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Genetic characterization and divergence studies of maize (Zea mays L.) lines developed from landraces indigenous to North Eastern Hill Region (NEHR) of India

Published online by Cambridge University Press:  09 October 2020

K. L. Naveenkumar ,
Devyani Sen Open the ORCID record for Devyani Sen [Opens in a new window] ,
Shimreiso Vashum  and
Miranda Sanjenbam
K. L. Naveenkumar
Affiliation:
School of Crop Improvement, College of Post-Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umroi Road, Umiam793103, Meghalaya, India
Devyani Sen*
Affiliation:
School of Crop Improvement, College of Post-Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umroi Road, Umiam793103, Meghalaya, India
Shimreiso Vashum
Affiliation:
School of Crop Improvement, College of Post-Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umroi Road, Umiam793103, Meghalaya, India
Miranda Sanjenbam
Affiliation:
School of Crop Improvement, College of Post-Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umroi Road, Umiam793103, Meghalaya, India
*
*Corresponding author. E-mail: [email protected]
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Abstract

The current study focused on characterization of the underlying genetic divergence in inbred lines developed from local landraces of North Eastern Hill Region of India – a designated Asiatic maize diversity centre – following six generations of inbreeding. Substantial genetic differentiation was indicated based on very high to moderate Fst values for 22 of the 38 simple sequence repeat markers studied. STRUCTURE analysis partitioned the subset into two distinct and one admixture subgroup (Populations I, II and III respectively) accompanied by a significant reduction in heterozygosity. Population II was further subdivided into subpopulations Pop-M9 and Pop-T9. Nei's pairwise genetic distance and population Fst values indicated that Populations I and II were more divergent with neighbour joining clustering analysis clearly defining landraces originating from the states of Tripura (Population II) and Sikkim (Population I) as most divergent. Principal coordinates analysis could explain 31.26% of the variation present in the subgroups wherein Population I was more variable. Analysis of molecular variance and Fst coefficients (P < 0.001) indicated 17% population structuring with 55% variation detected for individuals within populations. These results combined with the presence of phenotypic variability in the subgroups for yield traits supported by results of a preliminary partial diallel analysis strongly suggest the existence of distinct heterotic groups. Divergence studies are crucial for exploiting heterosis, and the current study would go a long way to help establish a germplasm base for developing varieties with improved agronomic performance and surer commercial prospects no reports of which are available thus far.

Keywords

Asiatic maize landracesgenetic divergencemaizeNorth East Indiapopulation structureSSR (simple sequence repeat) markers
Type
Research Article
Information
Plant Genetic Resources , Volume 18 , Issue 4 , August 2020 , pp. 231 - 242
Copyright
Copyright © The Author(s), 2020. Published by Cambridge University Press on behalf of NIAB

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References

Aci, MM, Revilla, P, Morsli, A, Djemel, A, Belalia, N, Kadri, Y, Khelifi-Saloui, M, Ordas, B and Khelifi, L (2013) Genetic diversity in Algerian maize (Zea mays L.) landraces using SSR markers. Maydica 58: 304–310.Google Scholar
Aci, MM, Lupini, A, Mauceri, A, Morsli, A, Khelifi, L and Sunseri, F (2018) Genetic variation and structure of maize populations from Saoura and Gourara Oasis in Algerian Sahara. BMC Genetics 19: 1–10.10.1186/s12863-018-0655-2CrossRefGoogle ScholarPubMed
Anonymous (2007) Guidelines for the conduct of tests for distinctness, uniformity and stability on maize (Zea mays. L). The Protection of Plant Varieties and Farmers Rights Authority, New Delhi. Plant Variety Journal India 1: 1–13.Google Scholar
