Evidence for divergence of response in Indica, Japonica, and wild rice to high CO2 × temperature interaction.

High CO2 and high temperature have an antagonistic interaction effect on rice yield potential and present a unique challenge to adapting rice to projected future climates. Understanding how the differences in response to these two abiotic variables are partitioned across rice germplasm accessions may be key to identifying potentially useful sources of resilient alleles for adapting rice to climate change. In this study, we evaluated eleven globally diverse rice accessions under controlled conditions at two carbon dioxide concentrations (400 and 600 ppm) and four temperature environments (29 °C day/21 °C night; 29 °C day/21 °C night with additional heat stress at anthesis; 34 °C day/26 °C night; and 34 °C day/26 °C night with additional heat stress at anthesis) for a suite of traits including five yield components, five growth characteristics, one phenological trait, and four photosynthesis-related measurements. Multivariate analyses of mean trait data from these eight treatments divide our rice panel into two primary groups consistent with the genetic classification of INDICA/INDICA-like and JAPONICA populations. Overall, we find that the productivity of plants grown under elevated [CO2 ] was more sensitive (negative response) to high temperature stress compared with that of plants grown under ambient [CO2 ] across this diversity panel. We report differential response to CO2 × temperature interaction for INDICA/INDICA-like and JAPONICA rice accessions and find preliminary evidence for the beneficial introduction of exotic alleles into cultivated rice genomic background. Overall, these results support the idea of using wild or currently unadapted gene pools in rice to enhance breeding efforts to secure future climate change adaptation.

More than one way to evolve a weed: parallel evolution of US weedy rice through independent genetic mechanisms.

Many different crop species were selected for a common suite of 'domestication traits', which facilitates their use for studies of parallel evolution. Within domesticated rice (Oryza sativa), there has also been independent evolution of weedy strains from different cultivated varieties. This makes it possible to examine the genetic basis of parallel weed evolution and the extent to which this process occurs through shared genetic mechanisms. We performed comparative QTL mapping of weediness traits using two recombinant inbred line populations derived from crosses between an indica crop variety and representatives of each of the two independently evolved weed strains found in US rice fields, strawhull (S) and blackhull awned (B). Genotyping-by-sequencing provided dense marker coverage for linkage map construction (average marker interval <0.25 cM), with 6016 and 13 730 SNPs mapped in F5 lines of the S and B populations, respectively. For some weediness traits (awn length, hull pigmentation and pericarp pigmentation), QTL mapping and sequencing of underlying candidate genes confirmed that trait variation was largely attributable to individual loci. However, for more complex quantitative traits (including heading date, panicle length and seed shattering), we found multiple QTL, with little evidence of shared genetic bases between the S and B populations or across previous studies of weedy rice. Candidate gene sequencing revealed causal genetic bases for 8 of 27 total mapped QTL. Together these findings suggest that despite the genetic bottleneck that occurred during rice domestication, there is ample genetic variation in this crop to allow agricultural weed evolution through multiple genetic mechanisms.

The impact of herbicide-resistant rice technology on phenotypic diversity and population structure of United States weedy rice.

The use of herbicide-resistant (HR) Clearfield rice (Oryza sativa) to control weedy rice has increased in the past 12 years to constitute about 60% of rice acreage in Arkansas, where most U.S. rice is grown. To assess the impact of HR cultivated rice on the herbicide resistance and population structure of weedy rice, weedy samples were collected from commercial fields with a history of Clearfield rice. Panicles from each weedy type were harvested and tested for resistance to imazethapyr. The majority of plants sampled had at least 20% resistant offspring. These resistant weeds were 97 to 199 cm tall and initiated flowering from 78 to 128 d, generally later than recorded for accessions collected prior to the widespread use of Clearfield rice (i.e. historical accessions). Whereas the majority (70%) of historical accessions had straw-colored hulls, only 30% of contemporary HR weedy rice had straw-colored hulls. Analysis of genotyping-by-sequencing data showed that HR weeds were not genetically structured according to hull color, whereas historical weedy rice was separated into straw-hull and black-hull populations. A significant portion of the local rice crop genome was introgressed into HR weedy rice, which was rare in historical weedy accessions. Admixture analyses showed that HR weeds tend to possess crop haplotypes in the portion of chromosome 2 containing the ACETOLACTATE SYNTHASE gene, which confers herbicide resistance to Clearfield rice. Thus, U.S. HR weedy rice is a distinct population relative to historical weedy rice and shows modifications in morphology and phenology that are relevant to weed management.

