The telomere-to-telomere genome of Fragaria vesca reveals the genomic evolution of Fragaria and the origin of cultivated octoploid strawberry

Fragaria vesca,commonly known as wild or woodland strawberry,is the most widely distributed diploid Fragaria species and is native to Europe and Asia.Because of its small plant size,low heterozygosity,and relative ease of genetic transformation,F.vesca has been a model plant for fruit research since the publication of its Illumina-based genome in 2011.However,its genomic contribution to octoploid cultivated strawberry remains a long-standing question.Here,we de novo assembled and annotated a telomere-to-telomere,gap-free genome of F.vesca‘Hawaii 4’,with all seven chromosomes assembled into single contigs,providing the highest completeness and assembly quality to date.The gap-free genome is 220785082 bp in length and encodes 36173 protein-coding gene models,including 1153 newly annotated genes.All 14 telomeres and seven centromeres were annotated within the seven chromosomes.Among the three previously recognized wild diploid strawberry ancestors,F.vesca,F.iinumae,and F.viridis,phylogenomic analysis showed that F.vesca and F.viridis are the ancestors of the cultivated octoploid strawberry F.×ananassa,and F.vesca is its closest relative.Three subgenomes of F.×ananassa belong to the F.vesca group,and one is sister to F.viridis.We anticipate that this high-quality,telomere-to-telomere,gap-free F.vesca genome,combined with our phylogenomic inference of the origin of cultivated strawberry,will provide insight into the genomic evolution of Fragaria and facilitate strawberry genetics and molecular breeding.

Significant reduction of ammonia emissions while increasing crop yields using the 4R nutrient stewardship in an intensive cropping system

Ammonia (NH_3) emissions should be mitigated to improve environmental quality.Croplands are one of the largest NH_3sources,they must be managed properly to reduce their emissions while achieving the target yields.Herein,we report the NH_3 emissions,crop yield and changes in soil fertility in a long-term trial with various fertilization regimes,to explore whether NH_3 emissions can be significantly reduced using the 4R nutrient stewardship (4Rs),and its interaction with the organic amendments (i.e.,manure and straw) in a wheat–maize rotation.Implementing the 4Rs significantly reduced NH_3 emissions to 6 kg N ha~(–1) yr~(–1) and the emission factor to 1.72%,without compromising grain yield (12.37 Mg ha~(–1) yr~(–1))and soil fertility (soil organic carbon of 7.58 g kg~(–1)) compared to the conventional chemical N management.When using the 4R plus manure,NH_3 emissions (7 kg N ha~(–1) yr~(–1)) and the emission factor (1.74%) were as low as 4Rs,and grain yield and soil organic carbon increased to 14.79 Mg ha~(–1) yr~(–1) and 10.09 g kg~(–1),respectively.Partial manure substitution not only significantly reduced NH_3 emissions but also increased crop yields and improved soil fertility,compared to conventional chemical N management.Straw return exerted a minor effect on NH_3 emissions.These results highlight that 4R plus manure,which couples nitrogen and carbon management can help achieve both high yields and low environmental costs.

Identification and profile of phenolamides with anthracnose resistance potential in tea(Camellia sinensis)

Tea anthracnose is a prevalent disease in China that can lead to reduced tea production and lower quality,yet there is currently a lack of effective means for controlling this disease.In this study,we identified 46 phenolamides(including 27 isomers)in different tissues and organs of tea plants based on a developed workflow,and the secondary mass spectra of all these compounds have been documented.It was revealed that tea plants predominantly accumulate protonated aliphatic phenolamides,rather than aromatic phenolamides.The profile of phenolamides indicate that their buildup in tea plants is specific to certain tissues and acyl-acceptors,and this distribution is associated with the extent of phenolamide acyl-modification.Additionally,it was observed that N-Feruloylputrescine(Fer-Put,a type of phenolamides)was responsive to the stimulated accumulation of the tea anthracnose pathogen.The findings of anti-anthracnose experiments in vitro and on tea leaf demonstrated that Fer-Put was capable of significantly inhibiting the growth of anthracnose pathogen colony,effectively prevented tea leaf disease.Furthermore,it was observed that Fer-Put treatment can enhance the antioxidant enzyme activity of tea leaves.TEA002780.1 and TEA013165.1 gene may be responsible for the biosynthesis of Fer-Put in the disease resistance process in tea plants.Through these studies,the types and distribution of phenolamides in tea plants have been elucidated,and Fer-Put’s ability to resist anthracnose has been established,providing new insights into the resistance of tea anthracnose.