Barbosa, AM, Geraldi, IO, Benchimol, LL, Garcia, AA, Souza, CL and Souza, AP (2003) Relationship of intra- and interpopulation tropical maize single cross hybrid performance and genetic distances computed from AFLP and SSR markers. Euphytica 130: 87–99.10.1023/A:1022381008721CrossRefGoogle Scholar
Bedoya, CA, Dreisigacker, S, Hearne, S, Franco, J, Mir, C, Prasanna, BM, Taba, S, Charcosset, A and Warburton, ML (2017) Genetic diversity and population structure of native maize populations in Latin America and the Caribbean. PLoS ONE 12: e0173488.10.1371/journal.pone.0173488CrossRefGoogle ScholarPubMed
Bellon, MR and Hellin, J (2011) Planting hybrids, keeping landraces: agricultural modernization and tradition among small-scale maize farmers in Chiapas, Mexico. World Development 39: 1434–1443.10.1016/j.worlddev.2010.12.010CrossRefGoogle Scholar
Bellon, MR and van Etten, J (2013) Climate change and on-farm conservation of crop landraces in centres of diversity. In: Jackson, M, Ford-Lloyd, B and Parry, ML (eds) Plant Genetic Resources and Climate Change. CABI Publishing, Wallingford, UK, pp. 137–150.10.1079/9781780641973.0137CrossRefGoogle Scholar
Berthaud, J and Gepts, P (2004) Assessment of effects on genetic diversity. In: CEC Secretariat of the Governments of Canada, Mexico and of the United States (eds.) Maize and Biodiversity: The Effects of Transgenic Maize in Mexico. Montreal: North American Commission on Environmental Cooperation, pp. 1–33.Google Scholar
Bhagat, D, Mishra, BK and Priyamvada, S (2015) Studies on changing livestock products scenario in Meghalaya. Journal of Hill Agriculture 6: 123–127.10.5958/2230-7338.2015.00005.1CrossRefGoogle Scholar
Casanas, F, Simo, J, Casals, J and Prohens, J (2017) Toward an evolved concept of landrace. Frontiers in Plant Science 8: 145.10.3389/fpls.2017.00145CrossRefGoogle ScholarPubMed
Charlesworth, D and Willis, JH (2009) The genetics of inbreeding depression. Nature Reviews Genetics 10: 783–796.10.1038/nrg2664CrossRefGoogle ScholarPubMed
Choukan, R, Hossainzadeh, A, Ghannadha, MR, Warburton, ML, Talei, AR and Mohammadi, SA (2006) Use of SSR data to determine relationships and potential heterotic groupings within medium to late maturing Iranian maize inbred lines. Field Crops Research 95: 212–222.10.1016/j.fcr.2005.02.011CrossRefGoogle Scholar
Dass, S, Kaul, J, Manivannan, A and Chikkappa, GK (2009) Single cross hybrid maize – a viable solution in the changing climate scenario. Indian Journal of Genetics and Plant Breeding 69: 331–334.Google Scholar
Dass, S, Kumar, A, Jat, SL, Parihar, CM, Singh, AK, Chikkappa, GK and Jat, ML (2012) Maize holds potential for diversification and livelihood security. Indian Journal of Agronomy 57: 32–37.Google Scholar
Dhawan, NL (1964) Primitive maize in Sikkim. Maize Genetics Co-op Newsletter 38: 69–70.Google Scholar
Doyle, JF and Doyle, JL (1990) Isolation of plant DNA from fresh tissue. Focus 12: 39–40.Google Scholar
Duvick, DN (2001) Biotechnology in the 1930s: the development of hybrid maize. Nature Reviews Genetics 2: 69–74.10.1038/35047587CrossRefGoogle ScholarPubMed
Duvick, DN (2005) The contribution of breeding to yield advances in maize (Zea mays L.). Advances in Agronomy, 86: 83–145.10.1016/S0065-2113(05)86002-XCrossRefGoogle Scholar
Evanno, G, Regnaut, S and Goudet, J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14: 2611–2620.10.1111/j.1365-294X.2005.02553.xCrossRefGoogle ScholarPubMed
FAO (2018) World Food and Agriculture – Statistical Pocketbook 2018. Rome, pp. 28, Licence: CC BY-NC-SA 3.0 IGO.Google Scholar
FAO (2019) Voluntary Guidelines for the Conservation and Sustainable Use of Farmers’ Varieties/Landraces. Rome.Google Scholar
Fenzi, M, Jarvis, DI, Reyes, LMA, Moreno, LL and Tuxill, J (2015) Longitudinal analysis of maize diversity in Yucatan, Mexico: influence of agro-ecological factors on landraces conservation and modern variety introduction. Plant Genetic Resources 15: 51–63.10.1017/S1479262115000374CrossRefGoogle Scholar
