Briefly Description about the mapping and tagging of aromatic genes

1. Master Seminar [GPB 591]
By: Prateek Chhari
M.Sc. (Ag) GPB
210116014
CoA, JNKVV, Jabalpur
)
on
Seminar Incharge -
Dr. R.S. Shukla
Dr. Yogendra Singh

2. Rice
Aromatic Rice
Gene Responsible for Aroma
GeneTagging
Gene Mapping
Step of Genetic Mapping
Significance of Genetic
Mapping &Tagging
Aroma Gene and Its Role in
Breeding Programme
Case Study 1
Case Study 2
Content
2 2/25/2023 Add a footer

3. RICE
• RicebelongstothegenusOryza,whichcontains2
cultivated (OryzasativaandOryzaglaberrima)and22
wildspecies.
• Asperthepresenttaxonomicdetailsofthiscrop, outof
22wildspecies,14arediploid (2n=2x=24)andrest8are
tetraploid(2n=4x=48). Thecultivatedspecies Oryza
sativaandOryzaglaberrimaarediploid.
• Riceproductiontotaled 503.27milliontonnes.Inwhich
Indiacontributed 124 milliontonnes.Outoftotaled
Production90%riceisproduced inAsiaalone
(Source: USDA(2022)
• Thevalueofriceissummed upintheiconicFAOslogan
"RiceisLife,"whichwascoinedduring theYearofRice
in2004

4. RICE
• Thegenomeis466megabasesinsize,withan
estimated46,022to55,615genes
• IndiaContributedforgenomesequencingof
shortarmofChromosome11&manyimportant
ResistanceGeneswereidentifiedonthis
chromosome
Source: www.ncbi.nlm.nih.gov/genome/

5. 5 2/25/2023 Add a footer
Rice Production By Continent
CONTINENT POPULATION PRODUCTION
OF RICE (Mt)
ASIA 4650M 6,77,276,789
AFRICA 1384 M 38,771,392
EUROPE 745M 4,023,638
NORTHAMERICA 504M 35,325,593
SOUTHAMERICA 438M
CENTERAL
AMERICA
51M
CARIBBEAN 44M DataNot
Available
OCEANIA 45M 76,388
Source : www.fao.org (FAO Statistical Data) 2020
Asia 89% Africa 5.1% Europe 0.53%
Americas
4.65%
Oceania 0.1%
Production 677,276,789 38,771,392 4,023,638 35,325,593 76,388
0
100,000,000
200,000,000
300,000,000
400,000,000
500,000,000
600,000,000
700,000,000
800,000,000
MT:
Million
Tons
Production

6. RiceProductionduring2021-22was 515.05milliontons.Thisyear's503.27 estimatedmillionstonscould
representadecreaseof11.78milliontonsor2.29%in riceproductionaroundtheglobe.
MAJOR COUNTRY PRODUCTION (Mt)
China 147,000,000
India 124,000,000
Bangladesh 35,650,000
Indonesia 34,600,000
Vietnam 27,225,000
Thailand 20,100,000
Burma 12,500,000
Philippines 12,411,000
Japan 7,450,000
Brazil 7,235,000
6 2/25/2023 Add a footer
China
34%
India
29%
Bangladesh
8%
Indonesia
8%
Vietnam
6%
Thailand
5%
Burma
3%
Philippines
3%
Japan
2%
Brazil
2%
Production (%)
China India Bangladesh Indonesia Vietnam Thailand Burma Philippines Japan Brazil
Source: USDA (2022)

7. 7 2/25/2023 Add a footer
Source: National Research Centre on
Plant Biotechnology India

8. AROMATIC RICE
• Aromainriceisconsideredasoneofthemajor
importantqualitytraitspreferred forconsumption.
• Aromainscentedandbasmatiriceisdueto2-acetyl-1-
pyrroline.
• Thearomadevelopmentinricegrainisinfluencedby
bothgeneticandenvironmentalfactors.
• Indiahasimmensewealthofaromaticrice,andthis
sub-continentisknownashomeforaromaticrice
diversity
• Basmatirice,jasminerice,Dehradunbasmati,Katarni
etc.aresomeimportanttypesoffragrantrice.
8