Pyramiding of multiple genes generates rapeseed introgression lines with clubroot and herbicide resistance, high oleic acid content, and early maturity

Clubroot and herbicide resistance,high oleic acid(OA)content,and early maturity are targets of rapeseed(Brassica napus L.)breeding.The objective of this study was to develop new male-fertility restorer lines by pyramiding favorable genes to improve these traits simultaneously.Seven elite alleles for the four traits were introduced into the restorer line 621R by speed breeding with marker-assisted and phenotypic selection.Six introgression lines(ILs)were developed with four-to seven-gene combinations and crossed with two elite parents to develop hybrids.All ILs and their corresponding hybrids displayed high resistance to both clubroot pathotype 4 and sulfonylurea herbicides.Three ILs and their hybrids showed large increases in OA contents and four showed earlier maturity.These new ILs may be useful in rapeseed hybrid breeding for the target traits.

Reduction of N2O emissions by DMPP depends on the interactions of nitrogen sources(digestate vs. urea) with soil properties

The inhibition of nitrification by mixing nitrification inhibitors(NI)with fertilizers is emerging as an effective method to reduce fertilizer-induced nitrous oxide(N_(2)O)emissions.The additive 3,4-dimethylpyrazole phosphate(DMPP)apparently inhibits ammonia oxidizing bacteria(AOB)more than ammonia oxidizing archaea(AOA),which dominate the nitrification in alkaline and acid soil,respectively.However,the efficacy of DMPP in terms of nitrogen sources interacting with soil properties remains unclear.We therefore conducted a microcosm experiment using three typical Chinese agricultural soils with contrasting pH values(fluvo-aquic soil,black soil and red soil),which were fertilized with either digestate or urea in conjunction with a range of DMPP concentrations.In the alkaline fluvo-aquic soil,fertilization with either urea or digestate induced a peak in N_(2)O emission(60μg N kg^(-1)d^(-1))coinciding with the rapid nitrification within 3 d following fertilization.DMPP almost eliminated this peak in N_(2)O emission,reducing it by nearly 90%,despite the fact that the nitrification rate was only reduced by 50%.In the acid black soil,only the digestate induced an N_(2)O emission that increased gradually,reaching its maximum(20μg N kg^(-1)d^(-1))after 5–7 d.The nitrification rate and N_(2)O emission were both marginally reduced by DMPP in the black soil,and the N_(2)O yield(N_(2)O-N per NO2–+NO3–-N produced)was exceptionally high at 3.5%,suggesting that the digestate induced heterotrophic denitrification.In the acid red soil,the N_(2)O emission spiked in the digestate and urea treatments at 50 and 10μg N kg^(-1)d^(-1),respectively,and DMPP reduced the rates substantially by nearly 70%.Compared with 0.5%DMPP,the higher concentrations of DMPP(1.0 to 1.5%)did not exert a significantly(P<0.05)better inhibition effect on the N_(2)O emissions in these soils(either with digestate or urea).This study highlights the importance of matching the nitrogen sources,soil properties and NIs to achieve a high efficiency of N_(2)O emission reduction.

