Plant genetic resources in India: management and utilization

Plant genetic resources (PGR) are the foundation of agriculture as well as food and nutritional security. The ICAR-NBPGR is the nodal institution at national level for management of PGR in India under the umbrella of Indian Council of Agricultural Research (ICAR), New Delhi. India being one of the gene-rich countries faces a unique challenge of protecting its natural heritage while evolving mutually beneficial strategies for germplasm exchange with other countries. The Bureaus activities include PGR exploration, collection, exchange, characterization, evaluation, conservation and documentation. It also has the responsibility to carry out quarantine of all imported PGR including transgenics meant for research purposes. The multifarious activities are carried out from ICAR-NBPGR headquarters and its 10 regional stations located in different agro-climatic zones of India. It has linkages with international organizations of the Consultative Group on International Agricultural Research (CGIAR) and national crop-based institutes to accomplish its mandated activities. NBPGR collects and acquires germplasm from various sources, conserves it in the Genebank, characterizes and evaluates it for different traits and provides ready material for breeders to develop varieties for farmers. ICAR-NBPGR encompasses the National Genebank Network and at present, the National Genebank conserves more than 0.40 million accessions. NBPGR works in service-mode for effective utilization of PGR in crop improvement programmes which depends mainly on its systematic characterization and evaluation, and identification of potentially useful germplasm. NBPGR is responsible for identifying trait-specific pre-adapted climate resilient genotypes, promising material with disease resistance and quality traits which the breeders use for various crop improvement programmes. The system has contributed immensely towards safeguarding the indigenous and introducing useful exotic PGR for enhancing the agricultural production. Presently, our focus is on characterization of ex situ conserved germplasm and detailed evaluation of prioritized crops for enhanced utilization; assessment of impact of on-farm conservation practices on genetic diversity; genome-wide association mapping for identification of novel genes and alleles for enhanced utilization of PGR; identification and deployment of germplasm/landraces using climate analog data; validation of trait-specific introduced germplasm for enhanced utilization.

1. Archak S., Agrawal R.C. PGR informatics at the National Bureau of Plant Genetic Resources: status, challenges and future. In: A Road Map for Implementing the Multilateral System of Access and Benefit-sharing in India. Halewood M. et al. (Eds.). Rome: ICAR-NBPGR and Bioversity International, 2012.

2. Arora R.K. Plant diversity in Indian gene centre. In: Paroda R.S., Arora R.K. (Eds.). Plant Genetic Resources - Conservation and Management. New Delhi, India: IPGRI, Regional Office for South Asia, 1991;25-54.

3. Arora R.K., Nayar E.R. Wild Relatives of Crop Plants in India. (NBPGR Monograph no. 7). New Delhi, India: National Bureau of Plant Genetic Resources, 1984;90.

4. Arora S., Singh N., Kaur S., Bains N.S., Uauy C., Poland J., Chhu-neja P. genome-wide association study of grain architecture in wild wheatAegilops tauschii. Front. Plant Sci. 2017;8:886. DOI 10.3389/fpls.2017.00886.

5. Arruda M.P., Brown P., Krill A., Brown-Guedira G., Thurber C., Fores-man B., Kolb F. Genome-wide association mapping of fusarium head blight resistance in wheat using genotyping-by-sequencing. Plant Genome. 2016;9(1):1-14.

6. Bailey-Serres J., Fukao T., Ronald P., Ismail A., Heuer S., Mackill D. Submergence tolerant rice: SUBJ’s journey from landrace to modern cultivar. Rice. 2010;3(2-3):138-147.

7. Bevan M.W., Uauy C., Wulff B.B., Zhou J., Krasileva K., Clark M.D. Genomic innovation for crop improvement. Nature. 2017;543(7645): 346-354. DOI 10.1038/nature22011.

8. Crossa J., Perez-Rodriguez P., Cuevas J., Montesinos-Lopez O., Jar-qum D., de los Campos G., Burgueno J., Gonzalez-Camacho J.M., Perez-Elizalde S., Beyene Y., Dreisigacker S., Singh R., Zhang X., Gowda M., Roorkiwal M., Rutkoski J., Varshney R.K. Genomic selection in plant breeding: methods, models, and perspectives. Trends Plant Sci. 2017;22:961-975.

