Abiotic stress tolerance:Genetics,genomics,and breeding

1.Tenth anniversary of The Crop Journal The Crop Journal will be 10 years old in October 2023.The journal is sponsored by the Crop Science Society of China,the Institute of Crop Sciences,Chinese Academy of Agricultural Sciences,and China Science Publishing&Media Group Ltd.(Science Press).It is published by Science Press and Ke Ai (founded by China Science Publishing&Media Ltd.and Elsevier).

水稻典型品种日本晴和IR24根系微生物组的解析

植物的各项生命活动与其根系微生物组密不可分,且根系微生物组的组成易受到植物生长环境和基因型的影响。为进一步探究中国北方地区种植的不同品种水稻根系微生物组的差异及其相互作用机制,本研究以种植于北京昌平和上庄农场的水稻典型品种日本晴(Nipponbare)和IR24为研究对象,基于16S rRNA基因扩增子测序技术获得根系微生物组序列,利用多样性分析、组成型分析、机器学习的随机森林和网络分析等方法,对旺盛生长期的两种不同品种的水稻根系微生物组进行详细比较。研究发现,种植地点和水稻基因型显著影响了水稻根系微生物组的群落结构,不同基因型导致了根系微生物组在物种分类组成上以及细菌间相互关系的差异,而且根系微生物组能作为生物标记跨地点区分宿主的基因型。本研究结果为深入理解我国北方种植的水稻根系微生物组的组成规律以及从根系微生物与植物互作的角度对品种进行改良提供了数据和理论基础。

Rice DENSE AND ERECT PANICLE 2 is essential for determining panicle outgrowth and elongation

The architecture of the panicle, including grain size and panicle morphology, directly determines grain yield. Panicle erectness, which is selected for achieving ideal plant arehitecture in the northern part of China, has drawn increasing attention of rice breeders. Here, dense and erect panicle 2 （dep2） mutant, which shows a dense and erect panicle phenotype, was identified. DEP2 encodes a plant-specific protein without any known functional domain. Expression profiling of DEP2 revealed that it is highly expressed in young tissues, with most abundance in young panicles. Morphological and expression analysis indicated that mutation in DEP2 mainly affects the rapid elongation of rachis and primary and secondary branches, but does not impair the initiation or formation of panicle primordia. Further analysis suggests that decrease of panicle length in dep2 is caused by a defect in cell proliferation during the exponential elongation of panicle. Despite a more compact plant type in the dep2 mutant, no significant alteration in grain production was found between wild type and dep2 mutant. Therefore, the study of DEP2 not only strengthens our understanding of the molecular genetic basis of panicle architecture but also has important implications for rice breeding.

The impact of high-temperature stress on rice: Challenges and solutions

Heat stress (HS) caused by rapidly warming climate has become a serious threat to global food security.Rice (Oryza sativa L.) is a staple food crop for over half of the world’s population,and its yield and quality are often reduced by HS.There is an urgent need for breeding heat-tolerant rice cultivars.Rice plants show various morphological and physiological symptoms under HS.Precise analysis of the symptoms(phenotyping) is essential for the selection of elite germplasm and the identification of thermotolerance genes.In response to HS,rice plants trigger a cascade of events and activate complex transcriptional regulatory networks.Protein homeostasis under HS is especially important for rice thermotolerance,which is affected by protein quality control,effective elimination of toxic proteins,and translational regulation.Although some agronomic and genetic approaches for improving heat tolerance have been adopted in rice,the molecular mechanisms underlying rice response to HS are still elusive,and success in engineering rice thermotolerance in breeding has been limited.In this review,we summarize HS-caused symptoms in rice and progress in heat-stress sensing and signal cascade research,and propose approaches for improving rice thermotolerance in future.

Salt tolerance in rice:Physiological responses and molecular mechanisms

Crop yield loss due to soil salinization is an increasing threat to agriculture worldwide.Salt stress drastically affects the growth,development,and grain productivity of rice(Oryza sativa L.),and the improvement of rice tolerance to salt stress is a desirable approach for meeting increasing food demand.The main contributors to salt toxicity at a global scale are Na^(+)and Cl^(-)ions,which affect up to 50%of irrigated soils.Plant responses to salt stress occur at the organismic,cellular,and molecular levels and are pleiotropic,involving(1)maintenance of ionic homeostasis,(2)osmotic adjustment,(3)ROS scavenging,and(4)nutritional balance.In this review,we discuss recent research progress on these four aspects of plant physiological response,with particular attention to hormonal and gene expression regulation and salt tolerance signaling pathways in rice.The information summarized here will be useful for accelerating the breeding of salt-tolerant rice.

