populations have separate origins. The two main U.S. weedy rice populations share genetic backgrounds with cultivated O. sativa varietal groups not grown commercially in the U.S., suggesting weed origins from domesticated ancestors. Hybridization between weedy groups and between weedy rice and local crops has also led to the evolution of distinct U.S. weedy rice populations. Demographic simulations indicate differences among the main weedy groups in the impact of bottlenecks on their establishment in the U.S., and in the timing of divergence from their cultivated relatives.ConclusionsUnlike prior research, we did not find unambiguous evidence for U.S. weedy rice originating via hybridization between cultivated and wild Oryza species. Our results demonstrate the potential for weedy life-histories to evolve directly from within domesticated lineages. The diverse origins of U.S. weedy rice populations demonstrate the multiplicity of evolutionary forces that can influence the emergence of weeds from a single species complex.

Cultivated rice fields worldwide are plagued with weedy rice, a conspecific weed of cultivated rice (Oryza sativa L.). The persistence of weedy rice has been attributed, in part, to its ability to shatter (disperse) seed prior to crop harvesting. In the United States, separately evolved weedy rice groups have been shown to share genomic identity with exotic domesticated cultivars. Here, we investigate the shattering phenotype in a collection of U.S. weedy rice accessions, as well as wild and cultivated relatives. We find that all U.S. weedy rice groups shatter seeds easily, despite multiple origins, and in contrast to a decrease in shattering ability seen in cultivated groups. We assessed allelic identity and diversity at the major shattering locus, sh4, in weedy rice; we find that all cultivated and weedy rice, regardless of population, share similar haplotypes at sh4, and all contain a single derived mutation associated with decreased seed shattering. Our data constitute the strongest evidence to date of an evolution of weeds from domesticated backgrounds. The combination of a shared cultivar sh4 allele and a highly shattering phenotype, suggests that U.S. weedy rice have re-acquired the shattering trait after divergence from their progenitors through alternative genetic mechanisms.

BackgroundSorghum is a tropical C4 cereal that recently adapted to temperate latitudes and mechanized grain harvest through selection for dwarfism and photoperiod-insensitivity. Quantitative trait loci for these traits have been introgressed from a dwarf temperate donor into hundreds of diverse sorghum landraces to yield the Sorghum Conversion lines. Here, we report the first comprehensive genomic analysis of the molecular changes underlying this adaptation.ResultsWe apply genotyping-by-sequencing to 1,160 Sorghum Conversion lines and their exotic progenitors, and map donor introgressions in each Sorghum Conversion line. Many Sorghum Conversion lines carry unexpected haplotypes not found in either presumed parent. Genome-wide mapping of introgression frequencies reveals three genomic regions necessary for temperate adaptation across all Sorghum Conversion lines, containing the Dw1, Dw2, and Dw3 loci on chromosomes 9, 6, and 7 respectively. Association mapping of plant height and flowering time in Sorghum Conversion lines detects significant associations in the Dw1 but not the Dw2 or Dw3 regions. Subpopulation-specific introgression mapping suggests that chromosome 6 contains at least four loci required for temperate adaptation in different sorghum genetic backgrounds. The Dw1 region fractionates into separate quantitative trait loci for plant height and flowering time.ConclusionsGenerating Sorghum Conversion lines has been accompanied by substantial unintended gene flow. Sorghum adaptation to temperate-zone grain production involves a small number of genomic regions, each containing multiple linked loci for plant height and flowering time. Further characterization of these loci will accelerate the adaptation of sorghum and related grasses to new production systems for food and fuel.

Genomic selection (GS) is a breeding method that uses markertrait models to predict unobserved phenotypes. This study developed GS models for predicting traits associated with resistance to Fusarium head blight (FHB) in wheat (Triticum aestivum L.). We used genotyping-by-sequencing (GBS) to identify 5054 singlenucleotide polymorphisms (SNPs), which were then treated as predictor variables in GS analysis. We compared how the prediction accuracy of the genomic-estimated breeding values (GEBVs) was affected by (i) five genotypic imputation methods (random forest imputation [RFI], expectation maximization imputation [EMI], k-nearest neighbor imputation [kNNI], singular value decomposition imputation [SVDI], and the mean imputation [MNI]); (ii) three statistical models (ridge-regression best linear unbiased predictor [RR-BLUP], least absolute shrinkage and operator selector [LASSO], and elastic net); (iii) marker density (p = 500, 1500, 3000, and 4500 SNPs); (iv) training population (TP) size (n TP = 96, 144, 192, and 218); (v) marker-based and pedigree-based relationship matrices; and (vi) control for relatedness in TPs and validation populations (VPs). No discernable differences in prediction accuracy were observed among imputation methods. The RR-BLUP outperformed other models in nearly all scenarios. Accuracies decreased substantially when marker number decreased to 3000 or 1500 SNPs, depending on the trait; when sample size of the training set was less than 192; when using pedigree-based instead of marker-based matrix; or when no control for relatedness was implemented. Overall, moderate to high prediction accuracies were observed in this study, suggesting that GS is a very promising breeding strategy for FHB resistance in wheat. It can be considered as a form of marker-assisted selection in which all markers are used to calculate GEBVs. It is assumed in GS that the quantitative trait loci (QTL) underlying the trait of interest are in linkage disequilibrium with at least one marker and that all the genetic variance can be explained by markers (Goddard and Hayes, 2007). For this reason, GS is particularly promising for predicting quantitative, complex traits where many small effect loci contribute to phenotypic variation. In GS, marker effects are estimated from a TP, for which phenotypes and genotypes are available. Marker effects are then used to predict phenotypes in a set of individuals, called the breeding population, which will only be