Harnessing genetic inheritance: Advances in groundnut breeding for drought and foliar disease resistance - Doctrol Seminar - II.pptx

Economic importance
Resistant sources and Introgression
Gene action
Gene mapping
Marker assisted breeding
Transcriptomics
Proteomics
Metabolomics
Transgenics
Constraints
Future prospects

1. Submitted by :- P .TEJASREE TAD/2023-010 Ph.D. 1 st Year Dept. of GPBR Submitted to :- Dr. M. Reddi Sekhar Senior Professor & Head Dept. of GPBR ACHARYA N.G. RANGA AGRICULTURAL UNIVERSITY S.V. AGRICULTURAL COLLEGE, TIRUPATI Course No :- GPB-692 Course Title :- Doctoral Seminar-II Harnessing genetic inheritance: Advances in groundnut breeding for drought and foliar disease resistance DEPARTMENT OF GENETICS AND PLANT BREEDING 1

2. Table of Contents 2 Resistance Breeding Economic importance Resistant sources and Introgression Gene action Gene mapping Marker assisted breeding Transcriptomics Proteomics Metabolomics Transgenics Constraints Future prospects

3. 3 E arly L eaf S pot (ELS) Cercospora arachidicola L ate L eaf S pot (LLS) Pheoisariopsis personatum Rust Puccinia arachidis Speg . Economic importance https://extension.okstate.edu/fact-sheets/foliar-diseases-of-peanuts.html

4. 4 Web Blotch Phoma arachidicola Pepper Spot Leptosphaerulina crassiasca B reeding resistant cultivars is one of the best means of reducing crop yield losses from biotic stresses and also the best strategy to overcome additional cost of production. https://extension.okstate.edu/fact-sheets/foliar-diseases-of-peanuts.html Alternaria leaf blight Alternaria arachidis

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6. 6 Phenotyping for foliar diseases Field Screening Detached Leaf Technique for Leaf Spots and Rust A rtificial inoculation Subrahmanyam et al ., 1995 Field Screening Detached Leaf Technique A rtificial inoculation

7. 7 The response of drought tolerance and susceptibility was assessed in terms of Drought susceptibility index ( DSI) for total dry matter (TDM), pod yield and HI and physiology indices for RWC, SLA , MSI and SCMR . DSI = [ 1 - ( Y d / Y p )] /D D = Drought Intensity = 1 - ( mean Y d of all genotypes in the non-irrigated treatment) (mean Y p of all genotypes in the irrigated treatment) DSI - < 1 - tolerance to drought DSI - > 1 - susceptibility J.C. Gutiérrez - 1998 - Proceedings of the World Cotton Research Conference -2 - 130-134. Phenotyping for drought Y d - yield of a genotype under stress Y p - yield of a genotype under well water

8. 8 Rating scale for field evaluation of leaf spot incidence Resistant Moderately resistant Susceptible Highly Susceptible Subrahmanyam et al ., 1995

9. 9 Rating scale for rust incidence Resistant Moderately Resistant Highly Susceptible Susceptible Subrahmanyam et al ., 1995

10. 10 Rathod et al ., (2020) - Plant Gene - 23 (2020)100243 Major defense mechanisms observed in peanut plants as a result of fungal infection

11. 11 Schematic demonstration of drought-tolerance mechanism in grain legumes Khatun et al ., 2021 - Agronomy – 11 : 2374

12. 12 Assembly of genetic resources ICRISAT, INDIA National Bureau of Plant Genetic Resources (NBPGR) Directorate of Groundnut Research (DGR) Chinese Academy of Agricultural Sciences (CAAS) Guangdong Academy of Agricultural Sciences , China U.S. Department of Agriculture (USDA) Texas A&M University (TAMU) North Carolina State University (NCSU), USA EMBRAPA – CENARGEN , Brazil Instituto Agronomico de Campinas in Brazil Instituto Nacional de Technologia Agropecuaria (INTA), Argentina Instituto de Botánica del Nordeste (IBONE), Argentina Pasupuleti and Nigam (2013)

13. 13 Germplasm Pools Rami et al ., 2014.

