title: Identification of QTLs for eight agronomically important traits using an ultra-high-density map based on SNPs generated from high-throughput sequencing in sorghum under contrasting photoperiods.
abstract: The productivity of sorghum is mainly determined by agronomically important traits. The genetic bases of these traits have historically been dissected and analysed through quantitative trait locus (QTL) mapping based on linkage maps with low-throughput molecular markers, which is one of the factors that hinder precise and complete information about the numbers and locations of the genes or QTLs controlling the traits. In this study, an ultra-high-density linkage map based on high-quality single nucleotide polymorphisms (SNPs) generated from low-coverage sequences (~0.07 genome sequence) in a sorghum recombinant inbred line (RIL) population was constructed through new sequencing technology. This map consisted of 3418 bin markers and spanned 1591.4 cM of genome size with an average distance of 0.5 cM between adjacent bins. QTL analysis was performed and a total of 57 major QTLs were detected for eight agronomically important traits under two contrasting photoperiods. The phenotypic variation explained by individual QTLs varied from 3.40% to 33.82%. The high accuracy and quality of this map was evidenced by the finding that genes underlying two cloned QTLs, Dw3 for plant height (chromosome 7) and Ma1 for flowering time (chromosome 6), were localized to the correct genomic regions. The close associations between two genomic regions on chromosomes 6 and 7 with multiple traits suggested the existence of pleiotropy or tight linkage. Several major QTLs for heading date, plant height, numbers of nodes, stem diameter, panicle neck length, and flag leaf width were detected consistently under both photoperiods, providing useful information for understanding the genetic mechanisms of the agronomically important traits responsible for the change of photoperiod.
authors.affiliation: State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences,  Hangzhou 310021  China.
authors.forename: Guihua
authors.initials: G
authors.lastname: Zou
authors.forename: Guowei
authors.initials: G
authors.lastname: Zhai
authors.forename: Qi
authors.initials: Q
authors.lastname: Feng
authors.forename: Song
authors.initials: S
authors.lastname: Yan
authors.forename: Ahong
authors.initials: A
authors.lastname: Wang
authors.forename: Qiang
authors.initials: Q
authors.lastname: Zhao
authors.forename: Jianfeng
authors.initials: J
authors.lastname: Shao
authors.forename: Zhipeng
authors.initials: Z
authors.lastname: Zhang
authors.forename: Jianqiu
authors.initials: J
authors.lastname: Zou
authors.forename: Bin
authors.initials: B
authors.lastname: Han
authors.forename: Yuezhi
authors.initials: Y
authors.lastname: Tao
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D032461:Chromosomes, Plant / Q000235:genetics; D018556:Crops, Agricultural; D008040:Genetic Linkage; D005819:Genetic Markers; D018745:Genome, Plant / Q000235:genetics*; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D007178:Inbreeding; D010641:Phenotype; D017440:Photoperiod; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D040641:Quantitative Trait Loci / Q000235:genetics*; D017422:Sequence Analysis, DNA; D045868:Sorghum / Q000235:genetics*
chemical_list: D005819:Genetic Markers