Grain weight is a major determinant of crop grain yield and is controlled by naturally occurring quantitative trait loci （QTLs）. We earlier identified a major QTL that controls rice grain width and weight, GW5, whic...Grain weight is a major determinant of crop grain yield and is controlled by naturally occurring quantitative trait loci （QTLs）. We earlier identified a major QTL that controls rice grain width and weight, GW5, which was mapped to a recombination hotspot on rice chromosome 5. To gain a better understanding of how GW5 controls rice grain width, we conducted fine mapping of this locus and uncovered a 1 212-bp deletion associated with the increased grain width in the rice cultivar Asominori, in comparison with the slender grain rice IR24. In addition, genotyping analyses of 46 rice cultivars revealed that this deletion is highly correlated with the grain-width phenotype, suggesting that the GW5 deletion might have been selected during rice domestication. GW5 encodes a novel nuclear protein of 144 amino acids that is localized to the nucleus. Furthermore, we show that GW5 physically interacts with polyubiquitin in a yeast two-hybrid assay. Together, our results suggest that GW5 represents a major QTL underlying rice width and weight, and that it likely acts in the ubiquitin-proteasome pathway to regulate cell division during seed development. This study provides novel insights into the molecular mechanisms controlling rice grain development and suggests that GW5 could serve as a potential tool for high-yield breeding of crops.展开更多
QTL Ici Mapping is freely available public software capable of building high-density linkage maps and mapping quantitative trait loci(QTL) in biparental populations. Eight functionalities are integrated in this softwa...QTL Ici Mapping is freely available public software capable of building high-density linkage maps and mapping quantitative trait loci(QTL) in biparental populations. Eight functionalities are integrated in this software package:(1) BIN: binning of redundant markers;(2) MAP: construction of linkage maps in biparental populations;(3) CMP: consensus map construction from multiple linkage maps sharing common markers;(4) SDL: mapping of segregation distortion loci;(5) BIP: mapping of additive, dominant, and digenic epistasis genes;(6) MET: QTL-by-environment interaction analysis;(7) CSL: mapping of additive and digenic epistasis genes with chromosome segment substitution lines; and(8) NAM: QTL mapping in NAM populations. Input files can be arranged in plain text, MS Excel 2003, or MS Excel 2007 formats. Output files have the same prefix name as the input but with different extensions. As examples, there are two output files in BIN, one for summarizing the identified bin groups and deleted markers in each bin, and the other for using the MAP functionality. Eight output files are generated by MAP, including summary of the completed linkage maps, Mendelian ratio test of individual markers, estimates of recombination frequencies, LOD scores, and genetic distances, and the input files for using the BIP, SDL,and MET functionalities. More than 30 output files are generated by BIP, including results at all scanning positions, identified QTL, permutation tests, and detection powers for up to six mapping methods. Three supplementary tools have also been developed to display completed genetic linkage maps, to estimate recombination frequency between two loci,and to perform analysis of variance for multi-environmental trials.展开更多
Seed plants have evolved to maintain the dormancy of freshly matured seeds until the appropriate time for germination. Seed dormancy and germination are distinct physiological processes, and the transition from dorman...Seed plants have evolved to maintain the dormancy of freshly matured seeds until the appropriate time for germination. Seed dormancy and germination are distinct physiological processes, and the transition from dormancy to germination is not only a critical developmental step in the life cycle of plants but is also impor- tant for agricultural production. These processes are precisely regulated by diverse endogenous hormones and environmental cues. Although ABA （abscisic acid） and GAs （gibberellins） are known to be the primary phytohormones that antagonistically regulate seed dormancy, recent findings demonstrate that another phytohormone, auxin, is also critical for inducing and maintaining seed dormancy, and therefore might act as a key protector of seed dormancy. In this review, we summarize our current understanding of the sophisticated molecular networks involving the critical roles of phytohormones in regulating seed dormancy and germination, in which AP2-domain-containing transcription factors play key roles. We also discuss the interactions （crosstalk） of diverse hormonal signals in seed dormancy and germination, focusing on the ABA/GA balance that constitutes the central node.展开更多
Today, about 30% of world nitrogen (N) fertilizer is consumed by China. Rice crops in China consume about 37% of the total N fertilizer used for rice production in the world. Average rate of N application for rice pro...Today, about 30% of world nitrogen (N) fertilizer is consumed by China. Rice crops in China consume about 37% of the total N fertilizer used for rice production in the world. Average rate of N application for rice production in China is high and fertilizer-N use efficiency is low compared with other major rice growing countries. Research progresses have been made internationally and domestically on the application method, fertilizer-N sources, computer-based decision support systems, and real-time N management in order展开更多
Plants have acquired sophisticated stress response systems to adapt to changing environments. It is important to understand plants＇ stress response mechanisms in the effort to improve crop productivity under stressfu...Plants have acquired sophisticated stress response systems to adapt to changing environments. It is important to understand plants＇ stress response mechanisms in the effort to improve crop productivity under stressful conditions. The AP2/ERF transcription factors are known to regulate diverse processes of plant development and stress responses. In this study, the molecular characteristics and biological functions of AP2/ERFs in a variety of plant species were analyzed. AP2/ERFs, especially those in DREB and ERF subfamilies, are ideal candidates for crop improvement because their overexpression enhances tolerances to drought, salt, freezing, as well as resistances to multiple diseases in the transgenic plants. The comprehensive analysis of physiological functions is useful in elucidating the biological roles of AP2/ERF family genes in gene interaction, pathway regulation, and defense response under stress environments, which should provide new opportunities for the crop tolerance engineering.展开更多
CRISPR/Cas9 （Clustered Regularly Interspaced Short Palin- dromic Repeats/CRISPR-associated Cas9 endonuclease）- mediated genome editing has revolutionized biological research and crop improvement because of its speci...CRISPR/Cas9 （Clustered Regularly Interspaced Short Palin- dromic Repeats/CRISPR-associated Cas9 endonuclease）- mediated genome editing has revolutionized biological research and crop improvement because of its specificity, simplicity, and versatility （reviewed in Komor et al., 2016a）.展开更多