Challenges and opportunities to improve tropical fruits in Hainan,China

Tropical fruits play a major role in the economic and social development of Hainan(China).Despite favorable climatic conditions,the yield of tropical fruits in Hainan remains low,in part due to the low genetic potential of currently grown tropical fruit varieties.Consequently,there is a need to improve yield potential by exploiting the genome and germplasm resources of tropical fruit species,minimizing post-harvest losses,and improving transportation standards.In this study,we intend to collect germplasm resources from a wide range of domestic and exotic sources to evaluate the genetic yield potential and nutritional quality of fruit using plant morphology,taxonomy and physiological parameters.In this review,we aim to identify current bottlenecks in the Hainan tropical fruit industry and propose solutions through the use of conventional breeding and new biotechnological tools,including the use of omics and CRISPR to enhance yield and tackle biotic and abiotic stresses of tropical fruit species.Producing new fruit cultivars in Hainan,either through conventional strategies or the use of genome editing technology such as CRISPR,could help improve the socioeconomic status of this region.Furthermore,increasing the genetic potential and production of new cultivars can help in meeting the demands of new trade agreements with various nations under the'One Belt,One Road'initiative,Boao Forum for Asia,ASEAN agreements,and the Shanghai Cooperation Organization.

Down-regulation of MeMYB2 leads to anthocyanin accumulation and increases chilling tolerance in cassava(Manihot esculenta Crantz)

Chilling-induced accumulation of reactive oxygen species(ROS) is harmful to plants,which usually produce anthocyanins to scavenge ROS as protection from chilling stress.As a tropical crop,cassava is hypersensitive to chilling,but the biochemical basis of this hypersensitivity remains unclear.We previously generated Me MYB2-RNAi transgenic cassava with increased chilling tolerance.Here we report that Me MYB2-RNAi transgenic cassava accumulated less ROS but more cyanidin-3-O-glucoside than the wild type under early chilling stress.Under this stress,the anthocyanin biosynthesis pathway was more active in Me MYB2-RNAi lines than in the wild type,and several genes involved in the pathway,including Me TT8,were up-regulated by Me MYB2-RNAi in the transgenic cassava.Me MYB2 bound to the Me TT8 promoter and blocked its expression under both normal and chilling conditions,thereby inhibiting anthocyanin accumulation.Me TT8 was shown to bind to the promoter of Dihydroflavonol 4-reductase(Me DFR-2)and increased Me DFR-2 expression.Me MYB2 appears to act as an inhibitor of chilling-induced anthocyanin accumulation during the rapid response of cassava to chilling stress.

Deep placement of nitrogen fertilizer increases rice yield and nitrogen use efficiency with fewer greenhouse gas emissions in a mechanical direct-seeded cropping system

Deep placement of nitrogen fertilizer is a key strategy for improving nitrogen use efficiency. A two-year field experiment was conducted during the early rice growing seasons(March–July) of 2016 and 2017.The experimental treatments comprised two rice cultivars: Wufengyou 615(WFY 615) and Yuxiangyouzhan(YXYZ), and three N treatments: mechanical deep placement of all fertilizers as basal dose at 10 cm soil depth(one-time deep-placement fertilization, namely OTDP fertilization);manual surface broadcast(the common farmer practice) of 40% N fertilizer at one day before sowing(basal fertilizer)followed by broadcast application of 30% each at tillering and panicle initiation stages;and no fertilizer application at any growth stage as a control. One-time deep-placement fertilization increased grain yield of both rice cultivars by 11.8%–19.6%, total nitrogen accumulation by 10.3%–13.1%, nitrogen grain production efficiency by 29.7%–31.5%, nitrogen harvest index by 27.8%–30.0%, nitrogen agronomic efficiency by 71.3%–77.2%, and nitrogen recovery efficiency by 42.4%–56.7% for both rice cultivars, compared with the multiple-broadcast treatment. One-time deep-placement fertilization reduced CH4-induced global warming potential(GWP) by 20.7%–25.3%, N2O-induced GWP by 7.2%–12.3%, and total GWP by 14.7%–22.9% for both rice cultivars relative to the multiple-broadcast treatment. The activities of glutamine synthetase and nitrate reductase were increased at both panicle-initiation and heading stages in both rice cultivars following one-time deep-placement fertilization treatment. Larger leaf area index at heading stage and more favorable root morphological traits expressed as larger total root length, mean root diameter, and total root volume per hill were also observed. One-time deep-placement fertilization could be an effective strategy for increasing grain yield and nitrogen use efficiency and lowering greenhouse-gas emissions under mechanical direct-seeded cropping systems.

