Plant Breeding Methods And Use Of Classical Plant Breeding. Molecular .

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Plant breedingMethods and use of classical plant breeding. Molecular markertechnology, Marker assisted selection in plant breeding. QTL(Quantitative Trait Loci), Genetic analysis and characterization of cropswith various DNA markers and isozymes. Application of Biotechnology inplant breeding programs., Testing GM cropsMitesh Shrestha

Plant Breeding Concept Plant breeding is the process by which humans change certain aspects ofplants over time in order to introduce desired characteristicsIncrease crop productivity

Domestication Plant Breeding activities began at least 10.000 years ago in the Fertile Crescentwith plant domesticationChallenges: transition from nomadicto a sedentary lifestyleIncrease plant yieldIncrease number of edible plants(reduce toxicity)

Landmarks in Plant BreedingWatson, Crick,Wilkins &Rosalind Franklinmodel for DNAstructureMendelEmpirical evidenceon heredity1694Camerariuscrossing as a methodto obtain new planttypes18661923WallaceFirst commercialhybrid corn1953

“The Green Revolution” (1960)Challenge: improve wheat andmaize to meet the productionneeds of developing countriesHigh yielding semi-dwarf, lodgingresistant wheat varietiesNorman Borlaug

Plant Breeding MethodsConventional breeding Mutation or crossing to introduce variability Selection based on morphological characteres Growth of selected seedsChallenge: reduce the time needed to complete a breeding program

Objective of plant breeding Aims to improve the characteristics of plant sothat they become more desirableagronomically and economically. Higher yield Improved quality Disease and insect resistance Change in maturity duration Agronomic characteristics

Classic/ traditional tools Emasculation Hybidization Wide crossing Selection Chromosome counting Chromosome doubling Male sterility Triploidy Linkage analysis Statistical tools

Quantitative trait locus Section of DNA (the locus) that correlates with variation in aphenotype (the quantitative trait). Linked to, or contains, the genes that control that phenotype. Mapped by identifying which molecular markers (such asSNPs or AFLPs) correlate with an observed trait. Early step in identifying and sequencing the actual genes thatcause the trait variation. Quantitative traits are phenotypes (characteristics) that varyin degree and can be attributed to polygenic effects, i.e., theproduct of two or more genes, and their environment.

Methods of plant breeding Self pollinated cropMass selectionPure line selectionPedigree selectionBulk methodBackcross methodSingle seed Descent and recurrent selection

Mass Selection In mass selection, a large number of plants ofsimilar phenotype are selected and theirseeds are mixed together to constitute thenew variety. The plants are selected on the basis of theirappearance or phenotype. The selection is done for easily observablecharacters like plant height, grain color, grainsize.

Merit of mass selection Since a large number of plants are selectedthe adaptation of original variety is notchange Often extensive and prolonged yield trials arenot necessary. This reduces time and costneeded for developing variety. It is less demanding method. Therefore thebreeder can devote more time to otherbreeding programs.

Demerits of Mass Selection The variety developed through mass selection showvariation and are not as uniform as pureline varieties Varieties developed by mass selection are moredifficult to identify than pureline in seed certificationprogram. Mass selection utilizes the variability already present ina variety or population. Therefore only thosevarieties/population that show genetic variation can beimproved through mass selection. Thus mass selectionis limited by the fact that it can not generate variability.

Pureline selection Pureline is the progeny of a single,homozygous, self pollinated plant. In purelineselection a large number of plants areselected from a self pollinated crop and areharvested individually. Individual plant progenies from them areevaluated and the best progeny is released asa pureline variety.

Advantages of pureline selection Pureline selection achieves the maximumpossible improvement over the originalvariety. This is because the variety is the bestpureline present in the population. Pureline variety are extremely uniform sinceall the plants in the variety have the samegenotype Due to its extreme uniformity, the variety iseasily identified in seed certification

Disadvantages of pureline selection The breeder has to devote more time topureline selection than to mass selection. Thisleaves less time for other breeding program. The variety developed through purelineselection generally do not have wideadaptation and stability in productionpossessed by local varieties from which theyare developed.

Pedigree selection In pedigree method, individual plants areselected from F2 and the subsequent segregatinggenerations and their progenies are tested. During the entire operation, a record of all theparent-offspring relationship is kept. This isknown as pedigree record. Individually plant selection is continued till theprogenies become virtually homozygous and theyshow no segregation, at this stage selection isdone among the progenies because there wouldbe no genetic variation within the progenies.