The disinfection of drinking water is an important public health service that generates high quality, safe and palatable tap water. The disinfection of drinking water to reduce waterborne disease was an outstanding pu...The disinfection of drinking water is an important public health service that generates high quality, safe and palatable tap water. The disinfection of drinking water to reduce waterborne disease was an outstanding public health achievement of the 20 th century.An unintended consequence is the reaction of disinfectants with natural organic matter,anthropogenic contaminants and bromide/iodide to form disinfection by-products（DBPs）.A large number of DBPs are cytotoxic, neurotoxic, mutagenic, genotoxic, carcinogenic and teratogenic. Epidemiological studies demonstrated low but significant associations between disinfected drinking water and adverse health effects. The distribution of DBPs in disinfected waters has been well defined by advances in high precision analytical chemistry. Progress in the analytical biology and toxicology of DBPs has been forthcoming.The objective of this review was to provide a detailed presentation of the methodology for the quantitative, comparative analyses on the induction of cytotoxicity and genotoxicity of103 DBPs using an identical analytical biological platform and endpoints. A single Chinese hamster ovary cell line was employed in the assays. The data presented are derived from papers published in the literature as well as additional new data and represent the largest direct quantitative comparison on the toxic potency of both regulated and emerging DBPs.These data may form the foundation of novel research to define the major forcing agents of DBP-mediated toxicity in disinfected water and may play an important role in achieving the goal of making safe drinking water better.展开更多
Since the official release of the stand-alone bioinformatics toolkit TBtools in 2020,its superior functionality in data analysis has been demonstrated by its widespread adoption by many thousands of users and referenc...Since the official release of the stand-alone bioinformatics toolkit TBtools in 2020,its superior functionality in data analysis has been demonstrated by its widespread adoption by many thousands of users and references in more than 5000 academic articles.Now,TBtools is a commonly used tool in biological laboratories.Over the past 3 years,thanks to invaluable feedback and suggestions from numerous users,we have optimized and expanded the functionality of the toolkit,leading to the development of an upgraded version—TBtools-II.In this upgrade,we have incorporated over 100 new features,such as those for comparative genomics analysis,phylogenetic analysis,and data visualization.Meanwhile,to better meet the increasing needs of personalized data analysis,we have launched the plugin mode,which enables users to develop their own plugins and manage their selection,installation,and removal according to individual needs.To date,the plugin store has amassed over 50 plugins,with more than half of them being independently developed and contributed by TBtools users.These plugins offer a range of data analysis options including co-expression network analysis,single-cell data analysis,and bulked segregant analysis sequencing data analysis.Overall,TBtools is now transforming from a stand-alone software to a comprehensive bioinformatics platform of a vibrant and cooperative community in which users are also developers and contributors.By promoting the theme“one for all,all for one”,we believe that TBtools-II will greatly benefit more biological researchers in this big-data era.展开更多
The majority of plant disease resistance （R） genes encode proteins that share common structural features. However, the transcription activator-like effector （TALE）-associated executor type R genes show no consider...The majority of plant disease resistance （R） genes encode proteins that share common structural features. However, the transcription activator-like effector （TALE）-associated executor type R genes show no considerable sequence homology to any known R genes. We adopted a map-based cloning approach and TALE-based technology to isolate and characterize Xa23, a new executor R gene derived from wild rice （Oryza rufipogon） that confers an extremely broad spectrum of resistance to bacterial blight caused by Xanthomonas oryzae pv. oryzae （Xoo）. Xa23 encodes a 113 amino acid protein that shares 50% identity with the known executor R protein XA10. The predicted transmembrane helices in XA23 also overlap with those of XA10. Unlike XalO, however, Xa23 transcription is specifically activated by AvrXa23, a TALE present in all examined Xoo field isolates. Moreover, the susceptible xa23 allele has an identical open reading frame of Xa23 but differs in promoter region by lacking the TALE binding element （EBE） for AvrXa23. XA23 can trigger a strong hypersensitive response in rice, tobacco, and tomato. Our results provide the first evidence that plant genomes have an executor R gene family of which members execute their function and spectrum of disease resistance by recognizing the cognate TALEs in the pathogen.展开更多
Grain size and shape are important determinants of grain weight and yield in rice. Here, we report a new major quantitative trait locus （QTL）, qTGW3, that controls grain size and weight in rice. This locus, qTGW3, e...Grain size and shape are important determinants of grain weight and yield in rice. Here, we report a new major quantitative trait locus （QTL）, qTGW3, that controls grain size and weight in rice. This locus, qTGW3, encodes OsSK41 （also known as OsGSK5）, a member of the GLYCOGEN SYNTHASE KINASE 3/SHAGGY-like family. Rice near-isogenic lines carrying the loss-of-function allele of OsSK41 have increased grain length and weight. We demonstrate that OsSK41 interacts with and phosphorylates AUXIN RESPONSE FACTOR 4 （OsARF4）. Co-expression of OsSK41 with OsARF4 increases the accumulation of OsARF4 in rice protoplasts. Loss of function of OsARF4 results in larger rice grains. RNA-sequencing analysis suggests that OsARF4 and OsSK41 repress the expression of a common set of downstream genes, including some auxin-responsive genes, during rice grain development. The loss-of-function form of OsSK41 at qTGW3 represents a rare allele that has not been extensively utilized in rice breeding. Suppression of OsSK41 function by either targeted gene editing or QTL pyramiding enhances rice grain size and weight. Thus, our study reveals the important role of OsSK41 in rice grain development and provides new candidate genes for genetic improvement of grain yield in rice and perhaps in other cereal crops.展开更多
Achieving both high yield and high nitrogen use efficiency （NUE） simultaneously has become a major challenge with increased global demand for food, depletion of natural resources, and deterioration of environment. A...Achieving both high yield and high nitrogen use efficiency （NUE） simultaneously has become a major challenge with increased global demand for food, depletion of natural resources, and deterioration of environment. As the greatest consumers of N fertilizer in the world, Chinese farmers have overused N, and there has been poor synchrony between crop N demand and N supply because of limited understanding of the N uptake-yield relationship. To address this problem, this study evaluated the total and dynamic N requirement for different yield ranges of two major crops （maize and wheat）, and suggested improvements to N management strategies. Whole-plant N aboveground uptake requirement per grain yield （Nreq） initially deceased with grain yield improvement and then stagnated, and yet most farmers still believed that more fertilizer and higher grain yield were synonymous. When maize yield increased from 〈 7.5 to 〉 12.0 Mg ha-I, Nreq decreased from 19.8 to 17.0 kg Mg-1 grain. For wheat, it decreased from 27.1 kg Mg-1 grain for grain yield 〈 4.5 Mg ha-1 to 22.7 kg Mg-1 grain for yield 〉 9.0 Mg ha-1. Meanwhile, the percentage of dry matter and N accumulation in the middle-late growing season increased significantly with grain yield, which indicated that N fertilization should be concentrated in the middle-late stage to match crop demand while farmers often applied the majority of N fertilizer either before sowing or during early growth stages. We accordingly developed an integrated soil-crop system management strategy that simultaneously increases both grain yield and NUE.展开更多
