Journal
JOURNAL OF EXPERIMENTAL BOTANY
Volume 72, Issue 4, Pages 1307-1320Publisher
OXFORD UNIV PRESS
DOI: 10.1093/jxb/eraa480
Keywords
EigenGWAS; GWAS; maize adaptation; popping traits; quality traits; tropical maize landrace
Categories
Funding
- National Key Research and Development Program of China [2016YFD0100303]
- CGIAR Genebank Platform
- CGIAR Research Program MAIZE (CRP-MAIZE)
- Government of Australia
- Government of Belgium
- Government of Canada
- Government of China
- Government of France
- Government of India
- Government of Japan
- Government of Korea
- Government of Mexico
- Government of Netherlands
- Government of New Zealand
- Government of Norway
- Government of Sweden
- Government of Switzerland
- Government of United Kingdom
- Government of United States
- World Bank
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This study characterized phenotypic variation for popping-related traits in maize kernels among 526 CIMMYT inbred lines and identified trait-associated loci through genome-wide association study. It revealed that many of these loci have undergone selection, with an average frequency of 55.27% for alleles promoting popping. This work not only pinpointed previously unknown loci for popping-related traits, but also provided evidence of the role of a gradual loss of popping ability throughout the evolution of teosinte-to-modern maize.
Popcorn (Zea mays L. var. Everta) is the most ancient type of cultivated maize. However, there is little known about the genetics of popping-related traits based on genotyping-by-sequencing (GBS) technology. Here, we characterized the phenotypic variation for seven popping-related traits in maize kernels among 526 CIMMYT inbred lines (CMLs). In total, 155 083 high-quality single nucleotide polymorphism (SNP) markers were identified by a GBS approach. Several trait-associated loci were detected by genome-wide association study for color, popping expansion volume, shape, pericarp, flotation index, floury/vitreous, and protein content, explaining a majority of the observed phenotypic variance, and these were validated by a diverse panel comprising 764 tropical landrace accessions. Sixty two of the identified loci were recognized to have undergone selection. On average, there was a 55.27% frequency for alleles that promote popping in CMLs. Our work not only pinpoints previously unknown loci for popping-related traits, but also reveals that many of these loci have undergone selection. Beyond establishing a new benchmark for the genetics of popcorn, our study provides a foundation for gene discovery and breeding. It also presents evidence to investigate the role of a gradual loss of popping ability as a by-product of diversification of culinary uses throughout the evolution of teosinte-to-modern maize.
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