9. AROMATIC RICE
9 2/25/2023 Add a footer
• Aromaticricecontributedaround20-22%inthe
ProductionWorldwide(www.ers.usda.gov) (2022)
• Morerecently,intraditionalBasmatiandJasmine-like
rice,Bradburyetal.(2005 a,b)demonstratedaroma
regionongenomeandidentifiedasinglerecessivegene
responsibleforaroma.Thisgeneisadefectivealleleofa
geneencodingbetainealdehydedehydrogenaseBADH2.
• AnumberofricearomaQTLshavebeenidentifiedon
chromosomes3, 4,5,8and12

10. SOME AROMATIC RICE ACROSSTHE WORLD
10

11. STRUCTURE OF COMPOUND 2-ACETYL-1-PYRROLINE (2 AP)
11 2/25/2023 Add a footer
Aromain riceisdueto2-acetyl-1-pyrroline

12. Biosynthetic Pathway of 2-Acetyl-1-Pyrroline (2AP)
Rice
12
• Ricearomaisaphenotypicalexpressionof
spontaneousrecessivemutationsofthe
OsBadh2gene(alsoknown asfgr/badh2/
osbadh2/os2APgene)
• 1-Pyrroline-5-carboxylatesynthetase(P5CS)
geneisreportedtoregulatetheproline
synthesisinplantsandactsastheprecursor
of2AP
• OsGlyI,improvesabioticstresstoleranceand
grainyieldinrice

13. Full Length of BADH2 & P5CS Gene
13 2/25/2023 Add a footer
Inaccordance,theintact,full-length
BADH2protein(503residues)
appearedexclusivelyinnonfragrant
transgeniclinesandricevarieties.
Theseresultsindicatethatthefull-
lengthBADH2proteinencoded
byBadh2rendersricenonfragrantby
inhibiting2APbiosynthesis.
Inaccordance,theintact,full-length
P5CSprotein(716residues) Source: www.uniprot.org/uniprotkb/Q84LK3/entry

14. DescriptionofSomePotentialGenesRelatedtoAromainRice
14 2/25/2023 Add a footer
Source : Prodhan and Qingyao (202

15. List of Badh2 Alleles Identified FromTheWhole
Genome Sequences ofThe Aromatic RiceVarieties
15 2/25/2023 Add a footer
Rice Genome
Imagecourtesyof GuotianLiandRashmiJain

16. List of Badh2 Alleles Identified FromThe Whole Genome
Sequences ofThe Aromatic RiceVarieties
16 2/25/2023 Add a footer

17. GENETAGGING
•Itreferstotheidentificationofexisting
DNAortheintroductionofnewDNAthat
canfunctionasatagorlabelforthegene
ofinterest.
•Itismostcommonmethodusedfor
selectionagainstdifferentbioticand
abioticstressresistancesstudiesincrop
plants.
17

18. STEPS IN GENETAGGING AND MAPPING
I. SelectionofTargetTraits
II. IdentificationofParentsdifferinginthetraitofinterest
III. Developmentofappropriatepopulationsegregatingforthetraitofinterest
IV. ScreeningthePopulationfortheTargetTrait(Phenotyping)
V. ParentalPolymorphismSurveywithMarkersandIdentificationofMarkersthatCo-
segregatewithGene(s)ofInterestintheIndividualsConstitutingthePopulation
VI. ConstructionofLinkageMap
VII. TestforReliabilityoftheIdentifiedMarkersinPredictingtheTraitinAlternate
Population(MarkerValidation)
VIII. UtilizationoftheMarkerinBreedingProgrammes
18 2/25/2023 Add a footer

19. GENE MAPPING
• Genemappingrefers totheprocessof
determiningthelocationofgeneson
chromosomes.Today,themostefficient
approachforgenemappinginvolves
sequencingagenomeandthenusing
computerprogramstoanalyzethe
sequencetoidentifythelocationof
genes.
• Agenomemaphighlightsthekey
‘landmarks’Inanorganism’sgenome
19 2/25/2023 Add a footer

20. MOLECULAR MAPPING
• Thelandmarksonagenomemapmay
includeshortDNAsequences,regulatory
sitesthatturngenesonandofforthegenes
themselves.
• Genomemappingprovidedthebasisfor
wholegenomesequencing
• SequencedDNAfragmentscanbealignedto
thegenomemaptoaidwiththeassemblyof
thegenome.
20 2/25/2023 Add a footer