Jasmonic acid （JA） is an important phytohormone that regulates plant defense responses against herbivore attack, pathogen infection and mechanical wounding. In this report, we provided biochemical and genetic eviden...Jasmonic acid （JA） is an important phytohormone that regulates plant defense responses against herbivore attack, pathogen infection and mechanical wounding. In this report, we provided biochemical and genetic evidence to show that the Arabidopsis thaliana NAC family proteins ANAC019 and ANAC055 might function as transcription activators to regulate JA-induced expression of defense genes. The role of the two NAC genes in JA signaling was examined with the anacO19 anac055 double mutant and with transgenic plants overexpressing ANACO19 or ANAC055. The anacO19 anac055 double mutant plants showed attenuated JA-induced VEGETATIVE STORAGE PROTEIN1 （VSP1） and LIPOXYGENASE2 （LOX2） expression, whereas transgenic plants overexpressing the two NAC genes showed enhanced JA-induced VSP1 and LOX2 expression. That the JA-induced expression of the two NAC genes depends on the function of COIl and AtMYC2, together with the finding that overexpression of ANACO19 partially rescued the JA-related phenotype of the atmyc2-2 mutant, has led us to a hypothesis that the two NAC proteins act downstream of AtMYC2 to regulate JA-signaled defense responses. Further evidence to substantiate this idea comes from the observation that the response of the anacO19 anac055 double mutant to a necrotrophic fungus showed high similarity to that of the atmyc2-2 mutant.展开更多
There is a rapidly rising trend in the development and application of molecular marker assays for gene map- ping and discovery in field crops and trees. Thus far, more than 50 SNP arrays and 15 different types of geno...There is a rapidly rising trend in the development and application of molecular marker assays for gene map- ping and discovery in field crops and trees. Thus far, more than 50 SNP arrays and 15 different types of genotyping-by-sequencing （GBS） platforms have been developed in over 25 crop species and perennial trees. However, much less effort has been made on developing ultra-high-throughput and cost-effective genotyping platforms for applied breeding programs. In this review, we discuss the scientific bottlenecks in existing SNP arrays and GBS technologies and the strategies to develop targeted platforms for crop mo- lecular breeding. We propose that future practical breeding platforms should adopt automated genotyping technologies, either array or sequencing based, target functional polymorphisms underpinning economic traits, and provide desirable prediction accuracy for quantitative traits, with universal applications under wide genetic backgrounds in crops. The development of such platforms faces serious challenges at both the technological level due to cost ineffectiveness, and the knowledge level due to large genotype- phenotype gaps in crop plants. It is expected that such genotyping platforms will be achieved in the next ten years in major crops in consideration of （a） rapid development in gene discovery of important traits, （b） deepened understanding of quantitative traits through new analytical models and population designs, （c） integration of multi-layer -omics data leading to identification of genes and pathways responsible for important breeding traits, and （d） improvement in cost effectiveness of large-scale genotyping. Crop breeding chips and genotyping platforms will provide unprecedented opportunities to accelerate the development of cultivars with desired yield potential, quality, and enhanced adaptation to mitigate the effects of climate change.展开更多
Heading date and photoperiod sensitivity are fundamental traits that determine rice adaptation to a wide range of geographic environments. By quantitative trait locus （QTL） mapping and candidate gene analysis using ...Heading date and photoperiod sensitivity are fundamental traits that determine rice adaptation to a wide range of geographic environments. By quantitative trait locus （QTL） mapping and candidate gene analysis using whole- genome re-sequencing, we found that Oryza sativa Pseudo-Response Regulator37 （OsPRR37; hereafter PRR37） is respon- sible for the Early heading7-2 （EH7-2）/Heading date2 （Hd2） QTL which was identified from a cross of late-heading rice ＇Milyang23 （M23）＇ and early-heading rice ＇H143＇. H143 contains a missense mutation of an invariantly conserved amino acid in the CCT （CONSTANS, CO-like, and TOC1） domain of PRR37 protein. In the world rice collection, different types of nonfunctional PRR37 alleles were found in many European and Asian rice cultivars. Notably, the japonica varieties harboring nonfunctional alleles of both Ghd7/Hd4 and PRR37/Hd2 flower extremely early under natural long-day condi- tions, and are adapted to the northernmost regions of rice cultivation, up to 53~ N latitude. Genetic analysis revealed that the effects of PRR37 and Ghd7 alleles on heading date are additive, and PRR37 down-regulates Hd3a expression to suppress flowering under long-day conditions. Our results demonstrate that natural variations in PRR37/Hd2 and GhdT/ Hd4 have contributed to the expansion of rice cultivation to temperate and cooler regions.展开更多
Intercropping is one of the most vital practice to improve land utilization rate in China that has limited arable land resource. However, the traditional intercropping systems have many disadvantages including illogic...Intercropping is one of the most vital practice to improve land utilization rate in China that has limited arable land resource. However, the traditional intercropping systems have many disadvantages including illogical field lay-out of crops, low economic value, and labor deficiency, which cannot balance the crop production and agricultural sustainability. In view of this, we developed a novel soybean strip intercropping model using maize as the partner, the regular maize-soybean strip intercropping mainly popularized in northern China and maize-soybean relay-strip intercropping principally extended in southwestern China. Compared to the traditional maize-soybean intercropping systems, the main innovation of field lay-out style in our present intercropping systems is that the distance of two adjacent maize rows are shrunk as a narrow strip, and a strip called wide strip between two adjacent narrow strips is expanded reserving for the growth of two or three rows of soybean plants. The distance between outer rows of maize and soybean strips are expanded enough for light use efficiency improvement and tractors working in the soybean strips. Importantly, optimal cultivar screening and increase of plant density achieved a high yield of both the two crops in the intercropping systems and increased land equivalent ratio as high as 2.2. Annually alternative rotation of the adjacent maize-and soybean-strips increased the grain yield of next seasonal maize, improved the absorption of nitrogen, phosphorus, and potasium of maize, while prevented the continuous cropping obstacles. Extra soybean production was obtained without affecting maize yield in our strip intercropping systems, which balanced the high crop production and agricultural sustainability.展开更多
