Skip to main content

Genetic Differentiation and Crop Evolution of Foxtail Millet

  • Chapter
  • First Online:
Genetics and Genomics of Setaria

Part of the book series: Plant Genetics and Genomics: Crops and Models ((PGG,volume 19))

Abstract

Several studies on genetic differentiation and crop evolution based on intraspecific hybrid pollen semi-sterility, isozymes, ribosomal DNA (rDNA) RFLP, nuclear RFLP, mitochondrial DNA (mtDNA) RFLP, RAPD, AFLP, transposon display (TD) markers, and single nucleotide polymorphisms (SNPs) have been carried out to elucidate genetic relationships of foxtail millet accessions, mainly from Eurasia. Most of the studies suggest that China is the center of diversity of foxtail millet and that landraces are grouped in geographical groups. Evolution of two genes, waxy gene controlling amylose content in endosperm and polyphenol oxidase (PPO) gene for phenol color reaction (Phr) in grains, was also reviewed. These analyses showed that multiple independent loss-of-function mutations occurred in each of the two genes under human/natural selection.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Afzal M, Kawase M, Nakayama H, Okuno K. Variation in electrophoregrams of total seed protein and Wx protein in foxtail millet. In: Janick J, editor. Progress in new crops. Alexandria, VA: ASHS Press; 1996. p. 191–5.

    Google Scholar 

  • Bennetzen JL, Schmutz J, Wang H, Percifield R, Hawkins J, Pontaroli AC, et al. Reference genome sequence of the model plant Setaria. Nat Biotechnol. 2012;30:555–61.

    Article  CAS  PubMed  Google Scholar 

  • Collins GN. A new type of Indian corn from China. USDA Bur Pl Ind Bull. 1909;16:1–30.

    Google Scholar 

  • de Wet JMJ, Oestry-Stidd LL, Cubero JI. Origins and evolution of foxtail millet (Setaria italica). Journ d’Agric et de Bot. 1979;26:53–64.

    Google Scholar 

  • Dekaprelevich LL, Kasparian AS. A contribution to the study of foxtail millet (Setaria italica P.B. maxima. Alef.) cultivated in Georgia (western Transcaucasia). Bull Appl Bot Plant Breed. 1928;19:533–72.

    Google Scholar 

  • Doebley J, Stec A, Hubbard L. The evolution of apical dominance in maize. Nature. 1997;386:485–8.

    Article  CAS  PubMed  Google Scholar 

  • Domon E, Fujita M, Ishikawa N. The insertion/deletion polymorphisms in the Waxy gene of barley genetic resources from East Asia. Theor Appl Genet. 2002a;104:132–8.

    Article  CAS  PubMed  Google Scholar 

  • Domon E, Saito A, Takeda K. Comparison of the waxy locus sequence from a non-waxy strain and two waxy mutants of spontaneous and artificial origins in barley. Genes Genet Syst. 2002b;77:351–9.

    Article  CAS  PubMed  Google Scholar 

  • Doust AD, Devos KM, Gadberry MD, Gale MD, Kellogg EA. Genetic control of branching in foxtail millet. Proc Natl Acad Sci U S A. 2004;101:9045–50.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Doust AD, Devos KM, Gadberry MD, Gale MD, Kellogg EA. The genetic basis for inflorescence variation between foxtail and green millet (Poaceae). Genetics. 2005;169:1659–72.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Eda M, Izumitani A, Ichitani K, Kawase M, Fukunaga K. Geographical variation of foxtail millet, Setaria italica (L.) P. Beauv. based on rDNA PCR–RFLP. Genet Res Crop Evol. 2013;60:265–74.

    Article  Google Scholar 

  • Fogg WH. Swidden cultivation of foxtail millet by Taiwan aborigines: a cultural analogue of the domestication of Setaria italica in China. In: Keighty DN, editor. The origins of Chinese civilization. Berkeley: University of California Press; 1983. p. 95–115.

