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Molecular profiling of foxtail millet (Setaria italica (L.) P. Beauv) from Central Himalayan Region for genetic variability and nutritional quality

  • A. K. Trivedi (a1), L. Arya (a2), S. K. Verma (a1), R. K. Tyagi (a2), A. Hemantaranjan (a3), M. Verma (a2), V. P. Sharma (a2) and D. Saha (a2)...

Abstract

Agriculture in the Central Himalayan Region depends on the availability of suitable germplasm as well as natural conditions. Due to extreme weather conditions, food and nutrition security is a major issue for communities inhabiting these remote and inaccessible areas. Millets are common crops grown in these areas. Foxtail millet (Setaria italica (L.) P. Beauv) is an important crop and forms a considerable part of the diet in this region. The aim of the present study was to explore, collect, conserve and evaluate the untapped genetic diversity of foxtail millet at the molecular level and discover variability in their nutritional traits. A total of 30 accessions having unique traits of agronomic importance were collected and molecular profiling was performed. A total of 63 alleles were generated with an average of 2.52 alleles per locus and average expected heterozygosity of 0.37 ± 0.231. Significant genetic variability was revealed through the genetic differentiation (Fst) and gene flow (Nm) values. Structure-based analysis divided whole germplasm into three sub-groups. Rich variability was found in nutritional traits such as dietary fibre in husked grains, carbohydrate, protein, lysine and thiamine content. The collected germplasm may be useful for developing nutritionally rich and agronomically beneficial varieties of foxtail millet and also designing strategies for utilization of unexploited genetic diversity for food and nutrition security in this and other similar agro-ecological regions.

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Author for correspondence: A.K. Trivedi, E-mail: ak.trivedi@icar.gov.in

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These authors contributed equally to this work.

Present address: Asia-Pacific Consortium on Agricultural Biotechnology (APCoAB), Asia-Pacific Association of Agricultural Research Institutions (APAARI), 4th Floor FAO Annex Building, 202/1 Larn Luang Road, Promprab Sattrupai, Khlong Mahanak, Bangkok 10100, Thailand.

