Exploring the Genetic Diversity among Weedy Rice Accessions Differing in Herbicide Tolerance and Allelopathic Potential

Increasing agricultural productivity is indispensable to meet future food demand. Crop improvement programs rely heavily on genetic diversity. The success of weeds in the ecosystem can be attributed to genetic diversity and plasticity. Weedy rice, a major weed of rice, has diverse morphology and phenology, implying wide genetic diversity. Study was conducted to genotype weedy rice accessions (n = 54) previously phenotyped for herbicide tolerance and allelopathic potential using 30 SSR markers. Cultivated rice (CL163, REX) and allelopathic rice (RONDO, PI312777, PI338047) were also included in the study. Nei’s genetic diversity among weedy rice (0.45) was found to be higher than cultivated rice (0.24) but less than allelopathic rice (0.56). The genetic relationship and population structure based on herbicide tolerance and allelopathic potential were evaluated. Herbicide-tolerant and susceptible accessions formed distinct clusters in the dendrogram, indicating their genetic variation, whereas no distinction was observed between allelopathic and non-allelopathic weedy rice accessions. Weedy rice accession B2, which was previously reported to have high allelopathy and herbicide tolerance, was genetically distinct from other weedy rice. Results from the study will help leverage weedy rice for rice improvement programs as both rice and weedy rice are closely related, thus having a low breeding barrier.

Flooding depths and burial effects on seedling emergence of five California weedy rice (Oryza sativa spontanea) accessions

Weedy rice (Oryza sativa f. spontanea Roshev.) has recently become a significant botanical pest in California rice (Oryza sativa L.) production systems. The conspecificity of this pest with cultivated rice, Oryza sativa (L.), negates the use of selective herbicides, rendering the development of non-chemical methods a necessary component of creating management strategies for this weed. Experiments were conducted to determine the emergence and early growth responses of O. sativa spontanea to flooding soil and burial conditions. Treatment combinations of four flooding depths (0, 5, 10, and 15 cm) and four burial depths (1.3, 2.5, 5, and 10 cm) were applied to test the emergence of five O. sativa spontanea accessions as well as ‘M-206’, a commonly used rice cultivar in California, for comparison. Results revealed that burial depth had a significant effect on seedling emergence. There was a 43-91% decrease in emergence between seedlings buried at 1.3 and 2.5 cm depending on the flooding depth and accession, and an absence of emergence from seedlings buried at or below 5 cm. Flooding depth did not affect emergence, but there was a significant interaction between burial and flooding treatments. There was no significant difference between total O. sativa spontanea emergence from the soil and water surfaces regardless of burial or flooding depths, implying that once the various accessions have emerged from the soil they will also emerge from the floodwater. Most accessions had similar total emergence compared to M-206 cultivated rice, but produced more dry weight than M-206 when planted at 1.3 cm in the soil. The results of this experiment can be used to inform stakeholders of the flooding conditions necessary as well as soil burial depths that will promote or inhibit the emergence of California O. sativa spontanea accessions from the weed seedbank.

An Allelic Variant of the Broad-Spectrum Blast Resistance Gene Ptr in Weedy Rice is Associated with Resistance to the Most Virulent Blast Race IB-33

Rice resistance (R) genes have been effectively deployed to prevent blast disease caused by the pathogen Magnaporthe oryzae, one of the most serious threats for stable rice production worldwide. Weedy rice competing with cultivated rice may carry novel or lost R genes. The QTL qBR12.3b was previously mapped between two single nucleotide polymorphism (SNP) markers 10,633,942 bp and 10,820,033 bp in a black hull awned (BHA) weed strain using a weed-crop mapping population under greenhouse conditions. In the present study, we found a portion of the known resistance gene Ptr encoding a protein with 4 armadillo repeats and confers a broad spectrum of blast resistance. We then analyzed the sequences of the Ptr gene from weedy rice, PtrBHA, identified a unique amino acid glutamine (Gln) at protein position 874. Minor changes of protein conformation of the PtrBHA gene were predicted through structural analysis of PtrBHA suggesting the product of PtrBHA is involved in disease resistance. A gene-specific codominant marker HJ17-13 from PtrBHA was then developed to distinguish alleles in weed and crop. The existence of the PtrBHA gene in 207 individuals of the same mapping population where qBR12.3b was mapped using this gene-specific marker. Disease reactions of 207 individuals and their parents to IB-33 were evaluated. The resistant individuals had the PtrBHA whereas the susceptible individuals did not suggest HJ17-13 is reliable to predict qBR12.3b. Taken together, this newly developed marker and weedy rice genotypes carrying qBR12.3b are useful for blast improvement using marker assisted selection.

Surveys of Weed Management on Flooded Rice Yields in Southern Brazil

One of the main limiting factors for high yields of flooded rice (Oryza sativa L.) is the presence of weeds, especially herbicide-resistant weeds. The aim of this study was to evaluate the association of weed management practices adopted by flooded rice farmers in the State of Rio Grande do Sul (RS) to grain yield. For this purpose, 324 interview surveys were administered to farmers who supplied information about the history of weed management and yields. The answers to the survey indicated that weedy rice (Oryza sativa L.) and Echinochloa sp. were the most important weeds that occurred in flooded rice areas in RS. Advanced growth stage of weeds and inadequate environmental conditions such as air temperature and relative humidity were listed as the main reasons for the low weed control efficacy. Farmers achieved greater rice yields when adopted rice-soybean [Glycine max (L.) Merr.] (9,140 kg ha−1 average yield) and herbicide site of action rotations (8,801 kg ha−1 average yield) along with tank-mixes (8,580 kg ha−1 average yield) as specific management practices for resistant weed control. The use of glyphosate with residual herbicides in tank-mix in rice spiking stage is the main factor related to greater yields. The postemergence applications and their relations with delaying of flooded rice is a factor that reduces rice yield when no spiking glyphosate applications was made. Identification of the most important weeds in terms of occurrence, as well as the knowledge of the main agronomic practices adopted by the farmers, are essential so that recommendations for integrated management practices can be adopted in an increasingly accurate and sustainable-flooded rice areas in Southern Brazil.