    Google Scholar 

  • Fukunaga K, Kato K. Mitochondrial DNA variation in foxtail millet, Setaria italica (L.) P. Beauv. Euphytica. 2003;129:7–13.

    Article  CAS  Google Scholar 

  • Fukunaga K, Domon E, Kawase M. Ribosomal DNA variation in foxtail millet, Setaria italica (L.) P. Beauv. and a survey of variation from Europe and Asia. Theor Appl Genet. 1997a;97:751–6.

    Article  Google Scholar 

  • Fukunaga K, Kawase M, Sakamoto S. Variation of caryopsis length and width among landraces of foxtail millet, Setaria italica (L.) P. Beauv. Jpn J Trop Agric. 1997b;41:235–40.

    Google Scholar 

  • Fukunaga K, Kawase M, Kato K. Structural variation in the Waxy gene and differentiation in foxtail millet [Setaria italica (L.) P. Beauv.]: implications for multiple origins of the waxy phenotype. Mol Genet Genomics. 2002a;268:214–22.

    Article  CAS  PubMed  Google Scholar 

  • Fukunaga K, Wang ZM, Kato K, Kawase M. Geographical variation of nuclear genome RFLPs and genetic differentiation in foxtail millet, Setaria italica (L.) P. Beauv. Genet Res Crop Evol. 2002b;49:95–101.

    Article  Google Scholar 

  • Fukunaga K, Ichitani K, Taura S, Sato M, Kawase M. Ribosomal DNA intergenic spacer sequence in foxtail millet, Setaria italica (L.) P. Beauv. and its characterization and application to typing of foxtail millet landraces. Hereditas. 2005;142:38–44.

    Article  PubMed  Google Scholar 

  • Fukunaga K, Ichiatani K, Kawase M. Phylogenetic analysis of rDNA intergenic spacer subrepeats and its implication for domestication history of foxtail millet, Setaria italica. Theor Appl Genet. 2006;113:261–9.

    Article  CAS  PubMed  Google Scholar 

  • Fukunaga K, Ichitani K, Kawase M. rDNA polymorphism of foxtail millet (Setaria italica ssp. italica) landraces in northern Pakistan and Afghanistan and in its wild ancestor (S. italica ssp. viridis). Genet Resour Crop Evol. 2011;58:825–30.

    Article  Google Scholar 

  • Hachiken T, Sato K, Hasegawa T, Ichitani K, Kawase M, Fukunaga K. Geographic distribution of Waxy gene SNPs and indels in foxtail millet, Setaria italica (L.) P. Beauv. Genet Res Crop Evol. 2013;60:1559–70.

    Article  Google Scholar 

  • Hammer K, Khoshbakht K. Foxtail millet (Setaria italica (L.) P. Beauv.) in Mazandaran/Northern Iran. Genet Res Crop Evol. 2007;54:907–11.

    Article  Google Scholar 

  • Harlan JR. Crops and man. Madison, WI: American Society of Agronomy, Crop Science Society of America; 1975.

    Google Scholar 

  • Hirano HY, Sano Y. Molecular characterization of the waxy locus of rice (Oryza sativa). Plant Cell Physiol. 1991;32:989–97.

    CAS  Google Scholar 

  • Hirano HY, Eighuchi M, Sano Y. A single base change altered the regulation of the Waxy gene at the posttranscriptional level during the domestication of rice. Mol Biol Evol. 1998;15:978–87.

    Article  CAS  PubMed  Google Scholar 

  • Hirano R, Naito K, Fukunaga K, Watanabe KN, Ohsawa R, Kawase M. Genetic structure of landraces in foxtail millet (Setaria italica (L.) P. Beauv.) revealed with transposon display and interpretation to crop evolution of foxtail millet. Genome. 2011;54:498–506.