Root distribution and potential interactions between allelopathic rice, sprangletop (Leptochloa spp.), and barnyardgrass (Echinochloa crus-galli) based on ¹³C isotope discrimination analysis.

Weed-suppressive rice cultivars hold promise for improved and more economical weed management in rice. Interactions between roots of rice and weeds are thought to be modulated by the weed-suppressive activity of some rice cultivars, but these phenomena are difficult to measure and not well understood. Thus, above-ground productivity, weed suppression, and root distribution of 11 rice cultivars and two weed species were evaluated in a drill-seeded, flood-irrigated system at Stuttgart, Arkansas, USA in a two-year study. The allelopathic cultivars, PI 312777 and Taichung Native 1 (TN-1), three other weed-suppressive cultivars, three indica-derived breeding selections, and three non-suppressive commercial cultivars were evaluated in field plots infested with barnyardgrass (Echinochloa crus-galli (L.) Beauv.) or bearded sprangletop (sprangletop, Leptochloa fusca (L.) Kunth var. fascicularis (Lam.) N. Snow). The allelopathic cultivars produced more tillers and suppressed both weed species to a greater extent than did the breeding selections or the non-suppressive cultivars. (13)C isotope discrimination analysis of mixed root samples to a depth of 15 cm revealed that the allelopathic cultivars typically produced a greater fraction of their total root mass in the surface 0-5 cm of soil depth compared to the breeding selections or the non-suppressive cultivars, which tended to distribute their roots more evenly throughout the soil profile. These trends in root mass distribution were apparent at both early (pre-flood) and late-season stages in weed-free and weed-infested plots. Cultivar productivity and root distribution generally responded similarly to competition with the two weed species, but barnyardgrass reduced rice yield and root mass more than did sprangletop. These findings demonstrate for the first time that roots of the allelopathic cultivars PI 312777 and TN-1 explore the upper soil profile more thoroughly than do non-suppressive cultivars under weed-infested and weed-free conditions in flood-irrigated U.S. rice production systems. They raise the interesting prospect that root proliferation near the soil surface might enhance the weed-suppressive activity of allelochemical exudates released from roots. Plant architectural design for weed suppressive activity should take these traits into consideration along with other proven agronomic traits such as high tillering and yield.

Food security and climate change: on the potential to adapt global crop production by active selection to rising atmospheric carbon dioxide.

Agricultural production is under increasing pressure by global anthropogenic changes, including rising population, diversion of cereals to biofuels, increased protein demands and climatic extremes. Because of the immediate and dynamic nature of these changes, adaptation measures are urgently needed to ensure both the stability and continued increase of the global food supply. Although potential adaption options often consider regional or sectoral variations of existing risk management (e.g. earlier planting dates, choice of crop), there may be a global-centric strategy for increasing productivity. In spite of the recognition that atmospheric carbon dioxide (CO(2)) is an essential plant resource that has increased globally by approximately 25 per cent since 1959, efforts to increase the biological conversion of atmospheric CO(2) to stimulate seed yield through crop selection is not generally recognized as an effective adaptation measure. In this review, we challenge that viewpoint through an assessment of existing studies on CO(2) and intraspecific variability to illustrate the potential biological basis for differential plant response among crop lines and demonstrate that while technical hurdles remain, active selection and breeding for CO(2) responsiveness among cereal varieties may provide one of the simplest and direct strategies for increasing global yields and maintaining food security with anthropogenic change.