Merits of pedigree method This method gives the maximum opportunityfor the breeder to use his skill and judgmentfor the selection of plants particularly in theearly segregating generation. It is well suited for the improvement ofcharacters which can be easily identified andare simply inherited It takes less time than the bulk method todevelop a new variety

Demerit of pedigree method Maintenance of accurate records takes upvaluable time. Sometimes it may be a limitingfactor in large breeding program. Selection among and within a large number ofprogenies in every generation is laborious andtime consuming. The success of this method largely dependsupon the skill of the breeder.

Bulk method In the bulk method, F2 and the subsequentgenerations are harvested in mass or as bulksto raise the next generation. At the end of bulking period, individual plantsare selected and evaluated in a similar manneras in the pedigree method of breeding. The duration of bulking may vary from 6-7 ormore generations

Merit of bulk method The bulk method is simple, convenient andinexpensive Little work and attention is needed in F2 andsubsequent generations No pedigree record is to be kept which savestime and labour Artificial selection may be practiced toincrease the frequency of desirable types

Demerit of bulk method It takes a much longer time to develop a newvariety. Information on the inheritance of characterscannot be obtained which is often availablefrom the pedigree method In some cases at least natural selection mayact against the agronomical desirable types

Backcross method A cross between a hybrid(F1 or segregatinggeneration) and one of its parents is known asbackcross. In this method the hybrid and the progenies inthe subsequent generation are repeatedlybackcrossed to one of their parents.

Merit of backcross method The genotype of new variety is nearly identicalwith of the recurrent parent except for thegenes transferred. It is not necessary to test the varietydeveloped by the backcross method inextensive yield tests because the performanceof the recurrent parent is already known. Much smaller populations are needed in thebackcross than in the case of pedigree method

Demerit of backcross method The new variety generally cannot be superiorto the recurrent parent except for thecharacter that is transferred Undesirable genes closely linked with the genebeing transferred may also be transmitted tothe new variety. Hybridization has to be done for eachbackcross. This is often difficult, time takingand costly

Cross pollinated crop Population improvement Hybrid and synthetic varieties development In case of Population improvement, massselection or its modifications are used toincrease the frequency of desirable alleles,thus improving the characteristics ofpopulation.

In case of hybrid and synthetic varieties avariable number of strains are crossed toproduce a hybrid population. The strains that are crossed are selected onthe basis of their combining ability.

Plant Breeding ApproachAbiotic and biotic resistance breeding(disease/pest resistance, drought and salt tolerance)Backcross breedingBC1F1P1xClassic BreedingF1P 1 x P2F2Main StreetF3F4-5F6-7F8-10PreliminaryMolecular Parent selectionbreeding Predictive breedingMASfor simple traitsTrue/false,self testingParent selection and progeny testingMarker-assisted selection (MAS)Genome-wide selection (GWS)Marker-assisted backcross breeding (MABB)QTL-based and genome-wide predictive breedingCultivarvarietyReleaseFinal Yield TestMASfor quantitative traitsGenotyping by sequencing (GBS)RAD-seq and RNA-seqSNP discovery and validationQTL mapping and association analysisCandidate gene identified and clone

Comparative of average physical distance and locusdistance in different organismsSpeciesGenome size (kb) Genetic distance (cM)kb / cMPhage T41.6 1028000.2E. coli4.2 1031,7502.4Yeast2.0 1044,2004.8Fungus2.7 1041,00027.0Nematode8.0 104320250.0Drosophila1.4 105280500.0Rice4.5 1051,500300.0Mouse3.0 1061,7001,800.0Human race3.3 1063,3001,000.0Maize2.5 1062,5001,000.0

Needed marker number to reach specificsaturated genetic mapSpeciesHuman raceRiceMaizeArabidopsisTomatoGenome size(kb)(cM)kb/cM3.3 106330010004.5 10515003002.5 106250010007.0 1045001407.1 1051500473Map 015003000

IntroductionCharacterization using molecular markers Molecular characterization is the description of an accessionusing molecular markers. Molecular makers are readily detectable sequence of DNA orproteins whose inheritance can be monitored. There are several methods that can be employed in molecularcharacterization ,which differ from each other in term of easeof analysis, reproducibility used techniques and theiradvantages and disadvantages are presented below.