    Article  CAS  PubMed  Google Scholar 

  • Hunt HV, Linden MV, Liu X, Motuzaite-Matuzeviciute G, Colledge S, Jones MK. Millets across Eurasia: chronology and context of early records of the genera Panicum and Setaria from archaeological sites in the Old World. Veg Hist Archaeobot. 2008;17(Suppl):5–18.

    Article  PubMed  PubMed Central  Google Scholar 

  • Inoue T, Yuo T, Ohta T, Hitomi E, Ichitani K, Kawase M, et al. Multiple origins of the phenol reaction negative phenotype in foxtail millet, Setaria italica (L.) P. Beauv, were caused by independent loss-of-function mutations of the polyphenol oxidase (Si7PPO) gene during domestication. Mol Genet Genomics. 2015;290:1563–74.

    Article  CAS  PubMed  Google Scholar 

  • Ishii T, Numaguchi K, Miura K, Yoshida K, Thanh PT, Htun TM, et al. OsLG1 regulates a closed panicle trait in domesticated rice. Nat Genet. 2013;45:462–5.

    Article  CAS  PubMed  Google Scholar 

  • Isshiki M, Morino K, Nakajima M, Okagaki RJ, Wessler SR, Izawa T, et al. A naturally occurring functional allele of the rice waxy locus has a GT to TT mutation at the 5′ splice site of the first intron. Plant J. 1998;15:133–8.

    Article  CAS  PubMed  Google Scholar 

  • Jia G, Huang X, Zhi H, Zhao Y, Zhao Q, Li W, et al. A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica). Nat Genet. 2013;45:957–61.

    Article  CAS  PubMed  Google Scholar 

  • Jusuf M, Pernes J. Genetic variability of foxtail millet (Setaria italica P. Beauv.). Theor Appl Genet. 1985;71:385–93.

    Article  CAS  PubMed  Google Scholar 

  • Kato S, Kosaka H, Hara S. On the affinity of rice varieties shown by the fertility of hybrid plants. Rep Bul Sci Fak Terkult Kyushu Imp Univ. 1928;3:132–47 (in Japanese with English summary).

    Google Scholar 

  • Kawase M. Genetic variation and landrace differentiation of foxtail millet, Setaria italica, in Eurasia. Ph.D. thesis. Kyoto University, Japan, 1986.

    Google Scholar 

  • Kawase M, Fukunaga K. Distribution of Type D, a landrace group newly determined by means of hybrid sterility in foxtail millet, Setaria italica (L.) P. Beauv. Breed Res. 1999;1:302 (in Japanese).

    Google Scholar 

  • Kawase M, Sakamoto S. Geographical distribution and genetic analysis of phenol color reaction in foxtail millet, Setaria italica (L.) P. Beauv. Theor Appl Genet. 1982;63:117–9.

    Article  CAS  PubMed  Google Scholar 

  • Kawase M, Sakamoto S. Variation, geographical distribution and genetical analysis of esterase isozymes in foxtail millet, Setaria italica (L.) P. Beauv. Theor Appl Genet. 1984;67:529–33.

    Article  CAS  PubMed  Google Scholar 

  • Kawase M, Sakamoto S. Geographical distribution of landrace groups classified by hybrid pollen sterility in foxtail millet, Setaria italica (L.) P. Beauv. J Jpn Breed. 1987;37:1–9.

    Article  Google Scholar 

  • Kawase M, Ochiai Y, Fukunaga K. Characterization of foxtail millet, Setaria italica (L.) P. Beauv. in Pakistan based on intraspecific hybrid pollen sterility. Breed Sci. 1997;47:45–9.

    Google Scholar 

  • Kawase M, Fukunaga K, Kato K. Diverse origins of waxy foxtail millet crops in East and Southeast Asia mediated by multiple transposable element insertions. Mol Genet Genomics. 2005;274:131–40.

    Article  CAS  PubMed  Google Scholar 

  • Kihara H, Kishimoto E. Bastarde zwischen Setaria italica und S. viridis. Bot Mag. 1942;20:63–7 (in Japanese with German summary).

