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SSR-Based Genetic Diversity, Population Structure, and Marker-Trait Associations for Popping-Related Traits in
Lin Yang1, Jialin Yu1, Ning Wang1
1Maize Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China.
Genetic analysis of popcorn quality traits using simple sequence repeat (SSR) markers revealed significant variation and identified key markers for breeding. This research provides a framework for understanding popcorn popping characteristics.
Area of Science:
- Genetics and Plant Breeding
- Agricultural Science
- Maize Genetics
Background:
- Popcorn (Zea mays L. var. everta) quality traits are crucial for breeding but lack comprehensive genetic characterization.
- Understanding the genetic basis of popping performance and flake morphology is essential for developing improved popcorn varieties.
Purpose of the Study:
- To characterize the genetic diversity of popcorn inbred lines using simple sequence repeat (SSR) markers.
- To identify SSR loci associated with popping-related quality traits, including expansion volume, expandability, and flake morphology.
- To propose a conceptual framework for the genetic organization of popcorn popping traits.
Main Methods:
- Analysis of 18 popcorn inbred lines with 25 SSR markers across all 10 maize chromosomes.
- Evaluation of popping performance and image-based flake morphology in 16 lines.
- Application of Principal Component Analysis (PCA), UPGMA clustering, and population structure analysis for genetic differentiation.
- Marker-trait association analysis to link SSR loci with phenotypic traits.
Main Results:
- Substantial phenotypic variation observed in expansion volume (173.33–343.33 mL) and expandability (16.79–32.46-fold).
- Image analysis confirmed flake morphology as a quantitative trait with continuous variation in circularity.
- SSR analysis revealed moderate-to-high genetic diversity (2–11 alleles/locus, PIC 0.05–0.85).
- Identification of putative SSR loci associated with expansion efficiency, flake morphology, pericarp retention, and popping dynamics, with marker M18 linked to expansion volume and expandability.
Conclusions:
- Popcorn popping-related traits can be organized into partially independent, interconnected functional modules.
- SSR markers provide valuable genetic information for popcorn germplasm characterization.
- Preliminary marker resources are available for quality-oriented popcorn breeding programs.
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