Scientia Agricultura Sinica ›› 2017, Vol. 50 ›› Issue (4): 599-611.doi: 10.3864/j.issn.0578-1752.2017.04.001

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS •     Next Articles

Association Analysis of Rice Cooking Quality Traits with Molecular Markers

GAO WeiWei, CHEN SiPing, WANG LiPing, CHEN LiKai, GUO Tao, WANG Hui, CHEN ZhiQiang   

  1. National Engineering Research Centre of Plant Space Breeding, South China Agricultural University, Guangzhou 510642
  • Received:2016-08-22 Online:2017-02-16 Published:2017-02-16

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Abstract: 【Objective】 In this study, the variation of major grain-quality traits and RVA profiles of representative rice germplasm were investigated, molecular markers significantly associated with the traits were identified, aiming to provide an important foundation for improvement of grain quality of rice. 【Method】 Global grain-quality properties and their differences were surveyed with a rice panel consisted of 48 diverse germplasms collected from both China and abroad. Starch RVA profile was examined with a Rapid Visco Analyzer. The markers reported to be related to starch biosynthesizing genes and QTLs for development of rice grain were used for genotyping. Trait-marker association for grain-quality properties was detected using the general linear model with Tassel 3.0 software. Moreover, stepwise regression analysis was performed with these detected markers significantly associated with grain-quality traits. The phenotypic effects of the alleles and allelic combinations were estimated and both elite alleles and typical carrier genotypes were identified. 【Result】There were wide phenotypic variance and diversity in amylose content (AC), gel consistency (GC) and alkali spreading value (ASV), and the coefficient of variation (CV.) ranged from 26.5% to 36.3%. Based on inspection of RVA profile, significant differences were found in breakdown (BDV), setback (SBV) and consistence (CSV), and these parameters have preferably reflected the diverse starch paste properties among different rice varieties. Correlation analysis showed the AC was positively correlated with cool paste viscosity (CPV), SBV and CSV, while negatively correlated with peak viscosity (PKV) and BDV. The GC was negatively correlated with SBV and CSV. A total of 491 alleles were identified with 154 polymorphic markers, with an average gene diversity of 0.447 and an average polymorphic information content of 0.390. Based on the analysis of trait-marker association, a total of 22 markers were detected to associate with grain-quality traits, which explained the phenotypic variance ranged from 14.11% to 75.62%. The GBSSI gene majorly affected the properties of AC and GC, and the SNP marker of Wx-G/T explained up to 61.44% and 41.87% of the phenotypic variation for AC and GC, respectively. While the SSIIa was the major gene affecting ASV, and the phenotypic variation of ASV explained by the markers of alk-GC/TT and SSIIa-F was up to 75.62% and 74.46%. The model equations based on stepwise regression analysis of AC, GC and ASV were developed using the significant markers, whose determination coefficients were 85.30%, 40.62%, and 80.38%, respectively. 【Conclusion】The starch RVA profile wass closely related to AC, GC and ASV. The RVA profile can be used to evaluate rice quality traits more comprehensively. With trait-marker association analysis, 22 markers were detected to be associated with grain-quality traits, and five of these sites were associated with both AC and GC. Regression models showed allelic combination can produce different phenotypic effects.

Key words: rice, grain-quality traits, trait-marker association, allelic variation

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