    Google Scholar 

  • Komatsuda T, Pourkheirandish M, He C, Azhaguvel P, Kanamori H, Perovic D, et al. Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene. Proc Natl Acad Sci U S A. 2007;104:1424–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Konishi S, Izawa T, Lin SY, Ebana K, Fukuta Y, Sasaki T, et al. An SNP caused loss of seed shattering during rice domestication. Science. 2006;312:1392–6.

    Article  CAS  PubMed  Google Scholar 

  • Kűster H. Neolithic plant remains from Eberdingenhochdo, southern Germany. In: Van Zeist WV, Casparoe WA, editors. Plants and ancient man (studies in palaeoethnobotany). Rotterdam: AA Bakame; 1984. p. 307–11.

    Google Scholar 

  • Le Thierry d’Ennequin M, Panaud O, Toupance B, Sarr A. Assessment of genetic relationships between Setaria italica and its wild relative S. viridis using AFLP markers. Theor Appl Genet. 2000;100:1061–6.

    Article  Google Scholar 

  • Li Y, Wu SZ. Traditional maintenance and multiplication of foxtail millet (Setaria italica (L.) P. Beauv) landraces in China. Euphytica. 1996;87:33–8.

    Article  Google Scholar 

  • Li HW, Li CH, Pao WK. Cytological and genetical studies of the interspecific cross of the cultivated foxtail millet, Setaria italica (L.) Beauv., and the green foxtail millet, S. viridis. J Am Soc Agron. 1945;37:32–54.

    Article  Google Scholar 

  • Li Y, Cao YS, Wu SZ, Zhang XZ. A diversity analysis of foxtail millet (Setaria italica (L.) P. Beauv.) landraces of Chinese origin. Genet Resour Crop Evol. 1995a;45:279–85.

    Article  Google Scholar 

  • Li Y, Wu SZ, Cao YS. Cluster analysis of an international collection of foxtail millet (Setaria italica (L.) P. Beauv). Euphytica. 1995b;83:79–85.

    Article  Google Scholar 

  • Li Y, Jia J, Wang W, Wu S. Intraspecific and interspecific variation in Setaria revealed by RAPD analysis. Genet Resour Crop Evol. 1998;45:279–85.

    Article  Google Scholar 

  • Lisitsina A. Main types of ancient farming on the Caucasus on the basis of palaeo-ethnobotanical research. Ber Deut Bot Ges. 1976;91:47–57.

    Google Scholar 

  • Mauro-Herrera M, Doust AN. Development and genetic control of plant architecture and biomass in the panicoid grass, Setaria. PLoS One. 2016;11(3):e0151346.

    Article  PubMed  PubMed Central  Google Scholar 

  • Mauro-Herrera M, Wang X, Barbier H, Brutnell TP, Devos KM, Doust AN. Genetic control and comparative genomic analysis of flowering time in Setaria (Poaceae). Genes, Genomes, and Genetics. 2013;3:283–95.

    Google Scholar 

  • McIntyre CL, Drenth J, Gonzalez N, Henzell RG, Jordan DR. Molecular characterization of the waxy locus in sorghum. Genome. 2008;51:524–33.

    Article  CAS  PubMed  Google Scholar 

  • Nakamura T. Production of waxy (amylose-free) wheats. Mol Gen Genet. 1995;248:253–9.

    Article  CAS  PubMed  Google Scholar 

  • Nakayama H, Afzal M, Okuno K. Intraspecific differentiation and geographical distribution of Wx alleles for low amylase content in endosperm of foxtail millet, Setaria italica (L.) Beauv. Euphytica. 1998;102:289–93.

    Article  Google Scholar 

  • Nakayama H, Namai H, Okuno K. Geographical variation of the alleles at the two prolamin loci, Pro1 and Pro2, in foxtail millet, Setaria italica (L.) P. Beauv. Genes Genet Syst. 1999;74:293–7.

