Evolutionary Genomics of Weedy Rice in the USA

Red rice Is an Interfertlle, weedy form of cultivated rice （Oryza sativa L.） that competes aggressively with the crop In the southern US, reducing yields and contaminating harvests. No wild Oryza species occur In North America and the weed has been proposed to have evolved through multiple mechanisms, Including ＂de-domestication＂ of US crop cultlvars, accidental introduction of Asian weeds, and hybridization between US crops and Asian wild/weedy Oryza strains. The phenotype of US red rice ranges from ＂crop mimics＂, which share some domestication traits with the crop, to strains closely resembling Asian wild Oryza species. Assessments of genetic diversity have Indicated that many weed strains are closely related to Asian taxa （Including indica and aus rice varieties, which have never been cultivated In the US, and the Asian crop progenitor O. ruflpogon）, whereas others show genetic similarity to the tropical Japonica varieties cultivated In the southern US. Herein, we review what Is known about the evolutionary origins and genetic diversity of US red rice and describe an ongoing research project to further characterize the evolutionary genomlcs of this aggressive weed.     

Manipulation of biotic signaling:a new theory for smarter pest control

正Modern agricultural bio-technologies have significantly increased the efficiency and quality of crop production and contributed to the improvement of people's life in the world.Widespread utilization of fertilizers,herbicides,fungicides,pesticides,antibiotics,and plant growth regulators has been instrumental in securing crop yields to feed over seven billions of human beings in the earth.However,during the recent half century,extensive uses of pesticides and other chemicals,which traditionally target the essential physiological pathways of pathogenic microbes and pests,have proverbial,negative impacts on the environmental and     

Progress of chromosome engineering mediated by asymmetric somatic hybridization

Plant somatic hybridization has progressed steadily over the past 35 years. Many hybrid plants have been generated from fusion combinations of different phylogenetic species, some of which have been utilized in crop breeding programs. Among them, asymmetric hybrid, which usually contains a fraction of alien genome, has received more attention because of its importance in crop improvement. However, few studies have dealt with the heredity of the genome of somatic hybrid for a long time, which has limited the progress of this approach. Over recent ten years, along with the development of an effective cytogenetical tool ＂in situ hybridization （ISH）＂, asymmetric fusion of common wheat （Triticum aestivum L.） with different grasses or cereals has been greatly developed. Genetics, genomes, functional genes and agricultt, ral traits of wheat asymmetric hybrids have been subject to systematic investigations using gene cloning, genomic in situ hybridization （GISH） and molecular makers. The future goal is to fully elucidate the functional relationships among improved agronomic traits, the genes and underlying molecular mechanisms, and the genome dynamics of somatic introgression lines. This will accelerate the development of elite germplasms via somatic hybridization and the application of these materials in the molecular improvement of crop plants.     

High-throughput Phenotyping and Genomic Selection:The Frontiers of Crop Breeding Converge

Genomic selection (GS) and high-throughput phenotyping have recently been captivating the interest of the crop breeding com-munity from both the public and private sectors world-wide.Both approaches promise to revolutionize the prediction of complex traits,including growth,yield and adaptation to stress.Whereas high-throughput phenotyping may help to improve understanding of crop physiology,most powerful techniques for high-throughput field phenotyping are empirical rather than analytical and compa-rable to genomic selection.Despite the fact that the two method-ological approaches represent the extremes of what is understood as the breeding process (phenotype versus genome),they both consider the targeted traits (e.g.grain yield,growth,phenology,plant adaptation to stress) as a black box instead of dissecting them as a set of secondary traits (i.e.physiological) putatively related to the target trait.Both GS and high-throughput phenotyping have in common their empirical approach enabling breeders to use genome profile or phenotype without understanding the underlying biology.This short review discusses the main aspects of both approaches and focuses on the case of genomic selection of maize flowering traits and near-infrared spectroscopy (NIRS) and plant spectral reflectance as high-throughput field phenotyping methods for complex traits such as crop growth and yield.     

Designing salt stress-resilient crops: Current progress and future challenges

Excess soil salinity affects large regions of land and is a major hindrance to crop production worldwide.Therefore, understanding the molecular mechanisms of plant salt tolerance has scientific importance and practical significance. In recent decades, studies have characterized hundreds of genes associated with plant responses to salt stress in different plant species. These studies have substantially advanced our molecular and genetic understanding of salt tolerance in plants and have introduce...     

