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

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.