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Genetic dissection of grain starch-related quality traits and identification of candidate genes in foxtail millet (Setaria italica)

Zhao Yuan-Lin1,Zhang Ming-Yang1,Zhang Wei-Wei1,Chen Long1,Xie Xun1,Han Yuan-Huai1,2,Sun Zhao-Xia1,2,*,Hou Si-Yu1,2,*   

  1. 1 College of Agronomy, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China; 2 Shanxi Houji Laboratory, Taiyuan 030001, Shanxi, China
  • Received:2026-03-26 Revised:2026-08-21 Accepted:2026-08-21 Published:2026-08-28
  • Supported by:
    This study was supported by the National Natural Science Foundation of China (32572336), Biological Breeding Project for the 15th Five-Year Plan of Shanxi Agricultural University (YZGC2026108), the Grand Science and Technology Special Project in Shanxi Province (202101140601027) and the Overseas Training Program for Young Talents of Shanxi Agricultural University.

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Abstract:

Systematic studies of the genetic basis and gene mining of starch-related traits in grains of the elite foxtail millet cultivar Jingu 21 remain limited. To elucidate the genetic basis underlying the starch quality traits of millet grains and identify candidate genes, a recombinant inbred line (RIL) population derived from Jingu 21 and a natural population were employed for phenotypic evaluation and genetic dissection of five starch-related quality traits across multiple environments. The results showed that the total starch content (SC), amylopectin content (APC), and amylose–to–amylopectin ratio (AC/APC) exhibited positive correlations, whereas they were significantly and negatively correlated with amylose content (AC) in both RIL and natural populations. Gel consistency (GEL) showed relatively weak correlations with the other traits. All starch-related quality traits displayed abundant phenotypic variation and approximately normal distributions. The broad-sense heritability estimates exceeded 58% for all traits, indicating that these traits were predominantly controlled by genetic factors. A total of 63 quantitative trait loci (QTLs) were identified on seven chromosomes and were further integrated into 11 QTL clusters, explaining 5.32%–17.51% of the phenotypic variation. Notably, a co-localized interval for four starch quality-related traits was identified on chromosome 2 at 40.43–41.27 Mb. In total, 1631 genes were annotated within the QTL mapping intervals. Genome-wide association study (GWAS) identified 58 significant SNPs associated with starch-related traits, with the phenotypic variance explained (PVE) ranging from 5.10% to 10.01%, and 636 genes were annotated within the associated genomic regions. Integration GWAS and QTL co-localization analyses yielded 15 repeatedly detected candidate genes. Combined with expression profiling, 10 of these genes were highly expressed during the late grain-filling stage. Haplotype analysis revealed that six genes, including Seita.2G282600, Seita.2G285500, Seita.2G301600, Seita.2G322700, Seita.3G011400, and Seita.4G041500, possessed superior haplotypes. Among them, SUS1 (sucrose synthase 1) was identified as an important candidate gene regulating grain starch content. Furthermore, pyramiding-effect analysis of superior haplotypes demonstrated that three varieties (B096, B292, and B261) simultaneously carried the superior haplotypes of five key genes. The mean phenotypic values of their grain starch-related traits were significantly higher than those of other haplotype combination types, suggesting that these favorable allelic variants may jointly affect foxtail millet grain starch quality through synergistic effects. In summary, this study preliminarily elucidated the genetic architecture of grain starch-related traits in foxtail millet and identified five key candidate genes. These findings provide valuable molecular markers and genetic resources for future molecular breeding and genetic improvement in foxtail millet.

Key words: Setaria italica, starch-related traits, quantitative trait loci (QTL), candidate genes, superior haplotypes, pyramiding-effect analysis

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