Abstract
The identification of the genes responsible for complex traits is highly promising to accelerate crop breeding, but such information is still limited for popcorn. Thus, in the present study, a mixed linear model-based association analysis (MLMA) was applied for six important popcorn traits: plant and ear height, 100-grain weight, popping expansion, grain yield and expanded popcorn volume per hectare. To this end, 196 plants of the open-pollinated popcorn population UENF-14 were sampled, selfed (S1), and then genotyped with a panel of 10,507 single nucleotide polymorphisms (SNPs) markers distributed throughout the genome. The six traits were studied under two environments [Campos dos Goytacazes-RJ (ENV1) and Itaocara-RJ (ENV2)] in an incomplete block design. Based on the phenotypic data of the S1 progenies and on the genetic characteristics of the parents, the MLMA was performed. Thereafter, genes annotated in the MaizeGDB platform were screened for potential linkage disequilibrium with the SNPs associated to the six evaluated traits. Overall, seven and eight genes were identified as associated with the traits in ENV1 and ENV2, respectively, and proteins encoded by these genes were evaluated for their function. The results obtained here contribute to increase knowledge on the genetic architecture of the six evaluated traits and might be used for marker-assisted selection in breeding programs.
Highlights
In maize (Zea mays L.), the economically most important traits are usually quantitatively inherited, and their genetic basis is attributed to polygenes, as well as to the interaction effects between genes and/or between genes and environment [1]
To measure the magnitude of the linkage disequilibrium (LD) and define the windows at which polymorphic locations are expected to be in high LD, the r2 among all single nucleotide polymorphisms (SNPs) belonging to the same chromosome was estimated
The mixed linear model-based association analysis (MLMA) strategy used in the present study proved useful and robust, complementary to biparental cross-mapping, and can map multiple genetic traits simultaneously [72]
Summary
In maize (Zea mays L.), the economically most important traits are usually quantitatively inherited, and their genetic basis is attributed to polygenes, as well as to the interaction effects between genes and/or between genes and environment [1]. Because Z. mays has been used as a model in classical genetics and cytogenetics, it has significantly contributed to the understanding of fundamental processes such as reproduction and photosynthesis, among others [2]. SNP-based mixed model association in popcorn but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section
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