Types of Marker The development of genetic marker– Morphologic marker (eg. flower color, plant height etc.)– Protein marker / Biochemical marker (eg. isozyme)– DNA marker / Molecular marker (RFLP, RAPD, SSR etc.) Molecular nature of naturally occurred polymorphism– Point mutation– Insertion / deletion– DNA rearrangement

Some regions of genome are significantly more polymorphicthan singly copy sequencesTandem repeatsSynteny In the use of molecular marker, an important observation is the finding thatmany distantly related species have co-linear maps for portions of their genomes.SolanaceaeGramineaeLocus & alleleAllele frequency & heterozygosityDominant & co-dominant

Application of Molecular Marker PhylogenyGenetic diversityMolecular MappingGene taggingMAS, marker assisted selectionGenebank management: duplicate identificationFingerprintingQuality testing

Classification of Molecular Marker byDetection Technology Based on DNA-DNA hybridizationBased on PCR technologyBased on restriction digest and PCRBased on DNA sequencing and microarray

Based on DNA-DNA hybridization RFLP, restriction fragment length polymorphism VNTR, variable number of tandem repeats

Based on PCR technology Based on random primers––––RAPD, random amplified polymorphismic DNAAP-PCR, arbitrarily primed PCRDAF, DNA amplification fingerprintingISSR, inter-simple sequence repeats Based on special primers––––SSR, simple sequence repeatsSCAR, sequence characterized amplified regionSTS, sequence-tagged siteRGA, resistance gene analogs

The molecular basic of DNA marker1. Point mutation between restriction sites (PCR primer binding sites)2. Insertion between restriction sites (PCR primer binding sites)Insertion3. Deletion between restriction sites (PCR primer binding sites)deletion4. Number of tandem repeats varying between restriction sites (PCR primer binding sites)5. Single nucleotide mutationrestriction sitePCR primertandem repeats

Restriction Fragment Length Polymorphism(RFLP) A Restriction Fragment Length Polymorphism , or RFLP, is avariation in the DNA sequence of a genome that can bedetected by cutting the DNA into pieces with restrictionenzymes and analyzing the size of the resulting fragments bygel electrophoresis. RFLPs are detected by fragmenting a sample of DNA using arestriction enzyme which can recognize and cut DNAwherever a specific short sequence occurs. The resulting DNA fragments are then separated by lengththough gel electrophoresis, and transferred to a membraneusing the Southern Blot Hybridization method.

Then the Length of the fragments is determined usingcomplementarily labeled DNA probe. Fragment lengths vary depending on the location of therestriction sites. Each fragment length (band) can be used in thecharacterization of genetic diversity. RFLPs are generally to be moderately polymorphic. In addition to their high genomic abundance and theirrandom distribution, RFLPs have the advantages of showingco-dominant alleles and having . The method has several disadvantages as well. The methodological procedures for RFLPs are expensive,laborious and require high skilled personal.

In addition, if the research is conducted with poorly studiedcrops or wild species, suitable probes may not yet beavailable. The procedures also requires large quantities of purified,high molecular weight DNA for each digestion. Species with large genome will need more time to probeeach blot . RFLPs are not amenable to automation, and collaborationamong research teams requires distribution of the probes.

Restriction Fragment LengthPolymorphism(RFLP)1. mutation in restriction site2. insertion mutation3. Deletion mutationrestriction siteWild typeprobeMutant

Variable Numbers of TandemRepeats(VNTR)Restriction digestHybridization with tandem repeats sequence as probeautoradiographyRestriction siteCore repeat sequences

Random Amplified Polymorphic DNA (RAPD) The method termed random amplification of polymorphicDNA (RAPD) uses a polymerase chain reaction (PCR) machineto produce many copies (amplification ) of random DNAsegments called random amplified polymorphic DNA (alsoRAPD). Several arbitrary, short primers (8-12 nucleotides) arecreated and applied in the PCR using a large template ofgenomic DNA, hoping that fragments will amplify. By resolving the resulting patterns using agarose gel andethidium bromide staining, a semi-unique profile can begleaned from a RAPD reaction.