Identification and characterization of MeERF genes and their targets in pathogen response by cassava(Manihot esculenta)

Cassava,Manihot esculenta Crantz (Me),is a major dietary source of calories for over 700 million people in tropical regions.The production of cassava is constantly threatened by cassava bacterial blight (CBB),caused by Xanthomonas axonopodis pv.manihotis (Xam).The gene resources for CBB-resistant breeding of cassava are limited.In model plant species,ethylene response factors play important roles in response to pathogen infection.In this study,cassava ethylene response factors (MeERFs) were identified and characterized as the first step in studying their potential for CBB-resistant breeding of cassava.In the cassava genome 155 MeERFs were identified,of which 23 were induced by Xam infection.The promoter regions of204 genes harbored GCC-box that had the potential to interact with MeERFs.Using 37 transcriptomes derived from Xam infection treatment,four gene co-expression modules for the MeERFs and GCC-box containing genes were constructed.Six MeERFs were associated with two GCC-box containing genes:transcription initiation factor TFIIE subunit beta (MeTFIIE),and histone-lysine N-methyltransferase ASHR1 (MeASHR1).Dual-luciferase reporter assays showed that MeERF10 and MeERF58 positively regulated Me TFIIE;MeERF137 negatively regulated Me TFIIE;MeERF10 and MeERF137 positively regulated Me ASHR1;and MeERF35 negatively regulated Me ASHR1.The four MeERFs may mediate pathogen response by regulating the expression of the two GCC-box containing genes.

Chromosomal-level genome of macadamia(Macadamia integrifolia)

Macadamia from the family Proteaceae is a plant native to Australia and has long been favoured by people for its crispy and high nutritional and medicinal value.Here,the genome of GUIRE 1(GR1),a highly heterozygous superior cultivar of macadamia nut,was sequenced and assembled using nanopore sequencing,and a 807-Mb genome(contig N50,1.9 Mb;scaffold N50,54.70 Mb)and 14 chromosomes were obtained.A total of 453 Mb(about 55.95%)repetitive sequences and 37,657 protein-coding genes were obtained by gene annotation and homologous protein comparison.Proteaceae diverged from Nelumbonaceae nearly 115.37 million years ago and from Rubiaceae about 140 million years ago.A genome-wide duplication(WGD)event occurred in macadamia 41 million years ago based on the WGD analysis.The functional enrichment analysis of M.integrifolia-specific gene families revealed their roles in signal transduction,protein phosphorylation,protein binding,and defense response.Here,a highly heterozygous genome of M.integrifolia was unlocked to provide a database for breeding and molecular mechanism research.

Distinct root system acclimation patterns of seagrass Zostera japonica in sediments of different trophic status:a research by X-ray computed tomography

Conspecific seagrass living in differing environments may develop different root system acclimation patterns.We applied X-ray computed tomography(CT)for imaging and quantifying roots systems of Zostera japonica collected from typical oligotrophic and eutrophic sediments in two coastal sites of northern China,and determined sediment physicochemical properties that might influence root system morphology,density,and distribution.The trophic status of sediments had little influence on the Z.japonica root length,and diameters of root and rhizome.However,Z.japonica in oligotrophic sediment developed the root system with longer rhizome node,deeper rhizome distribution,and larger allocation to below-ground tissues in order to acquire more nutrients and relieve the N deficiency.And the lower root and rhizome densities of Z.japonica in eutrophic sediment were mainly caused by fewer shoots and shorter longevity,which was resulted from the more serious sulfide inhibition.Our results systematically revealed the effect of sediment trophic status on the phenotypic plasticity,quantity,and distribution of Z.japonica root system,and demonstrated the feasibly of X-ray CT in seagrass root system research.