Exploration of rice yield potential: Decoding agronomic and physiological traits

Rice grain yield is determined by three major"visible"morphological traits:grain weight,grain number per panicle,and effective tiller number,which are affected by a series of"invisible"physiological factors including nutrient use efficiency and photosynthetic efficiency.In the past few decades,substantial progress has been made on elucidating the molecular mechanisms underlying grain yield formation,laying a solid foundation for improving rice yield by molecular breeding.This review outlines our current understanding of the three morphological yield-determining components and summarizes major progress in decoding physiological traits such as nutrient use efficiency and photosynthetic efficiency.It also discusses the integration of current knowledge about yield formation and crop improvement strategies including genome editing with conventional and molecular breeding.

The Arabidopsis Spontaneous Cell Death1 gene, encoding a ζ-carotene desaturase essential for carotenoid biosynthesis, is involved in chloroplast development, photoprotection and retrograde signalling

Carotenoids, a class of natural pigments found in all photosynthetic organisms, are involved in a variety of physiological processes, including coloration, photoprotection, biosynthesis of abscisic acid （ABA） and chloroplast biogenesis. Although carotenoid biosynthesis has been well studied biochemically, the genetic basis of the pathway is not well understood. Here, we report the characterization of two allelic Arabidopsis mutants, spontaneous cell death1-1 （spcl-1） and spc1-2. The weak allele spc1-1 mutant showed characteristics of bleached leaves, accumulation of superoxide and mosaic cell death. The strong mutant allele spc1-2 caused a complete arrest of plant growth and development shortly after germination, leading to a seedling-lethal phenotype. Genetic and molecular analyses indicated that SPC1 encodes a putative ζ-carotene desaturase （ZDS） in the carotenoid biosynthesis pathway. Analysis of carotenoids revealed that several major carotenoid compounds downstream of SPC 1/ZDS were substantially reduced in spc1-1, suggesting that SPC 1 is a functional ZDS. Consistent with the downregulated expression of CAO and PORB, the chlorophyll content was decreased in spc1-1 plants. In addition, expression of Lhcb1. 1, Lhcbl. 4 and RbcS was absent in spc1-2, suggesting the possible involvement of carotenoids in the plastid-to-nucleus retrograde signaling. The spc1-1 mutant also displays an ABA-deficient phenotype that can be partially rescued by the externally supplied phytohormone. These results suggest that SPC1/ZDS is essential for biosynthesis of carotenoids and plays a crucial role in plant growth and development.

岳西黑猪与北京黑猪和巴克夏猪的杂交效果分析

岳西黑猪为安徽省岳西县独有的地方猪品种。文章通过繁殖、胴体、肉质性能的测定和比较分析,综合评价北京黑猪和巴克夏猪与岳西黑猪的杂交效果,筛选可推广的杂交组合模式,为岳西黑猪的杂交利用奠定基础,旨在更好地促进岳西黑猪产业化开发。

The OsWRKY72-OsAAT30/OsGSTU26 module mediates reactive oxygen species scavenging to drive heterosis for salt tolerance in hybrid rice

Hybrid rice(Oryza sativa)generally outperforms its inbred parents in yield and stress tolerance,a phenomenon termed heterosis,but the underlying mechanism is not completely understood.Here,we combined transcriptome,proteome,physiological,and heterosis analyses to examine the salt response of super hybrid rice Chaoyou1000(CY1000).In addition to surpassing the mean values for its two parents(mid-parent heterosis),CY1000 exhibited a higher reactive oxygen species scavenging ability than both its parents(over-parent heterosis or heterobeltiosis).Nonadditive expression and allele-specific gene expression assays showed that the glutathione S-transferase gene OsGSTU26 and the amino acid transporter gene OsAAT30 may have major roles in heterosis for salt tolerance,acting in an overdominant fashion in CY1000.Furthermore,we identified OsWRKY72 as a common transcription factor that binds and regulates OsGSTU26 and OsAAT30.The salt-sensitive phenotypes were associated with the OsWRKY72^(paternal)genotype or the OsAAT30^(maternal)genotype in core rice germplasm varieties.OsWRKY72^(paternal)specifically repressed the expression of OsGSTU26 under salt stress,leading to salinity sensitivity,while OsWRKY72^(maternal)specifically repressed OsAAT30,resulting in salinity tolerance.These results suggest that the OsWRKY72-OsAAT30/OsGSTU26 module may play an important role in heterosis for salt tolerance in an overdominant fashion in CY1000 hybrid rice,providing valuable clues to elucidate the mechanism of heterosis for salinity tolerance in hybrid rice.