Recently developed CRISPR-mediated base editors,which enable the generation of num erous nucleotide changes in target genomic regions,have been widely adopted for gene correction and generation of crop germ plasms con...Recently developed CRISPR-mediated base editors,which enable the generation of num erous nucleotide changes in target genomic regions,have been widely adopted for gene correction and generation of crop germ plasms containing im portant gain-of-function genetic variations.How ever,to engineer target genes with unknown functional SNPs remains challenging.To address this issue,we present here abase-e diting-mediated gene evolution(BEMGE)m ethod,employing both Cas9n-based cytosine and adenine base editors as well as a single-guide RNA(sgRNA)library tiling the full-length coding region,for developing novel rice germ plasm swith mutations in any endogenous gene.To this end,OsALS1 was artificially evolved in rice cells using BEMGE through both Agrobacterium-mediated and particle-bom bardment-mediated transform ation.Four different types of amino acid substitutions in the evolved OsALS1,derived from two sites that have never been targeted by natural or human selection during rice dom estication,were identified,conferring varying levels of tolerance to the herbicide bispyribac-sodium.Furtherm ore,the P171F substitution identified in a strong OsALS1 allele was quickly introduced into the commercial rice cultivar Nangeng 46 through precise base editing w ith the corresponding base editor and sgRNA.Collectively,these data indicate great potential of BEMGE in creating important genetic variants of target genes for crop improvement.展开更多
Increasing plant density is an effective way to enhance maize yield, but often increases lodging rate and severity, significantly elevating the risk and cost of maize production. Therefore, lodging is a major factor r...Increasing plant density is an effective way to enhance maize yield, but often increases lodging rate and severity, significantly elevating the risk and cost of maize production. Therefore, lodging is a major factor restricting future increases in maize yield through high-density planting. This paper reviewed previous research on the relationships between maize lodging rate and plant morphology, mechanical strength of stalks, anatomical and biochemical characteristics of stalks, root characteristics, damage from pests and diseases, environmental factors, and genomic characteristics. The effects of planting density on these factors and explored possible ways to improve lodging resistance were also analyzed in this paper. The results provide a basis for future research on increasing maize lodging resistance under high-density planting conditions and can be used to develop maize cultivation practices and lodging-resistant maize cultivars.展开更多
A thorough understanding of the genetic basis of rice grain traits is critical for the improvement of rice （Oryza sativa L.） varieties. In this study, we generated an F2 population by crossing the large-grain japoni...A thorough understanding of the genetic basis of rice grain traits is critical for the improvement of rice （Oryza sativa L.） varieties. In this study, we generated an F2 population by crossing the large-grain japonica cultivar CW23 with Peiai 64 （PA64）, an elite indica small-grain cultivar. Using QTL analysis, 17 QTLs for five grain traits were detected on four different chromosomes. Eight of the QTLs were newly-identified in this study. In particular, qGL3-1, a newly-identified grain length QTL with the highest LOD value and largest phenotypic variation, was fine-mapped to the 17 kb region of chromosome 3. A serine/threonine protein phosphatase gene encoding a repeat domain containing two Kelch motifs was identified as the unique candidate gene corresponding to this QTL. A comparison of PA64 and CW23 sequences revealed a single nucleotide substitution （C→A） at position 1092 in exon 10, resulting in replacement of Asp （D） in PA64 with Glu （E） in CW23 for the 364th amino acid. This variation is located at the D position of the conserved sequence motif AVLDT of the Kelch repeat. Genetic analysis of a near-isogenic line （NIL） for qGL3-1 revealed that the allele qGL3-1 from CW23 has an additive or partly dominant effect, and is suitable for use in molecular marker-assisted selection.展开更多
A four-year field experiment was conducted to investigate the effect of subsoiling depth on root morphology, nitrogen(N), phosphorus(P), and potassium(K) uptake, and grain yield of spring maize. The results indicated ...A four-year field experiment was conducted to investigate the effect of subsoiling depth on root morphology, nitrogen(N), phosphorus(P), and potassium(K) uptake, and grain yield of spring maize. The results indicated that subsoil tillage promoted root development,increased nutrient accumulation, and increased yield. Compared with conventional soil management(CK), root length, root surface area, and root dry weight at 0–80 cm soil depth under subsoil tillage to 30 cm(T1) and subsoil tillage to 50 cm(T2) were significantly increased, especially the proportions of roots in deeper soil. Root length, surface area, and dry weight differed significantly among three treatments in the order of T2 > T1 > CK at the12-leaf and early filling stages. The range of variation of root diameter in different soil layers in T2 treatment was the smallest, suggesting that roots were more likely to grow downwards with deeper subsoil tillage in soil. The accumulation of N, P, and K in subsoil tillage treatment was significantly increased, but the proportions of kernel and straw were different. In a comparison of T1 with T2, the grain accumulated more N and P, while K accumulation in kernel and straw varied in different years. Grain yield and biomass were increased by 12.8% and 14.6% on average in subsoil tillage treatments compared to conventional soil treatment. Although no significant differences between different subsoil tillage depths were observed for nutrient accumulation and grain yield, lodging resistance of plants was significantly improved in subsoil tillage to 50 cm, a characteristic that favors a high and stable yield under extreme environments.展开更多
文摘Grain weight is a major determinant of crop grain yield and is controlled by naturally occurring quantitative trait loci （QTLs）. We earlier identified a major QTL that controls rice grain width and weight, GW5, which was mapped to a recombination hotspot on rice chromosome 5. To gain a better understanding of how GW5 controls rice grain width, we conducted fine mapping of this locus and uncovered a 1 212-bp deletion associated with the increased grain width in the rice cultivar Asominori, in comparison with the slender grain rice IR24. In addition, genotyping analyses of 46 rice cultivars revealed that this deletion is highly correlated with the grain-width phenotype, suggesting that the GW5 deletion might have been selected during rice domestication. GW5 encodes a novel nuclear protein of 144 amino acids that is localized to the nucleus. Furthermore, we show that GW5 physically interacts with polyubiquitin in a yeast two-hybrid assay. Together, our results suggest that GW5 represents a major QTL underlying rice width and weight, and that it likely acts in the ubiquitin-proteasome pathway to regulate cell division during seed development. This study provides novel insights into the molecular mechanisms controlling rice grain development and suggests that GW5 could serve as a potential tool for high-yield breeding of crops.