Effects of Storage Temperature on Postharvest Physiology of Amorphophallus cormifer Microbulb

[Objectives]The paper was to explore the optimum storage temperature of Amorphophallus cormifer microbulbs.[Methods]With A.cormifer as the raw material,the effects of different storage temperatures(4,12 and 20℃)on postharvest physiology of A.cormifer during the storage period of 80 d were investigated.[Results]There was no significant difference in starch content among the treatments,and the content of reducing sugar at 4℃was significantly higher than those of other treatments during the storage period.There was no significant difference in total water content among treatments,and the specific gravity of free water at 4℃was significantly lower than those at 12 and 20℃,respectively.At 60 d post storage,the POD activity at 4℃was significantly higher than those at 12 and 20℃,respectively.At the 80th day of storage,the PPO activity at 4℃was significantly lower than those at 12 and 20℃,respectively.[Conclusions]The low temperature of 4℃is more conducive to the storage of A.cormifer microbulbs,and the results also provide the theoretical basis for long-term storage of A.cormifer bulbs.

Identification and functional analysis of transcription factors related to coconut(Cocos nucifera L.)endosperm development based on ATAC-seq

Coconut(Cocos nucifera L.)is a member of the palm tree family(Arecaceae)and the only living species of the genus Cocos.In this paper,the regulatory relationship pathways between multiple transcription factors and functional genes were identified by combining ATAC-seq and RNAseq in coconut endosperm at four different developmental stages(fruit after pollination:7 months,8 months,9 months and 10 months,respectively).The results indicated that the peaks detected in the promoter-TSS area accounted for the largest proportion(11.99%)in the third stage.These results suggest that the chromatin open region of cells in this period is more functional and that there are more functional genes with active transcription.In addition,a large number of potential regulatory relationships between transcription factors and functional genes were detected via bioinformatics analysis at the genomic level.Among them,CnGATA20 was predicted to be an important transcription factor with a binding site on the promoter region of the CnOLE18 gene.The regulatory pathway by which CnGATA20 positively regulates the expression of CnOLE18 was further confirmed by yeast one-hybrid,protoplast transient expression and dual-luciferase reporter system experiments.The results provide a new research strategy for exploring the regulation at both the transcriptional and posttranscriptional levels during coconut endosperm growth and development.

De novo assembly of plant complete genomes

Plant genomes encode the mysteries of how plants cope with complex environments over long evolutionary histories.Over the past 20 years,rapidly developing technologies have allowed the decoding of hundreds of plant draft or reference genomes.The diversity,polyploidy and heterozygosity of plants make it technically challenging and time-consuming to generate high-quality plant genome assemblies.Recently invented ultra-long read sequencing technologies have achieved a milestone where several plant genomes have been gapless and assembled into telomere to telomere.Telomere-to-telomere(T2T)genome refers to a high-quality complete genome with high genomic accuracy,high continuity,and high integrity.With the release of the completed human genome and Arabidopsis thaliana genome,the era of complete T2T species genome has arrived.In this review,we summarize the history leading up to the gap free plant genomes based on emerging ultra-long read sequencing technologies.We discuss to close gaps relying on targeted genome sequencing and assembling technologies.However,there are still quite a lot of challenges in super large,polyploidy,and unstable genomes.Nevertheless,these complete genomes have already provided unprecedented information,which will certainly deepen our understanding of plant genomes and the exploration of more functional sequences.By taking advantage of the complete genomes,a series of important genes could be annotated,which will help achieve the goal of genome design in crop species.

Targeted approaches to improve tomato fruit taste

Tomato(Solanum lycopersicum)is the most valuable fruit and horticultural crop species worldwide.Compared with the fruits of their progenitors,those of modern tomato cultivars are,however,often described as having unsatisfactory taste or lacking f lavor.The f lavor of a tomato fruit arises from a complex mix of tastes and volatile metabolites,including sugars,acids,amino acids,and various volatiles.However,considerable differences in fruit f lavor occur among tomato varieties,resulting in mixed consumer experiences.While tomato breeding has traditionally been driven by the desire for continual increases in yield and the introduction of traits that provide a long shelf-life,consumers are prepared to pay a reasonable premium for taste.Therefore,it is necessary to characterize preferences of tomato f lavor and to define its underlying genetic basis.Here,we review recent conceptual and technological advances that have rendered this more feasible,including multi-omics-based QTL and association analyses,along with the use of trained testing panels,and machine learning approaches.This review proposes how the comprehensive datasets compiled to date could allow a precise rational design of tomato germplasm resources with improved organoleptic quality for the future.