14. 14 Wild arachis species with multiple resistance to disease and pests Singh and Oswalt – 1991 - Skill Development Series no.4

15. 15 Germplasm FESR-5-l-B-b4 FESR-5-2-B-64 NC3033 PI 109839 ICG 7878 ICG 6284 ICG 405 ICG 1705 UP 81206-1 UF 81206-2 72 x 32B 3-2-2-2-l-b3-B NC3033 AC3139 PI Nos. 203395 203397 261893-2-1-1-13 261893-1-3-B 261893-2-1-4-1-2B 261906-1-1-1-2-3B NC 3033 ICG 7756 ICG 1710 ICGV 86699 ICGV 99001 ICGV 99004 Early leaf spot Late leaf spot CS9 , CS30, CS22, CS62, CS31, CS26, CS36, CS2403, CS820/1, CS13-1-B1-B3-B1, CS16-B2-B2-B1, CS29/1-B2-B1-B1, and NC Ac 17090 (Interspecific hybrid crosses) Lines resistant to late leaf spot and rusts

16. 16 Rust PI 259747 PI 390593 ICGV 94114 ICGV-SM 86021 ICGV-SM 02536 ICG 02194 ICGV 01276 ICGV 02286 DTG 60 JL 776 (immune) TG 66 G 2-52 (highly resistant)  In India, six remarkable breeding lines have been identified for their immunity to rust—B3-F3-36-5, B3-F3-36-6, TFDRG 1, VG 9514, ICGV99003, and ICGV99005 Germplasm CSMG 84-1 ICGV 86031 ICGV 87128 Chico GNP 35 ICG 1660 ICG 3386 ICG 3736 ICG 296 ICG 405 ICG 1697 ICG 4790 ICG 4747 ICG 6997 ICG 2960 ICG 3301 ICG 4544 ICG 4728 ICG 3657 UP 67 Arbrook (PI 262817) Drought

17. 17 Incorporation of Genes from Wild Diploids into Cultivated Groundnut Methods of producing hexaploids and hybrid tetraploids for backcrossing to Arachis hypogaea to transfer genes from wild species into cultivated groundnut. ICRISAT 1980, and A.K.Singh , ICRISAT, personal communication 1989 Gene transfer from compatible species Ploidy manipulations Use of incompatible species Induced Mutagenesis

18. 18 (Dwivedi et al ., 2007; Holbrook and Stalker, 2003) Production and testing of tetraploids Production of hybrid tetraploids from diploids Gene transfer from compatible species

19. 19 Production of hybrid tetraploids from two wild diploids Production of tetraploids from diploids (Dwivedi et al ., 2007; Holbrook and Stalker, 2003)

20. 20 The hybrids produced by crossing cultivated groundnut with the diploid wild species are triploid and sterile. Their fertility could be restored by induction of polyploidy using the colchicine technique Ploidy manipulations sections Rhizomatosae and Erectoides have been crossed with A. hypogaea or diploid species of section Arachis’ with the help of hormone treatments (GA3, IAA, and Kinetin) and/or in vitro embryo rescue techniques. Use of incompatible species (Dwivedi et al ., 2007; Holbrook and Stalker, 2003)

21. 21 Physical mutagenesis: In groundnut 10, 20, 30, 40, 50 and 60 KR gamma irradiations are reported. Chemical mutagenesis: ethyl methane sulphonate (EMS), diethylsulfate (DES), ethylene-imine (EI), N-nitroso- N-methyl Urethane (NMUT), N-nitro-N-methyl urea (NMU), and ethyl bromide (EB). Induced Mutagenesis Gunasekaran, A. and Pavadai , P., 2015. Studies on induced physical and chemical mutagenesis in groundnut ( Arachis hypogaea ).  International Letters of Natural Sciences ,  8 .

22. 22 F irst generation Girnar 1 , ICGS(FDRS) 4 and ICGS (FDRS) 10 F oliar disease and drought resistant varieties S econd phase ICGV 86590, ICGV 86699 and ALR 2 GPBD-4, AK-265, ALR-1, JCG-88, VRI-( Gn ) 5, RHRG- 06083, JL-776, KDG-123, KDG-128 . Drought - Ajeya (R 2001-3), Jawahar Groundnut 23 (JGN 23), Greeshma, GKVK-5, Dh256 DIRECTORATE OF OILSEEDS DEVELOPMENT, Ministry of Agriculture & Farmers Welfare, Government of India

23. 23 Assessment of gene action Trait Method Type of gene action Reference Early leaf spot Diallel Additive Zongo et al ., 2019 Diallel Additive Tembo et al ., 2018 Late leaf spot GMA Additive Janila et al ., 2013 Rust Diallel Dominance Daudi et al ., 2021 Diallel cross analysis Line × Tester cross analysis Generation mean analysis

24. 24 I mprovement of peanut biotic stress resistance using integrated Omics technologies Huang et al ., (2023) - Front. Plant Sci. 14:1101994.