Genomic prediction and QTL mapping of root system architecture and above-ground agronomic traits in rice (Oryza sativa L.) with a multitrait index and Bayesian networks.

Root system architecture (RSA) is a crucial factor in resource acquisition and plant productivity. Roots are difficult to phenotype in the field, thus new tools for predicting phenotype from genotype are particularly valuable for plant breeders aiming to improve RSA. This study identifies quantitative trait loci (QTLs) for RSA and agronomic traits in a rice (Oryza sativa) recombinant inbred line (RIL) population derived from parents with contrasting RSA traits (PI312777 × Katy). The lines were phenotyped for agronomic traits in the field, and separately grown as seedlings on agar plates which were imaged to extract RSA trait measurements. QTLs were discovered from conventional linkage analysis and from a machine learning approach using a Bayesian network (BN) consisting of genome-wide SNP data and phenotypic data. The genomic prediction abilities (GPAs) of multi-QTL models and the BN analysis were compared with the several standard genomic prediction (GP) methods. We found GPAs were improved using multitrait (BN) compared to single trait GP in traits with low to moderate heritability. Two groups of individuals were selected based on GPs and a modified rank sum index (GSRI) indicating their divergence across multiple RSA traits. Selections made on GPs did result in differences between the group means for numerous RSA. The ranking accuracy across RSA traits among the individual selected RILs ranged from 0.14 for root volume to 0.59 for lateral root tips. We conclude that the multitrait GP model using BN can in some cases improve the GPA of RSA and agronomic traits, and the GSRI approach is useful to simultaneously select for a desired set of RSA traits in a segregating population.

Identification of Novel QTL Conferring Sheath Blight Resistance in Two Weedy Rice Mapping Populations.

BACKGROUND: Rice sheath blight (ShB) disease, caused by the pathogenic fungus Rhizoctonia solani, causes significant yield losses globally. US weedy rice populations, which are de-domesticated forms of indica and aus cultivated rice, appear to be more resistant to ShB than local japonica cultivated rice. We mapped quantitative trait loci (QTL) associated with ShB resistance using two F8 recombinant inbred line populations generated from crosses of an indica crop variety, Dee-Geo-Woo-Gen (DGWG), with individuals representing the two major US weed biotypes, straw hull (SH) and black hull awned (BHA). RESULTS: We identified nine ShB resistance QTL across both mapping populations. Five were attributable to alleles that affect plant height (PH) and heading date (HD), two growth traits that are known to be highly correlated with ShB resistance. By utilizing an approach that treated growth traits as covariates in the mapping model, we were able to infer that the remaining four QTL are involved in ShB resistance. Two of these, qShB1-2 and qShB4, are different from previously identified ShB QTL and represent new candidates for further study. CONCLUSION: Our findings suggest that ShB resistance can be improved through favorable plant growth traits and the combined effects of small to moderate-effect resistance QTL. Additionally, we show that including PH and HD as covariates in QTL mapping models is a powerful way to identify new ShB resistance QTL.

Phylogenetic origin and dispersal pattern of Taiwan weedy rice.

