Genetic characterization of hull color using BSR-Seq and genome re-sequencing approaches in foxtail millet

Abstract

Hull color of foxtail millet is an important indicator of certain nutritional quality parameters. An F2:6 recombinant inbred line (RIL) population developed by crossing a yellow-hulled cultivar Yugu 5 and a brown-hulled cultivar Jigu 31 was used to determine the genetic control of the hull color trait. This population segregated for yellow and brown hull colors in a ratio of 2:1, indicating that hull color is regulated by multiple genetic loci. A bulk segregant analysis-RNA sequencing (BSR-Seq) approach performed using the RNA bulks from 30 lines with brown and yellow hull colors each identified three genomic regions on chromosomes 1 (4,570,517-10,698,955 bp), 2 (40,301,380-46,168,003 bp), and 3 (44,469,860-50,532,757 bp). A new QTL for brown hull color of Jigu 31, QHC.czas1, was detected between bin markers Block43 and Block697 on chromosome 1 with the genetic linkage map constructed by re-sequencing a subset of the 147 RILs. This QTL explained a high level of phenotypic variation ranging from 28.0% to 47.0%. The corresponding genomic region of this QTL in the foxtail millet reference genome overlapped with that detected on chromosome 1 by the BSR-Seq analysis. Nineteen genes associated with biosynthesis of anthocyanin were annotated in this genomic region. Gene Si1g06530 encoding a SANT/Myb domain protein was highly expressed in developing panicles and seeds, which warrants further verification as the candidate gene for the brown color hull of Jigu 31. Moreover, several annotated genes for biosynthesis of anthocyanin were identified in the genomic regions of chromosomes 2 and 3.

Mapping of major QTL and candidate gene analysis for hull colour in foxtail millet (Setaria italica (L.) P. Beauv.)

“…There was a small physical distance between them, which might be because they were likely to be at the same locus. In addition, the minor QTL qHCL-2–1 (40,839,953–41,868,044) and qHCb-3–3 ( 47,561,089 – 48,177,283 ) overlapped with those QTL that Tian et al [ 7 ] identified.…”

“…Hull colour has been reported to be mainly controlled by a few major QTL on chromosomes 1, 2, 3, 6, 7, and 9 [ 2 , 7 , 13 , 21 ]. We compared the genomic regions of the QTL identified in this study with those detected in previous studies.…”

“…Jia et al [ 13 ] identified the QTL for hull colour in the interval of 1–5,480,917 bp (1–5,467,847 bp and 1–5,476,983 bp) on chromosome 1 by genome-wide association studies from five locations. Tian et al [ 7 ] identified the QTL for hull colour in the interval of 4,570,517–10,698,955 bp on chromosome 1 by the bulk segregant analysis-RNA sequencing (BSR-Seq) approach, which partially overlapped with qHCL-1–1 (5,392,854–5,553,418 bp), qHCa-1–1 (5,470,545–5,553,418 bp) and qHCC-1–1 (5,392,854–5,690,175 bp) identified in our research. Compared to the genomic region previously identified, the genomic region for QTL was narrowed down to smaller intervals in the current study, which allowed us to further narrow down the selection of plausible causal genes [ 16 ].…”

“…Hull colour is an important feature for evaluating the market value and appearance quality of foxtail millet [ 4 – 6 ]. The protein, lysine, fat, and selenium contents differ according to the hull colour of the foxtail millet [ 7 ].Cyan hull foxtail millet has high protein, fat, and lysine contents. Moreover, hull colour was related to bird feeding preferences during the mature phase of the foxtail millet crop.…”

“…In recent years, many researchers have used germplasm materials with various genetic backgrounds to construct segregated populations and applied them to the QTL mapping of important agronomic traits in foxtail millet. Regarding hull colour, several loci have been mapped to chromosomes 1, 2, 3, 6, 7, and 9 in foxtail millet [ 7 , 17 ]. Xie et al [ 2 ] showed that three QTL controlling hull colour are located on chromosome 1 of foxtail millet and identified a cinnamyl alcohol dehydrogenase ( CAD ) gene ( Seita.1G057300.v2.2 ) as a candidate gene for the hull colour.…”