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

BMC Plant Biology

Research Article

Chi Zhang¹  Kan Liu¹  Ismail M. Dweikat²  Malleswari Gelli²  David R. Holding³  Thomas E. Clemente³  Donald P. Weeks⁴  Sharon E. Mitchell⁵ 

[1] Center for Plant Science Innovation, University of Nebraska, 68588, Lincoln, NE, USA;School of Biological Sciences, University of Nebraska, 68588, Lincoln, NE, USA;Institute of Genomic Diversity, Cornell University, 14853, Ithaca, NY, USA;Department of Agronomy and Horticulture, University of Nebraska, 68583, Lincoln, NE, USA;Department of Agronomy and Horticulture, University of Nebraska, 68583, Lincoln, NE, USA;Center for Plant Science Innovation, University of Nebraska, 68588, Lincoln, NE, USA;Department of Biochemistry, University of Nebraska, 68588, Lincoln, NE, USA;Center for Plant Science Innovation, University of Nebraska, 68588, Lincoln, NE, USA;School of Biological Sciences, University of Nebraska, 68588, Lincoln, NE, USA;Institute of Genomic Diversity, Cornell University, 14853, Ithaca, NY, USA;

关键词: Sorghum;    Agronomic traits;    Differentially expressed gene transcripts;    Genotyping-by-sequencing;    Nitrogen fertilizer;    QTL mapping;    Illumina RNA-seq;   

DOI  :  10.1186/s12870-015-0696-x

 received in 2015-07-13, accepted in 2015-12-21,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundSorghum 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.ResultsA 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.ConclusionsCo-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.

【 授权许可】

CC BY   
© Gelli et al. 2016