BACKGROUND: Knowledge of the genetic diversity and spatial structure of Taiwan weedy red rice (WRR) populations, which adapted in a transplanting system, will facilitate the design of effective methods to control this weed by tracing its origins and dispersal patterns in a given region. RESULTS: Taiwan WRR is genetically most similar to Taiwan indica cultivars and landraces according to genetic distance. The inbreeding coefficient of the Taiwan WRR population is greater than 0.8, which is similar to the inbred cultivars. The ancestry coefficients map suggests a dispersal pattern of long-distance and seed-mediated contamination across Taiwan, often from warmer, earlier-planted regions to cooler, later-planted regions. Parentage analysis of Taiwan WRR revealed that mostly early indica landraces and indica cultivars were present in the genetic pool; in rare cases temperate japonica was present. Based on the above results, the phylogenetic origin of most Taiwan weedy rice appears to be from hybrid progenies of old cultivated red rice accessions crossed with 'DGWG'. The inbreeding coefficient trend of the six TWR clusters suggests a temporal shift from 'old' indica landraces with red bran (high inbreeding coefficient) to modern indica varieties (low inbreeding coefficient). CONCLUSION: Although there were sustained efforts to remove these old red rice accessions from paddy fields before 1945, some farmers continued to use low purity seed. This practice, along with volunteer cultivation of these old varieties in the second cropping season, apparently has facilitated the long-distance, seed-mediated contamination of rice seed, and the increase in weedy rice seed in paddy soil. © 2019 Society of Chemical Industry.

Impact of volunteer rice infestation on yield and grain quality of rice.

BACKGROUND: Volunteer rice (Oryza sativa L.) grains may differ in physicochemical traits from cultivated rice, which may reduce the quality of harvested rice grain. To evaluate the effect of volunteer rice on cultivated rice, fields were surveyed in Arkansas in 2012. RESULTS: Cropping history that included hybrid cultivars in the previous two years (2010 and 2011) had higher volunteer rice infestation (20%) compared with fields planted previously with inbred rice (5.5%). The total grain yield of rice was reduced by 0.4% for every 1% increase in volunteer rice density. The grain quality did not change in fields planted with the same cultivar for three years. Volunteer rice density of at least 7.6% negatively impacted the head rice and when infestation reached 17.7%, it also reduced the rice grain yield. The protein and amylose contents of rice were not affected until volunteer rice infestation exceeded 30%. CONCLUSION: Crop rotation systems that include hybrid rice are expected to have higher volunteer rice infestation than systems without hybrid rice. It is predicted that, at 8% infestation, volunteer rice will start to impact head rice yield and will reduce total yield at 18% infestation. It could alter the chemical quality of rice grain at >30% infestation. © 2016 Society of Chemical Industry.

Comparison of physicochemical properties and starch structure of red rice and cultivated rice.

Sixteen red rice accessions from the southern United States were studied for their physical, milling, pasting, and thermal properties, chemical composition, and starch fine structure relative to cultivated medium- and long-grain rice varieties. All red rice samples were medium-grain, but their physicochemical properties were different from those of Bengal, a cultivated medium-grain rice. Their apparent amylose and crude protein contents were generally higher, and their amylopectin structure consisted of a higher percentage of the shorter branch chains (DP6-24) and a lower percentage of the longer branch chains (DP25-65). Red rice starch pasting and thermal properties were similar to those of Wells, a long-grain rice cultivar. The red rice samples can be classified into two major clusters according to their kernel properties by hierarchical cluster analysis: one cluster with more resemblance to Wells and another cluster with more resemblance to Bengal. Starch structure and kernel physicochemical properties may offer an alternative way of classifying red rice in addition to phenotypic and genetic indices.

Evaluation of Host-Plant Resistance of Selected Rice Genotypes to the Rice Water Weevil (Coleoptera: Curculionidae).

The rice water weevil, Lissorhoptrus oryzophilus Kuschel, is the most important insect pest of rice in the United States. Management of L. oryzophilus mainly depends upon the use of insecticides due to the lack of effective alternative management tactics. A 3-yr field study was conducted to determine if difference exists among rice genotypes and cultivars of inbred tropical japonica subspecies commercially grown in the southern United States [Cocodrie (PI 606331), CL171, and CL151 (PI 654463)] and the germplasm lines of indica subspecies adapted to tropical climates of Asia [WC 4644 (PI 312777), TNI (PI 495830), Rondo (PI 615022), 4612 (PI 615039), TeQing (PI 536047), and 4593 (PI 615031)] for resistance to L. oryzophilus Experiments were established as a split-plot design with cultivars as main plots and insecticide treatment as subplots. No significant differences were observed in number of L. oryzophilus larvae recovered across cultivars and genotypes, indicating no significant variation in their preference to L. oryzophilus oviposition. Insecticide treatment had a significant impact on L. oryzophilus larval density. However, grain yield did not vary significantly between treated and untreated plots for any of the cultivars and genotypes. The amount of yield loss in response to L. oryzophilus infestation did not vary significantly across genotypes and cultivars, indicating no variation among these genotypes for resistance to L. oryzophilus.