Type-B response regulator OsRR22 forms a transcriptional activation complex with OsSLR1 to modulate OsHKT2;1 expression in rice

Soil salinity severely limits crop yields and quality. Plants have evolved several strategies to mitigate the adverse effects of salinity, including redistribution and compartmentalization of toxic ions using ion-specific transporters. However, the mechanisms underlying the regulation of these ion transporters have not been fully elucidated. Loss-of-function mutants of OsHKT2;1, which is involved in sodium uptake, exhibit strong salt stress-resistant phenotypes. In this study, OsHKT2;1 was ident...     

Evolutionary Genomics of Weedy Rice in the USA

Red rice is an interfertiie, weedy form of cultivated rice (Oryza sativa L.) that competes aggressively with the cropin the southern US, reducing yields and contaminating harvests. No wild Oryza species occur In North America andthe weed has been proposed to have evolved through multiple mechanisms, including "de-domestication" of UScrop cultivars, accidental introduction of Asian weeds, and hybridization between US crops and Asian wild/weedyOryza strains. The phenotype of US red rice ranges from "crop mimics", which share some domestication traitswith the crop, to strains closely resembling Asian wild Oryza species. Assessments of genetic diversity haveindicated that many weed strains are closely related to Asian taxa (including indica and aus rice varieties, whichhave never been cultivated in the US, and the Asian crop progenitor O. rufipogon), whereas others show geneticsimilarity to the tropical japonica varieties cultivated in the southern US. Herein, we review what is known aboutthe evolutionary origins and genetic diversity of US red rice and describe an ongoing research project to furthercharacterize the evolutionary genomics of this aggressive weed.     

Genetics of barley tiller and leaf development

In cereals, tillering and leaf development are key factors in the concept of crop ideotype, introduced in the 1960 s to enhance crop yield, via manipulation of plant architecture. In the present review, we discuss advances in genetic analysis of barley shoot architecture,focusing on tillering, leaf size and angle. We also discuss novel phenotyping techniques, such as 2 D and 3 D imaging, that have been introduced in the era of phenomics, facilitating reliable trait measurement. We discuss the identification of genes and pathways that are involved in barley tillering and leaf development,highlighting key hormones involved in the control of plant architecture in barley and rice. Knowledge on genetic control of traits related to plant architecture provides useful resources for designing ideotypes for enhanced barley yield and performance.     

Identification of Soybean Genes Involved in Circadian Clock Mechanism and Photoperiodic Control of Flowering Time by In Silico Analyses

Glycine max is a photoperiodic short-day plant and the practical consequence of the response is latitude and sowing period limitations to commercial crops. Genetic and physiological studies using the model plants Arabidopsis thaliana and rice （Oryza sativa） have uncovered several genes and genetic pathways controlling the process, however information about the corresponding pathways in legumes is scarce. Data mining prediction methodologies, including multiple sequence alignment, phylogeneUc analysis, bioinformaUcs expression and sequence motif pattern identification, were used to identify soybean genes involved in day length perception and photoperiodic flowering induction. We have investigated approximately 330 000 sequences from open-access databases and have identified all bona fide central oscillator genes and circadian photoreceptors from A. thaliana in soybean sequence databases. We propose a working model for the photoperiodic control of flowering time in G. max, based on the identified key components. These results demonstrate the power of comparative genomics between model systems and crop species to elucidate the several aspects of plant physiology and metabolism.     

Unveiling a half-century mystery of molecular bases for three-line hybrid rice breeding system

<正>Rice (Oryza sativa L.) is a staple crop for half the world’s population and an important contributor to world food security. The discovery and application of cytoplasmic male sterility (CMS) and fertility restoration (Rf) genetic materials have allowed the production of three-line hybrid rice (Kim and Zhang, 2018), successfully harnessing heterosis in crops.     