A nonsynonymous mutation in an acetolactate synthase gene (Gh_D10G1253) is required for tolerance to imidazolinone herbicides in cotton

Background Herbicide tolerance in crops enables them to survive when lethal doses of herbicides are applied to surrounding weeds.Herbicide-tolerant crops can be developed through transgenic approaches or traditional mutagenesis approaches.At present,no transgenic herbicide tolerant cotton have been commercialized in China due to the genetically-modified organism(GMO)regulation law.We aim to develop a non-transgenic herbicide-tolerant cotton through ethyl methanesulfonate(EMS)mutagenesis,offering an alternative choice for weed management.Results Seeds of an elite cotton cultivar Lumianyan 37(Lu37)were treated with EMS,and a mutant Lu37-1 showed strong tolerance to imidazolinone(IMI)herbicides was identified.A novel nonsynonymous substitution mutation Ser642Asn at acetolactate synthase(ALS)(Gh_D10G1253)in Lu37-1 mutant line was found to be the potential cause to the IMI herbicides tolerance in cotton.The Ser642Asn mutation in ALS did not present among the genomes of natural Gossypium species.Cleaved amplified polymorphic sequence(CAPS)markers were developed to identify the ALS mutant allele.The Arabidopsis overexpressing the mutanted ALS also showed high tolerance to IMI herbicides.Conclusion The nonsynonymous substitution mutation Ser642Asn of the ALS gene Gh_D10G1253 is a novel identi-fied mutation in cotton.This substitution mutation has also been identified in the orthologous ALS genes in other crops.This mutant ALS allele can be used to develop IMI herbicide-tolerant crops via a non-transgenic or transgenic approach.

A homeodomain-leucine zipper I transcription factor, MeHDZ14,regulates internode elongation and leaf rolling in cassava(Manihot esculenta Crantz)

Drought stress impairs plant growth and other physiological functions. MeHDZ14, a homeodomainleucine zipper I transcription factor, is strongly induced by drought stress in various cassava cultivars.However, the role of MeHDZ14 in cassava growth regulation has remained unclear. Here we report that MeHDZ14 affected plant height, such that a dwarf phenotype and altered internode elongation were observed in transgenic cassava lines. MeHDZ14 was found to negatively regulate the biosynthesis of lignin. Its overexpression resulted in abaxially rolled leaves. The morphogenesis of leaf epidermal cells was inhibited by overexpression of MeHDZ14, with decreased auxin and gibberellin and increased cytokinin contents. MeHDZ14 was found to regulate many drought-responsive genes, including genes involved in cell wall synthesis and expansion. MeHDZ14 bound to the promoter of caffeic acid 3-Omethyltransferase 1(MeCOMT1), acting as a transcriptional repressor of genes involved in cell wall development. MeHDZ14 appears to act as a negative regulator of internode elongation and epidermal cell morphogenesis during cassava leaf development.