25. Markers linked to foliar diseases and drought 25 Trait Markers Reference Early leaf spot GM1911, GM1883, GM1000, and Seq13E09 Zongo et al . (2017) Late leaf spot GM1954, GM1009 and GM1573 GKAMA02GL582, GKAMA02GL829 and GKAMA02GL975 pPGPseq5D05 Sukruth et al ., (2015) Danso et al ., (2024) Killada et al ., (2024) Rust SEQ16C6, GM 1733 , SEQ9H08, TC2A02, PM 384, PM 418 and SEQ15C10 srividya (2019) Drought GM2246, GM660,GM679, GM1911, GM694 , Seq16C06 , Seq13B08 , PM499 , PM375 , IPAHM10 8, TC3A12 , TC2D06, TC1A02 Gautami, 2012; Pandey et al ., 2020 Ravi et al ., 2011

26. 26 QTLs associated with foliar diseases and drought Trait QTL identified Phenotypic variance explained Reference Leaf spot 80 1.7–50.9 Khedikar et al ., (2010), Han et al ., (2018) Ahmad et al ., (2020), Kumari et al ., (2020), Khera et al ., (2018), Liang et al ., (2017) Rust 34 7.24–48.7 Bertioli et al ., (2015), Ahmad et al ., (2020), Kumari et al ., (2020), Khera et al ., (2018), Drought related traits Shoot dry weight 16 4.2–22.09 Gautami et al ., (2012), Pandey et al ., (2020) Transpiration efficiency 27 4.47–18.12 Ravi et al ., (2011), Pandey et al ., (2020) Leaf area 26 5.0–16.2 Transpiration rate 13 4.3–17.3 Ravi et al ., (2011), SCMR 29 4.00–19.53 Pandey et al ., (2020)

27. 27 F2 mapping population GJG17× GPBD4 1311 SSR markers ICIM mapping Also in accordance with Sujay et al . 2012; Khedikar et al . 2010; Gajjar et al . 2014 Ahmad et al ., (2020) - 3 Biotech - 10:458 QTLS for LLS and Rust

28. 28 Differentially expressed genes in QTL regions for LLS resistance Gangurde et al ., (2021) - Int. J. Mol. Sci - 22, 4491

29. 29 T TE CC CC CC TE TE SLA SLA SLA SLA SCMR SCMR SCMR SCMR SCMR SCMR DW DW DW CAs DM Bio Bio Pod Pod Pod Pod Seed Seed Ravi et al ., 2010 – Theory of Applied Genetics - 122:1119 –1132 TAG 24 (low TE) and ( high TE) ICGV 86031 318 RILs 3,215 SSR markers QTL Cartographer QTLs for DROUGHT

30. 30 Fine-mapping of the peanut web blotch resistance gene Arahy . 35VVQ3 Functional annotation of the genes in the candidate region Wu et al ., (2024) – Journal of Integrative Agriculture - 23(5): 1494–1506 QTLs for Web blotch

31. 31 Rathod et al ., (2020) - Plant Gene – 23:100243 Transcripts produced during ELS, Rust infection and drought ELS, RUST – GPBD 4 Rathod et al ., (2020) - 3 Biotech -10:284 F box MAPK signalling pathway Transcription Factors Starch and sucrose metabolism Flavonoid biosynthesis Phenylpropanoid biosynthesis Glutathione metabolism Hormone metabolism Zhao et al ., (2021) - Front. Genet - 12:672884 drought-tolerant cultivar, “L422”

32. 32 Photosynthesis Oxygen-evolving enhancer protein Ribulose-bisphosphate carboxylase activase , Light-harvesting chlorophyll a/b-binding protein Photosystem II stability/assembly factor Metabolism Sedoheptulose - 1,7-bisphosphatase, Glyoxalase I Malate dehydrogenase. secondary metabolism Dihydro flavonol reductase Terpenoid synthase. signal transduction Putative F-box protein Phytochrome A Defense Defensin like protein, Monodehydroascorbate reductase, Glyceraldehyde-3-phosphate dehydrogenase Proteins produced during LLS infection – A.diogi Kumar and Kriti (2015) - PLoS ONE 10(2): e0117559 Cytochrome P450 monoxygenase vacuolar processing enzyme heat shock 70 kDa protein 15-Hydroxyprostaglandin

33. 33 Katam et al ., (2016) – Journal of Proteomics - 143- 209-226 Drought responsive proteins lignification peroxidation

34. 34 Mahatma et al ., (2021) - Physiol Mol Biol Plants - 27(5):1027–1041 Metabolites associated with Rust, Late Leaf Spot Rathod et al. BMC Genomics (2023) 24:630