Root architecture

<正>Numerous research publications over the past 20 years have made it quite clear that a better understanding of the molecular and genetic basis for variation in root system architecture(RSA)will greatly aid the development of crop varieties with improved and more ef ficient nutrient and water acquisition under limiting conditions.In many parts of the world,especially in developing     

Shoot-Specific Down-Regulation of Protein Farnesyltransferase （α-Subunit） for Yield Protection against Drought in Canola

Canola （Brassica napus L.） is one of the most important oilseed crops in the world and its seed yield and quality are significantly affected by drought stress. As an innate and adaptive response to water deficit, land plants avoid potential damage by rapid biosynthesis of the phytohormone abscisic acid （ABA）, which triggers stomatal closure to reduce transpirational water loss. The ABA-mediated stomatal response is a dosage-dependent process; thus, one genetic engineering approach for achieving drought avoidance could be to sensitize the guard cell＇s responsiveness to this hormone. Recent genetic studies have pinpointed protein farnesyltransferase as a key negative regulator controlling ABA sensitivity in the guard cells. We have previously shown that down-regulation of the gene encoding Arabidopsis β-subunit of farnesyltransferase （ERA1） enhances the plant＇s sensitivity to ABA and drought tolerance. Although the β-subunit of famesyltransferase （AtFTA） is also implicated in ABA sensing, the effectiveness of using such a gene target for improving drought tolerance in a crop plant has not been validated. Here, we report the identification and characterization of the promoter of Arabidopsis hydroxypyruvate reductase （AtHPR1）, which expresses specifically in the shoot and not in non-photosynthetic tissues such as root. The promoter region of AtHPR1 contains the core motif of the well characterized dehydration-responsive cis-acting element and we have confirmed thatAtHPR1 expression is inducible by drought stress. Conditional and specific down-regulation of FTA in canola using the AtHPR1 promoter driving an RNAi construct resulted in yield protection against drought stress in the field. Using this molecular strategy, we have made significant progress in engineering drought tolerance in this important crop species.     

PAT： waking up a lazy sleeping beauty

Once upon a time, there was an unusual corn; and unlike its normal siblings, its stalk grew towards the ground rather than in an upward direction. The sleeping stature of the corn was portrayed in early 1930s as ＂lazy＂ by Jenkins and Gerhardt. Later, lazy appeared to be a fashion in the plant kingdom, found in rice, barley, tomato and several other species . These seemingly magic spellchanted plants have drawn considerable interests of plant biologists and breeders for many decades. To breeders, the lazy phenotype, viewed as tillering or branching angles of stems （or termed as culms in crop plants）, represents a key characteristic important for controlling photosynthesis efficiency and planting density, and thus a crucial factor in determining crop production .     

Relative importance of long‐term changes in climate and land‐use on the phenology and abundance of legume crop specialist and generalist aphids

Abstract Insect populations are prone to respond to global changes through shifts in phenology, distribution and abundance. However, global changes cover several factors such as climate and land-use, the relative importance of these being largely unknown. Here, we aim at disentangling the effects of climate, land-use, and geographical drivers on aphid abundance and phenology in France, at a regional scale and over the last 40 years. We used aerial data obtained from suction traps between 1978 and 2015 on five aphid species varying in their degree of specialization to legumes, along with climate, legume crop area and geographical data. Effects of environmental and geographical variables on aphid annual abundance and spring migration dates were analyzed using generalized linear mixed models. We found that within the last four decades, aphids have advanced their spring migration by a month, mostly due to the increase in temperature early in the year, and their abundance decreased by half on average, presumably in response to a combination of factors. The influence of legume crop area decreased with the degree of specialization of the aphid species to such crops. The effect of geographical variation was high even when controlling for environmental variables, suggesting that many other spatially structured processes act on aphid population characteristics. Multifactorial analyses helped to partition the effects of different global change drivers. Climate and land-use changes have strong effects on aphid populations, with important implications for future agriculture. Additionally, trait-based response variation could have major consequences at the community scale.     

10k-level integrated rice database shows power for exploiting rare variantsFA

<正>Rice is one of the most important staple crops, feeding half of the world’s population. In the 1990s, rice became a model plant to study monocots due to its relatively small genome and efficient transformation system(Izawa and Shimamoto, 1996).Rice is the first crop with a sequenced and assembled reference genome(Wang and Han, 2022), and rice genes have been cloned via the map-based cloning system,     

The role of calcium sensor-interacting protein kinases in plant adaptation to potassium-deficiency： new answers to old questions

Potassium （K^＋） is an essential macronutrient for all living organisms and large amounts are required for plant growth and development. In many regions of Asia K＋-fertilization has been neglected and soils have become K＋-depleted. K＋- deficiency in the field diminishes not only crop production but also leads to environmental problems due to inefficient usage and leaching of nitrate. Consequences of K^＋-deficiency on crop production range from decreased biomass, nutritional quality and taste of the crops to inferior harvest and storage properties, as well as increased susceptibility to disease. Effects of K^＋-deficiency on plant physiology include decreased photosynthetic rate, impaired tissue allocation of sugars and amino acids, decreased protein synthesis.     

