Abstract
Aromatic rice (Oryza sativa L. Indica) is popular among consumers. They provide significant economic benefit to producing countries as well as farmers. Aromatic germplasm is huge and diverse in terms of agro-morphological characters, grain types and aroma content. Development of a representative coreset of aromatic germplasm can be a good source for novel alleles identification and is required for its improvement. A collection of 552 aromatic accessions were screened for 40 DUS traits and 60 SSR markers. The data were processed in PowerCore software that implements the advanced M (or maximization) strategy using a modified heuristic algorithm and a coreset of 99 accessions was identified. The average Nei diversity and Shannon–Weaver diversity indices of the coreset were 0.635 and 0.823, representing the entire diversity of the collection. Statistical parameters like mean difference and variance difference were analysed to compare the mean and variance ratio between core and entire collections. Coreset has 3.45% mean difference and 14.4% variance difference. The coreset has 99.04% coincidence rate and 106.31% variable range which indicated the optimum properties of the coreset against the entire collection. This is the first attempt of making coreset of aromatic rice from larger germplasm.
This is a preview of subscription content, log in via an institution to check access.
References
Agrama HA, Yan WG, Lee F, Fjellstrom R, Chen MH, Jia M, McClung A (2009) Genetic assessment of a mini-core subset developed from the USDA rice gene bank. Crop Sci 49:1336–1346. https://doi.org/10.2135/cropsci2008.06.0551
Belaj A, Garcia MDCD, Atienza SG, Urdiroz NM, Rosa RDL, Satovic Z, Marti A, Kilian A, Trujillo I, Valpuesta V, Rio CD (2012) Developing a core collection of olive (Olea europaea L.) based on molecular markers (DArTs, SSRs, SNPs) and agronomic traits. Tree Genet Genomes 8:365–378. https://doi.org/10.1007/s11295-011-0447-6
Bhattacharjee R, Khairwal IS, Bramel PJ, Reddy KN (2007) Establishment of a pearl millet [Pennisetumglaucum (L.) R. Br.] core collection based on geographical distribution and quantitative traits. Euphytica 155:35–45. https://doi.org/10.1007/s10681-006-9298-x
Brown AHD (1989) Core collections: a practical approach to genetic resources management. Genome 31:818–824. https://doi.org/10.1139/g89-144
Brown AHD, Spillane C (1999) Implementing core collections-principles, procedures, progress, problems and promise. In: Johnson RC, Hodgkin T (eds) Core collections for today and tomorrow. International Plant Genetic Resources Institute, Rome, pp 1–9
Buttery RG, Ling LC, Juliano BO, Turnbaugh JG (1983) Cooked rice aroma and 2-acetyl-1-pyrroline. J Agric Food Chem 31:823–826. https://doi.org/10.1021/jf00118a036
Chung JW, Park YJ (2010) Population structure analysis reveals the maintenance of isolated sub-populations of weedy rice. Weed Res 50:606–620. https://doi.org/10.1111/j.1365-3180.2010.00810.x
Diwan N, McIntosh MS, Bauchan GR (1995) Methods of developing a core collection of annual Medicago species. Theor Appl Genet 90:755–761
Ebana K, Kojima Y, Fukuoka S, Nagamine T, Kawase M (2008) Development of mini core collection of Japanese rice landrace. Breed Sci 58:281–291. https://doi.org/10.1270/jsbbs.58.281
Escribano P, Viruel MA, Hormaza JI (2008) Comparison of different methods to construct a core germplasm collection in woody perennial species with SSR markers. A case study in cherimoya (Annona cherimola Mill., Annonaceae), an underutilized subtropical fruit tree species. Ann Appl Biol 153:25–32. https://doi.org/10.1111/j.1744-7348.2008.00232.x
FAO (2018) World food and agriculture—STATISTICALPOCKETBOOK 2018. Rome. Licence: CC BY-NC-SA 3.0 IGO
Frankel OH, Brown AHD (1984) Current plant genetic resources—a critical appraisal. Genetics: new frontiers, vol IV. Oxford and IBH Publishing Company, New Delhi, pp 1–11
Gao ZH, Zhang Z, Han ZH, Fang JG (2005) Development and evaluation of core collection of Japanese apricot germplasms in China. Sci Agric Sin 38:363–368
Gouesnard B, Bataillon TM, Decoux G, Rozale C, SchoenDJ DavidJL (2001) Mstrat: an algorithm for building germplasm core collections by maximizing allelic or phenotypic richness. J Hered 92:93–94. https://doi.org/10.1093/jhered/92.1.93