9. Dhillon B.S., Saxena S. India Chapter. In: Plant Genetic Resources in SAARC Countries, SAIC publication. Bangaldesh: SAARC Agricultural Information Center, 2003;241-296.

10. Ellur R.K., Khanna A., Gopala Krishnan S., Bhowmick P.K., Vinod K.K., Nagarajan M., Mondal K.K., Singh N.K., Singh K., Prabhu K.V., Singh A.K. Marker-aided incorporation of Xa38, a novel bacterial blight resistance gene, in PB1121 and comparison of its resistance spectrum with xa13 + Xa21. Sci. Rep. 2016;6:29188.

11. Esvelt K.M., Wang H.H. Genome-scale engineering for systems and synthetic biology. Mol. Syst. Biol. 2014;9:641.

12. Gopalakrishnan S., Sharma R.K., Anand Rajkumar K.A., Joseph M., Singh V.P., Bhat K.V., Singh N.K., Mohapatra T. Integrating marker assisted background analysis with foreground selection for identification of superior bacterial blight resistant recombinants in Basmati rice. Plant Breed. 2008;127:131-139.

13. Gupta D., Bhattacharjee O., Mandal D., Sen M.K., Dey D., Das-gupta A., Kazi T.A., Gupta R., Sinharoy S., Acharya K., Chatto-padhyay D., Ravichandiran V., CRISPR-Cas9 system: a new-fangled dawn in gene editing. Life Sci. 2019;232:116636. DOI 10.1016/j.lfs.2019.116636. Publ. online Jul 8, 2019.

14. Harlan J.R. Geographic patterns of variation in some cultivated plants. J. Heredity. 1975;66:182-191.

15. Harlan J.R., de Wet J.M.J. Towards a rational classification of cultivated plants. Taxon. 1971;20:505-517.

16. Heffner E.L., Jannink J.L., Iwata H., Souza E., Sorrellls M.E. Genomic selection acuracy for grain quality traits in biparental wheat populations. Crop Sci. 2011;51:2597-2606.

17. Hopkins J.J., Maxted N. Crop Wild Relatives: Plant Conservation for Food Security. Natural England Research Reports, Number 037. Natural England, Sheffield, 2010.

18. Huang S., Weigel D., Beachy R.N., Li J. A proposed regulatory framework for genome-edited crops. Nat. Genet. 2016;48:109-111.

19. Jenko J., Gorjanc G., Cleveland M.A., Varshney R.K., Whitelaw C.B., Woolliams J.A., Hickey J.M. Potential of promotion of alleles by genome editing to improve quantitative traits in livestock breeding programs. Genet. Sel. Evol. 2015;47:55.

20. Jia Y., Jannink J.L. Multiple-trait genomic selection methods increase genetic value prediction accuracy. Genetics. 2012;192:1513-1522.

21. Kim T.S., He Q., Kim K.W., Yoon M.Y., Ra W.H., Li F.P., Tong W., Yu J., Oo W.H., Choi B., Heo E.B., Yun B.K., Kwon S.J., Kwon S.W., Cho Y.H., Lee C.Y., Park B.S., Park Y.J. Genome-wide resequencing of KRICE_CORE reveals their potential for future breeding, as well as functional and evolutionary studies in the post-genomic era. BMC Genomics. 2016;17:408.

22. Lin Z., Cogan N.O.I., Pembleton L.W., Spangenberg G.C., Forster J.W., Hayes B.J., Daetwyler H.D. Genetic gain and inbreeding from genomic selection in a simulated commercial breeding program for perennial ryegrass. Plant Genome. 2016;9(1):1-12.

23. Maxted N., Ford-Lloyd B.V., Jury S., Kell S., Scholten M. Towards a definition of a crop wild relative. Biodivers. Conserv. 2006;15: 2673-2685.

24. Maxted N., Kell S. Establishment of a Global Network for the In Situ Conservation of Crop Wild Relatives: Status and Needs. 2009. http://www.fao.org/docrep/013/i1500e/i1500e18a

25. Maxted N., Kell S., Toledo A., Dulloo E., Heywood V, Hodgkin T., Hunter D., Guarino L., Jarvis A., Ford-Lloyd B. A global approach to crop wild relative conservation: securing the gene pool for food and agriculture. Kew Bull. 2011;65:1-16.

