Gene mapping and functional analysis of the novel leaf color gene SiYGL1 in foxtail millet [Setaria italica (L.) P. Beauv]

Abstract

Setaria italica and its wild ancestor Setaria viridis are emerging as model systems for genetics and functional genomics research. However, few systematic gene mapping or functional analyses have been reported in these promising C4 models. We herein isolated the yellow-green leaf mutant (siygl1) in S. italica using forward genetics approaches. Map-based cloning revealed that SiYGL1, which is a recessive nuclear gene encoding a magnesium-chelatase D subunit (CHLD), is responsible for the mutant phenotype. A single Phe to Leu amino acid change occurring near the ATPase-conserved domain resulted in decreased chlorophyll (Chl) accumulation and modified chloroplast ultrastructure. However, the mutation enhanced the light-use efficiency of the siygl1 mutant, suggesting that the mutated CHLD protein does not completely lose its original activity, but instead, gains novel features. A transcriptional analysis of Chl a oxygenase revealed that there is a strong negative feedback control of Chl b biosynthesis in S. italica. The SiYGL1 mRNA was expressed in all examined tissues, with higher expression observed in the leaves. Comparison of gene expression profiles in wild-type and siygl1 mutant plants indicated that SiYGL1 regulates a subset of genes involved in photosynthesis (rbcL and LHCB1), thylakoid development (DEG2) and chloroplast signaling (SRP54CP). These results provide information regarding the mutant phenotype at the transcriptional level. This study demonstrated that the genetic material of a Setaria species could be ideal for gene discovery investigations using forward genetics approaches and may help to explain the molecular mechanisms associated with leaf color variation.

Setaria viridis as a Model System to Advance Millet Genetics and Genomics

“…Empirically, the expense of this approach correlates with genome size, and the time to discovery largely depends on the generation time, so this approach is most suitable for model systems. Using this method, Li et al (2016) mapped a yellow–green leaf mutation in foxtail millet to a chlorophyll biosynthesis related gene SiYGL1 . Masumoto et al (2016) mapped a branching panicle mutation, a yield related trait in foxtail millet, to a candidate gene NEKODE1 .…”

Loose Panicle1 encoding a novel WRKY transcription factor, regulates panicle development, stem elongation, and seed size in foxtail millet [Setaria italica (L.) P. Beauv.]

“…In recent years, our group has used S . italica as a model for gene mapping and functional genomic studies [5–7]. We used an S .…”

“…italica variety with an available genome sequence, ‘Yugu1’, as the material for a large-scale ethyl methylsulfone (EMS)-induced mutant library. We identified an improved variety, ‘SSR41’, which has a similar flowering time and a high level of genetic polymorphism with ‘Yugu1’ [5]. ‘SSR41’ and a mutant originating from ‘Yugu1’ were used as pollen parents to construct mapping populations.…”

“…‘SSR41’ and a mutant originating from ‘Yugu1’ were used as pollen parents to construct mapping populations. Several functional genes, including SiYGL1 [5], SiDWARF2 [6], and SiAGO1b [7], were discovered recently through map-based cloning. These studies confirmed the potential of Setaria spp.…”

Setaria: A Food Crop and Translational Research Model for C4 Grasses

“…The high-quality genome sequence of foxtail millet has also allowed in-depth analyses of transposon family dynamics and locations that reveal hitherto unsuspected variation between transposon families in insertion site preference and turnover (Bennetzen et al, 2016). Mutant populations have been characterized in both foxtail millet and green foxtail millet, and the identity of candidate genes was revealed by novel high-throughput sequencing approaches (Li et al, 2016; Liu et al, 2016; Martins et al, 2016; Xue et al, 2016). S. italica and S. viridis have been used in the characterization of important agronomic traits, including yield-related architectural traits such as height, branching, biomass, flowering time and domestication-related traits such as shattering (Qian et al, 2012; Jia et al, 2013; Mauro-Herrera et al, 2013; Wang et al, 2013; Doust et al, 2014; Gupta et al, 2014; Layton and Kellogg, 2014; Qie et al, 2014; Fahlgren et al, 2015; Fang et al, 2016; Hodge and Kellogg, 2016; Liu et al, 2016; Mauro-Herrera and Doust, 2016).…”