A novel long non-coding RNA, DIR, increases drought tolerance in cassava by modifying stress-related gene expression

Cassava is an important tropical cash crop. Severe drought stresses affect cassava productivity and quality, and cause great economic losses in agricultural production. Enhancing the drought tolerance of cassava can effectively improve its yield. Long non-coding RNAs(lncRNAs) are present in a wide variety of eukaryotes. Recently, increasing evidence has shown that lncRNAs play a critical role in the responses to abiotic stresses. However, the function of cassava lncRNAs in the drought response remains largely unknown. In this study, we identified a novel lncRNA, DROUGHT-INDUCED INTERGENIC lncRNA(DIR). Gene expression analysis showed that DIR was significantly induced by drought stress treatment, but did not respond to abscisic acid(ABA) or jasmonic acid(JA) treatments. In addition, overexpression of the DIR gene enhanced proline accumulation and drought tolerance in transgenic cassava. RNA-seq analysis revealed that DIR preferentially affected drought-related genes that were linked to transcription and metabolism. Moreover, RNA pull-down mass spectrometry analysis showed that DIR interacted with 325 proteins. A protein–protein interaction(PPI)analysis found a marked enrichment in proteins associated with the mRNA export and protein quality control pathways.Collectively, these results suggest that DIR and its interacting proteins that regulate mRNA or protein metabolism are involved in mediating the drought stress response. Thus, regulating DIR expression has potential for improving cassava yield under drought conditions.

Genomic prediction using composite training sets is an effective method for exploiting germplasm conserved in rice gene banks

Germplasm conserved in gene banks is underutilized,owing mainly to the cost of characterization.Genomic prediction can be applied to predict the genetic merit of germplasm.Germplasm utilization could be greatly accelerated if prediction accuracy were sufficiently high with a training population of practical size.Large-scale resequencing projects in rice have generated high quality genome-wide variation information for many diverse accessions,making it possible to investigate the potential of genomic prediction in rice germplasm management and exploitation.We phenotyped six traits in nearly 2000 indica(XI)and japonica(GJ)accessions from the Rice 3K project and investigated different scenarios for forming training populations.A composite core training set was considered in two levels which targets used for prediction of subpopulations within subspecies or prediction across subspecies.Composite training sets incorporating 400 or 200 accessions from either subpopulation of XI or GJ showed satisfactory prediction accuracy.A composite training set of 600 XI and GJ accessions showed sufficiently high prediction accuracy for both XI and GJ subspecies.Comparable or even higher prediction accuracy was observed for the composite training set than for the corresponding homogeneous training sets comprising accessions only of specific subpopulations of XI or GJ(within-subspecies level)or pure XI or GJ accessions(across-subspecies level)that were included in the composite training set.Validation using an independent population of 281 rice cultivars supported the predictive ability of the composite training set.Reliability,which reflects the robustness of a training set,was markedly higher for the composite training set than for the corresponding homogeneous training sets.A core training set formed from diverse accessions could accurately predict the genetic merit of rice germplasm.

Metabolomics-centered mining of plant metabolic diversity and function:Past decade and future perspectives

Plants are natural experts in organic synthesis,being able to generate large numbers of specific metabolites with widely varying structures that help them adapt to variable survival challenges.Metabolomics is a research discipline that integrates the capabilities of several types of research including analytical chemistry,statistics,and biochemistry.Its ongoing development provides strategies for gaining a systematic understanding of quantitative changes in the levels of metabolites.Metabolomics is usually performed by targeting either a specific cell,a specific tissue,or the entire organism.Considerable advances in science and technology over the last three decades have propelled us into the era of multi-omics,in which metabolomics,despite at an earlier developmental stage than genomics,transcriptomics,and proteomics,offers the distinct advantage of studying the cellular entities that have the greatest influence on end phenotype.Here,we summarize the state of the art of metabolite detection and identification,and illustrate these techniques with four case study applications:(i)comparing metabolite composition within and between species,(ii)assessing spatio-temporal metabolic changes during plant development,(iii)mining characteristic metabolites of plants in different ecological environments and upon exposure to various stresses,and(iv)assessing the performance of metabolomics as a means of functional gene identification,metabolic pathway elucidation,and metabolomics-assisted breeding through analyzing plant populations with diverse genetic variations.In addition,we highlight the prominent contributions of joint analyses of plant metabolomics and other omics datasets,including those from genomics,transcriptomics,proteomics,epigenomics,phenomics,microbiomes,and ion-omics studies.Finally,we discuss future directions and challenges exploiting metabolomics-centered approaches in understanding plant metabolic diversity.