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References

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Abdul-Hamid, A and Luan, YS (2000) Functional properties of dietary fibre prepared from defatted rice bran. Food Chemistry 68, 1519.
Akoh, CC and Min, DB (2007) Food Lipids: Chemistry, Nutrition and Biotechnology, 3rd Edn. New York: Marcel Dekker.
Anderson, JA, Churchill, GA, Autrique, JE, Tanksley, SD and Sorrells, ME (1993) Optimizing parental selection for genetic linkage maps. Genome 36, 181186.
AOAC (1998) AOAC official method 996.01 fats (total, saturated, unsaturated and monounsaturated) in cereal products. In Horwitz, W (ed.), AOAC Official Methods of Analysis, 17th Edn. Arlington, VA: Association of Official Agricultural Chemists.
AOAC (2005) AOAC official methods 2001.03 dietary fiber in foods containing resistant maltodextrin. In Horwitz, W (ed.). AOAC Official Methods of Analysis, 18th Edn. Gaithersberg, MD: Association of Official Agricultural Chemists.
Backes, G and Østergard, H (2008) Molecular markers to exploit genotype-environment interactions of relevance in organic growing systems. Euphytica 163, 523531.
Baker, DH (2007) Lysine, arginine, and related amino acids: an introduction to the 6th amino acid assessment workshop. The Journal of Nutrition 137(suppl. 2), 1599S1601S.
Bennetzen, JL, Schmutz, J, Wang, H, Percifield, R, Hawkins, J, Pontaroli, AC, Estep, M, Feng, L, Vaughn, JN, Grimwood, J, Jenkins, J, Barry, K, Lindquist, E, Hellsten, U, Deshpande, S, Wang, X, W, X, Mitros, T, Triplett, J, Yang, X, Ye, CY, Mauro-Herrera, M, Wang, L, Li, P, Sharma, M, Sharma, R, Ronald, PC, Panaud, O, Kellogg, EA, Brutnell, TP, Doust, AN, Tuskan, GA, Rokhsar, D and Devos, KM (2012) Reference genome sequence of the model plant Setaria. Nature Biotechnology 30, 555561.
Bettendorff, L, Lakaye, B, Kohn, G and Wins, P (2014) Thiamine triphosphate: a ubiquitous molecule in search of a physiological role. Metabolic Brain Disease 29, 10691082.
Chakravarthi, BK and Naravaneni, R (2006) SSR marker based DNA fingerprinting and diversity study in rice (Oryza sativa L.). African Journal of Biotechnology 5, 684688.
Chen, Q, Li, D, Yang, H, Zhu, Q, Zheng, H and Xu, J (1999) Novel spectrofluorimetric method for the determination of thiamine with iron(III) tetrasulfonatophthalocyanine as a catalyst. The Analyst 124, 771775.
Chow, CK (ed.) (2008) Fatty Acids in Foods and Their Health Implications, 3rd Edn. Boca Raton, FL: CRC Press.
Coats, D, Shelton-Dodge, K, Ou, K, Khun, V, Seab, S, Sok, K, Prou, C, Tortorelli, S, Moyer, TP, Cooper, LE, Begley, TP, Enders, F, Fischer, PR and Topazian, M (2012) Thiamine deficiency in Cambodian infants with and without beriberi. Journal of Pediatrics 161, 843847.
Diao, X, Schnable, J, Bennetzen, JL and Li, J (2014) Initiation of Setaria as a model plant. Frontiers of Agricultural Science and Engineering 1, 1620.
Diniz, YS, Cicogna, ACC, Padovani, CR, Santana, LS, Faine, LA and Novelli, ELB (2004) Diets rich in saturated and poly unsaturated fatty acids: metabolic shifting and cardiac health. Nutrition 20, 230234.
Doust, AN, Kellogg, EA, Devos, KM and Bennetzen, JL (2009) Foxtail millet: a sequence-driven grass model system. Plant Physiology 149, 137141.
Duzyaman, E (2005) Phenotypic diversity within a collection of distinct okra (Abelmoschus esculentus) cultivars derived from Turkish land races. Genetic Resources and Crop Evolution 52, 10191030.
Dwivedi, SL, Crouch, JH, Mackill, DJ, Xu, Y, Blair, MW, Ragot, M, Upadhyaya, HD and Ortiz, R (2007) The molecularization of public sector crop breeding: progress, problems and prospects. Advances in Agronomy 95, 163318.
Dwyer, JT, Wiemer, KL, Dary, O, Keen, CL, King, JC, Miller, KB, Philbert, MA, Tarasuk, V, Taylor, CL, Gaine, PC, Jarvis, AB and Bailey, RL (2015) Fortification and health: challenges and opportunities. Advances in Nutrition 6, 124131.
Earl, DA and von Holdt, BM (2012) Structure harvester: a website and program for visualizing structure output and implementing the Evanno method. Conservation Genetics Resources 4, 359361.
Eastwood, M (2003) Principles of Human Nutrition, 2nd Edn. Malden, MA: Blackwell Science.
Flight, I (2006) Cereal grains and legumes in the prevention of coronary heart disease and stroke: a review of the literature. European Journal of Clinical Nutrition 60, 11451159.
Gupta, S, Kumari, K, Sahu, PP, Vidapu, S and Prasad, M (2012) Sequence-based novel genomic microsatellite markers for robust genotyping purposes in foxtail millet (Setaria italica (L.) P. Beauv.). Plant Cell Reports 31, 323337.
