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. 2025 Jan 6;138(1):17.
doi: 10.1007/s00122-024-04773-z.

Genetic dissection of a major locus SC9.1 conferring seed color in broomcorn millet (Panicum miliaceum)

Tianpeng Liu  1   2 , Kongjun Dong  1   2 , Jihong He  1   2 , Mei Wang  3 , Ruiyu Ren  1   2 , Lei Zhang  1   2 , Yawei Li  1   2 , Minxuan Liu  4 , Tianyu Yang  5   6
Affiliations

Genetic dissection of a major locus SC9.1 conferring seed color in broomcorn millet (Panicum miliaceum)

Tianpeng Liu et al. Theor Appl Genet. .

Abstract

A major locus SC9.1 was identified and finely mapped into a 92.68 Kb region, and longmi004412 was identified as the casual gene regulating brown seed color in broomcorn millet. Broomcorn millet is a cereal crop with abundant genetic variations in morphology, agronomy, and yield-related traits. The diversity of seed color is among the most distinctive morphological characteristics. However, genetic determinants governing seed coloration have rarely been reported. Here, the F2 and F3 populations from a cross between Longmi12 and Zhang778 were employed to elucidate the genetic basis of seed color. Statistical analysis conducted on the seed color in F1, F2, and F3 progeny conclusively demonstrated that brown seed color was controlled by a single dominant locus in broomcorn millet. The genetic control locus, SC9.1, was preliminarily located on chromosome 9 in the 32,175,878-44,281,406 bp region through bulked segregant analysis sequencing (BSA-seq). Furthermore, SC9.1 was narrowed down to a 92.68 kb interval harboring 11 genes using fine mapping with 260 recessive individual genotypes. Combined with gene structural variation, the transcriptome profile, and functional comparison, longmi004412 was identified as the causal gene resulting in brown seed color formation in broomcorn millet. In addition, haplotype analysis of the longmi004412 gene in 516 accessions was performed to clarify the types for broomcorn millet seed color. These findings lay the foundation for precise identification of germplasm at the molecular level, molecular-assisted selection breeding, and the application of gene editing technology in broomcorn millet.

Keywords: BSA-seq; Broomcorn millet; Fine mapping; Haplotype; Seed color; Transcriptome.

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Conflict of interest statement

Declarations. Conflict of interest: The authors declare that they have no conflicts of interest.

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