United States Department of Agriculture-Agricultural Research Service research on natural products for pest management.

Recent research of the Agricultural Research Service of USDA on the use of natural products to manage pests is summarized. Studies of the use of both phytochemicals and diatomaceous earth to manage insect pests are discussed. Chemically characterized compounds, such as a saponin from pepper (Capsicum frutescens L), benzaldehyde, chitosan and 2-deoxy-D-glucose are being studied as natural fungicides. Resin glycosides for pathogen resistance in sweet potato and residues of semi-tropical leguminous plants for nematode control are also under investigation. Bioassay-guided isolation of compounds with potential use as herbicides or herbicide leads is underway at several locations. New natural phytotoxin molecular target sites (asparagine synthetase and fructose-1,6-bisphosphate aldolase) have been discovered. Weed control in sweet potato and rice by allelopathy is under investigation. Molecular approaches to enhance allelopathy in sorghum are also being undertaken. The genes for polyketide synthases involved in production of pesticidal polyketide compounds in fungi are found to provide clues for pesticide discovery. Gene expression profiles in response to fungicides and herbicides are being generated as tools to understand more fully the mode of action and to rapidly determine the molecular target site of new, natural fungicides and herbicides.

Assessment of cultivated and wild, weedy rice lines to concurrent changes in CO2 concentration and air temperature: determining traits for enhanced seed yield with increasing atmospheric CO2.

Although several studies have examined intra-specific variability in growth and yield to projected atmospheric CO2 concentration, [CO2], few have considered concurrent increases in air temperature and [CO2], and none have compared the relative responses of cultivated and wild, weedy crop lines. In the current study we quantified the growth and seed yield response of three cultivated ('Rondo', 'Clearfield 161', 'M204') and one wild (red) rice line ('Stuttgart-S' or 'Stg-S'), grown at ambient or +200µmolmol-1 [CO2] at one of three day/night temperatures (29/21, 31/23 or 33/25°C). Averaged among all cultivars, [CO2] increased biomass and seed yield, but conversely, increasing air temperature reduced the [CO2] response of both parameters. Among the cultivated and weedy rice tested, 'Rondo' and 'Stg-S' showed significant increases in aboveground biomass and seed yield with elevated [CO2] at 29/21°C; however, only 'Stg-S', the weedy rice line, demonstrated a significant increase with [CO2] at all growth temperatures. A regression analysis for this line indicated that the relative increase in seed yield with [CO2] and air temperature was positively associated with panicle and tiller number, but negatively correlated with the percentage of immature seed. An analysis of all lines indicated that the ratio of tiller production between CO2 treatments at 30 days after sowing (DAS) was a significant predictor of seed yield response to increasing [CO2] for all temperatures. These results suggest that: (i) inclusion of wild lines may broaden genotypic or phenotypic variation and assist in selection to temperature/[CO2]; and (ii) early differences in tiller formation may be an effective means to facilitate screening for CO2 sensitive rice genotypes.

Recent and projected increases in atmospheric CO2 concentration can enhance gene flow between wild and genetically altered rice (Oryza sativa).