35. 35 Drought tolerant TAG 24 and drought-sensitive JL 24 genotypes GC-MS MetaboAnalyst 4.0 metabolites associated with drought stress Gundaraniya et al ., (2020) – 5: 31209−31219

36. Case studies 36

37. 37 Griffing’s ANOVA for the ELS severity score and AUDPC in 6 × 6 full diallel cross of groundnut. GENE ACTION FOR RESISTANCE TO EARLY LEAF SPOT OF GROUNDNUT Zongo et al ., 2019

38. 38 Covariance ( Wr )/variance ( Vr ) graph for the ELS severity score of groundnut. Wr : covariance between a parent r and its progeny; Vr : variance between a parent r and its progeny; Wr1: regression line; Wr2 : parabola; Wr : tangent to parabola. Estimates of the genetic parameters for the ELS severity score and AUDPC according to Hayman’s method in a 6 × 6 full diallel cross of groundnut. Covariance ( Wr )/variance ( Vr ) graph additive, dominance, and additive x additive genetic effects (Kornegay et al ., 1980; Hamid et al ., 1981; Anderson et al ., 1986; Green and Wynne, 1987). Maternal effects and/or cytoplasmic factors have also been reported ( Coffelt and Porter, 1986; Kornegay et al ., 1980; Sharief et al ., 1978). Zongo et al ., 2019

39. 39 GENE ACTION FOR RESISTANCE TO LATE LEAF SPOT OF GROUNDNUT R esistance to LLS is controlled by a combination of both, nuclear and maternal gene effects. The preponderance of additive genetic effects supports selection for LLS resistance in early generations Janila et al ., 2013 – Euphytica – 193:13-25

40. 40 GENE ACTION FOR RESISTANCE TO RUST OF GROUNDNUT Daudi et al ., 2021 – scientific reports 12 × 12 full diallel General combining ability effects Analysis of variance

41. 41 The inheritance of rust resistance is conditioned by dominance gene action. Trait improvement will only be effective after selection in the advanced generations. Variance components

42. 42 Marker assisted breeding for foliar disease resistance in groundnut IPAHM103, GM1536, GM2301, GM2079, GMRQ517, GMRQ786, GMRQ843- Rust SEQ8D09, GM1009, GMLQ975 - LLS Affymetrix SNP array 58 K SNPs Shasidhar et al ., (2020) - The crop journal – 1-15

43. 43 RPG recovery ranged from 83% to 90% in the genetic background of GJG 9, followed by GJGHPS 1 (72%– 92%) and GG 20 (71.0%–85.5%)

44. 44 Foliar disease-resistant varieties, namely, Improved JL 24 (DBG 3) and Super TMV 2 (DBG 4) have also been developed using the resistant donor GPBD 4 and released in the state of Karnataka, India for commercial cultivation. In addition, several promising marker assisted bred lines ( ICGV 181023, ICGV 181025 and ICGV 171025 ) in the genetic background of three elite varieties, ICGV 06142, ICGV 06420 and ICGV 061l0 which are under third-year testing in the All India Coordinated Research Project on Groundnut (AICRP-G).

45. 45 Marker assisted breeding for Rust resistance in groundnut Varshney et al ., (2014) - Theor Appl Genet - 127:1771–1781 An overview on improvement of rust resistance in peanut through marker-assisted backcrossing (MABC)

46. 46 Varshney et al ., (2014) - Theor Appl Genet - 127:1771–1781 Details of one of the best introgression line in each recurrent parent background of ‘ICGV 91114’, ‘JL 24’ and ‘TAG 24’

47. 47 PCR amplification of genomic DNA showing amplification of a 1200 bp fragment of the Tcchitinase -I gene RT-PCR of the cDNA showing amplification of a 1200 bp fragment of the Tcchitinase -I gene Transgenics for leaf spot and rust disease in peanut T-DNA portion of pBinAR -chitinase-I construct Hardened T transgenic plantlets Marka and Nanna, 2020 – Plant Growth Regulation – 93: 53-63

48. 48 ELS LLS Rust Transgenic Chitinase activity in the peanut transgenic plants Performance of peanut transgenic plants (T1) carrying Tcchitinase -I gene against ELS, LLS and rust diseases in peanut cv ICG 13942 Marka and Nanna, 2020 – Plant Growth Regulation – 93: 53-63

49. 49 Transgenics for drought in peanut –VIGS approach Govind et al ., 2009 - Mol Genet Genomics - 281:591–605