21. TYPES OF GENE/GENOME MAPPING
• Therearetwogeneraltypesofgenomemappingcalled
I. Genetic mapping
II. Physicalmapping
• Bothtypesofgenomemappingguidescientiststowardsthelocationofagene
(orsectionofDNA)onachromosome,however,theyrelyonverydifferentinformation.
• Genetic mappinglooksathowgeneticinformationisshuffledbetween
chromosomesorbetweendifferentregionsinthesamechromosome
duringmeiosis(atypeofcelldivision). Aprocesscalledrecombinationor‘crossing
over’.
• PhysicalmappinglooksatthephysicaldistancebetweenknownDNAsequences
(includinggenes)byworkingoutthenumberofbasepairs(A-T,C-G)betweenthem.
21 2/25/2023 Add a footer

22. Showingthedifferencebetweenthetwobasicwaysofmappingagenome
geneticmappingandphysicalmapping.
22 2/25/2023 Add a footer

23. Steps of Genetic Mapping &Tagging For Aroma Gene
23 2/25/2023 Add a footer
Field Work
•PlantMaterial
•Estimationofgrainaroma
LabWork
•SSRmakerdevelopment
•DNAextractionandPCRamplification
Lab + Software
Work
•ConstructionoflinkagemapandQTLmapping

24. 24 2/25/2023 Add a footer
StepsofGeneticMapping
RiceLeaf
DNA Extraction from Rice
leaf

25. 25 2/25/2023 Add a footer
Steps ofGenetic Mapping Part -2
GelScoring
GelElectrophoresis
P Srivong et al (2008)

26. 26 2/25/2023 Add a footer
ConstructionoflinkagemapandQTLmappingWiththeHelpofMAPMAKER
Image credit: Genome Research Limited.

27. IntegrationofReportedQtlsforAromaWithRespectiveCandidateGenes
inRice
27 2/25/2023 Add a footer
Source : Prodhan and Qingyao (2020)

28. Significance of Genetic Mapping &Tagging
• Genetic mappingorlinkagemappingprovides
evidencethatadiseasetransmittedfrom
parenttochildisofferlinkedtooneormore
genes.
• Thedetailedgeneticmaphelpstolocatethe
riskgenesforahostofgeneticdiseases.
• Knowledgeofthegeneticmapofplants&
animalsleadstodevelopmentofagricultural
crops&animalbreeds,thataremore
nutritious,productive&betterresistive.
• Moreovertherearegreatadvantagesinenergy
&environment,inforensicsciencetoo.
28 2/25/2023 Add a footer

29. AROMA GENES AND ITS APPLICATION IN RICE GENETICS
AND BREEDING
• Thegeneticbasis ofricearomageneiscomplexduetodifferentfragranttypessuch asjasmine,
popcorn,hickoryandvioletand duetotheenvironmentalfactors interactingwitharomagenes
• Asaromageneiscontrolledbyrecessive genesointroductionoftheBadh2mutantgeneintothe
existingelitevarietiesbyhybridizationandbackcrossing shouldbedone
• Chinesericebreedershavesuccessfully doneresearches onthehigh-yield,high-quality,multi-
resistancefragrantricevarieties,andscreenedaseriesofaromaticricerestorerlines,sterilelines,
andnewhybridcombinations
• Molecularmarkerassistedselectionhas beenwidelyusedinacceleratingtheprocessofscreening
andbreedingofnewvarietiesofaromaticrice.Molecularmarkerssuchas RG28, SCU015RM, and
RSP04coulddifferentiatebetweennon-aromaticandaromaticrice
• Genomeeditingtechnologycouldmakenon-aromaticriceproducefragrancebyinsertion,
replacementordeletionofBadh2 gene
29 2/25/2023 Add a footer

30. Case Study 1
30 2/25/2023 Add a footer

31. Case Study 2
31 2/25/2023 Add a footer

32. Sources & References
1. Source:Prodhanand Qingyao(2020)
2. https://www.ncbi.nlm.nih.gov/genome/
3. Source:Bradburyetal(2005)
4. FAOSTATUSDA
5. Source: Venkatesan,K.etal. (2015)
6. Source:Prodhan and Qingyao(2020)
7. USDA(2022)
8. GenomeResearchLimited
32 2/25/2023 Add a footer