Strigolactone regulates nitrogen-phosphorus balance in rice

Phosphorus(P) is one of the essential elements for growth and development of crops.Modern agriculture depends heavily on the application of large amounts of fertilizers,including P fertilizers.Excessive application of P fertilizers causes severe environmental pollution.Additionally,phosphate(Pi) mining is a non-renewable resource(Raghothama,1999).

reduced internode 1 shortens internode length while increasing soybean yield

Achieving high crop yields to meet the increasing food demands of a growing population has long been an important breeding goal and will continue to be so in the future.The grain yield per unit area of wheat and rice gradually increased from 1961 to 2021,with maximum increases of 2.21-and 1.55-fold,respectively(Figure 1A;source:https://www.fao.org/home/en/).During this period,breeding and selection gave rise to the so-called Green Revolution(GR)dwarf/semi-dwarf elite varieties of rice and wheat with remarkably increased yields.

Genetic improvement toward nitrogen-use efficiency in rice: Lessons and perspectives

The indispensable role of nitrogen fertilizer in ensuring world food security together with the severe threats it poses to the ecosystem makes the usage of nitrogen fertilizer a major challenge for sustainable agriculture.Genetic improvement of crops with high nitrogen-use efficiency(NUE)is one of the most feasible solutions for tackling this challenge.In the last two decades,extensive efforts toward dissecting the variation of NUE-related traits and the underlying genetic basis in different germplasms have been made,and a series of achievements have been obtained in crops,especially in rice.Here,we summarize the approaches used for genetic dissection of NUE and the functions of the causal genes in modulating NUE as well as their applications in NUE improvement in rice.Strategies for exploring the variants controlling NUE and breeding future crops with“less-input-more-output”for sustainable agriculture are also proposed.

The U-box ubiquitin ligase TUD1 promotes brassinosteroid-induced GSK2 degradation in rice

Brassinosteroids(BRs)are a class of steroid hormones with great potential for use in crop improvement.De-repression is usually one of the key events in hormone signaling.However,how the stability of GSK2,the central negative regulator of BR signaling in rice(Oryza sativa),is regulated by BRs remains elusive.Here,we identify the U-box ubiquitin ligase TUD1 as a GSK2-interacting protein by yeast two-hybrid screening.We show that TUD1 is able to directly interact with GSK2 and ubiquitinate the protein.Phenotypes of the tud1 mutant are highly similar to those of plants with constitutively activated GSK2.Consistent with this finding,GSK2 protein accumulates in the tud1 mutant compared with the wild type.In addition,inhibition of BR synthesis promotes GSK2 accumulation and suppresses TUD1 stability.By contrast,BRs can induce GSK2 degradation but promote TUD1 accumulation.Furthermore,the GSK2 degradation process is largely impaired in tud1 in response to BR.In conclusion,our study demonstrates the role of TUD1 in BR-induced GSK2 degradation,thereby advancing our understanding of a critical step in the BR signaling pathway of rice.

An activated form of NB-ARC protein RLS1 functions with cysteine-rich receptor-like protein RMC to trigger cell death in rice

A key event that follows pathogen recognition by a resistance(R)protein containing an NB-ARC(nucleotide-binding adaptor shared by Apaf-1,R proteins,and Ced-4)domain is hypersensitive response(HR)-type cell death accompanied by accumulation of reactive oxygen species and nitric oxide.However,the integral mechanisms that underlie this process remain relatively opaque.Here,we show that a gain-offunction mutation in the NB-ARC protein RLS1(Rapid Leaf Senescence 1)triggers high-light-dependent HR-like cell death in rice.The RLS1-mediated defense response is largely independent of salicylic acid accumulation,NPR1(Nonexpressor of Pathogenesis-Related Gene 1)activity,and RAR1(Required for Mla12 Resistance 1)function.A screen for suppressors of RLS1 activation identified RMC(Root Meander Curling)as essential for the RLS1-activated defense response.RMC encodes a cysteine-rich receptor-like secreted protein(CRRSP)and functions as an RLS1-binding partner.Intriguingly,their co-expression resulted in a change in the pattern of subcellular localization and was sufficient to trigger cell death accompanied by a decrease in the activity of the antioxidant enzyme APX1.Collectively,our findings reveal an NBARC-CRRSP signaling module that modulates oxidative state,the cell death process,and associated immunity responses in rice.

