Identification of QTLs for 14 Agronomically Important Traits in Setaria italica Based on SNPs Generated from High-Throughput Sequencing

G3 (Bethesda). 2017 May 5;7(5):1587-1594. doi: 10.1534/g3.117.041517.


Foxtail millet (Setaria italica) is an important crop possessing C4 photosynthesis capability. The S. italica genome was de novo sequenced in 2012, but the sequence lacked high-density genetic maps with agronomic and yield trait linkages. In the present study, we resequenced a foxtail millet population of 439 recombinant inbred lines (RILs) and developed high-resolution bin map and high-density SNP markers, which could provide an effective approach for gene identification. A total of 59 QTL for 14 agronomic traits in plants grown under long- and short-day photoperiods were identified. The phenotypic variation explained ranged from 4.9 to 43.94%. In addition, we suggested that there may be segregation distortion on chromosome 6 that is significantly distorted toward Zhang gu. The newly identified QTL will provide a platform for sequence-based research on the S. italica genome, and for molecular marker-assisted breeding.

Keywords: QTL mapping; SNP map; agronomic traits; foxtail millet; photoperiod.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Genome, Plant
  • High-Throughput Nucleotide Sequencing
  • Inbreeding
  • Plant Breeding
  • Polymorphism, Single Nucleotide*
  • Quantitative Trait Loci*
  • Quantitative Trait, Heritable*
  • Sequence Analysis, DNA
  • Setaria Plant / genetics*