Did maize domestication and early spread mediate the population genetics of corn leafhopper?

Investigating how crop domestication and early farming mediated crop attributes, distributions, and interactions with antagonists may shed light on today's agricultural pest problems. Crop domestication generally involved artificial selection for traits desirable to early farmers, for example, in creased productivity or yield, and enhanced qualities, though invariably it altered the interactions between crops and insects, and expanded the geographical ranges of crops. Thus, some studies suggest that with crop domestication and spread, insect populations on wild crop ancestors gave rise to pestiferous insect populations on crops. Here, we addressed whether the emergence of corn leafhopper (Dalbulus ma id is) as an agricultural pest may be associated with domestication and early spread of maize (Zea mays mays). We used AFLP markers and mitochondrial COI sequences to assess population genetic structuring and haplotype relationships among corn leafhopper samples from maize and its wild relative Zea diploperennis from multiple locations in Mexico and Argentina. We uncovered seven corn leafhopper haplotypes contained within two haplogroups, one haplogroup containing haplotypes associated with maize and the other containing haplotypes associated with Z. diploperennis in a mountainous habitat. Within the first haplogroup, one haplotype was predominant across Mexican locations, and another across Argentinean locations;both were considered pestiferous. We suggested that the divergence times of the maize-associated haplogroup and of the "pestiferous" haplotypes are correlated with the chronology of maize spread following its domestication. Overall, our results support a hypothesis positing that maize domestication favored corn leafhopper genotypes preadapted for exploiting maize so that they became pestiferous, and that with the geographical expansi on of maize farming, corn leafhopper colonized Z. diploperennis, a host exclusive to secluded habitats that serves as a refuge for archaic corn leafhopper genotypic diversity. Broadly, our results help explain the extents to which crop domestication and early spread may have mediated the emergence of today's agricultural pests.     

杂草科学管理——理论基础与实施途径

Scientific management of weeds is theoretically based on ecology.The implementation methods incladeIntensifying the weed biology and ecology research, especially those of the heavy weeds;Intensifying the research of developing competition between the crop and the weed;Utilizing a allelopathy the gene engineering and breeding against the weeds;Utilizing allelopathy between the crop and the weed, and utilizing biological and agricultural measurements to control the weeds.     

Epigenetic Regulation of a Powdery Mildew Resistance Gene in Medicago truncatula

Dear Editor, Medicago truncatula is a model legume that is conge- neric with alfalfa （Medicago sativa）, a forage crop of global importance. Over the last decade, tremendous genetic and genomic tools have been developed for this model system, which has greatly facilitated the study of various aspects of legume genomics and biology. From an applied perspective, genomic information gained from M. truncatula is particu- larly useful for genetic improvement of cultivated alfalfa, a crop that is not amenable to genetic analysis because of its allogamous and autotetraploid nature （Yang et al., 2008）. For instance, M. truncatula can be used to clone the orthologs of many economically important genes in alfalfa,     

A numerical study on impact of crop canopy on mesoscale climate

The impact of well watered mesoscale wheat planted on the mesoscale boundary layer structures of midlatitude arid area has been investigated by using a mesoscale biophysical meteorological model. The investigation indicates that mesoscale perturbations in temperature and specific humidity over crop area from the adjacent dry, bare soil, caused by the transpiration from the crop canopy and evaporation from underlying humid soil, result in a horizontal pressure gradient. A mesoscale circulation is forced by the pressure perturbation with a wind speed of about 5 m/s directing from the crop canopy to the bare soil in the lower boundary layer. In the daytime, the boundary layer structure over a complex terrain is determined by the interactions between upslope flow circulations and the circulations mentioned above when wheat crop canopies are located on plain and plateau. The impact of crop canopy scale on this thermally forced mesoscale circulation is also investigated.