RR125 is similar to bronzehull Type 2 weedy rice while RR126 is a strawhull type that is mostly awnless. In phylogenetic analysis, RR125 was grouped with Type 2 weedy rice and RR126 was grouped with Type 5 weedy rice . STRUCTURE indicated membership of RR125 to the genetic cluster composed primarily of Type 2 weedy rice with a small amount of admixture from the cluster composed primarily of Type 1 weedy rice . RR126 assigned with 100% membership to the genetic cluster composed of Type 5 weedy rice and japonica rice varieties . Our evaluation of seed shattering and seed dormancy at 35–40 days after flowering indicated that RR125 has low shattering and no seed dormancy , similar to cultivated rice . RR126 is also non-shattering, but has high seed dormancy . These results em‐ phasize the need for a consensus definition of weedy rice, as not all red‐pericarped rices are weedy. However, the clustering of both RR125 and RR126 with weedy rice biotypes does indicate possible genetic contributions from red‐pericarped varieties into weedy populations. This potentially problematic relationship calls for careful management of rice seed and certification to avoid the contamination of white‐pericarped cultivated rice acreage with red‐pericarped specialty rice or its weedy relatives. The genetic clustering of individuals by biotype observed in phylogenetic, STRUCTURE, curing cannabis and PCA analyses indicate that phenotypic similarity is a better indicator of relatedness than geographic proximity for California weedy rice.
The four major biotypes all contained samples from multiple different counties, and the only location where all individuals belong to the same biotype is Colusa County . The spread of biotypes across a large geographic area is likely the result of seed movement, as pollen of both cultivated and wild rice travels only up to 100 m from source plants . The most likely mode of weedy rice seed movement over long distance is dispersal by humans, either through contaminated seed stocks or equipment within California or through additional introductions of weedy rice from other rice‐growing regions. This highlights the need for growing weed‐free certified seed in California and encouraging growers to prevent the spread of weedy rice on contaminated equipment. Recent regulations regarding the importation of used equipment and the requirement for only planting certified seed or seed from a third‐party quality assurance program should aid in these efforts . Overall, the phylogenetic, population structure, and principal component analyses above allow some insights into the ancestry of California weedy rice and into the prevalence of evolutionary histories of de-domestication. Type 1 weedy rice is likely evolutionarily derived from aus rice or possibly a wild rice species, as is the black‐ hull awned rice from the southern United States . These two American weedy rice biotypes may have a single origin from Asian rice or separate origins followed by hybridization with each other. However, they are both genetically and phenotypically distinct, as Type 1 rice is neither blackhulled or awned . Because the specific origins and any subsequent hybridization are unclear, it cannot be determined whether this biotype is derived from endoferal de‐domestication directly from the crop cultivars or exoferal de‐domestication through hybridization of cultivars and/or weedy populations.
Type 2 weedy rice is most closely related to strawhull weedy rice from the southern United States, and these two groups likely evolved by exoferal de‐domestication from indica rice. Alternatively, these two groups were also placed with wild rice species in several analyses and could have some ancestry from undomesticated rice. Regardless, it is unclear whether Type 2 and southern strawhull weedy rice have a single or separate origins. Type 3 weedy rice of California is highly differentiated from other rice types and has ambiguous evolutionary origins. Based on its closest relationship in the phylogenetic analysis, it appears to have evolved from wild rice and may have retained wild traits such as pubescence of leaves, presence of long awn, high seed dor‐ mancy, and shattering, consistent with the results of Londo and Schaal using a single California weedy rice genotype . In another study of Type 3 weedy rice by Kanapeckas et al. , California strawhull weedy rice had the lowest mean population divergence from O. rufipogon from South East Asia, but was interpreted as having diverged from California cultivated rice based on coalescent modeling analysis. More study of this weedy rice bio‐ type may be needed to fully understand its evolutionary origins. Type 4 weedy rice is most likely descended from Type 3 weedy rice. Type 5 weedy rice is endoferally derived from japonica rice, and it is not clear whether the direct ancestor is tropical japonica rice or temperate japonica rice grown inside or outside of California. For all California weedy rice biotypes, the presence of the causative Rc allele for red pericarp associated with wild rice or landrace rice never selected for white pericarp means that genetic contributions of endoferal ancestry from landrace rice or exoferal ancestry from wild rice cannot be ruled out. In conclusion, the five major California weedy rice biotypes are not all closely related to each other and have diverse parentage from several major lineages of cultivated rice and wild rice, as well as relationships with weedy rice from the southern United States.
