Abstract
Barnyard millet (Echinochloa spp) is a wide-adaptive crop that produces larger seeds compared to other minor millets. It is one of the most important minor millet crops that is predominantly cultivated for human consumption in Asia and livestock feed in the United States. Barnyard millet has incredible resilience to biotic and abiotic stresses. Grains are highly nutritious with significant amount of protein, carbohydrate, fiber, and, most notably, micronutrients (iron and zinc) than other staple cereals. Despite these benefits, barnyard millet has received little attention in genetic and genomic studies for many years. Progress has been made in develo** genetic and genomic resources over last few years, thanks to the reducing cost of sequencing technologies in polyploid and orphan millets species as well. Recently, the genome of wild and transcriptome sequences of cultivated Echinochloa species has facilitated the understanding of the genetic architecture of important agronomic and micronutrient traits. In this chapter, we discuss the importance of barnyard millet in the current climatic scenario and highlight the up-to-date status of genetic and genomics research and the research gaps that need to be addressed in this crop. This chapter also provides an overview of deploying omics approaches to study the barnyard millet for better understanding of crops’ nutritional richness and tolerance to environmental stresses.
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References
Arya L, Chauhan D, Yadav Y, Verma M (2014) Transferability of simple sequence repeat (SSR) markers developed in Finger Millet, and Pearl Millet to Kodo Millet and barnyard Millet. Innovative Approach in Stem Cell Research, Cancer Biology and Applied Biotechnology, 60–64
Aslam B, Basit M, Nisar MA, Khurshid M, Rasool MH (2017) Proteomics: technologies and their applications. J Chromatogr Sci 55:182–196. https://doi.org/10.1093/chromsci/bmw167
Babu B, Chauhan R (2017) In-silico identification of EST based microsatellite markers and SNPs, and comparative genomic analysis of ESTs in barnyard millet for their omics applications. Curr Agric Res J 5:279–287. https://doi.org/10.12944/CARJ.5.3.03
Babu B, Rashmi C, Sood S (2018a) Cross transferability of finger millet and maize genomic SSR markers for genetic diversity and population structure analysis of barnyard millet. Indian J Genet Plant Breed 78:364–372. https://doi.org/10.31742/IJGPB.78.3.5
Babu B, Sood S, Kumar D, Joshi A, Pattanayak A, Kant L et al (2018b) Cross-genera transferability of rice and finger millet genomic SSRs to barnyard millet (Echinochloa spp.). 3 Biotech 8. https://doi.org/10.1007/s13205-018-1118-1
Bajwa A, Jabran K, Shahid M, Ali HH, Chauhan B, Ehsanullah (2015). Eco-biology and management of Echinochloa crus-galli. Crop Prot 75, 151–162. doi:https://doi.org/10.1016/j.cropro.2015.06.001
Chen G, Zhang W, Fang J, Dong L (2017) Identification of massive molecular markers in Echinochloa phyllopogon using a restriction-site associated DNA approach. Plant Divers 39. https://doi.org/10.1016/j.pld.2017.08.004
Danquah EY, Hanley SJ, Brookes RC, Aldam C, Karp A (2002) Isolation and characterization of microsatellites in Echinochloa (L.) Beauv. spp. Mol Ecol Notes 2:54–56
Gao Y, Li J, Pan X, Liu D, Napier R, Dong L (2018) Quinclorac resistance induced by the suppression of the expression of 1-aminocyclopropane-1-carboxylic acid (ACC) synthase and ACC oxidase genes in Echinochloa crusgall i var. zelayensis. Pestic Biochem Physiol 146:25–32. https://doi.org/10.1016/j.pestbp.2018.02.005