Exploring the Genetic Diversity Among Weedy Rice Accessions Differing in Herbicide Tolerance and Allelopathic Potential

Increasing agricultural productivity is indispensable to meet future food demand. Crop im-provement programs rely heavily on genetic diversity. The success of weeds in the ecosystem can be attributed to genetic diversity and plasticity. Weedy rice, a major weed of rice, has diverse morphology and phenology, implying wide genetic diversity. Study was conducted to genotype weedy rice accessions (n =54) previously phenotyped for herbicide tolerance and allelopathic potential using 30 SSR markers. Cultivated rice (CL163, REX) and allelopathic rice (RONDO, PI312777, PI338047) were also included in the study. Nei’s genetic diversity among weedy rice (0.45) was found to be higher than cultivated rice (0.24) but less than allelopathic rice (0.56). The genetic relationship and population structure based on herbicide tolerance and allelopathic po-tential were evaluated. Herbicide-tolerant and susceptible accessions formed distinct clusters in the dendrogram, indicating their genetic variation, whereas no distinction was observed between allelopathic and non-allelopathic weedy rice accessions. Weedy rice accession B2, which was previously reported to have high allelopathy and herbicide tolerance, was genetically distinct from other weedy rice. Results from the study will help leverage weedy rice for rice improvement programs as both rice and weedy rice are closely related, thus having a low breeding barrier.

Phenotypic Differentiation between Weedy Rice Populations Associated with their Local Adaptation in Early-and Late-Season Rice Fields

Background: Temperatures and photoperiods can profoundly affect plant growth and development and play vital roles in the local adaptation of plant species. Weedy rice (Oryza sativa f. spontanea) is a conspecific weed of cultivated rice, and it was found in the same rice fields (sympatry) of early and late rice-cultivation seasons in Leizhou, Guangdong Province of China. Generally, the phenological conditions, such as temperature and photoperiod, are different in the two seasons. Therefore, the early- and late-season weedy rice populations in the same rice fields provide a perfect system for estimating sympatric divergence in plant species. The previous study had demonstrated considerable genetic divergence between the early- and late-season weedy rice populations. Here, we designed in situ common garden experiments to estimate the phenotypical differences between the two-season weedy rice populations and disclose the local adaptation in weedy rice populations associated with their ambient temperature and photoperiod.Results: Distinct air temperature and day length variation patterns were recognized between the early and late rice-cultivation seasons, based on the 10-year historical climate data. More stressful conditions, indicated by low air temperature and long day length, were found for weedy rice growth in the early seasons. Noticeably, significant differences in plant heights, the number of tillers, flowering time, and reproductive traits were detected between the two-season weedy rice populations according to the early-season common garden experiment. The early-season populations showed evident higher plant heights, more tillers, and earlier flowering time than the late-season populations. However, such differences were not detected in the late-season common garden experiment. In addition, evident local adaptation represented by the traits such as plant heights, flowering time, and reproductive traits was only detected in the early-season weedy rice populations. The principal component analysis also showed clear population clusters between the two-season populations using the phenotypical data.Conclusions: This study provided clear evidence of phenotypic differentiation between the sympatric early- and late-season weedy rice populations, probably associated with the local adaptation to their ambient temperature and photoperiod. Our findings also have potential roles in facilitating the design of strategies for effective weedy rice control practices.

High-Quality Genomes and High-Density Genetic Map Facilitate the Identification of Genes From a Weedy Rice

Genes have been lost or weakened from cultivated rice during rice domestication and breeding. Weedy rice (Oryza sativa f. spontanea) is usually recognized as the progeny between cultivated rice and wild rice and is also known to harbor an gene pool for rice breeding. Therefore, identifying genes from weedy rice germplasms is an important way to break the bottleneck of rice breeding. To discover genes from weedy rice germplasms, we constructed a genetic map based on w-hole-genome sequencing of a F2 population derived from the cross between LM8 and a cultivated rice variety. We further identified 31 QTLs associated with 12 important agronomic traits and revealed that ORUFILM03g000095 gene may play an important role in grain length regulation and participate in grain formation. To clarify the genomic characteristics from weedy rice germplasms of LM8, we generated a high-quality genome assembly using single-molecule sequencing, Bionano optical mapping, and Hi-C technologies. The genome harbored a total size of 375.8 Mb, a scaffold N50 of 24.1 Mb, and originated approximately 0.32 million years ago (Mya) and was more closely related to Oryza sativa ssp. japonica. and contained 672 unique genes. It is related to the formation of grain shape, heading date and tillering. This study generated a high-quality reference genome of weedy rice and high-density genetic map that would benefit the analysis of genome evolution for related species and suggested an effective way to identify genes related to important agronomic traits for further rice breeding.