Unlike traditional PCR analysis, RAPD does not requireany specific knowledge of the DNA sequence of the targetorganism: the identical 10-mer primers will or will notamplify a segment of DNA, depending on positions thatare complementary to the primers' sequence. For example, no fragment is produced if primersannealed too far apart or 3' ends of the primers are notfacing each other. Therefore, if a mutation has occurred in the templateDNA at the site that was previously complementary to theprimer, a PCR product will not be produced, resulting in adifferent pattern of amplified DNA segments on the gel.

Limitations of RAPD Nearly all RAPD markers are dominant, i.e. it is not possible to distinguish whethera DNA segment is amplified from a locus that is heterozygous (1 copy) orhomozygous (2 copies). Codominant RAPD markers, observed as different-sizedDNA segments amplified from the same locus, are detected only rarely.PCR is an enzymatic reaction, therefore the quality and concentration of templateDNA, concentrations of PCR components, and the PCR cycling conditions maygreatly influence the outcome. Thus, the RAPD technique is notoriously laboratorydependent and needs carefully developed laboratory protocols to be reproducible.Mismatches between the primer and the template may result in the total absenceof PCR product as well as in a merely decreased amount of the product. Thus, theRAPD results can be difficult to interpret.

Random Amplified Polymorphic DNA(RAPD)1. Point mutation in PCR primer binding site -12. Point mutation in PCR primer binding site -23. Insertion mutation4. Deletion mutationprimerWild typeMutant

Simple Sequence Repeats(SSRs) Simple Sequence Repeats(SSRs) or microsatellites, are polymorphic locipresented in nuclear and organellar DNA. They consist of repeating unitsof 1-6 base pair in length. They are multi-allelic and co-dominant. SSRs are used in population studies, genetic diversity analysis and tolook for duplications or deletions of a particular genetic region. Microsatellites can be amplified through PCR, using the uniquesequences of flanking regions as primers. Point mutation in the primer annealing sites in such species may lead tothe occurrence of ‘null alleles’, where microsatellites fail to amplify in PCRassays.

Importance of characterization and evaluationInformation derived from characterization and evaluation of germplasmcollection can be used to: Identify an accession Monitor identify of an accession over a number of regenerations Locate specific traits Assess genetic diversity of the collection Fingerprint genotypes Identify duplications Determine gap in the collection Facilitates preliminary selection of germplasm by end-users Study genetic diversity and taxonomic relationships Develop core collection

Simple Sequence Repeat (SSR)

Developing SSR PrimersGenome DNADigested fragments cloned to plasmid vectorHybridized by poly GA/CT probeExtract plasmid DNA from positive clonesSequencing of cloned fragmentsDesigning primers according to flanking sequence

Based on restriction digest and PCR AFLP, amplified fragment length polymorphism CAPS, cleaved amplified polymorphic sequence

Amplified Fragments Length Polymorphism(AFLP) Amplified Fragments Length Polymorphism(AFLP) are DNAfragments obtained by using restriction enzymes to cutgenomic DNA, followed by ligation of adaptors to the stickyends of the restriction fragments. The amplified fragments are visualized an denaturingpolyacrylamide gels either through autoradiography or viafluorescence methodologies. AFLP has many advantages compare with other markertechnologies. AFLP-PCR is a highly sensitive method for detectingpolymorphisms in DNA. AFLP has higher reproductively, resolution and sensitivelyat the whole genome level compared to other techniques.

It also has the capacity to amplify between 50 and 100 fragments at onetime. In addition, no prior sequence information is needed foramplification AFLP is widely used for the identification of genetic variation in strains orclosely related plant species. The AFLP technology has been used in population genetics to determineslight differences within populations, as well as in linkage studies togenerate maps for quantitative trait locus(QTL) analysis. AFLPs can be applied in studies involving genetic identity, parentage andidentification of clones and cultivars, and phylogenetic studies of closelyrelated species. The disadvantage of AFLP includes the need for purified, high molecularweight DNA, the dominance of alleles, and the possible non-homology ofcomigrating fragments belonging to different loci.