Guo L, Qiu J, Ye CY, ** G, Lingfeng M, Zhang H et al (2017) Echinochloa crus-galli genome analysis provides insight into its adaptation and invasiveness as a weed. Nat Commun 8. https://doi.org/10.1038/s41467-017-01067-5
Gupta S, Kumari K, Muthamilarasan M, Alagesan S, Prasad M (2013) Development and utilization of novel SSRs in foxtail millet [Setaria italica (L.) P. Beauv.]. Plant Breed 132. https://doi.org/10.1111/pbr.12070
Hereward JP, Werth JA, Thornby DF, Keenan M, Chauhan BS, Walter GH (2016) Complete chloroplast genome sequences of six lines of Echinochloa colona (L.) link. Mitochondrial DNA Part B 1:945–946
Hilu K (1994) Evidence from RAPD markers in the evolution of Echinochloa millets (Poaceae). Plant Syst Evol 189:247–257. https://doi.org/10.1007/BF00939730
IIMR (2018) Annual Report 2017–18. Indian Institute of Millets Research, Hyderabad
Ishikawa G, Seimiya Y, Saito M, Nakamura T, Hoshino T (2013) Molecular characterization of spontaneous and induced mutations in the three homoeologous waxy genes of Japanese barnyard millet [Echinochloa esculenta (A. Braun) H. Scholz]. Mol Breed 31:69–78. https://doi.org/10.1007/s11032-012-9769-9
Iwakami S, Uchino A, Kataoka Y, Shibaike H, Watanabe H, Inamura T (2014) Cytochrome P450 genes induced by bispyribac-sodium treatment in a multiple-herbicide-resistant biotype of Echinochloa phyllopogon. Pest Manag Sci 70:549–558. https://doi.org/10.1002/ps.3572
Jiang B, Lao S, Wu D, Fan L, Ye CY (2021) The complete chloroplast genome of Echinochloa haploclada. Mitochondrial DNA Part B 6:3105–3106
Krishna TPA, Maharajan T, David RHA, Ramakrishnan MS, Ceasar A, Duraipandiyan V, Roch GV, Ignacimuthu S (2018) Microsatellite markers of finger millet (Eleusine coracana (L.) Gaertn) and foxtail millet (Setaria italica (L.) Beauv) provide resources for cross-genome transferability and genetic diversity analyses in other millets. Biocatal Agric Biotechnol 16:493–450
Kumari K, Muthamilarasan M, Misra G, Gupta S, Alagesan S, Parida S et al (2013) Development of eSSR-markers in Setaria italica and their applicability in studying genetic diversity, cross-transferability and comparative map** in millet and non-millet species. PLoS One 8:e67742. https://doi.org/10.1371/journal.pone.0067742
Kumari KS, Thayumanavan B (1998) Characterization of starches of proso, foxtail, barnyard, kodo, and little millets. Plant Foods Hum Nutr 53:47. https://doi.org/10.1023/A:1008083020810
Lee J, Kim C-S, Lee I-Y (2017) Discrimination of Echinochloa colona (L.) Link from other Echinochloa species using DNA barcode. Weed Turfgrass Sci 4:225–229. https://doi.org/10.5660/WTS.2015.4.3.225
Li G, Wu S, Cai L, Wang Q, Zhao X, Wu C (2013b) Identification and mRNA expression profile of glutamate receptor-like gene in quinclorac-resistant and susceptible Echinochloa crus-galli. Gene 531(2):489–495. https://doi.org/10.1016/j.gene.2013.09.013
Li G, Wu SG, Yu RX, Cang T, Chen LP, Zhao XP, Cai LM, Wu CX (2013a) Identification and expression pattern of a glutathione S-transferase in Echinochloa crus-galli. Weed Res 53. https://doi.org/10.1111/wre.12031
Lin H-S, Chiang CY, Chang S-B, Kuoh C-S (2011) Development of simple sequence repeats (SSR) markers in Setaria italica (Poaceae) and cross-amplification in related species. Int J Mol Sci 12:7835–7845. https://doi.org/10.3390/ijms12117835
Manimekalai M, Dhasarathan M, Karthikeyan A, Murukarthick J, Renganathan VG, Thangaraj K et al (2018) Genetic diversity in the barnyard millet (Echinochola frumentacea) germplasms revealed by morphological traits and simple sequence repeat markers. Curr Plant Biol 14:71–78. https://doi.org/10.1016/j.cpb.2018.09.006
