4.7 Article

The Integration of Genome-Wide Association Study and Homology Analysis to Explore the Genomic Regions and Candidate Genes for Panicle-Related Traits in Foxtail Millet

Journal

Publisher

MDPI
DOI: 10.3390/ijms232314735

Keywords

foxtail millet; panicle-related traits; genome-wide association study; homology analysis; haplotype analysis

Funding

  1. National Natural Science Foundation of China
  2. Joint Research Program on Foxtail Millet Breeding of Shanxi Province [U21A20216]
  3. Fundamental Research Program of Shanxi Province [2022XCZX04-10]
  4. Research Program of Agricultural Science and Technology Innovation of the Shanxi Academy of Agricultural Sciences [202103021223157]
  5. Ministerial and Provincial Co-Innovation Centre [YCX2020YQ30]

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In this study, a large-scale genome-wide association study was conducted to identify candidate genes and quantitative trait loci associated with panicle traits in foxtail millet. The detected genes and loci provide important information for gene cloning and marker-assisted selection in foxtail millet breeding.
Panicle traits are important factors affecting yield, and their improvement has long been a critical goal in foxtail millet breeding. In order to understand the genetic basis of panicle formation, a large-scale genome-wide association study (GWAS) was performed in this study for six panicle-related traits based on 706,646 high-polymorphism SNP loci in 407 accessions. As a result, 87 quantitative trait loci (QTL) regions with a physical distance of less than 100 kb were detected to be associated with these traits in three environments. Among them, 27 core regions were stably detected in at least two environments. Based on rice-foxtail millet homologous comparison, expression, and haplotype analysis, 27 high-confidence candidate genes in the QTL regions, such as Si3g11200 (OsDER1), Si1g27910 (OsMADS6), Si7g27560 (GS5), etc., affected panicle-related traits by involving multiple plant growth regulator pathways, a photoperiod response, as well as panicle and grain development. Most of these genes showed multiple effects on different panicle-related traits, such as Si3g11200 affecting all six traits. In summary, this study clarified a strategy based on the integration of GWAS, a homologous comparison, and haplotype analysis to discover the genomic regions and candidate genes for important traits in foxtail millet. The detected QTL regions and candidate genes could be further used for gene clone and marker-assisted selection in foxtail millet breeding.

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