基金supported by the Natural Science Foundation of China (31271798)the Generation Challenge Program (GCP)HarvestP lus Challenge Program of CGIAR
文摘QTL Ici Mapping is freely available public software capable of building high-density linkage maps and mapping quantitative trait loci(QTL) in biparental populations. Eight functionalities are integrated in this software package:(1) BIN: binning of redundant markers;(2) MAP: construction of linkage maps in biparental populations;(3) CMP: consensus map construction from multiple linkage maps sharing common markers;(4) SDL: mapping of segregation distortion loci;(5) BIP: mapping of additive, dominant, and digenic epistasis genes;(6) MET: QTL-by-environment interaction analysis;(7) CSL: mapping of additive and digenic epistasis genes with chromosome segment substitution lines; and(8) NAM: QTL mapping in NAM populations. Input files can be arranged in plain text, MS Excel 2003, or MS Excel 2007 formats. Output files have the same prefix name as the input but with different extensions. As examples, there are two output files in BIN, one for summarizing the identified bin groups and deleted markers in each bin, and the other for using the MAP functionality. Eight output files are generated by MAP, including summary of the completed linkage maps, Mendelian ratio test of individual markers, estimates of recombination frequencies, LOD scores, and genetic distances, and the input files for using the BIP, SDL,and MET functionalities. More than 30 output files are generated by BIP, including results at all scanning positions, identified QTL, permutation tests, and detection powers for up to six mapping methods. Three supplementary tools have also been developed to display completed genetic linkage maps, to estimate recombination frequency between two loci,and to perform analysis of variance for multi-environmental trials.
文摘Seed plants have evolved to maintain the dormancy of freshly matured seeds until the appropriate time for germination. Seed dormancy and germination are distinct physiological processes, and the transition from dormancy to germination is not only a critical developmental step in the life cycle of plants but is also impor- tant for agricultural production. These processes are precisely regulated by diverse endogenous hormones and environmental cues. Although ABA （abscisic acid） and GAs （gibberellins） are known to be the primary phytohormones that antagonistically regulate seed dormancy, recent findings demonstrate that another phytohormone, auxin, is also critical for inducing and maintaining seed dormancy, and therefore might act as a key protector of seed dormancy. In this review, we summarize our current understanding of the sophisticated molecular networks involving the critical roles of phytohormones in regulating seed dormancy and germination, in which AP2-domain-containing transcription factors play key roles. We also discuss the interactions （crosstalk） of diverse hormonal signals in seed dormancy and germination, focusing on the ABA/GA balance that constitutes the central node.
文摘Today, about 30% of world nitrogen (N) fertilizer is consumed by China. Rice crops in China consume about 37% of the total N fertilizer used for rice production in the world. Average rate of N application for rice production in China is high and fertilizer-N use efficiency is low compared with other major rice growing countries. Research progresses have been made internationally and domestically on the application method, fertilizer-N sources, computer-based decision support systems, and real-time N management in order
基金supported by the National Transgenic Key Project of MOA(201 1ZX08002-002 and 2009ZX08009-083B)
文摘Plants have acquired sophisticated stress response systems to adapt to changing environments. It is important to understand plants＇ stress response mechanisms in the effort to improve crop productivity under stressful conditions. The AP2/ERF transcription factors are known to regulate diverse processes of plant development and stress responses. In this study, the molecular characteristics and biological functions of AP2/ERFs in a variety of plant species were analyzed. AP2/ERFs, especially those in DREB and ERF subfamilies, are ideal candidates for crop improvement because their overexpression enhances tolerances to drought, salt, freezing, as well as resistances to multiple diseases in the transgenic plants. The comprehensive analysis of physiological functions is useful in elucidating the biological roles of AP2/ERF family genes in gene interaction, pathway regulation, and defense response under stress environments, which should provide new opportunities for the crop tolerance engineering.
文摘CRISPR/Cas9 （Clustered Regularly Interspaced Short Palin- dromic Repeats/CRISPR-associated Cas9 endonuclease）- mediated genome editing has revolutionized biological research and crop improvement because of its specificity, simplicity, and versatility （reviewed in Komor et al., 2016a）.
文摘The disinfection of drinking water is an important public health service that generates high quality, safe and palatable tap water. The disinfection of drinking water to reduce waterborne disease was an outstanding public health achievement of the 20 th century.An unintended consequence is the reaction of disinfectants with natural organic matter,anthropogenic contaminants and bromide/iodide to form disinfection by-products（DBPs）.A large number of DBPs are cytotoxic, neurotoxic, mutagenic, genotoxic, carcinogenic and teratogenic. Epidemiological studies demonstrated low but significant associations between disinfected drinking water and adverse health effects. The distribution of DBPs in disinfected waters has been well defined by advances in high precision analytical chemistry. Progress in the analytical biology and toxicology of DBPs has been forthcoming.The objective of this review was to provide a detailed presentation of the methodology for the quantitative, comparative analyses on the induction of cytotoxicity and genotoxicity of103 DBPs using an identical analytical biological platform and endpoints. A single Chinese hamster ovary cell line was employed in the assays. The data presented are derived from papers published in the literature as well as additional new data and represent the largest direct quantitative comparison on the toxic potency of both regulated and emerging DBPs.These data may form the foundation of novel research to define the major forcing agents of DBP-mediated toxicity in disinfected water and may play an important role in achieving the goal of making safe drinking water better.
