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Microsatellite marker-based characterization of waxy maize inbreds for their utilization in hybrid breeding

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Abstract

Waxy corn possesses 95–100% amylopectin, compared to 70–75% in normal maize, owing to mutation in Wx gene encoding a granule-bound starch synthase I. Amylopectin is used as an ingredient in textile, adhesive and paper industries. Further, waxy green cob is popular as breakfast item in South Asia and an important constituent of diet in north-eastern states of India as well. We developed a series of waxy inbreds from diverse exotic sources and through introgression breeding. To characterize and unravel the genetic relationships, 24 diverse waxy inbreds were analysed using 77 SSRs distributed throughout the genome. The study generated a total of 203 polymorphic alleles, with a mean of 2.69 alleles per locus. A total of nine unique and 20 rare alleles were detected. The polymorphism information content ranged from 0.08 to 0.68 with an average value of 0.40. Molecular profiling suggested sufficient attainment of homozygosity among the inbreds. Jaccard’s dissimilarity coefficient between pairs of genotypes varied from 0.26 to 0.83 which revealed the diverse nature of the inbred lines. Cluster analyses grouped 24 genotypes into three major clusters. Principle coordinate analysis based on SSR also depicted the diverse origin of the genotypes as per the pedigree more reliably than agro-morphological traits. These inbreds were also promising for various cob and grain characteristics including grain yield. The study identified a set of potential cross-combinations that can be planned to develop highly heterotic waxy hybrid combinations. This is the first report of development and characterization of waxy inbreds in India.

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References

  • Aguiar CG, Schuster I, Amaral Junior AT, ScapimCA Vieira ESN (2008) Heterosis groups in tropical maize germplasm by test crosses and simple sequence repeat markers. Genet Mol Res 7:1233–1244

    Article  CAS  Google Scholar 

  • Ajmone-Marsan Castiglioni P, Fusari F, Kuiper M, Motto M (1998) Genetic diversity and its relationship to hybrid performance in maize as revealed by RFLP and AFLP markers. Theor Appl Genet 96:219–227

    Article  Google Scholar 

  • Bao JD, Yao JQ, Zhu JQ (2012) Identification of glutinous maize landraces and inbred lines with altered transcription of waxy gene. Mol Breed 30:1707–1714

    Article  CAS  Google Scholar 

  • Chakraborti M, Prasanna BM, Hossain F, Mazumdar S, Singh AM, Guleria SK, Gupta HS (2011) Identification of kernel iron- and zinc-rich maize inbreds and analysis of genetic diversity using microsatellite markers. J Plant Biochem Biotechnol 20:224–233

    Article  CAS  Google Scholar 

  • Choudhary M, Hossain F, Muthusamy V, Thirunavukkarasu N, Saha S, Pandey N, Jha SK, Gupta HS (2015) Microsatellite marker-based genetic diversity analyses of novel maize inbreds possessing rare allele of β-carotene hydroxylase (crtRB1) for their utilization in β-carotene enrichment. J Plant Biochem Biotechnol 25:12–20

    Article  Google Scholar 

  • Collard BCY, Jahufer MZZ, Brouwer JB, Pang ECK (2005) An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: the basic concepts. Euphytica 142:169–196

    Article  CAS  Google Scholar 

  • Dellaporta SL, Wood J, Hicks JB (1983) A plant DNA mini preparation: version II. Plant Mol Biol Rep 1:19–21

    Article  CAS  Google Scholar 

  • Drinic SM, Trifunovic S, Drinic G, Konstantinov K (2002) Genetic divergence and its correlation to heterosis in maize as revealed by SSR -based markers. Maydica 47:1–8

    Google Scholar 

  • Fan LJ, Quan LY, Leng XD, Guo XY, Hu WM, Ruan S, Ma H, Zeng M (2008) Molecular evidence for post-domestication selection in the Waxy gene of Chinese waxymaize. Mol Breed 22:329–338

    Article  CAS  Google Scholar 

  • Hao D, Zhang Z, Cheng Y, Chen G, Lu H, Mao Y, Shi M, Huang X, Zhou G, Xue L (2015) Identification of genetic differentiation between waxy and common maize by SNP genotyping. PLoS One 10:e0142585. doi:10.1371/journal.pone.0142585

    Article  Google Scholar 

  • Hung TN, Huyen TN, Loc NV, Cuong BM (2012) The application of SSR molecular indicator to assess the purity and genetic diversity of waxy corn inbred lines. J ISSASS 18:45–54

    Google Scholar 

  • Kaur H, Sarao K, Vikal Y, Singh K, Sharma RC (2011) Microsatellite fingerprinting of maize cultivars (Zea mays L.). Cereal Res Commun 39:507–514

