Skip to main content
SpringerLink
Log in

Genetic analysis of adaptive syndromes interrelated with seed dormancy in weedy rice (Oryza sativa)

  • Original Paper
  • Published:
Theoretical and Applied Genetics Aims and scope Submit manuscript

Abstract

Seed dormancy in rice interrelates to the weedy characteristics shattering, awn, black hull color, and red pericarp color. A cross between the weedy strain SS18-2 and the breeding line EM93-1 was developed to investigate the genetic basis and adaptive significance of these interrelationships. These characteristics or their components differed in average degree of dominance from −0.8 to 1.5, in heritability from 0.5 to 0.96, and in their contribution to phenotypic or genotypic variation in dormancy by up to 25%. Five dormancy, four shattering, and three awn-length quantitative trait loci (QTLs) were detected in the BC1 population replicated in 2 years. Two QTLs for hull color were identified, and the SS18-2-derived and EM93-1-derived alleles increased the intensity of black, and red or yellow pigmentations, respectively. The only QTL for pericarp color co-located with the red pericarp gene Rc, with the SS18-2-derived allele increasing the intensity of black and red pigmentations. Four of the five dormancy QTLs were flanked or bracketed by one to four QTLs for the interrelated characteristics. The QTL organization pattern indicates the central role of seed dormancy in adaptive syndromes for non-domesticated plants, implies that the elimination of dormancy from cultivars could arise from the selections against multiple interrelated characteristics, and challenges the use of dormancy genes at these loci in breeding varieties for resistance to pre-harvest sprouting (PHS). However, another QTL (qSD12) provides candidate gene(s) for PHS resistance because it has a large effect in the population and it is independent of the loci for interrelated characteristics.

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

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Anderson JA, Sorrells ME, Tanksley SD (1993) RFLP analysis of genomic regions associated with resistance to pre-harvest sprouting in wheat. Crop Sci 33:453–459

    Google Scholar 

  • Bres-Patry C, Lorieu M, Clement G, Bangratz M, Ghesquiere A (2001) Heredity and genetic mapping of domestication-related traits in a temperate japonica weedy rice. Theor Appl Genet 102:118–126

    Google Scholar 

  • Burke JM, Tang S, Knapp SJ, Rieseberg LH (2002) Genetic analysis of sunflower domestication. Genetics 161:1257–1267

    CAS  PubMed  Google Scholar 

  • Cai HW, Morishima H (2000) Genomic regions affecting seed shattering and seed dormancy in rice. Theor Appl Genet 100:840–846

    Article  CAS  Google Scholar 

  • Cai HW, Morishima H (2002) QTL clusters reflect character associations in wild and cultivated rice. Theor Appl Genet 104:1217–1228

    Google Scholar 

  • Chang TT, Yen ST (1969) Inheritance of grain dormancy in four rice crosses. Bot Bull Acad Sin 10:1–9

    Google Scholar 

  • Devos KM, Gale MD (2000) Genome relationships: the grass model in current research. Plant Cell 12:637–646

    Article  CAS  PubMed  Google Scholar 

  • Doebley J, Stec A (1991) Genetic analysis of the morphological differences between maize and teosinte. Genetics 129:285–295

    CAS  PubMed  Google Scholar 

  • Dong Y, Tsozuki E, Kamiunten H, Terao H, Lin D, Matsuo M, Zheng Y (2002) Identification of quantitative trait loci associated with pre-harvest sprouting resistance in rice (Oryza sativa L.). Field Crops Res 81:133–139

    Google Scholar 

  • Flintham JE, Adlam R, Bassoi M, Holdsworth M, Gale MD (2002) Mapping genes for resistance to sprouting damage in wheat. Euphytica 126:39–45

    Google Scholar 

  • Frary A, Nesbitt TC, Frary A, Grandillo S, Knaap E, Cong B, Liu J, Meller J, Elber R, Alpert KB, Tanksley SD (2000) fw2.2: a quantitative trait locus key to the evolution of tomato fruit size. Science 289:85–88

    Google Scholar 

  • Gale MD, Flintham JE, Devos KM (2002) Cereal comparative genetics and preharvest sprouting. Euphytica 126:21–25

    Google Scholar 

  • Gfeller F, Svejda F (1960) Inheritance of post-harvest seed dormancy and kernel colour in spring wheat lines. Can J Plant Sci 40:1–6

