Validation of QTL mapping and transcriptome profiling for identification of candidate genes associated with nitrogen stress tolerance in sorghum

BMC Plant Biology

Research Article

Chi Zhang¹  Kan Liu¹  Malleswari Gelli²  Ismail M. Dweikat²  David R. Holding³  Thomas E. Clemente³  Anji Reddy Konda⁴ 

[1] Center for Plant Science Innovation, University of Nebraska, 68588, Lincoln, NE, USA;School of Biological Sciences, University of Nebraska, 68588, Lincoln, NE, 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;

关键词: Sorghum;    Nitrogen use efficiency (NUE);    N-stress tolerance;    Genotyping-by-sequencing (GBS);    QTL mapping;    QTL validation;    Agronomic traits;    Illumina RNA-seq;    Differentially expressed gene transcripts;    Candidate genes;    Marker assisted selection (MAS);   

DOI  :  10.1186/s12870-017-1064-9

 received in 2016-12-13, accepted in 2017-06-25,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundQuantitative trait loci (QTLs) detected in one mapping population may not be detected in other mapping populations at all the time. Therefore, before being used for marker assisted breeding, QTLs need to be validated in different environments and/or genetic backgrounds to rule out statistical anomalies. In this regard, we mapped the QTLs controlling various agronomic traits in a recombinant inbred line (RIL) population in response to Nitrogen (N) stress and validated these with the reported QTLs in our earlier study to find the stable and consistent QTLs across populations. Also, with Illumina RNA-sequencing we checked the differential expression of gene (DEG) transcripts between parents and pools of RILs with high and low nitrogen use efficiency (NUE) and overlaid these DEGs on to the common validated QTLs to find candidate genes associated with N-stress tolerance in sorghum.ResultsAn F7 RIL population derived from a cross between CK60 (N-stress sensitive) and San Chi San (N-stress tolerant) inbred sorghum lines was used to map QTLs for 11 agronomic traits tested under different N-levels. Composite interval mapping analysis detected a total of 32 QTLs for 11 agronomic traits. Validation of these QTLs revealed that of the detected, nine QTLs from this population were consistent with the reported QTLs in earlier study using CK60/China17 RIL population. The validated QTLs were located on chromosomes 1, 6, 7, 8, and 9. In addition, root transcriptomic profiling detected 55 and 20 differentially expressed gene (DEG) transcripts between parents and pools of RILs with high and low NUE respectively. Also, overlay of these DEG transcripts on to the validated QTLs found candidate genes transcripts for NUE and also showed the expected differential expression. For example, DEG transcripts encoding Lysine histidine transporter 1 (LHT1) had abundant expression in San Chi San and the tolerant RIL pool, whereas DEG transcripts encoding seed storage albumin, transcription factor IIIC (TFIIIC) and dwarfing gene (DW2) encoding multidrug resistance-associated protein-9 homolog showed abundant expression in CK60 parent, similar to earlier study.ConclusionsThe validated QTLs among different mapping populations would be the most reliable and stable QTLs across germplasm. The DEG transcripts found in the validated QTL regions will serve as future candidate genes for enhancing NUE in sorghum using molecular approaches.

【 授权许可】

CC BY   
© The Author(s). 2017