    Article  CAS  Google Scholar 

  • Klosgen RB, Gierl A, Schwarz-Sommer Z, Saedler H (1986) Molecular analysis of the waxy locus of Zea mays. Mol Genet Genom 203:237–244

    Article  Google Scholar 

  • Lanza LLB, Sauza CL Jr, Vieira MLC, Ottoboni LMM, Souza AP (1997) Genetic distance of inbred lines and prediction of maize single cross performance using RAPD markers. Theor Appl Genet 94:1023–1030

    Article  CAS  Google Scholar 

  • Liet VV, Thinh TT (2009) Genetic diversity of local maize (Zea mays L.) accessions collected in highland areas of Vietnam revealed by RAPD markers. J Sci Dev 7:192–201

    Google Scholar 

  • Liu K, Muse SV (2005) PowerMarker: integrated analysis environment for genetic marker data. Bioinformatics 21:2128–2129

    Article  CAS  Google Scholar 

  • Lu D, Lu W (2012) Effects of protein removal on the physico-chemical properties of waxy maize flours. Starch/Stärke 64:874–881

    Article  CAS  Google Scholar 

  • Mason-Gamer RJ, Well CF, Kellogg EA (1998) Granule-bound starch synthase: structure, function, and phylogenetic utility. Mol Biol Evol 15:1658–1673

    Article  CAS  Google Scholar 

  • Mehta B, Hossain F, Muthusamy V, Baveja A, Zunjare RU, Jha SK, Gupta HS (2017) Microsatellite-based genetic diversity analyses of sugary1-, shrunken2- and double mutant-sweet corn inbreds for their utilization in breeding programme. Physiol Mol Biol Plants. doi:10.1007/s12298-017-0431-1

    Google Scholar 

  • Melchinger AE, Lee M, Lamkey KR, Hallauer AR, Woodman WL (1990) Genetic diversity for restriction fragment length polymorphism and heterosis for two diallel sets of maize inbreds. Theor Appl Genet 80:488–496

    Article  CAS  Google Scholar 

  • Muthusamy V, Hossain F, Thirunavukkarasu N, Pandey N, Vishwakarma AK, Saha S, Gupta HS (2015) Molecular characterization of exotic and indigenous maize inbreds for biofortification with kernel carotenoids. Food Biotechnol 29:276–295

    Article  CAS  Google Scholar 

  • Pandey N, Hossain F, Kumar K, Vishwakarma AK, Muthusamy V, Manjaiah KM, Agrawal PK, Guleria SK, Reddy SS, Thirunavukkarasu N, Gupta HS (2015a) Microsatellite marker-based genetic diversity among quality protein maize (QPM) inbreds differing for kernel iron and zinc. Mol Plant Breed 6:1–10

    Google Scholar 

  • Pandey N, Hossain F, Kumar K, Vishwakarma AK, Muthusamy V, Saha S, Agrawal PK, Guleria SK, Reddy SS, Thirunavukkarasu N, Gupta HS (2015b) Molecular characterization of endosperm and amino acids modifications among quality protein maize inbreds. Plant Breed. doi:10.1111/pbr.12328

    Google Scholar 

  • Park JS, Park JY, Park KJ, Lee JK (2008) Genetic diversity among waxy corn accessions in Korea revealed by microsatellite markers. Korean J Breed Sci 40:250–257

    Google Scholar 

  • Perrier X, Flori A, Bonnot F (2003) Data analysis methods. In: Hamon P, Seguin M, Perrier X, Glaszmann JC (eds) Genetic diversity of cultivated tropical plants. Science Publishers Montpellier, Enfield, pp 43–76

    Google Scholar 

  • Prasanna BM, Pixley KV, Warburton M, Xie C (2010) Molecular marker-assisted breeding for maize improvement in Asia. Mol Breed 26:339–356

    Article  CAS  Google Scholar 

  • Sa KJ, Park JY, Choi SH, Kim BW, Park KJ, Lee JK (2015) Genetic diversity, population structure, and association mapping of agronomic traits in waxy and normal maize inbred lines. Genet Mol Res 14:7502–7518

    Article  CAS  Google Scholar 

  • Semagn K, Bjornstad A, Ndjiondjop MN (2006) Progress and prospects of marker assisted backcrossing as a tool in crop breeding programmes. Afr J Biotechnol 5:2588–2603

    CAS  Google Scholar 

  • Senior ML, Murphy JP, Goodman MM, Stuber C (1998) Utility of SSRs for determining genetic similarities and relationships in maize using an agarose gel system. Crop Sci 38:1088–1098