    Google Scholar 

  • Grist DH (1986) Rice, 6th edn. Longman, London

    Google Scholar 

  • Groos C, Gay G, Perretant MR, Gervais L, Bernard M, Dedryver F, Charmet G (2002) Study of the relationship between pre-harvest sprouting and grain color by quantitative trait loci analysis in a white × red grain bread-wheat cross. Theor Appl Genet 104:39–47

    Article  CAS  PubMed  Google Scholar 

  • Gu X-Y, Chen Z-X, Foley ME (2003) Inheritance of seed dormancy in weedy rice. Crop Sci 43:835–843

    Google Scholar 

  • Gu X-Y, Kianian SF, Foley ME (2004) Multiple loci and epistases control genetic variation for seed dormancy in weedy rice (Oryza sativa). Genetics 166:1503–1516

    Google Scholar 

  • Gu X-Y, Kianian SF, Foley ME (2005) Seed dormancy imposed by covering tissues interrelates to shattering and seed morphological characteristics in weedy rice. Crop Sci 45 (in press)

  • Han F, Ullrich SE, Clancy JA, Jitkov V, Kilian A, Romogosa I (1996) Verification of barley seed dormancy loci via linked molecular markers. Theor Appl Genet 92:87–91

    Article  Google Scholar 

  • Harlan JR (1965) The possible role of weed races in the evolution of cultivated plants. Euphytica 14:173–176

    Google Scholar 

  • Harlan JR, de Wet JMJ (1965) Some thoughts about weeds. Econ Bot 19:16–24

    Google Scholar 

  • Harlan JR, de Wet JMJ, Price EG (1973) Comparative evolution of cereals. Evolution 27:311–325

    Google Scholar 

  • Johnson LPV (1935) The inheritance of delayed germination in hybrids of Avena fatua and A. sativa. Can J Res 13:367–387

    Google Scholar 

  • Kato K, Nakamura W, Tabiki T, Miura H (2001) Detection of loci controlling seed dormancy on group 4 chromosomes of wheat and comparative mapping with rice and barley genomes. Theor Appl Genet 102:980–985

    Article  Google Scholar 

  • Kearsey MJ, Pooni HS (1996) The genetical analysis of quantitative traits. Chapman and Hall, London

    Google Scholar 

  • Khan M, Cavers PB, Kane M, Thompson K (1996) Role of the pigmented seed coat of proso millet (Panicum miliaceum L.) in imbibition, germination and seed persistence. Seed Sci Res 7:21–25

    Google Scholar 

  • Kinoshita T (1984) Gene analysis and linkage map. In: Tsunoda S, Takahashi N (eds) Biology of rice. JSSP/Elsevier, Tokyo, pp 187–274

    Google Scholar 

  • Li C, Ni P, Francki M, Hunter A, Zhang Y, Schibeci D, Li H, Tarr A, Wang J, Cakir M, Yu J, Bellgard M, Lance R, Appels R (2004) Genes controlling seed dormancy and pre-harvesting sprouting in a rice-wheat-barley comparison. Funct Integr Genomics 4:84–93

    Article  CAS  PubMed  Google Scholar 

  • Lijavetzky D, Martinez MC, Carrari F, Hopp HE (2000) QTL analysis and mapping of pre-harvest sprouting resistance in sorghum. Euphytica 112:125–135

    Google Scholar 

  • Lin SY, Sasaki T, Yano M (1998) Mapping quantitative trait loci controlling seed dormancy and heading date in rice. Theor Appl Genet 96:997–1003

    Article  CAS  Google Scholar 

  • Lincoln S, Daly M, Lander E (1992) Constructing genetic maps with mapmaker/exp 3.0, 3rd edn. Whitehead Institute, Cambridge

    Google Scholar 

  • Matus I, Corey A, Filichkin T, Hayes PM, Vales MI, Kling J, Riera-Lizarazu O, Sato K, Powell W, Waugh R (2003) Development and characterization of recombinant chromosome substitution lines (RCSLs) using Hordeum vulgare subsp. spontaneum as a source of donor alleles in a Hordeum vulgare subsp. vulgare background. Genome 46:1010–1023

    Article  CAS  PubMed  Google Scholar 

  • McCouch SR, Teytelman L, Xu Y, Lobos KB, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y, Zhang Q, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L (2002) Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res 9:199–207

    CAS  PubMed  Google Scholar 

  • Miura K, Lin SY, Yano M, Nagamine T (2002) Mapping quantitative trait loci controlling seed longevity in rice (Oryza sativa L.). Theor Appl Genet 104:981–986

