title: Mapping QTLs and association of differentially expressed gene transcripts for multiple agronomic traits under different nitrogen levels in sorghum.
abstract: BACKGROUND
  Sorghum is an important C4 crop which relies on applied Nitrogen fertilizers (N) for optimal yields, of which substantial amounts are lost into the atmosphere. Understanding the genetic variation of sorghum in response to limited nitrogen supply is important for elucidating the underlying genetic mechanisms of nitrogen utilization.
  
  
  RESULTS
  A bi-parental mapping population consisting of 131 recombinant inbred lines (RILs) was used to map quantitative trait loci (QTLs) influencing different agronomic traits evaluated under normal N (100 kg.ha(-1) fertilizer) and low N (0 kg.ha(-1) fertilizer) conditions. A linkage map spanning 1614 cM was developed using 642 polymorphic single nucleotide polymorphisms (SNPs) detected in the population using Genotyping-By-Sequencing (GBS) technology. Composite interval mapping detected a total of 38 QTLs for 11 agronomic traits tested under different nitrogen levels. The phenotypic variation explained by individual QTL ranged from 6.2 to 50.8%. Illumina RNA sequencing data generated on seedling root tissues revealed 726 differentially expressed gene (DEG) transcripts between parents, of which 108 were mapped close to the QTL regions.
  
  
  CONCLUSIONS
  Co-localized regions affecting multiple traits were detected on chromosomes 1, 5, 6, 7 and 9. These potentially pleiotropic regions were coincident with the genomic regions of cloned QTLs, including genes associated with flowering time, Ma3 on chromosome 1 and Ma1 on chromosome 6, gene associated with plant height, Dw2 on chromosome 6. In these regions, RNA sequencing data showed differential expression of transcripts related to nitrogen metabolism (Ferredoxin-nitrate reductase), glycolysis (Phosphofructo-2-kinase), seed storage proteins, plant hormone metabolism and membrane transport. The differentially expressed transcripts underlying the pleiotropic QTL regions could be potential targets for improving sorghum performance under limited N fertilizer through marker assisted selection.
authors.affiliation: Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA. malleswari.gelli@gmail.com.
authors.forename: Malleswari
authors.initials: M
authors.lastname: Gelli
authors.affiliation: School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588, USA. sem30@cornell.edu.|Institute of Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA. sem30@cornell.edu.
authors.forename: Sharon E
authors.initials: SE
authors.lastname: Mitchell
authors.affiliation: Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA. kliu7@unl.edu.|School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588, USA. kliu7@unl.edu.|Institute of Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA. kliu7@unl.edu.
authors.forename: Kan
authors.initials: K
authors.lastname: Liu
authors.affiliation: Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA. tclemente1@unl.edu.|Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA. tclemente1@unl.edu.
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Clemente
authors.affiliation: Department of Biochemistry, University of Nebraska, Lincoln, NE, 68588, USA. donald.weeks@unl.edu.|Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA. donald.weeks@unl.edu.
authors.forename: Donald P
authors.initials: DP
authors.lastname: Weeks
authors.affiliation: Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA. czhang5@unl.edu.|School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588, USA. czhang5@unl.edu.|Institute of Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA. czhang5@unl.edu.
authors.forename: Chi
authors.initials: C
authors.lastname: Zhang
authors.affiliation: Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA. dholding2@unl.edu.|Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA. dholding2@unl.edu.
authors.forename: David R
authors.initials: DR
authors.lastname: Holding
authors.affiliation: Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA. idweikat2@unl.edu.
authors.forename: Ismail M
authors.initials: IM
authors.lastname: Dweikat
mesh_terms: D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D002523:Edible Grain / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D008040:Genetic Linkage; D009584:Nitrogen / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D045868:Sorghum / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism
chemical_list: D009584:Nitrogen