    Article  CAS  PubMed  Google Scholar 

  • Nasu H, Momohra A, Yasuda Y, He J. The occurrence and identification of Setaria italica (L.) P. Beauv. (foxtail millet) grains from the Chengtoushan site (ca. 5800 cal B.P.) in central China, with reference to the domestication centre in Asia. Veg Hist Archaeobot. 2007;16:481–94.

    Article  Google Scholar 

  • Nguyen Van F, Pernes J. Genetic diversity of foxtail millet (Setaria italica). In: Jacquard P, editor. Genetic differentiation and dispersal in plants. NATO ASI Series, vol. G5. Berlin: Springer; 1985. p. 113–128.

    Google Scholar 

  • Ochiai Y. Variation in tillering and geographical distribution of foxtail millet (Setaria italica P. Beauv.). Breed Sci. 1996;46:143–6.

    Google Scholar 

  • Ochiai Y, Kawase M, Sakamoto S. Variation and distribution of foxtail millet (Setaria italica P. Beauv.) in the mountainous areas of northern Pakistan. Breed Sci. 1994;44:413–8.

    Google Scholar 

  • Oka HI. Phylogenetic differentiation of the cultivated rice plant. 1. Variations in respective characteristics and their combinations in rice cultivars. Jpn J Breed. 1953;3:33–43 (in Japanese with English summary).

    Article  Google Scholar 

  • Okuno K, Fuwa H, Yano M. A new mutant gene lowering amylose content in endosperm starch in rice, Oryza sativa L. Japan J Breed. 1983;33:387–94.

    Article  CAS  Google Scholar 

  • Olsen KM, Purugganan MD. Molecular evidence on the origin and evolution of glutinous rice. Genetics. 2002;162:941–50.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Patron NJ, Smith AM, Fahy BF, Hylton CM, Naldrett MJ, Rossnagel BG, et al. The altered pattern of amylose accumulation in the endosperm of low-amylose barley cultivars is attributable to a single mutant allele of granule-bound starch synthase I with a deletion in the 5-non-coding region. Plant Physiol. 2002;130:190–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Prasada Rao KE, de Wet JMJ, Brink DE, Mengesha MH. Infraspecific variation and systematics of cultivated Setaria italica, foxtail millet (Poaceae). Econ Bot. 1987;41:108–16.

    Article  Google Scholar 

  • Sakamoto S. Origin and dispersal of common millet and foxtail millet. Japan Agr Res Quart. 1987;21:84–9.

    Google Scholar 

  • Sakamoto S. Glutinous-endosperm starch food culture specific to Eastern and Southeastern Asia. In: Ellen R, Fukui K, editors. Redefining nature: ecology, culture and domestication. Oxford: Berg; 1996. p. 215–31.

    Google Scholar 

  • Sano Y. Differential regulation of gene expression in rice endosperm. Theor Appl Genet. 1984;68:467–73.

    Article  CAS  PubMed  Google Scholar 

  • Sato K, Mukainari Y, Naito K, Fukunaga K. Construction of a foxtail millet linkage map and mapping spikelet-tipped bristles 1(stb1) by using transposon display markers and simple sequence repeat markers with genome sequence information. Mol Breed. 2013;31:675–84.

    Article  CAS  Google Scholar 

  • Sattler SE, Singh J, Haas EJ, Guo L, Sarath G, Pedersen JF. Two distinct waxy alleles impact the granule-bound starch synthase in sorghum. Mol Breed. 2009;24:349–59.

    Article  CAS  Google Scholar 

  • Schontz D, Rether B. Genetic variability in foxtail millet, Setaria italica (L.) P. Beauv. RFLP using a heterologous rDNA probe. Plant Breed. 1998;117:231–4.

    Article  Google Scholar 

  • Schontz D, Rether B. Genetic variability in foxtail millet, Setaria italica (L.) P. Beauv.: Identification and classification of lines with RAPD markers. Plant Breed. 1999;118:190–2.