基金supported by the Key Area Research and Development Program of Guangdong Province(2022B0202070003,and 2021B0707010004)supported by the National Science Foundation of China(#32072547,and#32102320)+5 种基金the National Key Research and Development Program(2021YFF1000101,and 2019YFD1000500)the Special Support Program of Guangdong Province(2019TX05N193)the Scientific Research Foundation of the Hunan Provincial Education Department(20A261),)the open competition program of top ten critical priorities of Agricultural Science and Technology Innovation for the 14th Five-Year Plan of Guangdong Province(2022SDZG05)C.C.is supported by the Guangzhou Municipal Science and Technology Plan Project(2023A04J0113)J.F.is supported by the Hainan Provincial Natural Science Foundation of China(323QN279).
文摘Since the official release of the stand-alone bioinformatics toolkit TBtools in 2020,its superior functionality in data analysis has been demonstrated by its widespread adoption by many thousands of users and references in more than 5000 academic articles.Now,TBtools is a commonly used tool in biological laboratories.Over the past 3 years,thanks to invaluable feedback and suggestions from numerous users,we have optimized and expanded the functionality of the toolkit,leading to the development of an upgraded version—TBtools-II.In this upgrade,we have incorporated over 100 new features,such as those for comparative genomics analysis,phylogenetic analysis,and data visualization.Meanwhile,to better meet the increasing needs of personalized data analysis,we have launched the plugin mode,which enables users to develop their own plugins and manage their selection,installation,and removal according to individual needs.To date,the plugin store has amassed over 50 plugins,with more than half of them being independently developed and contributed by TBtools users.These plugins offer a range of data analysis options including co-expression network analysis,single-cell data analysis,and bulked segregant analysis sequencing data analysis.Overall,TBtools is now transforming from a stand-alone software to a comprehensive bioinformatics platform of a vibrant and cooperative community in which users are also developers and contributors.By promoting the theme“one for all,all for one”,we believe that TBtools-II will greatly benefit more biological researchers in this big-data era.
文摘The majority of plant disease resistance （R） genes encode proteins that share common structural features. However, the transcription activator-like effector （TALE）-associated executor type R genes show no considerable sequence homology to any known R genes. We adopted a map-based cloning approach and TALE-based technology to isolate and characterize Xa23, a new executor R gene derived from wild rice （Oryza rufipogon） that confers an extremely broad spectrum of resistance to bacterial blight caused by Xanthomonas oryzae pv. oryzae （Xoo）. Xa23 encodes a 113 amino acid protein that shares 50% identity with the known executor R protein XA10. The predicted transmembrane helices in XA23 also overlap with those of XA10. Unlike XalO, however, Xa23 transcription is specifically activated by AvrXa23, a TALE present in all examined Xoo field isolates. Moreover, the susceptible xa23 allele has an identical open reading frame of Xa23 but differs in promoter region by lacking the TALE binding element （EBE） for AvrXa23. XA23 can trigger a strong hypersensitive response in rice, tobacco, and tomato. Our results provide the first evidence that plant genomes have an executor R gene family of which members execute their function and spectrum of disease resistance by recognizing the cognate TALEs in the pathogen.
基金This work was financially supported by grants from the National Key Research and Development Program of China （2016YFD0100902）, the National Natural Science Foundation of China （numbers 31400223, 31471461, and 31625004）, the Basic Research Program from the Shanghai Municipal Science and Technology Commission （14JC1400800）, the Basic Application Research Program from the Shanghai Municipal Agriculture Commission （2014-7-1-2）, and the Agricultural Seed Project of Shandong Province.
文摘Grain size and shape are important determinants of grain weight and yield in rice. Here, we report a new major quantitative trait locus （QTL）, qTGW3, that controls grain size and weight in rice. This locus, qTGW3, encodes OsSK41 （also known as OsGSK5）, a member of the GLYCOGEN SYNTHASE KINASE 3/SHAGGY-like family. Rice near-isogenic lines carrying the loss-of-function allele of OsSK41 have increased grain length and weight. We demonstrate that OsSK41 interacts with and phosphorylates AUXIN RESPONSE FACTOR 4 （OsARF4）. Co-expression of OsSK41 with OsARF4 increases the accumulation of OsARF4 in rice protoplasts. Loss of function of OsARF4 results in larger rice grains. RNA-sequencing analysis suggests that OsARF4 and OsSK41 repress the expression of a common set of downstream genes, including some auxin-responsive genes, during rice grain development. The loss-of-function form of OsSK41 at qTGW3 represents a rare allele that has not been extensively utilized in rice breeding. Suppression of OsSK41 function by either targeted gene editing or QTL pyramiding enhances rice grain size and weight. Thus, our study reveals the important role of OsSK41 in rice grain development and provides new candidate genes for genetic improvement of grain yield in rice and perhaps in other cereal crops.
基金supported by the National Basic Research Program(973 Program) of China(No.2015CB150402)the National Maize Production System in China(No.CARS-02-24)+1 种基金the Special Fund for Agroscientific Research in the Public Interest of China (No.201103003)the Innovative Group Grant of the NSFC,China(No.31421092)
文摘Achieving both high yield and high nitrogen use efficiency （NUE） simultaneously has become a major challenge with increased global demand for food, depletion of natural resources, and deterioration of environment. As the greatest consumers of N fertilizer in the world, Chinese farmers have overused N, and there has been poor synchrony between crop N demand and N supply because of limited understanding of the N uptake-yield relationship. To address this problem, this study evaluated the total and dynamic N requirement for different yield ranges of two major crops （maize and wheat）, and suggested improvements to N management strategies. Whole-plant N aboveground uptake requirement per grain yield （Nreq） initially deceased with grain yield improvement and then stagnated, and yet most farmers still believed that more fertilizer and higher grain yield were synonymous. When maize yield increased from 〈 7.5 to 〉 12.0 Mg ha-I, Nreq decreased from 19.8 to 17.0 kg Mg-1 grain. For wheat, it decreased from 27.1 kg Mg-1 grain for grain yield 〈 4.5 Mg ha-1 to 22.7 kg Mg-1 grain for yield 〉 9.0 Mg ha-1. Meanwhile, the percentage of dry matter and N accumulation in the middle-late growing season increased significantly with grain yield, which indicated that N fertilization should be concentrated in the middle-late stage to match crop demand while farmers often applied the majority of N fertilizer either before sowing or during early growth stages. We accordingly developed an integrated soil-crop system management strategy that simultaneously increases both grain yield and NUE.