50. 50

51. 51 M achine learning to enhance selection for Leaf spot-resistant genotypes Chapu et al ., (2024) – Agronomy- 14 : 947 Associations between the actual and predicted LLS scores of the test dataset using six models derived from the testing dataset

52. 52 Tripati et al ., (2014) – Computers and Electronics in Agriculture – 107 : 104-114 Data Mining for disease dynamics Zigbee based wireless sensor network Naïve Bayes with Gaussian distribution Rapid association rule mining

53. 53 Major constraints to genetic improvement of foliar disease resistance Absence of high levels of resistance in cultivated peanut and the linkage of resistance with long duration. Wild Arachis spp . showed very high level of resistance to ELS and LLS but possess very small and catenate pods. Limited gene introgression from wild Arachis spp. to cultivated groundnut. Disease resistant germplasm are late maturing types, have lower partitioning Disease resistant germplasm are sensitive to photoperiod than agronomically elite susceptible materials. Large genotype-by-environment interactions for traits of economic importance.

54. 54 LLS resistance is polygenic in nature, recombination breeding coupled with some amount of recurrent selection to accumulate minor genes in elite susceptible/ tolerant backgrounds may be rewarding. Wild species of Arachis are known for resistance to LLS and therefore, it would be necessary to include those species as donors to broaden the genetic base of resistance to late leaf spot. It is important to use the resistance donor as female parent to tap cytoplasmic inheritance of resistance to LLS. Efforts to overcome incompatibility in wide crosses, by using non-conventional techniques i ,e ., transgenics Genome editing could be used to domesticate wild plants and reunite lost but desirable traits, including nutritional features or stress tolerance, with yield potential and other agronomically valuable characteristics. Future prospect of genetic improvement of foliar disease resistance

55. References 55 Chapu , I., Chandel, A., Sie, E.K., Okello, D.K., Oteng -Frimpong, R., Okello, R.C.O., Hoisington, D and Balota , M. 2024. Comparing regression and classification models to estimate leaf spot disease in peanut ( Arachis hypogaea L.) for implementation in breeding selection. Agronomy . 14(5): 947. Daudi , H., Shimelis , H., Mathew, I., Rathore, A and Ojiewo , C.O. 2021. Combining ability and gene action controlling rust resistance in groundnut ( Arachis hypogaea L.). Scientific Reports . 11(1): 16513. Govind, G., ThammeGowda , H. V, Kalaiarasi , P. J, Iyer, D.R., Muthappa , S.K., Nese , S and Makarla , U.K. 2009. Identification and functional validation of a unique set of drought-induced genes preferentially expressed in response to gradual water stress in peanut. Molecular Genetics and Genomics . 281: 591-605. Janila , P., Ramaiah, V., Rathore, A., Rupakula , A., Reddy, R.K., Waliyar , F and Nigam, S.N. 2013. Genetic analysis of resistance to late leaf spot in interspecific groundnuts. Euphytica . 193:13–25. Leal-Bertioli, S. C., José, A. C., Alves-Freitas, D. M., Moretzsohn , M. C., Guimarães , P. M and Nielen , S. 2009. Identification of candidate genome regions controlling disease resistance in Arachis. BMC Plant Biology . 9: 112.

56. 56 Marka , R and Nanna, R.S. 2021. Expression of Tcchitinase -I gene in transgenic peanut ( Arachis hypogaea L.) confers enhanced resistance against leaf spot and rust diseases. Plant Growth Regulation . 93: 53-63. Shasidhar , Y., Variath , M.T., Vishwakarma, M.K., Manohar, S.S., Gangurde , S.S., Sriswathi , M., Sudini , H.K., Dobariya, K.L., Bera, S.K., Radhakrishnan, T and Pandey, M.K. 2020. Improvement of three popular Indian groundnut varieties for foliar disease resistance and high oleic acid using SSR markers and SNP array in marker-assisted backcrossing. The Crop Journal . 8(1): 1-15. Varshney, R.K., Pandey, M.K., Janila , P., Nigam, S.N., Sudini , H., Gowda, M.V.C., Sriswathi , M., Radhakrishnan, T., Manohar, S.S and Nagesh, P. 2014. Marker-assisted introgression of a QTL region to improve rust resistance in three elite and popular varieties of peanut ( Arachis hypogaea L.). Theoretical and Applied Genetics . 127: 1771-1781. Zongo, A., Konate, A.K., Koïta , K., Sawadogo, M., Sankara, P., Ntare, B.R. and Desmae , H. 2019. Diallel analysis of early leaf spot ( Cercospora arachidicola Hori) disease resistance in groundnut. Agronomy . 9(1): 15

57. Thank you 57