Murukarthick J, Manimekalai M, Karthikeyan A, Perumal S, Dhasarathan M, Kandasamy T et al (2019) Transcriptomes of Indian barnyard millet and barnyard grass reveal putative genes involved in drought adaptation and micronutrient accumulation. Acta Physiol Plant 41:66. https://doi.org/10.1007/s11738-019-2855-4
Muthamilarasan M, Prasad M (2014) Advances in Setaria genomics for genetic improvement of cereals and bioenergy grasses. Theor Appl Genet. https://doi.org/10.1007/s00122-014-2399-3
Nah G, Im JH, Kim JW, Kim K, Lim J, Choi AY, Choi IY, Yang TJ, Park TS, Lee D, Kim DS (2016) The complete chloroplast genomes of three Korean Echinochloa crus-galli accessions. Mitochondrial DNA Part A 27:4357–4358
Nah G, Im J-H, Kim J-W, Park H-R, Yook M-J, Yang T-J et al (2015) Uncovering the differential molecular basis of adaptive diversity in three Echinochloa leaf transcriptomes. PLoS One 10:e0134419. https://doi.org/10.1371/journal.pone.0134419
Nozawa S, Takahashi M, Nakai H, Sato Y-I (2006) Difference in SSR variations between Japanese Barnyard Millet (Echinochloa esculenta) and its wild relative E. crus-galli. Breed Sci 56:335–340. https://doi.org/10.1270/jsbbs.56.335
Odintsova TI, Rogozhin EA, Baranov Y, Musolyamov AK, Yalpani N, Egorov TA et al (2008) Seed defensins of barnyard grass Echinochloa crusgalli (L.) Beauv. Biochimie 90:1667–1673. https://doi.org/10.1016/j.biochi.2008.06.007
Padulosi S, Mal B, Ravi SB, Gowda J, Gowda KTK et al (2009) Food security and climate change: role of plant genetic resources of minor millets. Indian J Plant Genet Resour 22:1–16
Pandey G, Misra G, Kumari K, Gupta S, Kumar Parida S, Chattopadhyay D et al (2013) Genome-wide development and use of microsatellite markers for large-scale genoty** applications in Foxtail Millet [Setaria italica (L.)]. DNA Res 20. https://doi.org/10.1093/dnares/dst002
Pareek A, Dhankher OP, Foyer C (2020) Mitigating the impact of climate change on plant productivity and ecosystem sustainability. J Exp Bot 71:451–456. https://doi.org/10.1093/jxb/erz518
Perumal S, Jayakodi M, Kim D-S, Yang T-J, Natesan S (2016) The complete chloroplast genome sequence of Indian barnyard millet, Echinochloa frumentacea (Poaceae). Mitochondrial DNA B 1(1):79–80. https://doi.org/10.1080/23802359.2015.1137832
Prabha D, Negi YK, Khanna VK (2010) Morphological and isozyme diversity in the accessions of two cultivated species of barnyard millet. Nat Sci 8:71–76
Renganathan VG, Vanniarajan C, Karthikeyan A, Ramalingam J (2020) Barnyard millet for food and nutritional security: current status and future research direction. Front Genet 11:500. https://doi.org/10.3389/fgene.2020.00500
Renganathan VG, Vanniarajan C, Senthil N, Nirmalakumari A, Karthikeyan A, Veni K, Ramalingam J (2021) Genetics and molecular markers for anthocyanin pigmentation in barnyard millet (Echinochloa frumentacea (Roxb.) link). Plant Breed 140:246–253. https://doi.org/10.1111/pbr.12892
Ruiz-Santaella PJ, Bastida F, Franco A, Prado R (2006) Morphological and molecular characterization of different Echinochloa spp. and Oryza sativa populations. J Agric Food Chem 54:1166–1172. https://doi.org/10.1021/jf0520746
Rutledge J, Talbert RE, Sneller CH (2000) RAPD analysis of genetic variation among propanil-resistant and -susceptible Echinochloa crus-galli populations in Arkansas. Weed Sci 48:669–674
Sebastin R, Lee KJ, Cho GT, Lee JR, Shin MJ, Kim SH et al (2019) The complete chloroplast genome sequence of Japanese millet Echinochloa esculenta (A. braun) H. scholz (Poaceae). Mitochondrial DNA Part B Resour 4:1392–1393. https://doi.org/10.1080/23802359.2019.1598787
