title: A high density genetic map and QTL for agronomic and yield traits in Foxtail millet [Setaria italica (L.) P. Beauv].
abstract: Foxtail millet [Setaria italica (L.) P. Beauv.], a crop of historical importance in China, has been adopted as a model crop for studying C-4 photosynthesis, stress biology and biofuel traits. Construction of a high density genetic map and identification of stable quantitative trait loci (QTL) lay the foundation for marker-assisted selection for agronomic traits and yield improvement.
  
  
  
  A total of 10598 SSR markers were developed according to the reference genome sequence of foxtail millet cultivar 'Yugu1'. A total of 1013 SSR markers showing polymorphism between Yugu1 and Longgu7 were used to genotype 167 individuals from a Yugu1 × Longgu7 F2 population, and a high density genetic map was constructed. The genetic map contained 1035 loci and spanned 1318.8 cM with an average distance of 1.27 cM between adjacent markers. Based on agronomic and yield traits identified in 2 years, 29 QTL were identified for 11 traits with combined analysis and single environment analysis. These QTL explained from 7.0 to 14.3 % of phenotypic variation. Favorable QTL alleles for peduncle length originated from Longgu7 whereas favorable alleles for the other traits originated from Yugu1 except for qLMS6.1.
  
  
  
  New SSR markers, a high density genetic map and QTL identified for agronomic and yield traits lay the ground work for functional gene mapping, map-based cloning and marker-assisted selection in foxtail millet.
authors.affiliation: Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, People's Republic of China.
authors.forename: Xiaomei
authors.initials: X
authors.lastname: Fang
authors.affiliation: Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, Gansu, People's Republic of China.
authors.forename: Kongjun
authors.initials: K
authors.lastname: Dong
authors.affiliation: Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, People's Republic of China.
authors.forename: Xiaoqin
authors.initials: X
authors.lastname: Wang
authors.affiliation: Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, Gansu, People's Republic of China.
authors.forename: Tianpeng
authors.initials: T
authors.lastname: Liu
authors.affiliation: Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, Gansu, People's Republic of China.
authors.forename: Jihong
authors.initials: J
authors.lastname: He
authors.affiliation: Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, Gansu, People's Republic of China.
authors.forename: Ruiyu
authors.initials: R
authors.lastname: Ren
authors.affiliation: Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, Gansu, People's Republic of China.
authors.forename: Lei
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, People's Republic of China.
authors.forename: Rui
authors.initials: R
authors.lastname: Liu
authors.affiliation: Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, People's Republic of China.
authors.forename: Xueying
authors.initials: X
authors.lastname: Liu
authors.affiliation: Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, People's Republic of China.
authors.forename: Man
authors.initials: M
authors.lastname: Li
authors.affiliation: Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, People's Republic of China.
authors.forename: Mengzhu
authors.initials: M
authors.lastname: Huang
authors.affiliation: Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, People's Republic of China. zhangzs@swu.edu.cn.
authors.forename: Zhengsheng
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, Gansu, People's Republic of China. yty681001@yahoo.com.cn.
authors.forename: Tianyu
authors.initials: T
authors.lastname: Yang
mesh_terms: D002681:China; D002874:Chromosome Mapping / Q000379:methods*; D005819:Genetic Markers; D018745:Genome, Plant; D018895:Microsatellite Repeats; D010641:Phenotype; D010802:Phylogeny; D040641:Quantitative Trait Loci; D017422:Sequence Analysis, DNA; D032983:Setaria Plant / Q000235:genetics*
chemical_list: D005819:Genetic Markers
keywords: Agronomic traits; Foxtail millet (Setaria italica L.); Genetic map; QTL; Yield traits