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Mining of favorable alleles for lodging resistance traits in rice (oryza sativa) through association mapping

Planta volume 248, pages 155–169 (2018)Cite this article

Abstract

Main conclusion

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.

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Notes

  1. All the rice seeds used in this research were collected during long-term rice science studies and properly kept in our State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University. Accession numbers 1–543 were selected from our previous studies on rice grain sizes and weight (Rf. https://www.frontiersin.org/articles/10.3389/fpls.2016.00787/full).

Abbreviations

ANOVA:

Analysis of variance

AT/S:

Anti-thrust per stem

GWA:

Genome-wide association

\(H_{\text{B}}^{2}\) :

Heritability in the broad sense

LD:

Linkage disequilibrium

MAS:

Marker-assisted selection

MTAs:

Marker–trait associations

PH:

Plant height

PIC:

Polymorphic information content

PVE:

Proportion of phenotypic variance explained

QTL:

Quantitative trait locus

SD:

Stem diameter

SI:

Stem index

SL:

Stem length

SSR:

Simple sequence repeat

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Acknowledgements

We thank Jianhua Ji, a technician at Nanjing Agricultural University Farm, for help with the daily management of the paddy field.

Funding

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).

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  1. State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China

    Ognigamal Sowadan, Dalu Li, Yuanqing Zhang, Shangshang Zhu, Xiaoxiao Hu, Lal Bux Bhanbhro, Wisdom M. Edzesi, Xiaojing Dang & Delin Hong

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  1. Ognigamal Sowadan
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  2. Dalu Li
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Correspondence to Delin Hong.

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The raw genotypic data are available in Supplementary Table 5.

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Sowadan, O., Li, D., Zhang, Y. et al. Mining of favorable alleles for lodging resistance traits in rice (oryza sativa) through association mapping. Planta 248, 155–169 (2018). https://doi.org/10.1007/s00425-018-2885-y

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Keywords

  • Oryza sativa
  • Lodging resistance
  • Linkage disequilibrium
  • Association mapping
  • Favorable allele
  • Phenotypic and genetic diversities