Mining of favorable alleles for lodging resistance traits in rice (oryza sativa) through association mapping
Fourteen new quantitative trait loci (QTLs) and ten favorable alleles were identified for lodging resistance traits in a natural population of rice. Parental combinations were designed to improve lodging resistance.
Lodging is one of the most critical constraints to rice yield, and therefore, mining favorable alleles for lodging resistance traits is imperative for the advancement of cultivated rice and selection for market demand. This investigation was performed on a selected sample of 521 rice cultivars using 262 SSR markers in 2016 and 2017. Lodging resistance traits were evaluated by plant height (PH), stem length (SL), stem diameter (SD), anti-thrust per stem (AT/S), and stem index (SI), with AT/S, used as the lodging resistance index. A genome-wide association map was generated by combining phenotypic and genotypic data. Eight subpopulations were found by structure software, and the linkage disequilibrium (LD) ranged from 30 to 80 cM. Identification of 68 marker–trait associations (MTAs) linking in 64 SSR markers for five traits was done. QTL were detected, including 15 for PH, 14 for SL, 14 for SD, 7 for AT/S, and 18 for SI. A number of favorable alleles were also discovered, including 22, 24, 19, 12, and 28 alleles for PH, SL, SD, AT/S, and SI, respectively. These favorable alleles might be used to design parental combinations, and the predictable results found by relieving the favorable alleles per QTL. The accessions containing favorable alleles for lodging resistant traits mined in this study could be useful for breeding superior rice cultivars.
KeywordsOryza sativa Lodging resistance Linkage disequilibrium Association mapping Favorable allele Phenotypic and genetic diversities
Analysis of variance
Anti-thrust per stem
Heritability in the broad sense
Polymorphic information content
Proportion of phenotypic variance explained
Quantitative trait locus
Simple sequence repeat
We thank Jianhua Ji, a technician at Nanjing Agricultural University Farm, for help with the daily management of the paddy field.
Funding support was a grant provided by National Natural Science Foundation of China (31671658), a Grant from doctoral found of Educational Ministry (B0201300662), and a Grant from the China national “863” program (2010AA101301).
Compliance with ethical standards
Consent for publication
Availability of data and materials
The raw genotypic data are available in Supplementary Table 5.
Conflict of interest
The authors declare no competing financial interests.
- Chandler RF Jr (1969) Plant morphology and stand geometry in relation to nitrogen. Agronomy and Horticulture Department (Digital Commons), University of Nebraska–Lincoln. 196. http://digitalcommons.unl.edu/agronomyfacpub/196. Accessed 2 Feb 2018
- Chang T-T, Vergara BS (1972) Ecological and genetic information on adaptability and yielding ability in tropical rice varieties. In: Rice breeding. International Rice Research Institute, Los Baños, Philippines, pp 431–453Google Scholar
- Chen GH, Deng HB, Zhang GL, Tang WB, Huang H (2016) The correlation of stem characters and lodging resistance and combining ability analysis in rice. Sci Agric Sin 49:407–417. https://doi.org/10.3864/j.issn.0578-1752.2016.03.001 (in Chinese) CrossRefGoogle Scholar
- FAO I (2016) WFP (2015) The state of food insecurity in the world 2015. Meeting the 2015 international hunger targets: Taking stock of uneven progress. Food and Agriculture Organization Publications, RomeGoogle Scholar
- GRiSP (2013) Rice almanac, 4th edn. International Rice Research Institute, Los BañosGoogle Scholar
- Hojyo Y (1974) Lodging and stiffness of culms in crops. Agric Technol 29:157–162Google Scholar
- Larson JC, Maranville JW (1977) Alterations of yield, test weight, and protein in lodged grain sorghum. Agron J 69:629–630. https://doi.org/10.2134/agronj1977.00021962006900040027x CrossRefGoogle Scholar
- Noor RBM, Caviness CE (1980) Influence of induced lodging on pod distribution and seed yield in soybeans. Agron J 72:904–906. https://doi.org/10.2134/agronj1980.00021962007200060010x CrossRefGoogle Scholar
- Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425Google Scholar
- Siripoonwiwat W, O’Donoughue LS, Wesenberg D, Hoffman DL, Barbosa-Neto JF, Sorrells ME (1996) Chromosomal regions associated with quantitative traits in oat. J Quant Trait Loci 2:830Google 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 11:1441–1452CrossRefPubMedPubMedCentralGoogle Scholar
- Weber CR, Fehr WR (1966) Seed yield losses from lodging and combine harvesting in soybeans. Agron J 58:287–289. https://doi.org/10.2134/agronj1966.00021962005800030012x CrossRefGoogle Scholar