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Background  Foxtail millet ( Setaria italica ) is one of the oldest domesticated crops and has been considered as an ideal model plant for C 4  grasses. It has abundant type of anther and hull colors which is not only a most intuitive morphological marker for color selection in seed production, but also has very important biological significance for the study of molecular mechanism of regulating the synthesis and metabolism of flavonoids and lignin. However, only a few genetic studies have been reported for anther color and hull color in foxtail millet.    Results  Quantitative trait loci (QTL) analysis for anther color and hull color was conducted using 400 F 6  and F 7  recombinant inbreed lines (RILs) derived from a cross between parents Yugu18 and Jigu19. Using restriction-site associated DNA sequencing, 43,001 single-nucleotide polymorphisms (SNPs) and 3,022 indels were identified between both the parents and the RILs. A total of 1,304 bin markers developed from the SNPs and indels were used to construct a genetic map that spanned 2196 cM of the foxtail millet genome with an average of 1.68 cM/bin. Combined with this genetic map and the phenotypic data observed in two locations for two years, two QTL located on chromosome 6 (Chr6) in a 1.215-Mb interval (33,627,819–34,877,940 bp) for anther color (yellow - white) and three QTL located on Chr1 in a 6.23-Mb interval (1–6,229,734 bp) for hull color (gold-reddish brown) were detected. To narrow the QTL regions identified from the genetic map and QTL analysis, we developed a new method named “inconsistent rate analysis” and efficiently narrowed the QTL regions of anther color into a 60-kb interval (34.13–34.19 Mb) in Chr6, and narrowed the QTL regions of hull color into 70-kb (5.43–5.50 Mb) and 30-kb (5.69–5.72 Mb) intervals in Chr1. Two genes ( Seita.6G228600.v2.2  and  Seita.6G228700.v2.2 ) and a  cinnamyl alcohol dehydrogenase  ( CAD ) gene ( Seita.1G057300.v2.2 ) with amino acid changes between the parents detected by whole-genome resequencing were identified as candidate genes for anther and hull color, respectively.    Conclusions  This work presents the related QTL and candidate genes of anther and hull color in foxtail millet and developed a new method named inconsistent rate analysis to detect the chromosome fragments linked with the quality trait in RILs. This is the first study of the QTL related to hull color in foxtail millet and clarifying that the  CAD  gene ( Seita.1G057300.v2.2 ) is the key gene responsible for this trait. It lays the foundation for further cloning of the functional genes and provides a powerful tool to detect the chromosome fragments linked with quality traits in RILs.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-07882-x.

Identification of QTL related to anther color and hull color by RAD sequencing in a RIL population of Setaria italica