Fernandez, EH, Schuster, I, Scapim, CA, Vieira, ES and Coan, MM (2015) Genetic diversity in elite inbred lines of maize and its association with heterosis. Genetics and Molecular Research 14: 6509–6517.10.4238/2015.June.12.3CrossRefGoogle Scholar
Feroze, SM, Raju, VT, Singh, R and Tripathi, AK (2010) Status of livestock sector: a micro study of North Eastern India. Indian Journal of Hill Farming 23: 43–51.Google Scholar
Ficiciyan, A, Loos, J, Sievers-Glotzbach, S and Tscharntke, T (2018) More than yield: ecosystem services of traditional versus modern crop varieties revisited. Sustainability 10: 2834.10.3390/su10082834CrossRefGoogle Scholar
Gichuru, L, Derera, J, Tongoona, P and Murenga, M (2016) Combining ability and molecular genetic distances in tropical maize lines for grain yield and agronomic traits. South African Journal of Plant and Soil 34: 175–183.10.1080/02571862.2016.1213323CrossRefGoogle Scholar
Grogan, P, Lalnunmawia, F and Tripathi, SK (2012) Shifting cultivation in steeply sloped regions: a review of management options and research priorities for Mizoram state, Northeast India. Agroforestry Systems 84: 163–177.10.1007/s10457-011-9469-1CrossRefGoogle Scholar
Hallauer, AR, Carena, MJ and Miranda Filho, JD (2010) Quantitative Genetics in Maize Breeding, vol. 6. New York: Springer Science & Business Media, p. 432.Google Scholar
Hochholdinger, F and Baldauf, JA (2018) Heterosis in plants. Current Biology 28: R1089–R1092.10.1016/j.cub.2018.06.041CrossRefGoogle ScholarPubMed
Holsinger, KE and Weir, BS (2009) Genetics in geographically structured populations: defining, estimating and interpreting F ST. Nature Reviews Genetics 10 : 639–650.10.1038/nrg2611CrossRefGoogle Scholar
Hossain, F, Muthusamy, V, Bhat, JS, Jha, SK, Zunjare, R, Das, A, Sarika, K and Kumar, R (2016) Maize. In: Singh, M and Kumar, S (eds) Broadening the Genetic Base of Grain Cereals. New Delhi: Springer, pp. 67–88.10.1007/978-81-322-3613-9_4CrossRefGoogle Scholar
Kumar, M and Sachan, JK (1994) Cytological basis of racial diversity in Indian maize: an overview. Indian Journal of Genetics and Plant Breeding 54: 409–417.Google Scholar
Kumar, R, Srinivas, K and Sivaramane, N (2013) Assessment of the maize situation, outlook and investment opportunities in India. Country Report – Regional Assessment Asia (MAIZE-CRP), National Academy of Agricultural Research Management, Hyderabad, India.Google Scholar
Lai, J, Li, R, Xu, X, Jin, W, Xu, M, Zhao, H, Xiang, Z, Song, W, Ying, K, Zhang, M and Jiao, Y (2010) Genome-wide patterns of genetic variation among elite maize inbred lines. Nature Genetics 42: 1027–1030.10.1038/ng.684CrossRefGoogle ScholarPubMed
Lee, EA and Kannenberg, LW (2004) Effect of inbreeding method and selection criteria on inbred and hybrid performance. Maydica 49: 191–197.Google Scholar
Lia, VV, Poggio, L and Confalonieri, VA (2009) Microsatellite variation in maize landraces from North Western Argentina: genetic diversity, population structure and racial affiliations. Theoretical and Applied Genetics 119: 1053–1067.10.1007/s00122-009-1108-0CrossRefGoogle Scholar
Liu, K, Goodman, M, Muse, S, Smith, JS, Buckler, E and Doebley, J (2003) Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites. Genetics 165: 2117–2128.Google ScholarPubMed
Louette, D and Smale, M (2000) Farmers’ seed selection practices and traditional maize varieties in Cuzalapa, Mexico. Euphytica 113: 25–24.10.1023/A:1003941615886CrossRefGoogle Scholar
Meirmans, PG (2006) Using the AMOVA framework to estimate a standardized genetic differentiation measure. Evolution 60 : 2399–2402.10.1554/05-631.1CrossRefGoogle ScholarPubMed
Melani, MD and Carena, MJ (2005) Alternative maize heterotic patterns for the northern corn belt. Crop Science 45: 2186–2194.10.2135/cropsci2004.0289CrossRefGoogle Scholar
Melchinger, AE and Gumber, RK (1998) Overview of heterosis and heterotic groups in agronomic crops. In: Larnkey, KR and Staub, JE (eds) Concepts and Breeding of Heterosis in Crop Plants. Madison, WI: CSSA Special Publication, pp. 29–44.Google Scholar
