Plant model systems have contributed greatly to the dramatic progress in understanding the fundamental aspects of plant biology. Using model weeds will also help facilitate focused funding and research in the weed science community. Criteria for developing model weeds require attention to weedy characteristics that impart economic losses and a wide geographic distribution, attributes that present the potential for political and scientific support. Expressed sequence tag (EST) databases for model weeds are the most practical approach to identifying new genes and obtaining data on the gene expression underlying weedy characteristics. Weeds such as Canada thistle, eastern black nightshade, johnsongrass, jointed goatgrass, leafy spurge, waterhemp, and weedy rice are proposed as model systems.

Seed dormancy, a major adaptive trait in plants, facilitates the survival of weeds and provides for resistance to preharvest sprouting (PHS) in cereal crops. Seventeen weedy strains and 24 cultivars of rice (Oryza sativa L.) were evaluated for germinability to screen for donors of dormancy genes. Extremely dormant genotypes were identified from the weedy strains. These genotypes displayed hull‐ and pericarp/testa‐imposed dormancy. Three dormant weedy strains, LD, TKN12‐2, and SS18‐2, were crossed and backcrossed with the nondormant breeding line EM93‐1 to determine the relationship between dormancy and the shattering, awn, hull color, and pericarp/testa color characteristics. All these characteristics interrelated to the covering‐imposed dormancy; the weedy forms of the characteristics significantly reduced germination in the BC1F1 populations. Moreover, multiple linear regression analyses revealed significant effects of interaction between the characteristics on dormancy in the populations. The interrelation and interaction reflect the importance of combined effects of dormancy and other weedy characteristics in the adaptation of weedy populations to agroecosystems, and suggest that domestication and breeding activities have eliminated dormancy alleles at loci near the genes for shattering and the morphological characteristics from improved cultivars.

Genes interacting with seed developmental environments control primary dormancy. To understand how a multigenic system evolved to adapt to the changing environments in weedy rice, we evaluated genetic components of three dormancy QTL in a synchronized nondormant genetic background. Two genetically identical populations segregating for qSD1, qSD7-1, and qSD12 were grown under greenhouse and natural conditions differing in temperature, relative humidity, and light intensity during seed development. Low temperatures tended to enhance dormancy in both conditions. However, genotypes responded to the environments divergently so that two populations displayed similar distributions for germination. Additive and/or dominance effects of the three loci explained ∼90% of genetic variances and their epistases accounted for the remainder in each environment. The qSD1 and qSD7-1 main effects were increased, while the qSD12 additive effect was decreased by relatively low temperatures. Both gene main and epistatic effects were involved in G × E interactions, which in magnitude were greater than environmental main effect. The divergent responses of dormancy genes observed in this simple multigenic system presumably have selective advantages in natural populations adapted to changing environments and hence represent a genetic mechanism stabilizing the dormancy level of weedy rice ripened in different seasons or temperature regimes.

Association of seed dormancy with shattering, awn, and black hull and red pericarp colors enhances survival of wild and weedy species, but challenges the use of dormancy genes in breeding varieties resistant to preharvest sprouting. A phenotypic selection and recurrent backcrossing technique was used to introduce dormancy genes from a wild-like weedy rice to a breeding line to determine their effects and linkage with the other traits. Five generations of phenotypic selection alone for low germination extremes simultaneously retained dormancy alleles at five independent QTL, including qSD12 (R2 > 50%), as determined by genome-wide scanning for their main and/or epistatic effects in two BC4F2 populations. Four dormancy loci with moderate to small effects colocated with QTL/genes for one to three of the associated traits. Multilocus response to the selection suggests that these dormancy genes are cumulative in effect, as well as networked by epistases, and that the network may have played a “sheltering” role in maintaining intact adaptive haplotypes during the evolution of weeds. Tight linkage may prevent the dormancy genes from being used in breeding programs. The major effect of qSD12 makes it an ideal target for map-based cloning and the best candidate for imparting resistance to preharvest sprouting.

Weedy rice has much stronger seed dormancy than cultivated rice. A wild-like weedy strain SS18-2 was selected to investigate the genetic architecture underlying seed dormancy, a critical adaptive trait in plants. A framework genetic map covering the rice genome was constructed on the basis of 156 BC(1) [EM93-1 (nondormant breeding line)//EM93-1/SS18-2] individuals. The mapping population was replicated using a split-tiller technique to control and better estimate the environmental variation. Dormancy was determined by germination of seeds after 1, 11, and 21 days of after-ripening (DAR). Six dormancy QTL, designated as qSD(S)-4, -6, -7-1, -7-2, -8, and -12, were identified. The locus qSD(S)-7-1 was tightly linked to the red pericarp color gene Rc. A QTL x DAR interaction was detected for qSD(S)-12, the locus with the largest main effect at 1, 11, and 21 DAR (R(2) = 0.14, 0.24, and 0.20, respectively). Two, three, and four orders of epistases were detected with four, six, and six QTL, respectively. The higher-order epistases strongly suggest the presence of genetically complex networks in the regulation of variation for seed dormancy in natural populations and make it critical to select for a favorable combination of alleles at multiple loci in positional cloning of a target dormancy gene.