Grenier C, Bramel-Cox PJ, Hamon P (2001a) Core collection of sorghum. I. Stratification based on eco-geographical data. Crop Sci 41:234–240. https://doi.org/10.2135/cropsci2001.411234x
Grenier C, Hamon P, Bramel-Cox PJ (2001b) Core collection of sorghum. II. Comparison of three random sampling strategies. Crop Sci 41:241–246
Hamon S, Dussert S, Noirot M, Anthony F, Hodgkin T (1995) Core collections—accomplishments and challenges. Plant Breed Abstr 65(8):1125–1133
Hokanson SC, Szewc-McFadden AK, Lamboy WF, McFerson JR (1998) Microsatellite (SSR) markers reveal genetic identities, genetic diversity and relationships in a Malus domesticaborkh core subset collection. Theor Appl Genet 97:671–683. https://doi.org/10.1007/s001220050943
Holbrook CC, Anderson WF, Pittman RN (1993) Selection of a core collection from the U.S. germplasm collection of peanut. Crop Sci 33:859–861. https://doi.org/10.2135/cropsci1993.0011183X003300040044x
Hu J, Zhu J, Xu HM (2000) Methods of constructing core collections by stepwise clustering with three sampling strategies based on the genotypic values of crops. Theo Appl Genet 101:264–268. https://doi.org/10.1007/s001220051478
Jambhulkar NN, Patra BC, Reddy JN, Sarkar RK (2018) Developing mini core of rice germplasm for submergence tolerance. Indian J Plant Genet Resour 31(1):89–96. https://doi.org/10.5958/0976-1926.2018.00013.X
Kim KW, Chung HK, Cho GT, Ma KH, Chandrabalan D, Gwag JG, Kim TS, Cho EG, Park YJ (2007) PowerCore: a program applying the advanced M strategy with a heuristic search for establishing allele mining sets. Bioinformatics 23:2155–2162. https://doi.org/10.1093/bioinformatics/btm313
Kumar et al (2020) Designing a mini-core collection effectively representing 3004 diverse rice accessions. Plant Commun. https://doi.org/10.1016/j.xplc.2020.100049
Liu W, Muhammad QS, Bai L, Lu Z, Chen Y, Jiang L, Diao M, Liu X, Lu Y (2015) Evaluation of genetic diversity and development of a core collection of wild rice (Oryza rufipogon Griff.) populations in China. PLoS ONE 10(12):e0145990. https://doi.org/10.1371/journal.pone.0145990
Moe KT, Gwag JG, Park YG (2012) Efficiency of POWERCORE in coreset development using amplified fragment length polymorphic markers in mungbean. Plant Breed 131:110–117. https://doi.org/10.1111/j.1439-0523.2011.01896.x
Nei M (1973) Analysis ofgene diversity in subdivided populations. Proc Natl Acad Sci USA 70:3321–3323. https://doi.org/10.1073/pnas.70.12.3321
Noreen R, Khan S, Ashique Rabbani M, Kanwal A, Uzair B (2020) Screening of diverse rice (Oryza sativa L.) varieties for genetic diversity and bacterial blight resistance gene. Pak J Bot 52(3):1087–1096. https://doi.org/10.30848/PJB2020-3(41)
Orjuela J, Garavito A, Bouniol M, Arbelaez JD, Moreno L, Kimball J, Wilson G, Rami JF, Tohme J, McCouch SR, Lorieux M (2010) A universal core genetic map for rice. Theor Appl Genet 120:563–572. https://doi.org/10.1007/s00122-009-1176-1
Ortiz R, Ruiz-Tapia EN, Mujica-Sanchez A (1998) Sampling strategy for a core collection of Peruvian quinoa germplasm. Theor Appl Genet 96:475–483. https://doi.org/10.1007/s001220050764
Powell W, Morgante M, Andre C, Hanafey M, Vogel J et al (1996) The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breed 3:225–238
PPV&FRA (2007) Guidelines for the conduct of Test for distinctiveness, uniformity, and stability on rice (Oryza Sativa L.). Protection of Plant Varieties and Farmers’ Rights Authority (PPV&FRA), Government of India. SG/01/2007. www.Plantauthority.gov.in/pdf/GRice.pdf. Accessed 9 Apr 2012
Rachana B, Eswari KB, Jyothi B, Lakshmi Devi G, Jai Vidhya LRK, Laxmi Bhavani P, Bharath M, Raghuveer Rao P, Aravind Kumar J, Fiyaz Abdul R, Neeraja CN, Subba Rao LV, Ram T (2019) Characterization of new plant type coreset of rice (Oryza sativa L.) using QTL/gene-linked markers. Oryza 56(4):352–360. https://doi.org/10.35709/ory.2019.56.4.2
Rodino AP, Santalla M, Ron AMD, Singh SP (2003) A core collection of common bean from the Iberian peninsula. Euphytica 131:165–175. https://doi.org/10.1023/A:1023973309788
Schoen DJ, Brown AHD (1993) Conservation of allelic richness in wild crop relatives is aided by assessment of genetic markers. Proc Natl Acad Sci USA 90:10623–10627. https://doi.org/10.1073/pnas.90.22.10623