    Article  Google Scholar 

  • Takeda K, Chang CL. Inheritance and geographical distribution of phenol reaction-less varieties of barley. Euphytica. 1996;90:217–21.

    Article  Google Scholar 

  • Takei E. Characteristics and ethnobotany of millets in the Southwestern (Nansei) Islands of Japan (in Japanese with English abstract). Ph.D. thesis, Faculty of Agriculture, Kyoto University, 1994.

    Google Scholar 

  • Takei E, Sakamoto S. Geographical variation of heading response to daylength in foxtail millet (Setaria italica P. Beauv.). Jpn J Breed. 1987;37:150–8.

    Article  Google Scholar 

  • Takei E, Sakamoto S. Further analysis of geographical variation of heading response to daylength in foxtail millet (Setaria italica P. Beauv.). Japan J Breed. 1989;39:285–98.

    Article  Google Scholar 

  • Taketa S, Amano S, Tsujino Y, Sato T, Saisho D, Kakeda K, et al. Barley grain with adhering hulls is controlled by an ERF family transcription factor gene regulating a lipid biosynthesis pathway. Proc Natl Acad Sci U S A. 2008;105:4062–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Taketa S, Matsuki K, Amano S, Saisho D, Himi E, Shitsukawa N, et al. Duplicate polyphenol oxidase genes on barley chromosome 2H and their functional differentiation in the phenol reaction of spikes and grains. J Exp Bot. 2010;61:3983–93.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Van S, Onoda S, Kim MY, Kim KD, Lee SH. Allelic variation of the Waxy gene in foxtail millet [Setaria italica (L.) P. Beauv.] by single nucleotide polymorphisms. Mol Genet Genomics. 2008;279:255–66.

    Article  CAS  PubMed  Google Scholar 

  • Vavilov NI. Studies on the origin of cultivated plants. Inst Appl Bot Plant Breed. 1926;16:1–248.

    Google Scholar 

  • Vrinten P, Nakamura T. Molecular characterization of waxy mutations in wheat. Mol Gen Genet. 1999;261:463–71.

    Article  CAS  PubMed  Google Scholar 

  • Wanchana S, Toojinda T, Tragoonrung S, Vanavichit A. Duplicated coding sequence in the waxy allele of tropical glutinous rice (Oryza sativa L.). Plant Sci. 2003;165:1193–9.

    Article  CAS  Google Scholar 

  • Wang H, Nussbaum-Wagler T, Li B, Zhao Q, Vigouroux Y, Faller M, et al. The origin of the naked grains of maize. Nature. 2005;436:714–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wessler SR, Varagona MJ. Molecular basis of mutations at Waxy locus of maize: correlation with the fine structure genetic map. Proc Natl Acad Sci U S A. 1985;82:4177–81.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yoshida S. Wild food plants and vegeculture. In: Yoshida S, Matthews PJ, editors. Vegeculture in Eastern Asia and Oceania, JCAS Symposium Series, vol. 16. Osaka: National Museum of Ethnology; 2002. p. 31–44.

    Google Scholar 

  • Yu Y, Tang T, Qian Q, Wang Y, Yan M, Zeng D, et al. Independent losses of function in a polyphenol oxidase in rice: differentiation in grain discoloration between subspecies and the role of positive selection under domestication. Plant Cell. 2008;20:2946–59.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Kenji Fukunaga .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer International Publishing Switzerland

About this chapter

Cite this chapter

Fukunaga, K. (2017). Genetic Differentiation and Crop Evolution of Foxtail Millet. In: Doust, A., Diao, X. (eds) Genetics and Genomics of Setaria. Plant Genetics and Genomics: Crops and Models, vol 19. Springer, Cham. https://doi.org/10.1007/978-3-319-45105-3_7

Download citation

Publish with us

Policies and ethics