Melchinger, AE, Messmer, MM, Lee, M, Woodman, WL and Lamkey, KR (1991) Diversity and relationships among US maize inbreds revealed by restriction fragment length polymorphisms. Crop Science 31: 669–678.10.2135/cropsci1991.0011183X003100030025xCrossRefGoogle Scholar
Mengoni, A and Bazzicalupo, M (2002) The statistical treatment of data and the Analysis of Molecular Variance (AMOVA) in molecular microbial ecology. Annals of Microbiology 52: 95–101.Google Scholar
Mercer, KL and Perales, HR (2010) Evolutionary response of landraces to climate change in centers of crop diversity. Evolutionary Applications 3: 480–493.10.1111/j.1752-4571.2010.00137.xCrossRefGoogle ScholarPubMed
Moll, RH, Lonnquist, JH, Fortuno, JV and Johnson, EC (1965) The relationship of heterosis and genetic divergence in maize. Genetics 52: 139.Google ScholarPubMed
Morrell, PL, Buckler, ES and Ross-Ibarra, J (2012) Crop genomics: advances and applications. Nature Reviews Genetics 13: 85–96.10.1038/nrg3097CrossRefGoogle Scholar
Nei, M (1973) Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences 70: 3321–3323.10.1073/pnas.70.12.3321CrossRefGoogle ScholarPubMed
Nyaligwa, L, Hussein, S, Amelework, B and Ghebrehiwot, H (2015) Genetic diversity analysis of elite maize inbred lines of diverse sources using SSR markers. Maydica 60 : 1–8.Google Scholar
Pavithra, S, Boeber, C, Shah, SA, Subash, SP, Birthal, PS and Mittal, S (2018) Adoption of modern maize varieties in India: insights based on expert elicitation methodology. Agricultural Research 7: 391–401.10.1007/s40003-018-0330-xCrossRefGoogle Scholar
Peakall, RO and Smouse, PE (2012) Genalex 6.5: genetic analysis in excel. Population genetic software for teaching and research-an update. Bioinformatics (Oxford, England) 28: 2537–2539.10.1093/bioinformatics/bts460CrossRefGoogle ScholarPubMed
Portwood, JL, Woodhouse, MR, Cannon, EK, Gardiner, JM, Harper, LC, Schaeffer, ML, Walsh, JR, Sen, TZ, Cho, KT, Schott, DA, Braun, BL, Dietze, M, Dunfee, B, Elsik, CG, Manchanda, N, Coe, E, Sachs, M, Stinard, P, Tolbert, J, Zimmerman, S and Andorf, CM (2018) Maize GDB 2018: the maize multi-genome genetics and genomics database. Nucleic Acids Research 47: 1146–1154.10.1093/nar/gky1046CrossRefGoogle Scholar
Prasanna, BM (2010) Phenotypic and molecular diversity of maize landraces: characterization and utilization. Indian Journal of Genetics and Plant Breeding 70: 315–327.Google Scholar
Prasanna, BM (2012) Diversity in global maize germplasm: characterization and utilization. Journal of Bioscience 37: 843–855.10.1007/s12038-012-9227-1CrossRefGoogle ScholarPubMed
Pressoir, G and Berthaud, J (2004) Population structure and strong divergent selection shape phenotypic diversification in maize landraces. Heredity 92: 95–101.10.1038/sj.hdy.6800388CrossRefGoogle ScholarPubMed
Pritchard, JK, Stephens, M and Donnelly, P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945–959.Google ScholarPubMed
Punya, Sharma VK and Kumar, P (2018) Microsatellite marker dependent genetic divergence assessment within and among heterotic groups of tropical maize inbred lines. Maydica 63: 13.Google Scholar
Rebourg, C, Chastanet, M, Gouesnard, B, Welcker, C, Dubreuil, P and Charcosset, A (2003) Maize introduction into Europe: the history reviewed in the light of molecular data. Theoretical and Applied Genetics 106: 895–903.10.1007/s00122-002-1140-9CrossRefGoogle ScholarPubMed
Reif, JC, Melchinger, AE, Xia, XC, Warburton, ML, Hoisington, DA, Vasal, SK, Srinivasan, G, Bohn, M and Frisch, M (2003) Genetic distance based on simple sequence repeats and heterosis in tropical maize populations. Crop Science 43: 1275–1282.10.2135/cropsci2003.1275CrossRefGoogle Scholar
Reif, JC, Hamrit, S, Heckenberger, M, Schipprack, W, Maurer, HP, Bohn, M and Melchinger, AE (2005) Genetic structure and diversity of European flint maize populations determined with SSR analyses of individuals and bulks. Theoretical and Applied Genetics 111: 906–913.10.1007/s00122-005-0016-1CrossRefGoogle ScholarPubMed