Sekhar BPS, Reddy GM (1982) Amino acid profiles in some scented rice varieties. Theor Appl Genet 62:35–37. https://doi.org/10.1007/BF00276278
Shannon CE, Weaver W (1949) The mathematical theory of communication. University of Illinois Press, Urbana
Singh RK, Gautam PL, Saxena S, Singh S (2000a) Scented rice germplasm: conservation, evaluation and utilization. In: Singh RK, Singh US, Khush GS (eds) Aromatic rices. Oxford & IBH, New Delhi, pp 107–133
Singh RK, Singh US, Khush GS, Rohilla R, Singh JP, Singh G, Shekhar KS (2000b) Small and medium grained aromatic rices of India. In: Singh RK, Singh US, Khush GS (eds) Aromatic rices. Oxford & IBH, New Delhi, pp 155–177
Sun Q, Bai L, Ke L, Xiang X, Zhao J, Ou L (2012) Developing a core collection of litchi (Litchi chinensis Sonn.) based on EST-SSR genotype data and agronomic traits. Sci Hortic 146:29–38. https://doi.org/10.1016/j.scienta.2012.08.012
Taba S, Diaz J, Franco J, Crossa J (1998) Evaluation of Caribbean maize accessions to develop a core collection. Crop Sci 38:1378–1386. https://doi.org/10.2135/cropsci1998.0011183X003800050037x
Tiwari KK, Singh A, Pattnaik S (2014) Identification of a diverse mini-core panel of Indian rice germplasm based on genotyping using microsatellite markers. Plant Breed. https://doi.org/10.1111/pbr.12252
Umakanth B, Vishalakshi B, Sathish Kumar P, Rama Devi SJS, Bhadana VP, Senguttuvel P, Kumar S, Sharma SK, Sharma PK, Prasad MS, Madhav MS (2017) Diverse rice landraces of North-East India enables the identification of novel genetic resources for Magnaporthe Resistance. Front Plant Sci 8:1500. https://doi.org/10.3389/fpls.2017.01500
Upadhyaya HD, Ortiz R (2001) A mini core subset for capturing diversity and promoting utilization of chickpea genetic resources in crop improvement. Theor Appl Genet 102:1292–1298. https://doi.org/10.1007/s00122-001-0556-y
Upadhyaya HD, Gowda CLL, Pundir RPS, Reddy VG, Singh S (2006) Development of core subset of finger millet germplasm using geographical origin and data on 14 quantitative traits. Genet Resour Crop Evol 53:679–685. https://doi.org/10.1007/s10722-004-3228-3
Yan WG, Ruter JN, Bryant RJ, Bockelman HE, Fjellstrom RG, Chen MH, Tai TH, McClung AM (2007) Development and evaluation of a core subset of the USDA rice germplasm collection. Crop Sci 47:869–876. https://doi.org/10.2135/cropsci2006.07.0444
Yoneazwa K, Nomura T, Morish H (1995) Sampling strategies for use in stratified germplasm collection. In: Hodgkin T, Brown AHD, van Hintum THL (eds) Core collection of plant genetic resources. Wily, Chichester, pp 35–53
Zhang P, Li J, Li X, Liu X, Zhao X et al (2011) Population structure and genetic diversity in a rice core collection (Oryza sativa L.) investigated with SSR markers. PLoS ONE 6(12):e27565. https://doi.org/10.1371/journal.pone.0027565
Zhao WG, Cho GT, Ma KH, Chung JW, Gwag JG, Park YJ (2010) Development of an allele-mining set in rice using a heuristic algorithm and SSR genotype data with least redundancy for the post-genomic era. Mol Breed 26:639–651. https://doi.org/10.1007/s11032-010-9400-x
Zheng K, Huang N, Bennett J, Khush GS (1995) PCR-based marker assisted selection in rice breeding. IRRI discussion paper series No. 12. IRRI, Los Banos, Philippines
Acknowledgements
The authors acknowledge all the collaborators of Indian Aromatic Rice Network Project funded by Department of Biotechnology (DBT) Govt. of India, New Delhi, India for their active collaboration in the project. We thank DBT for providing funds for this project. Sathish Kumar P and Praveen R thank Dr. P. Sudhakar and Dr. A. Krishna Satya, Department of Biotechnology, Acharya Nagarjuna University (ANU), Guntur, India for the Ph.D. registration.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare no conflict of interest.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
P, S.K., R, P.K., Maddala, S.S. et al. Development of coreset of aromatic rice (Oryza sativa L. Indica) based on molecular and morphological diversity. Genet Resour Crop Evol 68, 441–450 (2021). https://doi.org/10.1007/s10722-020-01074-4
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10722-020-01074-4