Two awn-development-related peptides,GAD1 and OsEPFL2,promote seed dispersal and germination in rice

In nature,seed dispersal and germination are crucial for plant survival and propagation.Elaborate mechanisms have evolved that enhance the success of these events(Peart,1981;Bewley,1997),and the widespread distribution of grass species has been associated with the evolution of these traits.Many of these mechanisms are associated with characteristics that are intrinsic to the seed,such as awn development,seed shattering,and germination(Ntakirutimana et al.,2019).Awns and/or other seed appendages often help mature seeds to disperse widely and germinate under various challenging environments(Elbaum et al.,2007).

Nitrate confers rice adaptation to high ammonium by suppressing its uptake but promoting its assimilation

Dear Editor,earEaltor,Nitrogen(N)is the most important macronutrient driving plant growth and development.For higher plants,inorganic N including nitrate(NO_(3)^(-))and ammonium(NH_(4)^(+))are predominant N sources(Hu et al.,2023).Nitrate needs to be firstly reduced into ammonium to implement its assimilation,thus requiring a higher energy consumption than ammonium,making ammonium more cost effective for plants.However,ammonium usually causes severe growth retardation of plants under high concentration,which is known as ammonium toxicity.The concentrations of nitrate and ammonium greatly vary in different soil environments.Nitrate is the major inorganic N form in dry land,while ammonium accounts for thehighest proportion of inorganic N in the paddy field,where nitrification is suppressed(Haynes and Goh,1978).Although nitrogen is generally one of the most important contributing factors for yield increase,irrational fertilization strategies can cause negative effects.

Interplay between ethylene and nitrogen nutrition:How ethylene orchestrates nitrogen responses in plants

The stress hormone ethylene plays a key role in plant adaptation to adverse environmental conditions.Nitrogen(N)is the most quantitatively required mineral nutrient for plants,and its availability is a major determinant for crop production.Changes in N availability or N forms can alter ethylene biosynthesis and/or signaling.Ethylene serves as an important cellular signal to mediate root system architecture adaptation,N uptake and translocation,ammonium toxicity,anthocyanin accumulation,and premature senescence,thereby adapting plant growth and development to external N status.Here,we review the ethylenemediated morphological and physiological responses and highlight how ethylene transduces the N signals to the adaptive responses.We specifically discuss the N-ethylene relations in rice,an important cereal crop in which ethylene is essential for its hypoxia survival.

Crosstalk between brassinosteroid signaling and variable nutrient environments

Brassinosteroid(BR)represents a group of steroid hormones that regulate plant growth and development as well as environmental adaptation.The fluctuation of external nutrient elements is a situation that plants frequently face in the natural environment,in which nitrogen(N)and phosphorus(P)are two of the most critical nutrients restraint of the early growth of plants.As the macronutrients,N and P are highly required by plants,but their availability or solubility in the soil is relatively low.Since iron(Fe)and P always modulate each other’s content and function in plants mutually antagonistically,the regulatory mechanisms of Fe and P are inextricably linked.Recently,BR has emerged as a critical regulator in nutrient acquisition and phenotypic plasticity in response to the variable nutrient levels in Arabidopsis and rice.Here,we review the current understanding of the crosstalk between BR and the three major nutrients(N,P,and Fe),highlighting how nutrient signaling regulates BR synthesis and signaling to accommodate plant growth and development in Arabidopsis and rice.

Coordinating gibberellin and brassinosteroid signaling beyond Green Revolution

The Green Revolution,which took place in the 1960s,was instrumental in increasing grain yields and mitigating the world’s food crisis.Breeding semi-dwarfing crops was a critical activity that significantly improved lodging resistance,field management,and harvesting convenience.Subsequent molecular genetic studies revealed that the semi-dwarfing genes used in rice and wheat,two major staple crops,are related to the plant hormone gibberellin(GA).In rice,SD1 encodes a defective GA synthetic enzyme GA20ox-2,while in wheat,Rht-1(Rht-B1b or Rht-D1b)encodes the gain-of-function form of the GA signaling inhibitors known as DELLA proteins(Peng et al.,1999;Sasaki et al.,2002).However,defects in either GA synthesis or signaling can decrease nitrogen use efficiency(NUE)and potentially lead to inferior grain development.Ultimately,the success of the Green Revolution relies heavily on the massive input of nitrogen fertilizer,which causes severe environmental issues.

OsDREB1C,an integrator for photosynthesis,nitrogen use efficiency,and early flowering

Food security is a major challenge for people around the world.Despite the continuous growth of food supply in the past sixty years,more than 800 million people in the world are still suffering from hunger due to climate change and geographical conflicts(Food and Agriculture Organization of the United Nations,FAO,2020,https://www.fao.org/hunger/en/).