Procedure of AFLPPre-selective amplificationSelective amplificationDenatured Gel Electrophoresis

Based on DNA sequencing and microarray SNP, single nucleotide polymorphism––––––SSCP (Single-strand conformation polymorphism)DGGE (Denaturing gradient gel electrophoresis)ASA (Allele-specific amplification)GBA (Genetic bit analysis)Oligonucleotide chip-based hybridizationMALDI-TOF MS (Matrix assisted laser desorption ionization,time of flight mass spectrometry)

Marker Development for Molecular BreedingDonor ScreeningPopulation DevelopmentPhenotypic DataGenotypic DataData AnalysisQTL MappingAssociation AnalysisMarker IdentificationMarker ImplementationMolecular Breeding

Molecular Plant Breeding ApproachSNP is a single nucleotide (A, T, C orG) mutation, and can be discoveredfrom PCR, Next generation sequencing(NGS) such as RNA-Seq, RAD-Seq, GBS.Tool: BioEdit, DNASTAR, SAMtools,SOAPsnp, or GATKMarker Discovery(SNP, SSR)SSR is repeating sequences of 2-5 (most of them)base pairs of DNA such as (AT)n, (CTC)n, (GAGT)n,(CTCGA)nTool: SSRLocator, BatchPrimer3, MEGA6, BioEditGenetic diversityGeneticDiversityGenetic ngAssociation analysisMAS/GWSQTL mappingGenetic MapMarker Identification(SNP, SSR Markers)AddeffectDomeffectLODR 2(%)CoP930721 82 -0.123-0.1224.4636.1CoP930934 82 me-wideSelectionMolecular BreedingSNP markers

Fall 2016 HORT603310/31/2016Marker-assisted SelectionMarker-assisted Selection (MAS): using marker(s) to select trait of interest.Marker type: SSR and SNPQTL mapping :Linkage analysisAssociation AnalysisMarker: traitMarker IdentificationMarker ImplementationParent selection and progeny testingEarly generation selection for simple traitMarker-assisted backcrossingLate generation selection for complex traitGene-pyramidingCultivar identity/assessment of ‘purity’

Marker Assisted Selection(MAS) Inplant breeding Marker assisted selection refers to themanipulation of genomic regions that areinvolved in the expression of traits of interestthrough molecular markers. MAS of parental Lines for trait improvement: Molecular markers can be used to genotype aset of germplasm and the data used toestimate the genetic divergence among theevaluated materials

Use of Molecular Markers Clonal identity, Family structure, Population structure, Phylogeny (Genetic Diversity) Mapping Parental analysis, Gene flow, Hybridisation

Foreground selection and backgroundselection using molecular markerMolecular markers are now increasingly beingemployed to trace the presence of the targetgenes(foreground selection) as well as foraccelerating the recovery of the recurrentparent genome(background selection) inbackcross program.MAS for improvement of qualitative traits:MAS in developing quality protein maize(QPM)genotypes

MAS for improvement of quantitativetraits MAS for improving heterotic performance inmaize MAS for drought tolerance in maize Germplasm enhancement in tomatousingAB QTL QTL mapping Single marker approach Simple interval mapping (SIM)

Composite interval mapping (CIM)Application of biotechnology in plant breedingSomclonal variationDirected selectionHaploidyGene transferGermplasm and pedigree identification

Jian-Long Xu, Institute of Crop Sciences, CAAS. Molecular Marker-assisted Breeding in Rice

Population Size for MASJian-Long Xu, Institute of Crop Sciences, CAAS. Molecular Marker-assisted Breeding in RiceEquation to Estimate Sample Size Required for QTL Detection

Marker Assisted SelectionUseful when the gene(s) of interest is difficultto select:1. Recessive Genes2. Multiple Genes for Disease Resistance3. Quantitative traits4. Large genotype x environment interaction

MARKER ASSISTEDBREEDING SCHEMES1.2.3.4.Marker-assisted backcrossingPyramidingEarly generation selection‘Combined’ approaches

Marker-assisted backcrossing(MAB) MAB has several advantages over conventionalbackcrossing:– Effective selection of target loci– Minimize linkage drag– Accelerated recovery of recurrent parent123412341234TargetlocusTARGET IONBACKGROUNDSELECTIONBACKGROUND SELECTION

Gene Pyramiding Widely used for combining multiple disease resistancegenes for specific races of a pathogen Pyramiding is extremely difficult to achieve usingconventional methodsConsider: phenotyping a single plant for multiple forms ofseedling resistance – almost impossible Important to develop ‘durable’ disease resistance againstdifferent races