基金Acknowledgments We are grateful to Dr Xinnian Dong （Duke University, Durham, NC, USA） for critical reading of the manuscript and valuable suggestions. We thank Dr Jianmin Zhou （National Institute of Biological Sciences, Beijing, China） for providing the fungus strain Botrytis cinerea, Dr Salome Prat （Institut de Biologia Molecular de Barcelona, Barcelona, Spain） for providing homozygous atmyc2-2 （T-DNA insertion line SALK_083483） seeds and Dr Daoxin Xie （Tsinghua University, Beijing, China） for providing the coil-I seeds. This work was supported by grants from The National Natural Science Foundation of China （30530440）, The Ministry of Science and Technology of China （2006CB 102004, 2006AA10A 116）, and The Chinese Academy of Sciences （KSCX2-YW-N-045）.
文摘Jasmonic acid （JA） is an important phytohormone that regulates plant defense responses against herbivore attack, pathogen infection and mechanical wounding. In this report, we provided biochemical and genetic evidence to show that the Arabidopsis thaliana NAC family proteins ANAC019 and ANAC055 might function as transcription activators to regulate JA-induced expression of defense genes. The role of the two NAC genes in JA signaling was examined with the anacO19 anac055 double mutant and with transgenic plants overexpressing ANACO19 or ANAC055. The anacO19 anac055 double mutant plants showed attenuated JA-induced VEGETATIVE STORAGE PROTEIN1 （VSP1） and LIPOXYGENASE2 （LOX2） expression, whereas transgenic plants overexpressing the two NAC genes showed enhanced JA-induced VSP1 and LOX2 expression. That the JA-induced expression of the two NAC genes depends on the function of COIl and AtMYC2, together with the finding that overexpression of ANACO19 partially rescued the JA-related phenotype of the atmyc2-2 mutant, has led us to a hypothesis that the two NAC proteins act downstream of AtMYC2 to regulate JA-signaled defense responses. Further evidence to substantiate this idea comes from the observation that the response of the anacO19 anac055 double mutant to a necrotrophic fungus showed high similarity to that of the atmyc2-2 mutant.
基金This study was supported by the National Key Research and Development Program of China （2016YFD0101802 and 2016YFE0108600） and National Natural Science Foundation of China （31550110212）.
文摘There is a rapidly rising trend in the development and application of molecular marker assays for gene map- ping and discovery in field crops and trees. Thus far, more than 50 SNP arrays and 15 different types of genotyping-by-sequencing （GBS） platforms have been developed in over 25 crop species and perennial trees. However, much less effort has been made on developing ultra-high-throughput and cost-effective genotyping platforms for applied breeding programs. In this review, we discuss the scientific bottlenecks in existing SNP arrays and GBS technologies and the strategies to develop targeted platforms for crop mo- lecular breeding. We propose that future practical breeding platforms should adopt automated genotyping technologies, either array or sequencing based, target functional polymorphisms underpinning economic traits, and provide desirable prediction accuracy for quantitative traits, with universal applications under wide genetic backgrounds in crops. The development of such platforms faces serious challenges at both the technological level due to cost ineffectiveness, and the knowledge level due to large genotype- phenotype gaps in crop plants. It is expected that such genotyping platforms will be achieved in the next ten years in major crops in consideration of （a） rapid development in gene discovery of important traits, （b） deepened understanding of quantitative traits through new analytical models and population designs, （c） integration of multi-layer -omics data leading to identification of genes and pathways responsible for important breeding traits, and （d） improvement in cost effectiveness of large-scale genotyping. Crop breeding chips and genotyping platforms will provide unprecedented opportunities to accelerate the development of cultivars with desired yield potential, quality, and enhanced adaptation to mitigate the effects of climate change.
文摘Heading date and photoperiod sensitivity are fundamental traits that determine rice adaptation to a wide range of geographic environments. By quantitative trait locus （QTL） mapping and candidate gene analysis using whole- genome re-sequencing, we found that Oryza sativa Pseudo-Response Regulator37 （OsPRR37; hereafter PRR37） is respon- sible for the Early heading7-2 （EH7-2）/Heading date2 （Hd2） QTL which was identified from a cross of late-heading rice ＇Milyang23 （M23）＇ and early-heading rice ＇H143＇. H143 contains a missense mutation of an invariantly conserved amino acid in the CCT （CONSTANS, CO-like, and TOC1） domain of PRR37 protein. In the world rice collection, different types of nonfunctional PRR37 alleles were found in many European and Asian rice cultivars. Notably, the japonica varieties harboring nonfunctional alleles of both Ghd7/Hd4 and PRR37/Hd2 flower extremely early under natural long-day condi- tions, and are adapted to the northernmost regions of rice cultivation, up to 53~ N latitude. Genetic analysis revealed that the effects of PRR37 and Ghd7 alleles on heading date are additive, and PRR37 down-regulates Hd3a expression to suppress flowering under long-day conditions. Our results demonstrate that natural variations in PRR37/Hd2 and GhdT/ Hd4 have contributed to the expansion of rice cultivation to temperate and cooler regions.
基金supported by the National Natural Science Foundation of China (31401308, 31371555 and 31671445)
文摘Intercropping is one of the most vital practice to improve land utilization rate in China that has limited arable land resource. However, the traditional intercropping systems have many disadvantages including illogical field lay-out of crops, low economic value, and labor deficiency, which cannot balance the crop production and agricultural sustainability. In view of this, we developed a novel soybean strip intercropping model using maize as the partner, the regular maize-soybean strip intercropping mainly popularized in northern China and maize-soybean relay-strip intercropping principally extended in southwestern China. Compared to the traditional maize-soybean intercropping systems, the main innovation of field lay-out style in our present intercropping systems is that the distance of two adjacent maize rows are shrunk as a narrow strip, and a strip called wide strip between two adjacent narrow strips is expanded reserving for the growth of two or three rows of soybean plants. The distance between outer rows of maize and soybean strips are expanded enough for light use efficiency improvement and tractors working in the soybean strips. Importantly, optimal cultivar screening and increase of plant density achieved a high yield of both the two crops in the intercropping systems and increased land equivalent ratio as high as 2.2. Annually alternative rotation of the adjacent maize-and soybean-strips increased the grain yield of next seasonal maize, improved the absorption of nitrogen, phosphorus, and potasium of maize, while prevented the continuous cropping obstacles. Extra soybean production was obtained without affecting maize yield in our strip intercropping systems, which balanced the high crop production and agricultural sustainability.
