Mapping QTLs and association of differentially expressed gene transcripts for multiple agronomic traits under different nitrogen levels in sorghum

• Published in: BMC plant biology Vol. 16; no. 1; p. 16
• Main Authors: Gelli, Malleswari, Mitchell, Sharon E., Liu, Kan, Clemente, Thomas E., Weeks, Donald P., Zhang, Chi, Holding, David R., Dweikat, Ismail M.
• Format: Journal Article
• Language: English
• Published: London BioMed Central 13.01.2016; BioMed Central Ltd
• Subjects: Agriculture; agronomic traits; Biomedical and Life Sciences; Chromosome Mapping; chromosomes; Chromosomes, Plant; Edible Grain - genetics; flowering; gene expression; gene expression regulation; Gene Expression Regulation, Plant; genes; Genetic Linkage; genetic variation; Genetics and crop biotechnology; glycolysis; hormone metabolism; inbred lines; Life Sciences; marker-assisted selection; messenger RNA; nitrogen; Nitrogen - metabolism; Nitrogen fertilizers; parents; phenotypic variation; physiological transport; plant hormones; Plant Sciences; Polymorphism, Single Nucleotide; Quantitative Trait Loci; Research Article; RNA sequencing; seed storage proteins; seedlings; sequence analysis; single nucleotide polymorphism; Single nucleotide polymorphisms; Sorghum (Poaceae); Sorghum - genetics; Sorghum - growth & development; Sorghum - metabolism; tissues; Tree Biology; United States; Illumina RNA-seq; Genotyping-by-sequencing; Sorghum; Differentially expressed gene transcripts; Nitrogen fertilizer; Agronomic traits; QTL mapping
• ISSN: 1471-2229; 1471-2229
• DOI: 10.1186/s12870-015-0696-x

Background Sorghum is an important C 4 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.