Process of combining several genes, usually from 2 different parents,together into a single genotypeBreeding planP1xP1Gene AGene BGenotypesP1: AAbbF1Gene A BF2MASSelect F2 plants that haveGene A and Gene BP2: aaBBxF1: aBAaBBAaBbaaBBaaBbabAaBbAabbaaBbaabb

Early generation MAS MAS conducted at F2 or F3 stage Plants with desirable genes/QTLs are selected andalleles can be ‘fixed’ in the homozygous state– plants with undesirable gene combinations can bediscarded Advantage for later stages of breeding programbecause resources can be used to focus on fewerlines

P1xSusceptibleP2ResistantF1F2large populations (e.g. 2000 plants)MAS for 1 QTL – 75% elimination of (3/4) unwanted genotypesMAS for 2 QTLs – 94% elimination of (15/16) unwanted genotypes

SINGLE-LARGE SCALE MARKERASSISTED SELECTION (SLS-MAS)PEDIGREE METHODP1xP2P1F1F2xP2F1PhenotypicscreeningPlants spaceplanted in rowsfor individualplant selectionF3F3Families grownin progeny rowsfor selection.F4F5Families grownin progeny rowsfor selection.F5Pedigreeselection basedon local needsF6F6F7Furtheryield trialsF7Multi-location testing, licensing, seedOnly desirableF3 lines plantedin fieldF4Preliminary yieldtrials. Selectsingle plants.F8 – F12 increase and cultivar releaseMASF2Multi-location testing, licensing, seedF8 – F12 increase and cultivar releaseBenefits: breeding program can be efficientlyscaled down to focus on fewer lines

Combined approaches In some cases, a combination of phenotypicscreening and MAS approach may be useful1. To maximize genetic gain (when some QTLs havebeen unidentified from QTL mapping)2. Level of recombination between marker and QTL(in other words marker is not 100% accurate)3. To reduce population sizes for traits where markergenotyping is cheaper or easier than phenotypicscreening

‘Marker-directed’ phenotyping(Also called ‘tandem selection’)P1 (S) x P2 (R)RecurrentParentDonorParentF1 (R) x P1 (S)BC1F1 phenotypes: R and SUse when markers are not100% accurate or whenphenotypic screening ismore expensive comparedto marker genotypingMARKER-ASSISTED SELECTION (MAS)1 2345 6 789 10 11 12 13 14 15 16 17 18 19 20 SAVE TIME & REDUCECOSTSPHENOTYPIC SELECTION*Especially for quality traits*

Crop characterization by identifyingisozymes Enzymes electrophoresis relies on quantifying aseries of enzymes that are present in a specifictissue such as germinating seedlings Within each enzyme measured differentalleles(allozymes or isozymes) can be measuredby their differential migration on a starch orpolyacrylamide gel Enzyme electrophoresis refers to the migration ofproteins(enzymes) from a starting point at thebase of the gel and across an electric field.

The amount of migration is dependent on the molecular weight ofthe enzyme, charge differences, and three-dimensional structure. Early studies in maize could resolve approximately 85% of a sampleof inbred with known pedigrees (Stuber and Goodman, 1983).Smithet al.(1987)were able to distinguish 94% of 62 inbred lines of knownpedigree. Furthermore, these inbred could be identified in hybridcombinations and hybrid yield could be predicted based on theirenzymes profile. Biochemical data is generally accepted as one method of identifyinggermplasm and in at least one legal case in United States has beenused to verify ownership of a maize inbred .

Advanced tools for Plant Breeding Mutagenesis Tissue culture Haploidy In situ hybridization DNA markers

Advanced technology Molecular markers Marker-assisted selection DNA sequencing Plant genomic analysis Bioinformatics Microarray analysis Primer design Plant transformation

Modern Breeding ToolsIn vitro cultureGenomic toolsGenomic engineeringIncrease of breeding effectiveness and efficiency

Future ChallengesMultidisciplinary FieldPathologyChallenge: Increase of humanpopulation by 60-80%, requiring tonearly double the global foodproductionBiometry/Statistics

Molecular characterization is the description of an accession using molecular markers. Molecular makers are readily detectable sequence of DNA or proteins whose inheritance can be monitored. There are several methods that can be employed in molecular characterization ,which differ from each other in term of ease

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