Seed dormancy contributes to the adaptability of plants in nature and is of considerable importance in agriculture. The weedy rice (Oryza sativa L.) strains LD, SS18‐2, and TKN12‐2 and cultivar ‘N22’ were selected to investigate the inheritance of dormancy in controlled conditions. Initial investigations using intact seeds, caryopses, caryopses with pericarp/testa removed, and excised embryos demonstrated that seed dormancy was imposed by the hull in SS18‐2 and TKN12‐2, and by the hull and pericarp/testa in LD and N22. Seed dormancy at 0 d after harvest (DAH) was dominant with average degree of dominance (ADD) > 0.8 in the crosses with weedy strains. Dominance for duration of seed dormancy was incomplete when judged by days to 50% germination. Broad‐sense heritability (h2b) for seed germination was lower at 0 DAH and highest at 20 DAH in all the crosses. The weedy strain‐derived F2 populations maintained a higher h2b during afterripening. The effects of three and two major genes on seed germination at 20 DAH were detected in the SS18‐2‐ and N22‐derived F2 populations, respectively. A positive ADD, a high h2b, and major gene effect for caryopsis germination at 0 DAH were detected only in the cross with LD. Seed or caryopsis dormancy was correlated with the characteristics awn and black hull or red pericarp colors in the SS18‐2‐ or LD‐derived F2 populations. This research demonstrates that weedy rice provides ideal gene resources to elucidate mechanisms of dormancy and to improve resistance to preharvest sprouting.

AbstractA study was conducted to map-based clone and characterize genes that directly regulate germinability in grasses using rice as a model system. Germinability was evaluated for 45 accessions, including 17 cultivars of Oryza sativa indica, seven of japonica and 4 of O. glaberrima, and 17 weedy rice strains. Weedy strains SS18 and LD were selected as dormancy parents to cross with non-dormant cultivars (CO39, EM93-1 and WY) for genetic analysis of seed covering-imposed dormancy. Seed dormancy was imposed by the seed coverings (hull/pericarp/testa). Genotypes with a higher level or a much longer duration of seed covering-imposed dormancy were present in weedy rice strains. A high positive dominance and a high level of heritability detected in the F1 and F2 generations confirmed that the 2 weedy strains were appropriate as parents and gene donors for map-based cloning of quantitative trait loci for seed covering-imposed dormancy.

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Dormancy is a critical factor for the survival and persistence of weedy species. Contemporary approaches can be used to identify genes that regulate dormancy directly or indirectly to elucidate key mechanisms, signals, and pathways. Several domesticated plant species have been used as model systems to mark quantitative trait loci (QTL) that affect dormancy in seeds and vegetative propagules directly. A few weedy species have also been used to mark QTL and to determine dormancy genes using microarray analysis. Given the number of serious weeds worldwide and the role that dormancy plays in their persistence, developing fundamental knowledge on dormancy is an important step toward developing new strategies for weed management. This paper describes current research and outlines some weeds that might be candidates for dormancy investigations using molecular genetic and genomics approaches. An underlying theme in the selection of weeds for dormancy investigations is their relation to crop species and the ability to adapt existing resources to investigate dormancy in weedy plants.

Dormancy is a form of developmental arrest and is an adaptive trait that promotes the survival of many organisms. In flowering plants, dormancy occurs in seeds and vegetative propagules (Lang 1996). Seed dormancy increases the distribution of germination over time, thus enhancing the survival of plants in an ever-changing environment. Seed dormancy is of intrinsic interest to weed scientists because it is one of 12 adaptive characteristics associated with weeds (Baker 1974). The sporadic emergence of seedlings derived from populations of dormant and nondormant weed seeds in the soil (Benech-Arnold et al. 2000; Forcella et al. 2000) is a key factor that dictates the need to apply weed control measures repeatedly within, between, and across growing seasons. My objective in writing this paper is to provide weed scientists, advanced students, and others with limited background information, some recent findings concerning the physiological genetics of dormancy, and steps toward identifying genes that directly regulate seed dormancy and germination. Molecular aspects of dormancy and germination will not be covered here because they have been reviewed recently (Bewley 1997; Li and Foley 1997). Readers can obtain additional and more extensive information on the biology and ecology of seed dormancy and germination from several recent books and reviews (Baskin and Baskin 1998; Benech-Arnold et al. 2000; Bewley and Black 1994; Casal and Sánchez 1998; Cohn 1996, 1998; Fennell 1999; Forcella et al. 2000; Hilhorst 1995, 1998; Hilhorst and Toorop 1997; Kelley et al. 1992; Kigel and Galili 1995; Simpson 1990; Vleeshouwers et al. 1995).

Dormant wild oat seed require afterripening under warm-dry conditions for conversion to a nondormant state capable of germination. Research was conducted to determine the relationship between temperature and seed moisture levels on afterripening of dormant wild oat line M73 seed, and to evaluate the status of water binding in the dormant seed. Conversion of dormant wild oat seed to a nondormant state at 20 to 40 C occurs primarily in the range of 5 to 20% seed moisture. There is an inverse relationship between temperature and seed moisture content for afterripening as measured by seed germination. As the afterripening temperature increases, the seed moisture content must decrease for maximum afterripening (germination) to occur. Moisture isotherms and derived enthalpy curves indicate three regions of water binding which reflect decreased binding of water to seed components as the moisture content in the dormant seed increases. Maximum afterripening, in the second region of water binding, corresponds to seed moisture contents of 7 to 22%. In this region water is weakly associated with macromolecular surfaces and begins to have solvent properties. Because afterripening occurs mainly in the second region of water binding it is likely that individual enzymatic and nonenzymatic reactions, rather than metabolic processes, mediate the conversion of wild oat seed to the nondormant state.