基金This work was supported by grants from the National Natural Science Foundation of China(31871948)the Fundamental Research Funds,and the Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences to H.Z.a grant from the Fundamental Research Funds for the Central Universities to S.L.
文摘Recently developed CRISPR-mediated base editors,which enable the generation of num erous nucleotide changes in target genomic regions,have been widely adopted for gene correction and generation of crop germ plasms containing im portant gain-of-function genetic variations.How ever,to engineer target genes with unknown functional SNPs remains challenging.To address this issue,we present here abase-e diting-mediated gene evolution(BEMGE)m ethod,employing both Cas9n-based cytosine and adenine base editors as well as a single-guide RNA(sgRNA)library tiling the full-length coding region,for developing novel rice germ plasm swith mutations in any endogenous gene.To this end,OsALS1 was artificially evolved in rice cells using BEMGE through both Agrobacterium-mediated and particle-bom bardment-mediated transform ation.Four different types of amino acid substitutions in the evolved OsALS1,derived from two sites that have never been targeted by natural or human selection during rice dom estication,were identified,conferring varying levels of tolerance to the herbicide bispyribac-sodium.Furtherm ore,the P171F substitution identified in a strong OsALS1 allele was quickly introduced into the commercial rice cultivar Nangeng 46 through precise base editing w ith the corresponding base editor and sgRNA.Collectively,these data indicate great potential of BEMGE in creating important genetic variants of target genes for crop improvement.
基金supported by the National Basic Research Program of China (973 Program, 2015CB150401)the National Key Research and Development Program of China (2016YFD0300101)the National Maize Industrial Technology System, China
文摘Increasing plant density is an effective way to enhance maize yield, but often increases lodging rate and severity, significantly elevating the risk and cost of maize production. Therefore, lodging is a major factor restricting future increases in maize yield through high-density planting. This paper reviewed previous research on the relationships between maize lodging rate and plant morphology, mechanical strength of stalks, anatomical and biochemical characteristics of stalks, root characteristics, damage from pests and diseases, environmental factors, and genomic characteristics. The effects of planting density on these factors and explored possible ways to improve lodging resistance were also analyzed in this paper. The results provide a basis for future research on increasing maize lodging resistance under high-density planting conditions and can be used to develop maize cultivation practices and lodging-resistant maize cultivars.
基金supported by grants from the Geneti-cally Modified Organisms Breeding Major Projects of China(2011ZX08001-004-009)the National Natural Science Foun-dation of China(30900881)+2 种基金the Jiangxi Province Major Science and Technology Projects and Super Hybrid Rice BreedingDemonstration and Dissemination Projects(20114ABF03105)the Natural Science Foundation of Shandong Province(Y2006D22)
文摘A thorough understanding of the genetic basis of rice grain traits is critical for the improvement of rice （Oryza sativa L.） varieties. In this study, we generated an F2 population by crossing the large-grain japonica cultivar CW23 with Peiai 64 （PA64）, an elite indica small-grain cultivar. Using QTL analysis, 17 QTLs for five grain traits were detected on four different chromosomes. Eight of the QTLs were newly-identified in this study. In particular, qGL3-1, a newly-identified grain length QTL with the highest LOD value and largest phenotypic variation, was fine-mapped to the 17 kb region of chromosome 3. A serine/threonine protein phosphatase gene encoding a repeat domain containing two Kelch motifs was identified as the unique candidate gene corresponding to this QTL. A comparison of PA64 and CW23 sequences revealed a single nucleotide substitution （C→A） at position 1092 in exon 10, resulting in replacement of Asp （D） in PA64 with Glu （E） in CW23 for the 364th amino acid. This variation is located at the D position of the conserved sequence motif AVLDT of the Kelch repeat. Genetic analysis of a near-isogenic line （NIL） for qGL3-1 revealed that the allele qGL3-1 from CW23 has an additive or partly dominant effect, and is suitable for use in molecular marker-assisted selection.
基金supported by the National Key Technology R&D Program of China(2012BAD04B02,2013BAD07B02,and2011BAD16B10)the Special Fund for Agro-Scientific Research in the Public Interest(201103003 and 201303126-4)the Key Technology R&D Program of Jilin province,China(20126026)
文摘A four-year field experiment was conducted to investigate the effect of subsoiling depth on root morphology, nitrogen(N), phosphorus(P), and potassium(K) uptake, and grain yield of spring maize. The results indicated that subsoil tillage promoted root development,increased nutrient accumulation, and increased yield. Compared with conventional soil management(CK), root length, root surface area, and root dry weight at 0–80 cm soil depth under subsoil tillage to 30 cm(T1) and subsoil tillage to 50 cm(T2) were significantly increased, especially the proportions of roots in deeper soil. Root length, surface area, and dry weight differed significantly among three treatments in the order of T2 > T1 > CK at the12-leaf and early filling stages. The range of variation of root diameter in different soil layers in T2 treatment was the smallest, suggesting that roots were more likely to grow downwards with deeper subsoil tillage in soil. The accumulation of N, P, and K in subsoil tillage treatment was significantly increased, but the proportions of kernel and straw were different. In a comparison of T1 with T2, the grain accumulated more N and P, while K accumulation in kernel and straw varied in different years. Grain yield and biomass were increased by 12.8% and 14.6% on average in subsoil tillage treatments compared to conventional soil treatment. Although no significant differences between different subsoil tillage depths were observed for nutrient accumulation and grain yield, lodging resistance of plants was significantly improved in subsoil tillage to 50 cm, a characteristic that favors a high and stable yield under extreme environments.