Smarda P, Bures P, Horova L, Leitch IJ, Mucina L et al (2014) Ecological and evolutionary significance of genomic GC content diversity in monocots. Proc Natl Acad Sci U S A 111:E4096-102. https://doi.org/10.1073/pnas.1321152111
Sood S, Khulbe R, Kumar RA, Agrawal PK, Upadhyaya H (2015) Barnyard millet global core collection evaluation in the sub mountain Himalayan region of India using multivariate analysis. Crop J 3(6):517–525. https://doi.org/10.1016/j.cj.2015.07.005
Tabacchi M, Mantegazza R, Spada A, Ferrero A (2009) Morphological traits and molecular markers for classification of Echinochloa species from Italian rice fields. Weed Sci 54:1086–1093. https://doi.org/10.1614/WS-06-018R1.1
Ugare R, Chimmad B, Naik R, Bharati P, Itagi S (2014) Glycemic index and significance of barnyard millet (Echinochloa frumentacae) in type II diabetics. J Food Sci Technol 51(2):392–395. https://doi.org/10.1007/s13197-011-0516-8
Wallace GJ, Upadhyaya H, Vetriventhan M, Buckler E, Hash Charles J, Ramu P (2015) The genetic makeup of a global barnyard millet germplasm collection. Plant Genome 08(01):01–07. https://doi.org/10.3835/plantgenome2014.10.0067
Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63. https://doi.org/10.1038/nrg2484
Weber A (2015) Discovering new biology through RNA-Seq. Plant Physiol 169:01081.2015. https://doi.org/10.1104/pp.15.01081
Wu LM, Fang Y, Yang HN, Bai LY (2019) Effects of drought-stress on seed germination and growth physiology of quinclorac-resistant Echinochloa crusgalli. PLoS One 14(4):e0214480
Yadav S, Gaur V, Jaiswal JP, Kumar A (2014) Simple sequence repeat (SSR) analysis in relation to calcium transport and signaling genes reveals transferability among grasses and a conserved behavior within finger millet genotypes. Plant Syst Evol 300:1–8. https://doi.org/10.1007/s00606-014-0982-3
Yamaguchi H, Utano AYA, Yasuda K, Yano A, Soejima A (2005) A molecular phylogeny of wild and cultivated Echinochloa in East Asia inferred from non-coding region sequences of trnT-L-F. Weed Biol Manage 5:210–218. https://doi.org/10.1111/j.1445-6664.2005.00185.x
Yang X, Yu X-Y, Li YF (2013) De novo assembly and characterization of the barnyard grass (Echinochloa crus-galli) transcriptome using next-generation pyrosequencing. PLoS One 8:e69168. https://doi.org/10.1371/journal.pone.0069168
Yasuda K, Yano A, Nakayama Y, Yamaguchi H (2006) Molecular identification of Echinochloa oryzicola Vasing. And E. crus-galli (L.) Beauv. Using a polymerase chain reaction–restriction fragment length polymorphism technique. Weed Biol Manage 2:11–17. https://doi.org/10.1046/j.1445-6664.2002.00041.x
Ye C-Y, Lin Z, Li G, Wang Y, Qiu J, Fu F et al (2014) Echinochloa chloroplast genomes: insights into the evolution and taxonomic identification of two weedy species. PLoS One 9(11):e113657. https://doi.org/10.1371/journal.pone.0113657
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All the authors sincerely acknowledge Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India. The first author extends his thanks to AAIC, the Centre of Excellence in Innovation-Postdoctoral program.
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Renganathan, V.G., Vanniarajan, C., Renuka, R., Veni, K., Vetriventhan, M. (2022). Current Status and Future Prospects of Omics Strategies in Barnyard Millet. In: Pudake, R.N., Solanke, A.U., Sevanthi, A.M., Rajendrakumar, P. (eds) Omics of Climate Resilient Small Millets. Springer, Singapore. https://doi.org/10.1007/978-981-19-3907-5_3
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