Although recent and projected increases in atmospheric carbon dioxide can alter plant phenological development, these changes have not been quantified in terms of floral outcrossing rates or gene transfer. Could differential phenological development in response to rising CO(2) between genetically modified crops and wild, weedy relatives increase the spread of novel genes, potentially altering evolutionary fitness? Here we show that increasing CO(2) from an early 20(th) century concentration (300 µmol mol(-1)) to current (400 µmol mol(-1)) and projected, mid-21(st) century (600 µmol mol(-1)) values, enhanced the flow of genes from wild, weedy rice to the genetically altered, herbicide resistant, cultivated population, with outcrossing increasing from 0.22% to 0.71% from 300 to 600 µmol mol(-1). The increase in outcrossing and gene transfer was associated with differential increases in plant height, as well as greater tiller and panicle production in the wild, relative to the cultivated population. In addition, increasing CO(2) also resulted in a greater synchronicity in flowering times between the two populations. The observed changes reported here resulted in a subsequent increase in rice dedomestication and a greater number of weedy, herbicide-resistant hybrid progeny. Overall, these data suggest that differential phenological responses to rising atmospheric CO(2) could result in enhanced flow of novel genes and greater success of feral plant species in agroecosystems.

Molecular evolution of the rice blast resistance gene Pi-ta in invasive weedy rice in the USA.

The Pi-ta gene in rice has been effectively used to control rice blast disease caused by Magnaporthe oryzae worldwide. Despite a number of studies that reported the Pi-ta gene in domesticated rice and wild species, little is known about how the Pi-ta gene has evolved in US weedy rice, a major weed of rice. To investigate the genome organization of the Pi-ta gene in weedy rice and its relationship to gene flow between cultivated and weedy rice in the US, we analyzed nucleotide sequence variation at the Pi-ta gene and its surrounding 2 Mb region in 156 weedy, domesticated and wild rice relatives. We found that the region at and around the Pi-ta gene shows very low genetic diversity in US weedy rice. The patterns of molecular diversity in weeds are more similar to cultivated rice (indica and aus), which have never been cultivated in the US, rather than the wild rice species, Oryza rufipogon. In addition, the resistant Pi-ta allele (Pi-ta) found in the majority of US weedy rice belongs to the weedy group strawhull awnless (SH), suggesting a single source of origin for Pi-ta. Weeds with Pi-ta were resistant to two M. oryzae races, IC17 and IB49, except for three accessions, suggesting that component(s) required for the Pi-ta mediated resistance may be missing in these accessions. Signatures of flanking sequences of the Pi-ta gene and SSR markers on chromosome 12 suggest that the susceptible pi-ta allele (pi-ta), not Pi-ta, has been introgressed from cultivated to weedy rice by out-crossing.

Gene flow from weedy red rice (Oryza sativa L.) to cultivated rice and fitness of hybrids.

BACKGROUND: Gene transfer from weeds to crops could produce weedy individuals that might impact upon the evolutionary dynamics of weedy populations, the persistence of escaped genes in agroecosystems and approaches to weed management and containment of transgenic crops. The present aim was to quantify the gene flowrate from weedy red rice to cultivated rice, and evaluate the morphology, phenology and fecundity of resulting hybrids. Field experiments were conducted at Stuttgart and Rohwer, Arkansas, USA. Twelve red rice accessions and an imazethapyr-resistant rice (Imi-R; Clearfield) were used. RESULTS: Hybrids between Imi-R rice x red rice were 138-150 cm tall and flowered 1-5 days later than the rice parent, regardless of the red rice parent. Hybrids produced 20-50% more seed than the rice parent, but had equivalent seed production to the majority of red rice parents. Seeds of all hybrids were red, pubescent and dehisced at maturity. For the majority of hybrids, seed germination was higher than that of the red rice parent. The gene flowrate from red rice to rice was 0.01-0.2% and differed by red rice biotype. The hybrids had higher fecundity and potential competitive ability than the rice parent, and in some cases also the red rice parent. CONCLUSIONS: Red rice plants are vectors of gene flow back to cultivated rice and other weedy populations. The progeny of red rice hybrids from cultivated rice mother plants have higher chances of persistence than those from red rice mother plants. Gene flow mitigation strategies should consider this scenario.