Hurrell, RF and Carpenter, KJ (1981) The estimation of available lysine in foodstuffs after Maillard reactions. Progress in Food and Nutrition Science 5, 159176. (Accessed 13 March 2018).
Jali, MV, Kamatar, MY, Jali, SM, Hiremath, MB and Naik, RK (2012) Efficacy of value added foxtail millet therapeutic food in the management of diabetes and dyslipidamea in type 2 diabetic patients. Recent Research in Science and Technology 4, 34.
Jia, G, Huang, X, Zhi, H, Zhao, Y, Zhao, Q, Li, W, Chai, Y, Yang, L, Liu, K, Lu, H, Zhu, C, Lu, Y, Zhou, C, Fan, D, Weng, Q, Guo, Y, Huang, T, Zhang, L, Lu, T, Feng, Q, Hao, H, Liu, H, Lu, P, Zhang, N, Li, Y, Guo, E, Wang, S, Wang, S, Liu, J, Zhang, W, Chen, G, Zhang, B, Li, W, Wang, Y, Li, H, Zhao, B, Li, J, Diao, X and Han, B (2013) A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica). Nature Genetics 45, 957961.
Jia, X, Zhang, Z, Liu, Y, Zhang, C, Shi, Y, Song, Y, Wang, T and Li, Y (2009) Development and genetic mapping of SSR markers in foxtail millet (Setaria italica (L.) P. Beauv.). Theoretical and Applied Genetics 118, 821829.
Jones, JM (2001) The benefits of eating breakfast cereals. Cereal Foods World 46, 461464, 466–467.
Jones, JR, Lineback, DM and Levine, MJ (2006) Dietary reference intakes: implications for fiber labeling and consumption: a summary of the international life sciences institute North America fiber workshop, June 1–2, 2004, Washington, DC. Nutrition Reviews 64, 3138.
Kam, J, Puranik, S, Yadav, R, Manwaring, HR, Pierre, S, Srivastava, RK and Yadav, RS (2016) Dietary interventions for type 2 diabetes: how millet comes to help. Frontiers in Plant Science 7, 1454.
Khounnorath, S, Chamberlain, K, Taylor, AM, Soukaloun, D, Mayxay, M, Lee, SJ, Phengdy, B, Luangxay, K, Sisouk, K, Soumphonphakdy, B, Latsavong, K, Akkhavong, K, White, NJ and Newton, PN (2011) Clinically unapparent infantile thiamin deficiency in Vientiane, Laos. PLoS Neglected Tropical Diseases 5, e969. https://doi.org/10.1371/journal.pntd.0000969
Kumari, K, Muthamilarasan, M, Misra, G, Gupta, S, Subramanian, A, Parida, SK, Chattopadhayay, D and Prasad, M (2013) Development of eSSR-markers in Setaria italica and their applicability in studying genetic diversity, cross-transferability and comparative mapping in millet and non-millet species. PLoS ONE 8, e67742.
Lammerts van Bueren, ET, Backes, G, de Vriend, H and Østergärd, H (2010) The role of molecular markers and marker assisted selection in breeding for organic agriculture. Euphytica 175, 5164.
Lata, C, Gupta, S and Prasad, M (2013) Foxtail millet: a model crop for genetic and genomic studies in bioenergy grasses. Critical Reviews in Biotechnology 33, 328343.
Lee, YK (1994) The Beri-beri Hospital, Singapore (1907–1925). Singapore Medical Journal 35, 306311.
Leonard, WH and Martin, JH (1963) Cereal Crops. New York: Macmillan.
Li, P and Brutnell, TP (2011) Setaria viridis and Setaria italica, model genetic systems for the Panicoid grasses. Journal of Experimental Botany 62, 30313037.
Li, HW, Meng, CJ and Liu, TM (1935) Problems in the breeding of millet (Setaria italica (L.) Beauv.). Agronomy Journal 27, 963970.
Li, S, An, S, Liu, Z, Cheng, R and Wang, Z (2014) Innovation of the new superior quality foxtail millet (Setaria italica (L.) P. Beauv) variety-Jigu32 with characteristics of stress resistance, stable and high yield and its physiological mechanism. Agricultural Sciences 5, 304316.
Lin, HS, Chiang, CY, Chang, SB, Liao, GI and Kuoh, CS (2012) Genetic diversity in the foxtail millet (Setaria italica) germplasm as determined by agronomic traits and microsatellite markers. Australian Journal of Crop Science 6, 342349.
Liu, Z, Bai, G, Zhang, D, Zhu, C, Xia, X, Cheng, R and Shi, Z (2011) Genetic diversity and population structure of elite foxtail millet (Setaria italica (L.) P. Beauv.) germplasm in China. Crop Science 51, 16551663.
Lonsdale, D (1990) Thiamine deficiency and sudden deaths (letter; comment). The Lancet 336, 376.
Lowry, OH, Rosenbrough, NJ, Farr, AL and Randall, RJ (1951) Protein measurement with the Folin-phenol reagent. Journal of Biological Chemistry 193, 265275.
Mehta, RS (2005) Dietary fiber benefits. Cereal Foods World 50, 6671.
Morris, DL (1948) Quantitative determination of carbohydrates with Dreywood's anthrone reagent. Science 107, 254255.
Muthamilarasan, M and Prasad, M (2015) Advances in Setaria genomics for genetic improvement of cereals and bioenergy grasses. Theoretical and Applied Genetics 128, 114.
Muthamilarasan, M, Venkata Suresh, B, Pandey, G, Kumari, K, Parida, SK and Prasad, M (2014) Development of 5123 intron-length polymorphic markers for large-scale genotyping applications in foxtail millet. DNA Research 21, 4152.