26. Maxted N., Scholten M., Codd R., Ford-Lloyd B. Creation and use of a national inventory of crop wild relatives. Biol. Conserv. 2007; 140:142-159.

27. Meuwissen T.H.E., Hayes B.J., Goddard M.E. Prediction of total genetic value using genome-wide dense marker maps. Genetics. 2001; 157:1819-1829.

28. Myers N. Threatened biotas: “hotspots” in tropical forests. Environmentalist. 1988;8:187-208.

29. Myers N., Mittermeier R.A., Mittermeier C.G., da Fonseca G.A.B., Kent J. Biodiversity hotspots for conservation priorities. Nature. 2000;403:853-858.

30. Nayar M.P. Endemism and pattern of distribution of endemic genera (angiosperm) in India. J. Econ. Tax. Bot. 1980;1:99-110.

31. Qualset C.O., McGuire P.E., Warbuton M.L. ‘Agrobiodiversity’ key to agricultural productivity. Calif. Agric. 1995;49:45-49.

32. Riar A.K., Kaur S., Dhaliwal H.S., Singh K., Chhuneja P. Introgression of a leaf rust resistance gene from Aegilops caudate to bread wheat. J. Genetics. 2012;91(2):1-7.

33. Rodrigues J.I.S., Arruda K.M.A., Piovesan N.D., de Barros E.G. Plant pre-breeding for increased protein content in soybean Glycine max (L.) Merrill. Acta Agron. 2017;66(4):618-624.

34. Saint Pierre C., Burgueno J., Crossa J., Fuentes Davila G., Figueroa Lopez P., Solis Moya E., Ireta Moreno J., Hernandez Muela V.M., Zamora Villa V.M., Vikram P., Mathews K., Sansaloni C., Sehgal D., Jarquin D., Wenzl P., Singh S. Genomic prediction models for grain yield of spring bread wheat in diverse agro-ecological zones. Sci. Rep. 2016;6:27312.

35. Sauer N.J., Mozoruk J., Miller R.B., Warburg Z.J., Walker K.A., Beetham P.R., Schopke C.R., Gocal G.F. Oligonucleotide-directed mutagenesis for precision gene editing. Plant Biotech. J. First publ. 27 Oct. 2015. Publ. 2016;14:496-502.

36. Scheben A., Edwards D. Genome editors take on crops. Science. 2017; 355:1122-1123.

37. Scheben A., Wolter F., Batley J., Puchta H., Edwards D. Towards CRISPR/Cas crops-bringing together genomics and genome editing. New Phytol. 2017;216:682-698.

38. Scheben A., Yuan Y., Edwards D. Advances in genomics for adapting crops to climate change. Curr. Plant Biol. 2016;6:2-10.

39. Shukla V.K., Doyon Y., Miller J.C., DeKelver R.C., Moehle E.A., Worden S.E., Mitchell J.C., Arnold N.L., Gopalan S., Meng X., Choi V.M., Rock J.M., Wu Y.Y., Katibah G.E., Zhifang G., McCaskill D., Simpson M.A., Blakeslee B., Greenwalt S.A., Butler H.J., Hinkley S.J., Zhang L., Rebar E.J., Gregory P.D., Ur-nov F.D. Precise genome modification in the crop species Zea mays using zinc-finger nucleases. Nature. 2009;459:437-441.

40. Singh S., Vikram P., Sehgal D., Burgueno J., Sharma A., Singh S.K., Sansaloni C.P., Joynson R., Brabbs T., Ortiz C., Solis-Moya E., Govindan V., Gupta N., Sidhu H.S., Basandrai A.K., Basandrai D., Ledesma-Ramires L., Suaste-Franco M.P., Fuentes-Davila G., Moreno J.I., Sonder K., Singh V.K., Singh S., Shokat S., Arif M.A.R., Laghari K.A., Srivastava P., Bhavani S., Kumar S., Pal D., Jais-wal J.P., Kumar U., Chaudhary H.K., Crossa J., Payne T.S., Im-tiaz M., Sohu V.S., Singh G.P., Bains N.S., Hall A., Pixley K.V. Harnessing genetic potential of wheat germplasm banks through impact-oriented-prebreeding for future food and nutritional security. Sci. Rep. 2018;8:12527.

