Characterization and Fine Mapping of SiDWARF2 (D2) in Foxtail Millet

Abstract

Elongation of grass internodes determines the plant height and underlies the grain yield of grass crop species, by enhancing of lodging resistance in elite cultivars. Foxtail millet [Setaria italica (L.) P. Beauv.] is an ancient cereal crop that served as a staple food during early civilization in China and is still grown widely across South and East Asia, Europe, and Africa. In this study, a foxtail millet dwarf mutant (Sidwarf2), derived from ‘Yugu1’, was characterized. In the dwarf mutant, significantly reduced cell lengths caused the observed shorter internodes. Gibberellin sensitivity analyses suggested that the height of the mutant could be restored under out spraying of gibberellic acid (GA3). In both the wild‐type and the mutant, endogenous levels of GA3 in elongated internodes stayed the same, while the abscisic acid (ABA) content of the dwarf mutant was greatly elevated. The dwarf gene (D2) was finally mapped on chromosome 3 and located to a genome region spanning 52.7 kb using combined bulked segregation analysis and map‐based approaches. Twelve transcripts were annotated in the target region and a cytochrome P450 encoding gene was deduced to be the candidate gene of D2. This study highlighted the potential of fast‐mapping‐favorable loci in foxtail millet, which will aid molecular selection and modification of foxtail millet in the future.

Identification and Fine Mapping of SiDWARF3 (D3), a Pleiotropic Locus Controlling Environment‐Independent Dwarfism in Foxtail Millet

“…This type of pleiotropic effect of dwarfing genes has also been observed in other crop species (Duan et al, 2012; Zhang et al, 2014a; Chen et al, 2015; Jin et al, 2015; Liu et al, 2015). In Setaria, Sidwarf2 ( D2 ) has also been characterized as a mutant with multitrait variations (Xue et al, 2016), and many dwarf mutants identified in Setaria (Ratnaswamy and Dhanaraj, 1961; Yao and Liang, 1990; Dineshkumar et al, 1992) were the result of shortened internodes with no change in the number of internodes. Interestingly, only one previously reported mutant in rice, nl1 , has ever been identified as having a changed number of stem internodes (Wang et al, 2009), which was similar to Sidwarf3 , suggesting that dwarfism involving changed internode number may be conditioned by specific regulators in plants.…”

“…A bulked segregant analysis, followed by map‐based cloning, is a powerful tool for gene isolation in model plants, such as Arabidopsis and rice. In Setaria, this approach was found to be efficient for rapid mapping of favorable loci (Li et al, 2016; Liu et al, 2016; Xue et al, 2016). A MutMap method was developed on the basis of high‐throughput genome resequencing techniques (Abe et al, 2012; Fekih et al, 2013; Takagi et al, 2013).…”

“…Many types of dwarfing mutants have been analyzed in cereal crop species (Gale and Youssefian, 1985; Phinney, 1985; Federizzi and Qualset, 1989; Mitsunaga et al, 1994). In foxtail millet breeding programs, several naturally occurring dwarfing mutants, such as 84133 , An'ai3 , sic24 , sic25 , and sic26 , have been identified (Ratnaswamy and Dhanaraj, 1961; Yao and Liang, 1990; Dineshkumar et al, 1992; Li and Diao, 1994; Gao et al, 2003; Qian et al, 2012); however, dwarfing mutants created in foxtail millet have not been genetically characterized, with the exception of Sidwarf2 ( D2 ), a mutant identified from callus‐based regeneration of Yugu1 (Xue et al, 2016).…”

Genetic analysis of NEKODE1 gene involved in panicle branching of foxtail millet, Setaria italica (L.) P. Beauv., and mapping by using QTL-seq

“…QTL-seq was useful not only for analysis of QTL but also for a gene for qualitative traits between cultivars. For construction of linkage Wang et al 1998;Jia et al 2009;Sato et al 2013), QTL of morphological/agronomic traits (Doust et al 2004(Doust et al , 2005Mauro-Herrera et al 2013) and positional cloning (Li et al 2015;Xue et al 2016), combinations between distantly related parents such as between a S. italica cultivar and the wild ancestor, ssp. viridis, between a Japanese landrace and a Taiwanese landrace and between divergent Chinese cultivars have been used.…”

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).…”