Nathoo, T, Holmes, CP and Ostry, A (2005) An analysis of the development of Canadian food fortification policies: the case of vitamin B. Health Promotion International 20, 375382.
Pandey, G, Misra, G, Kumari, K, Gupta, S, Parida, SK, Chattopadhyay, D and Prasad, M (2013) Genome-wide development and use of microsatellite markers for large-scale genotyping applications in foxtail millet (Setaria italica (L.)). DNA Research 20, 197207.
Pritchard, JK, Stephens, M and Donnelly, P (2000) Inference of population structure using multilocus genotype data. Genetics 155, 945959.
Rohlf, FJ (2000) NTSYS-PC, Numerical Taxonomy System for the PC Exeter Software, Version 2.1. Setauket: Applied Biostatistics Inc.
Ronald, P (2011) Plant genetics, sustainable agriculture and global food security. Genetics 188, 1120.
Saghai-Maroof, MA, Soliman, KM, Jorgensen, RA and Allard, RW (1984) Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location and population dynamics. Proceedings of the National Academy of Sciences of the United States of America 81, 80148018.
Sahley, BJ and Birkner, KM (2000) Healing with Amino Acids and Nutrients. San Antonio, TX: Pain and Stress Publications, Inc.
Sankhala, A, Chopra, S and Sankhala, AK (2004) Effect of processing on tannin, phytate and in vitro iron in underutilized millets – bajra (Pennisetum typhoideum) and Kangni (Setaria italica). Indian Journal of Nutrition and Dietetics 41, 5562.
Shewry, PR and Halford, NG (2002) Cereal seed storage proteins: structures, properties and role in grain utilization. Journal of Experimental Botany 53, 947958.
Sica, DA (2007) Loop diuretic therapy, thiamine balance, and heart failure. Congestive Heart Failure 13, 244247.
Staub, JC, Serquen, FC and Mccreight, JD (1997) Genetic diversity in cucumber (Cucumis sativus L.). III. An evaluation of Indian germplasm. Genetic Resources and Crop Evolution 44, 315326.
Suresh, VB, Muthamilarasan, M, Misra, G and Prasad, M (2013) FmMDb: a versatile database of foxtail millet markers for millets and bioenergy grasses research. PLoS ONE 8, e71418.
Tome, D and Bos, C (2007) Lysine requirement through the human life cycle. Journal of Nutrition 137(suppl. 2), 1642S1645S.
Trivedi, AK, Arya, L, Verma, M, Verma, SK, Tyagi, RK and Hemantaranjan, A (2015) Genetic variability in proso millet (Panicum miliaceum) germplasm of Central Himalayan region based on morpho-physiological traits and molecular markers. Acta Physiologiae Plantarum 37, 23. https://doi.org/10.1007/s11738-014-1770-y
Tuvesson, S, Svensson, E, Happstadius, I, Henriksson, T and Kazman, E (2009) Application of markers when breeding for baking quality. In Østergård, H, Lammerts van Bueren, ET and Bouwman-Smits, L (eds), Proceedings of the BioExploit/Eucarpia Workshop on the Role of Marker Assisted Selection in Breeding Varieties for Organic Agriculture. Wageningen, The Netherlands: BioExploit, pp. 3839. Available at https://www.eucarpia.org/organic-and-low-input-agriculture/190-workshop-on-the-role-of-marker-assisted-selection-in-breeding-varieties-for-organic-agriculture.html (Accessed 13 March 2018).
Wang, ZM, Devos, KM, Liu, CJ, Wang, RQ and Gale, MD (1998) Construction of RFLP-based maps of foxtail millet, Setaria italica (L.) P. Beauv. Theoretical and Applied Genetics 96, 3136.
Wooley, JA (2008) Characteristics of thiamin and its relevance to the management of heart failure. Nutrition in Clinical Practice 23, 487493.
Wright, S (1931) Evolution in Mendelian populations. Genetics 16, 97159.
Xu, Y and Crouch, JH (2008) Marker-assisted selection in plant breeding: from publications to practice. Crop Science 48, 391407.
Yadav, CB, Bonthala, VS, Muthamilarasan, M, Pandey, G, Khan, Y and Prasad, M (2015) Genome-wide development of transposable elements-based markers in foxtail millet and construction of an integrated database. DNA Research 22, 7990.
Yeh, FC, Yang, RC and Boyle, T (1999) Popgene Version 1.32. Microsoft Window-Based Freeware for Population Genetic Analysis. Edmonton, Canada: Quick User Guide, University of Alberta and Center for International Forestry Research. Available at https://sites.ualberta.ca/~fyeh/popgene_download.html (Accessed 13 March 2018).
Zhang, S, Tang, C, Zhao, Q, Li, J, Yang, L, Qie, L, Fan, X, Li, L, Zhang, N, Zhao, M, Liu, X, Chai, Y, Zhang, X, Wang, H, Li, Y, Li, W, Zhi, H, Jia, G and Diao, X (2014) Development of highly polymorphic simple sequence repeat markers using genome-wide microsatellite variant analysis in foxtail millet (Setaria italica (L.) P. Beauv.). BMC Genomics 15, 78.

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