Identification and candidate gene screening of qHC1.2 , a Major QTL associated with hull color in foxtail millet ( Setaria italica L.)

Abstract

Abstract Hull color is a crucial characteristic that helps assess the nutritional value and economic potential of foxtail millet. However, the reports on quantitative trait locus (QTL) mapping and map-based cloning for hull color are limited. Here, we mapped QTLs responsible for hull color by using 215 recombinant inbred lines (RILs) derived from Yugu 18 (Light yellow hull) × Hongjiugu (Red hull) and a high-density bin map. A total of 36 QTLs for hull color were detected in all four environments by four phenotypic evaluation methods. Among these QTLs, a major QTL for hull color (HC) named qHC1.2 was repeatedly mapped on chromosome 1 and explained 8.89 – 69.63% of the phenotypic variation. In addition, RNA sequencing (RNA-seq) was performed 7, 14, and 21 days after flowering for the YRRIL-145 and YRRIL-229, and three differentially expressed genes (DEGs) were detected in the candidate region. The qRT-PCR results showed the same expression patterns as the RNA-seq data. Among them, DEGs, only one gene, Seita.1G057300, encoding a cinnamyl alcohol dehydrogenase (CAD), was located in the candidate region of qHC1.2. Furthermore, sequence analysis revealed One SNP (A to G), located at the third exon, resulted in an amino acid change from isoleucine to valine in YRRIL-145 compared with YRRIL-229. Our results provide a foundation for further cloning of qHC1.2 and will be very useful in clarifying the regulatory mechanism for hull color synthesis in foxtail millet.