41. Spindel J.E., Begum H., Akdemir D., Collard B., Redona E., Jan-nink J.L., McCouch S. Genome-wide prediction models that incorporate de novo GWAS are a powerful new tool for tropical rice improvement. Heredity. 2016;116:395-408.

42. Takhtajan A. Flowering Plants: Origin and Dispersal (Engl. trans. C. Jeffrey). Edinburgh: Oliver & Boyd, 1969.

43. Urnov F.D., Rebar E.J., Holmes M.C., Zhang H.S., Gregory P.D. Genome editing with engineered zinc finger nucleases. Nat. Rev. Genet. 2010;11:636-646.

44. Varshney R.K., Terauchi R., McCouch S.R. Harvesting the promising fruits of genomics: applying genome sequencing technologies to crop breeding. PLoS Biol. 2014;12:e1001883.

45. Varshney R.K., Singh V.K., Kumar A., Powell W., Sorrells M.E. Can genomes deliver climate-change ready crops? Curr. Opin. Plant Biol. 2018;45:205-211.

46. Vavilov N.I. Centres of origin of cultivated plants. Trudy po Prikladnoy Botanike, Genetike i Selektsii = Proceedings on Applied Botany, Genetics, and Breeding. 1926;16(2):139-248. (in Russian)

47. Vavilov N.I. Phyto-geographical basis of plant breeding. In: Selected Writings of N.I. Vavilov and translated by K.S. Chester. The Origin, Variation, Immunity and Breeding of Cultivated Plants, Chronica Botanica. 1951;13:364. Waltham Mass., USA.

48. Vikal Y., Chawla H., Sharma R., Lore J.S., Singh K. Mapping of bacterial blight resistance gene xa8 in rice (Oryza sativa L.). Ind. J. Genet. 2014;74(4):589-595.

49. Vikram P., Franco J., Burgueno-Ferreira J., Li H., Sehgal D., Saint Pierre C., Ortiz C., Sneller C., Tattaris M., Guzman C., Sansaloni C.P., Ellis M., Fuentes-Davila G., Reynolds M., Sonders K., Singh P., Payne T., Wenzl P., Sharma A., Bains N.S., Singh G.P., Crossa J., Singh S. Unlocking the genetic diversity of Creole wheats. Sci. Rep. 2016;6:23092.

50. Wang C., Hu S., Gardner C., Lubberstedt T. Emerging avenues for utilization of exotic germplasm. Trends Plant Sci. 2017;22(7):624-637.

51. Xu Y., Crouch J. Marker-assisted selection in plant breeding: from theory to practice. Crop Sci. 2008;48:391-407.

52. Xu Y., Lu Y., Xie C., Gao S., Wan J., Prassana B.M. Whole genome strategies for marker assisted plant breeding. Mol. Breed. 2012;29: 833-854.

53. Zhao J., Sauvage C., Zhao J., Bitton F., Bauchet G., Liu D., Huang S., Tieman D.M., Klee H.J., Causse M. Meta-analysis of genome-wide association studies provides insights into genetic control of tomato flavor. Nat. Commun. 2019;10:1534. DOI 10.1038/s41467-019-09462-w.

54. Zhou Q., Zhou C., Zheng W., Mason A.S., Fan S., Wu C., Fu D., Huang Y. Genome-wide SNP markers based on SLAF-Seq uncover breeding traces in rapeseed (Brassica napus L.). Front. Plant Sci. 2017;8:648.

55. Zhang Y., Liang Z., Zong Y., Wang Y., Liu J., Chen K., Qiu J.L., Gao C.X. Efficient and transgene-free genome editing in wheat through transient expression of CRISPR/Cas9 DNA or RNA. Nat. Commun. 2016;7:12617.

56. Zhukovsky P.M. New centres of origin and new gene centres of cultivated plants including specifically endemic microcentres of species closely allied to cultivated species. Bot. J. (Russian Bot. Z.). 1968; 53:430-460. (in Russian)

57. Conflict of interest. The authors declare no conflict of interest. Received April 3, 2019. Revised April 3, 2020. Accepted April 3, 2020.