QTL-Guided Prioritization of SiMGT2 as a Candidate Gene Associated with Grain Fat Content in Foxtail Millet

Grain fat content contributes to nutritional quality in foxtail millet, but its genetic basis remains incompletely understood. We evaluated a 256-line recombinant inbred population derived from Jingu21 and Chuang29 in two environments. Among the individual environments, qFC5 was detected only in Sanya (2022_SY; LOD 5.86; phenotypic variance explained: 9.24%), exceeding the LOD threshold of 3.58. Across-environment mapping using best linear unbiased estimates identified an overlapping chromosome 5 region (LOD: 5.99; phenotypic variance explained: 7.67%), exceeding the threshold of 4.14 from 1000 permutations. Among 248 annotated genes in the 1.80 Mb Sanya interval, Arabidopsis and rice homology, functional annotation and expression information supported prioritization of Seita.5G394800.1 (SiMGT2), a predicted MGT/MRS2 magnesium transporter. Six SiMGT family members were identified. In the parental panicle dataset, SiMGT2 had a higher mean expression in Jingu21 at three sampling stages; only the middle-stage difference remained significant after correction across 18 comparisons. In 534 phenotyped accessions, H1 had a higher grain fat content than H2, but not H3; these comparisons were not corrected for population structure or kinship. The results prioritize SiMGT2 as a candidate associated with grain fat content, with environment-dependent QTL support. Causality and the proposed connection with magnesium homeostasis require functional validation.