Most bio‐ types are likely derived from independent origins outside of California, although hybridization between biotypes or with local cultivars may contribute to the evolution of weedy rice populations. Future study of California weedy rice with sequence data may help elucidate the evolutionary relationships of weedy rice types with currently ambiguous origins. The recent rediscovery and rapid spread of multiple weedy rice biotypes with evolutionary origins outside of California highlights the need for management of current weedy populations and measures to prevent further introductions of weedy rice into California.Rice is produced on about 500,000 acres in the Sacramento Valley annually, making it the region’s major crop. Rice is a cereal crop that has been grown in California since the early 1900s. It is grown in flooded soils, so it is ideally suited to the poorly drained soils common to much of the Sacramento Valley. Most rice growers till both in the fall to incorporate rice straw and in the spring to prepare the seedbed. Typical spring tillage involves six to eight tractor passes that include chisel plowing, disking and planing before applying fertilizer, and rolling the field in preparation for planting. No-till rice systems are not likely to be successful in California because harvesting equipment can leave deep tracks in the field that results in poor rice establishment and weed problems. Fall tillage is necessary to level the field and incorporate rice straw, but minimum-till rice systems with no spring tillage may be an option. Minimum-till systems are not new to rice and are being evaluated in the southern United States and Asia . In these areas, weed dryer rice is grown in rotation with other crops such as soybean and wheat, respectively. In contrast, most California rice systems do not involve crop rotations due to the heavy soils on which they are grown. Nevertheless, there is increasing interest in growing rice in California with no spring tillage due to the potential for reduced fuel costs, earlier planting , better control of herbicide-resistant weeds, and potential air-quality improvements due to reduced dust. Herbicide-resistant weeds are one of the main problems threatening the long-term sustainability of California’s rice-based systems. In fact, California rice has seven herbicide-resistant weed species, more than any other crop or geographic area in the United States . Herbicide resistance has evolved in rice weed populations due to repeated use of the same herbicide, herbicides having the same mode of action, or herbicides detoxified by a common mechanism in plants and weeds. Minimum tillage with a stale seedbed offers new opportunities to control herbicide-resistant weeds in California rice fields.
The approach entails preparing a stale seedbed before planting by flushing or flooding the field with water to induce weed-seed germination, and then killing the weeds, usually with glyphosate. The choice between flushing or flooding depends on whether or not the field is infested with weeds that require water saturation to germinate. The soil is then left untilled to ensure that buried weed seeds are not brought to the surface to germinate. This combination of a stale seedbed and no spring tillage can currently control all types of herbicide-resistant weeds in California rice systems, because they are not resistant to glyphosate.An experiment was initiated in 2004 at the California Rice Experiment Station near Biggs in Butte County, to evaluate crop establishment methods and their effects on rice yield, weed and pest populations, and nitrogen cycling. The experiment was set up as a randomized complete block design with four replications on 0.5-acre plots. In this paper we discuss two treatments: water-seeded conventional till and water-seeded minimum till with a stale seedbed. Water-seeding refers to broadcasting rice seed into a flooded field, a practice used by more than 90% of California rice growers. In both treatments, the plots were tilled in the fall to incorporate rice straw and then flooded to encourage straw decomposition. The conventional-till treatment replicated the practice of most California rice growers, and entailed spring tillage , flooding and planting. The minimum-till treatment had no spring tillage but the plots were flushed with water to prepare a stale seedbed prior to planting. Both the conventional- and minimumtill plots were flooded and planted on the same day. The plots remained flooded until a few weeks before harvest. Weed control. In the minimum-till treatment a stale seedbed was prepared, which entailed flushing the plots with water in April and then draining. After the weeds germinated, glyphosate was applied at a rate of 1.2 pounds acid equivalent per acre. Other than this, weeds in both tillage treatments were managed similarly during the growing season with the objective of obtaining full control. This was accomplished using propanil and penoxsulam applied at the four- to five-leaf stage of rice. This mixture of broad-spectrum herbicides with different modes of action is the currently recommended practice for managing herbicide-resistant weeds. A 3,000-square-foot portion of each plot was left untreated to monitor weed recruitment and evaluate the effectiveness of the stale seedbed. In the minimum-till treatment, this area received glyphosate prior to planting but not the other herbicides used in the the leaf-eating adults. Adult weevil feeding was monitored from the three-to-five rice leaf stage. Larvae were counted twice in 10 soil samples in all plots in July. Fertilizer management. Fertilizer management varied between the two study treatments due to differences in water management and tillage. Phosphorus and potassium fertilizer were applied on all plots prior to permanent flooding. In the conventional tillage plots the phosphorus and potassium were tilled into the soil with the tillage operations, but in the minimumtill system it remained on the surface. Nitrogen fertilizer was applied at a rate of 150 pounds per acre, within the recommended range for rice . In the conventional till system, the field remained permanently flooded and anaerobic, and all of the nitrogen was applied in a single dose incorporated 3 to 4 inches below the soil surface prior to planting. In the minimum-till system, since the soil was left undisturbed following the stale seedbed treatment, nitrogen fertilizer was applied on the soil surface instead of below it. Two-thirds of the nitrogen was broadcast on the surface just before flooding for planting, and the remaining third was broadcast between 40 and 50 days after planting. Nitrogen fertility trial. To determine the most efficient nitrogen management practices for each tillage system, a nitrogen fertility trial was conducted in 2004 and 2006. This trial included five 400-square-foot subplots within each plot to which no nitrogen fertilizer had previously been applied. The location of these subplots within the main plots changed each year to avoid the compounding effects of the nitrogen fertility treatments. Nitrogen fertilizer rates ranged from 0 to 200 pounds per acre in the subplots . In the conventional-till treatment, nitrogen was always applied as a single dose and incorporated below the soil surface before flooding for planting. In the minimum-till treatment, nitrogen was applied either as a single dose or split between two doses. Data analysis. All data were analyzed using Statistical Analysis System software. Main plot yields, weed data and water weevil data were analyzed using a randomized complete block design. The nitrogen fertility trial was analyzed using a split-plot design.