Hostname: page-component-cd9895bd7-7cvxr Total loading time: 0 Render date: 2024-12-25T05:48:51.544Z Has data issue: false hasContentIssue false

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

Published online by Cambridge University Press:  28 May 2018

A. K. Trivedi*
Affiliation:
ICAR – National Bureau of Plant Genetic Resources, Regional Station Bhowali – 263132, Nainital (Uttarakhand), India
L. Arya
Affiliation:
ICAR – National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi – 110012, India
S. K. Verma
Affiliation:
ICAR – National Bureau of Plant Genetic Resources, Regional Station Bhowali – 263132, Nainital (Uttarakhand), India
R. K. Tyagi
Affiliation:
ICAR – National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi – 110012, India
A. Hemantaranjan
Affiliation:
Department of Plant Physiology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi – 221005, India
M. Verma
Affiliation:
ICAR – National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi – 110012, India
V. P. Sharma
Affiliation:
ICAR – National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi – 110012, India
D. Saha
Affiliation:
ICAR – National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi – 110012, India
*
Author for correspondence: A.K. Trivedi, E-mail: [email protected]

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.

Type
Crops and Soils Research Paper
Copyright
Copyright © Cambridge University Press 2018 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

Footnotes

*

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.

References

Abdul-Hamid, A and Luan, YS (2000) Functional properties of dietary fibre prepared from defatted rice bran. Food Chemistry 68, 1519.Google Scholar
Akoh, CC and Min, DB (2007) Food Lipids: Chemistry, Nutrition and Biotechnology, 3rd Edn. New York: Marcel Dekker.Google Scholar
Anderson, JA, Churchill, GA, Autrique, JE, Tanksley, SD and Sorrells, ME (1993) Optimizing parental selection for genetic linkage maps. Genome 36, 181186.Google Scholar
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.Google Scholar
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.Google Scholar
Backes, G and Østergard, H (2008) Molecular markers to exploit genotype-environment interactions of relevance in organic growing systems. Euphytica 163, 523531.CrossRefGoogle Scholar
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.Google Scholar
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.CrossRefGoogle ScholarPubMed
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.Google Scholar
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.Google Scholar
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.Google Scholar
Chow, CK (ed.) (2008) Fatty Acids in Foods and Their Health Implications, 3rd Edn. Boca Raton, FL: CRC Press.Google Scholar
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.Google Scholar
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.Google Scholar
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.CrossRefGoogle Scholar
Doust, AN, Kellogg, EA, Devos, KM and Bennetzen, JL (2009) Foxtail millet: a sequence-driven grass model system. Plant Physiology 149, 137141.CrossRefGoogle ScholarPubMed
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.Google Scholar
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.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
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.Google Scholar
Eastwood, M (2003) Principles of Human Nutrition, 2nd Edn. Malden, MA: Blackwell Science.Google Scholar
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.CrossRefGoogle ScholarPubMed
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.Google Scholar
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).Google Scholar
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.Google Scholar
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.Google Scholar
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.CrossRefGoogle ScholarPubMed
Jones, JM (2001) The benefits of eating breakfast cereals. Cereal Foods World 46, 461464, 466–467.Google Scholar
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.Google Scholar
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.Google Scholar
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.0000969CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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.CrossRefGoogle Scholar
Lee, YK (1994) The Beri-beri Hospital, Singapore (1907–1925). Singapore Medical Journal 35, 306311.Google Scholar
Leonard, WH and Martin, JH (1963) Cereal Crops. New York: Macmillan.Google Scholar
Li, P and Brutnell, TP (2011) Setaria viridis and Setaria italica, model genetic systems for the Panicoid grasses. Journal of Experimental Botany 62, 30313037.Google Scholar
Li, HW, Meng, CJ and Liu, TM (1935) Problems in the breeding of millet (Setaria italica (L.) Beauv.). Agronomy Journal 27, 963970.CrossRefGoogle Scholar
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.Google Scholar
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.Google Scholar
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.Google Scholar
Lonsdale, D (1990) Thiamine deficiency and sudden deaths (letter; comment). The Lancet 336, 376.Google Scholar
Lowry, OH, Rosenbrough, NJ, Farr, AL and Randall, RJ (1951) Protein measurement with the Folin-phenol reagent. Journal of Biological Chemistry 193, 265275.Google Scholar
Mehta, RS (2005) Dietary fiber benefits. Cereal Foods World 50, 6671.Google Scholar
Morris, DL (1948) Quantitative determination of carbohydrates with Dreywood's anthrone reagent. Science 107, 254255.CrossRefGoogle ScholarPubMed
Muthamilarasan, M and Prasad, M (2015) Advances in Setaria genomics for genetic improvement of cereals and bioenergy grasses. Theoretical and Applied Genetics 128, 114.Google Scholar
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.CrossRefGoogle ScholarPubMed
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.Google Scholar
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.Google Scholar
Pritchard, JK, Stephens, M and Donnelly, P (2000) Inference of population structure using multilocus genotype data. Genetics 155, 945959.Google Scholar
Rohlf, FJ (2000) NTSYS-PC, Numerical Taxonomy System for the PC Exeter Software, Version 2.1. Setauket: Applied Biostatistics Inc.Google Scholar
Ronald, P (2011) Plant genetics, sustainable agriculture and global food security. Genetics 188, 1120.Google Scholar
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.CrossRefGoogle ScholarPubMed
Sahley, BJ and Birkner, KM (2000) Healing with Amino Acids and Nutrients. San Antonio, TX: Pain and Stress Publications, Inc.Google Scholar
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.Google Scholar
Shewry, PR and Halford, NG (2002) Cereal seed storage proteins: structures, properties and role in grain utilization. Journal of Experimental Botany 53, 947958.Google Scholar
Sica, DA (2007) Loop diuretic therapy, thiamine balance, and heart failure. Congestive Heart Failure 13, 244247.Google Scholar
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.Google Scholar
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.Google Scholar
Tome, D and Bos, C (2007) Lysine requirement through the human life cycle. Journal of Nutrition 137(suppl. 2), 1642S1645S.Google Scholar
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-yCrossRefGoogle Scholar
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).Google Scholar
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.Google Scholar
Wooley, JA (2008) Characteristics of thiamin and its relevance to the management of heart failure. Nutrition in Clinical Practice 23, 487493.Google Scholar
Wright, S (1931) Evolution in Mendelian populations. Genetics 16, 97159.Google Scholar
Xu, Y and Crouch, JH (2008) Marker-assisted selection in plant breeding: from publications to practice. Crop Science 48, 391407.Google Scholar
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.Google Scholar
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).Google Scholar
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.Google Scholar
Supplementary material: File

Trivedi et al. supplementary material 1

Supplementary Table

Download Trivedi et al. supplementary material 1(File)
File 3.9 KB