    Article  Google Scholar 

  • Sivaranjani R, Santha IM, Pandey N, Vishwakarma AK, Nepolean T, Hossain F (2014) Microsatellite-based genetic diversity in selected exotic and indigenous maize (Zea mays L.) inbred lines differing in total kernel carotenoids. Indian J Genet 74:34–41

    CAS  Google Scholar 

  • Smith JSC, Smith OS (1992) Fingerprinting crop varieties. Adv Agron 47:85–140

    Article  CAS  Google Scholar 

  • Smith JSC, Chin ECL, Shu H, Smith OS, Wall SJ, Senior LM, Mitchell SE, Kresovich S, Ziegel J (1997) An evaluation of the utility of SSR loci as molecular markers in maize (Zea maysL.): comparisons with data from RFLPs and pedigree. Theor Appl Genet 95:163–173

    Article  CAS  Google Scholar 

  • Tian ML, Tan GX, Liu YJ, Rong TZ, Huang YB (2009) Origin and evolution of Chinese waxy maize: evidence from the Globulin-1 gene. Genet Resour Crop Evol 56:247–255

    Article  CAS  Google Scholar 

  • Xiaoyang W, Dan C, Yuqing L, Weihua L, Xinming Y, Xiuquan L, Juan D, Lihui L (2017) Molecular characteristics of two new waxy mutations in China waxy maize. Mol Breed 37:27

    Article  Google Scholar 

  • Yu RH, Wang YL, Sun Y, Liu B (2012) Analysis of genetic distance by SSR in waxy maize. Genet Mol Res 11(1):254–260

    Article  CAS  Google Scholar 

  • Zhang W, Yang W, Wang M, Wang W, Zeng G, Chen Z, Cai Y (2013) Increasing lysine content of waxy maize through introgression of opaque-2 and opaque-16 genes using molecular assisted and biochemical development. PLoS One 8(2):e56227. doi:10.1371/journal.pone.0056227

    Article  CAS  Google Scholar 

  • Zheng H, Wang H, Yang H, Wu J, Shi B, Cai R, Xu Y, Wu A, Luo L (2013) Genetic diversity and molecular evolution of Chinese waxy maize germplasm. PLoS One 8:1–11

    CAS  Google Scholar 

  • Zhou Z, Song L, Zhang Li X, Yan N, Xia R, Zhu H, Weng J, Hao Z, Zhang D, Yong H, Li M, Zhang S (2016) Introgression of opaque2 into waxy maize causes extensive biochemical and proteomic changes in endosperm. PLoS One. doi:10.1371/journal.pone.0158971

    Google Scholar 

  • Zunjare R, Hossain F, Muthusamy V, Vishwakarma AK, Pandey N, Kumar P, Sekhar JC, Jha SK, Nepolean T, Gupta HS (2015) Analyses of genetic diversity among exotic- and indigenous-maize inbreds differing for responses to stored grain weevil (Sitophilus oryzae L.) infestation. Maydica 60:1–7

    Google Scholar 

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Acknowledgements

We thank Dr. B.M. Prasanna, Director, Global Maize Program, CIMMYT, for providing the source germplasm for waxy character. The authors also thank ICAR–Indian Agricultural Research Institute for the financial support. The help received from Dr. Rajesh Kumar, Chief Technical Officer, and Sh. Manish Kapasia, Technical Assistant, is acknowledged.

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Author notes

  1. Elangbam Lamalakshmi Devi

    Present address: ICAR Research Complex for North Eastern Hill Region, Manipur Centre, Manipur, India

Authors and Affiliations

  1. ICAR-Indian Agricultural Research Institute, New Delhi, India

    Elangbam Lamalakshmi Devi, Firoz Hossain, Vignesh Muthusamy, Rashmi Chhabra, Rajkumar Uttamrao Zunjare, Aanchal Baveja, Sunil Kumar Jaiswal, Rajat Goswami & Sweta Dosad

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  1. Elangbam Lamalakshmi Devi
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  2. Firoz Hossain
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  3. Vignesh Muthusamy
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Contributions

ELD conducted the experiment; FH involved in development of waxy inbred; RC and AB contributed to genotyping; RUZ, RC, AB and SKJ participated in data analysis; RUZ and SD involved in phenotyping for morphological characteristics; MV, RUZ and RG participated in field evaluation and maintenance of lines; FH and MV involved in design of experiment and drafting the manuscript.

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Correspondence to Firoz Hossain.

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Devi, E.L., Hossain, F., Muthusamy, V. et al. Microsatellite marker-based characterization of waxy maize inbreds for their utilization in hybrid breeding. 3 Biotech 7, 316 (2017). https://doi.org/10.1007/s13205-017-0946-8

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