Abstract
Maize starch plays a critical role in food processing and industrial application. The pasting properties, the most important starch characteristics, have enormous influence on fabrication property, flavor characteristics, storage, cooking, and baking. Understanding the genetic basis of starch pasting properties will be beneficial for manipulation of starch properties for a given purpose. Genome-wide association studies (GWAS) are becoming a powerful tool for dissecting the complex traits. Here, we carried out GWAS for seven pasting properties of maize starch with a panel of 230 inbred lines and 145,232 SNPs using one single-locus method, genome-wide efficient mixed model association (GEMMA), and three multi-locus methods, FASTmrEMMA, FarmCPU, and LASSO. We totally identified 60 quantitative trait nucleotides (QTNs) for starch pasting properties with these four GWAS methods. FASTmrEMMA detected the most QTNs (29), followed by FarmCPU (19) and LASSO (12), GEMMA detected the least QTNs (7). Of these QTNs, seven QTNs were identified by more than one method simultaneously. We further investigated locations of these significantly associated QTNs for possible candidate genes. These candidate genes and significant QTNs provide the guidance for further understanding of molecular mechanisms of starch pasting properties. We also compared the statistical powers and Type I errors of the four GWAS methods using Monte Carlo simulations. The results suggest that the multi-locus method is more powerful than the single-locus method and a combination of these multi-locus methods could help improve the detection power of GWAS.
Highlights
Maize (Zea mays L.) is the world’s most important crop for food, feed and industrial materials
The main objectives of this study were to (i) identify loci that are significantly associated with pasting properties of maize starch using single-locus and multi-locus Genome-wide association studies (GWAS) methods, and (ii) compare three multi-locus methods (FASTmrEMMA, LASSO, and FarmCPU) with one single-locus method (GEMMA) in terms of their detection powers and Type I errors
The narrow sense heritability, defined as the ratio of additive genetic variance to total phenotypic variance, ranges from 0.46 for pasting time (PT) to 0.77 for trough viscosity (TV) (Table 2). These results indicate that the phenotypic variations of starch pasting properties are mainly affected by genetic factors, and this panel can be used for further genetic analyses
Summary
Maize (Zea mays L.) is the world’s most important crop for food, feed and industrial materials. Benefitting from its characteristics such as slow tendency of retrogradation and low pasting temperature (PTP), maize starch serves as an essential ingredient for industrial production of food, and has been widely used to thicken sauces or soups and make. Great progress has been made in dissection of starch content in maize kernels (Wang et al, 2015; Li et al, 2018). Further improvements in starch quality are needed to meet demands of food processing and industrial application. The pasting properties are important characteristics of starch, determining the starch quality and functionality. Dissection the genetic basis of pasting properties will facilitate the improvement of starch quality in maize
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