Rodrigues, MC, Valva, FD, Brasil, EM and Chaves, LJ (2001) Comparison among inbreeding systems in maize. Crop Breeding and Applied Biotechnology 1: 105–114.10.13082/1984-7033.v01n02a02CrossRefGoogle Scholar
Romay, MC, Butron, A, Ordas, A, Revilla, P and Ordas, B (2012) Effect of recurrent selection on the genetic structure of two broad-based Spanish maize populations. Crop Science 52: 1493–1502.10.2135/cropsci2011.10.0552CrossRefGoogle Scholar
Sanjenbam, M, Sen, D, Tyagi, W and Chand, R (2018) Phenotypic diversity analysis and screening for northern corn leaf blight resistance in maize (Zea mays L.) landraces grown in North Eastern hill region of India. Indian Journal of Plant Genetic Resources 31: 286–294.10.5958/0976-1926.2018.00033.5CrossRefGoogle Scholar
Semagn, K, Magorokosho, C, Vivek, BS, Makumbi, D, Beyene, Y, Mugo, S, Prasanna, BM and Warburton, ML (2012) Molecular characterization of diverse CIMMYT maize inbred lines from Eastern and Southern Africa using single nucleotide polymorphic markers. BMC Genomics 13: 113.10.1186/1471-2164-13-113CrossRefGoogle ScholarPubMed
Sharma, SK and Brahmi, P (2011) Gene bank curators: towards implementation of the international treaty on plant genetic resources for food and agriculture by the Indian National Gene Bank. In: Frison, C, López, F and Esquinas-Alcázar, JT (eds) Plant Genetic Resources and Food Security: Stakeholder Perspectives on the International Treaty on Plant Genetic Resources for Food and Agriculture. Oxon: FAO and Bioversity International, pp. 183–196.Google Scholar
Sharma, L, Prasanna, BM and Ramesh, B (2010) Analysis of phenotypic and microsatellite-based diversity of maize landraces in India, especially from the north east Himalayan region. Genetica 138: 619–631.10.1007/s10709-010-9436-1CrossRefGoogle ScholarPubMed
Singh, B (1977) Races of Maize in India. New Delhi: Indian Council of Agricultural Research.Google Scholar
Singode, A and Prasanna, BM (2010) Analysis of genetic diversity in the North Eastern Himalayan maize landraces using microsatellite markers. Journal of Plant Biochemistry and Biotechnology 19: 33–41.10.1007/BF03323433CrossRefGoogle Scholar
Springer, NM and Stupar, RM (2007) Allelic variation and heterosis in maize: how do two halves make more than a whole? Genome Research 17: 264–275.10.1101/gr.5347007CrossRefGoogle ScholarPubMed
Tripathi, AK, Singh, SB and Datta, KK (2003) Prospects, problems and scope of maize and pulses in north eastern hill region of India. Indian Journal of Hill Farming 16: 48–52.Google Scholar
van Heerwaarden, J, Hellin, J, Visser, RF and van Eeuw, FA (2009) Estimating maize genetic erosion in modernized smallholder agriculture. Theoretical and Applied Genetics 119: 875–888.10.1007/s00122-009-1096-0CrossRefGoogle ScholarPubMed
Villa, TCC, Maxted, N, Scholten, M and Ford-Lloyd, B (2005) Defining and identifying crop landraces. Plant Genetic Resources 3: 373–384.10.1079/PGR200591CrossRefGoogle Scholar
Wang, L, Beissinger, TM, Lorant, A, Ross-Ibarra, C, Ross-Ibarra, J and Hufford, MB (2017) The interplay of demography and selection during maize domestication and expansion. Genome Biology 18: 215.10.1186/s13059-017-1346-4CrossRefGoogle ScholarPubMed
Wasala, SK and Prasanna, BM (2012) Microsatellite marker-based diversity and population genetic analysis of selected lowland and mid-altitude maize landrace accessions of India. Journal of Plant Biochemistry Biotechnology 22: 392–400.10.1007/s13562-012-0167-5CrossRefGoogle Scholar
Yang, Q, Balint-Kurti, P and Xu, M (2017) Quantitative disease resistance: dissection and adoption in maize. Molecular Plant 10: 402–413.10.1016/j.molp.2017.02.004CrossRefGoogle ScholarPubMed
Yao, Q, Yang, K, Pan, G and Rong, T (2007) Genetic diversity of maize (Zea mays L.) landraces from Southwest China based on SSR data. Journal of Genetic and Genomics 34: 851–860.10.1016/S1673-8527(07)60096-4CrossRefGoogle ScholarPubMed
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