    Google Scholar 

  • Oberthur L, Blake TK, Dyer WE, Ullrich SE (1995) Genetic analysis of seed dormancy in barley (Hordeum vulgare L.). J Quant Trait Loci 1:5

    Google Scholar 

  • Oka HI (1988) Origin of cultivated rice. Japan Science Society Press, Tokyo

    Google Scholar 

  • Paterson AH, Sorrells ME (1990) Inheritance of grain dormancy in white-kerneled wheat. Crop Sci 30:25–30

    Google Scholar 

  • Paterson AH, Schertz KF, Lin YR, Liu SC, Chang YL (1995) The weediness of wild plants: molecular analysis of genes influencing dispersal and persistence of johnsongrass, Sorghum halepense (L) Pers. Proc Natl Acad Sci USA 92:6127–6131

    CAS  PubMed  Google Scholar 

  • Peng J, Ronin Y, Fahima T, Roder MS, Li Y, Nevo E, Korol A (2003) Domestication quantitative trait loci in Triticum dicoccoides, the progenitor of wheat. Proc Natl Acad Sci USA 100:2489–2494

    Article  CAS  PubMed  Google Scholar 

  • Prada D, Ullrich SE, Molina-Cano JL, Cistue L, Clancy JA, Romagosa I (2004) Genetic control of dormancy in a Triumph/Morex cross in barley. Theor Appl Genet 109:62–70

    Article  CAS  PubMed  Google Scholar 

  • SAS Institute Inc (1999) SAS/STAT user’s guide. Version 8 Cary, N.C.

  • Simpson GM (1992) The adaptive significance of awns and hairs in grasses. J Biol Educ 26:10–11

    Google Scholar 

  • Tang L-H, Morishima H (1997) Genetic characterization of weedy rices and the inference on their origins. Breed Sci 47:153–160

    Google Scholar 

  • Tanksley SD, McCouch SR (1997) Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277:1063–1066

    Article  CAS  PubMed  Google Scholar 

  • Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res 11:441–1452

    Google Scholar 

  • Thomson MJ, Tai TH, McClung AM, Lai XH, Hinga ME, Lobos KB, Xu Y, Martinez CP, McCouch SR (2003) Mapping quantitative trait loci for yield, yield components and morphological traits in an advanced backcross population between Oryza rufipogon and the Oryza sativa cultivar Jefferson. Theor Appl Genet 107:479–493

    Google Scholar 

  • Tinker NA, Mather DE (1995) MQTL: software for simplified composite interval mapping of QTL in multiple environments. J Agric Genomics 1:2 http://www.ncgr.org/jag/

  • Wang D, Dowell FE, Lacey RE (1999) Predicting the number of dominant R alleles in single wheat kernels using visible and near-infrared reflectance spectra. Cereal Chem 76:6–8

    Google Scholar 

  • Xiong LZ, Liu KD, Dai XK, Xu CG, Zhang Q (1999) Identification of genetic factors controlling domestication-related traits of rice using an F2 population of a cross between Oryza sativa and O. rufipogon. Theor Appl Genet 98:243–251

    Google Scholar 

Download references

Acknowledgements

We thank T. Nelson, C. Kimberlin, D. Puhr, and J. Wear for their technical assistance and anonymous reviewers for their insightful comments. Funding for this work was provided by USDA-National Research Initiative (020068).

Author information

Authors and Affiliations

  1. Department of Plant Sciences, North Dakota State University, Fargo, ND, 58105, USA

    Xing-You Gu & Shahryar F. Kianian

  2. Northern Crop Sciences Research Laboratory, USDA-Agricultural Research Service, Fargo, ND, 58105-5674, USA

    Gary A. Hareland

  3. Biosciences Research Laboratory, USDA-Agricultural Research Service, Fargo, ND, 58105-5674, USA

    Barry L. Hoffer & Michael E. Foley

Authors
  1. Xing-You Gu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Shahryar F. Kianian
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Gary A. Hareland
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Barry L. Hoffer
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Michael E. Foley
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Michael E. Foley.

Additional information

Communicated by D.J. Mackill

Rights and permissions

Reprints and permissions

About this article

Cite this article

Gu, XY., Kianian, S.F., Hareland, G.A. et al. Genetic analysis of adaptive syndromes interrelated with seed dormancy in weedy rice (Oryza sativa). Theor Appl Genet 110, 1108–1118 (2005). https://doi.org/10.1007/s00122-005-1939-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-005-1939-2

Keywords

Search

Navigation