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Journal of Integrative Agriculture  2022, Vol. 21 Issue (4): 917-932    DOI: 10.1016/S2095-3119(21)63700-0
Special Issue: 麦类遗传育种合辑Triticeae Crops Genetics · Breeding · Germplasm Resources
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Identification of QTL and underlying genes for root system architecture associated with nitrate nutrition in hexaploid wheat
Marcus GRIFFITHS1, Jonathan A. ATKINSON2, 3, Laura-Jayne GARDINER4, Ranjan SWARUP1, Michael P. POUND5, Michael H. WILSON2, 3, Malcolm J. BENNETT1, 2, 3, Darren M. WELLS1, 2, 3
1 School of Biosciences, University of Nottingham, Sutton Bonington Campus, LE12 5RD, UK
2 Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington Campus, LE12 5RD, UK
3 Integrative Phenomics Group, School of Biosciences, University of Nottingham, Sutton Bonington Campus, LE12 5RD, UK
4 IBM Research, The Hartree Centre, Warrington, WA4 4AD, UK
5 School of Computer Science, University of Nottingham, Nottingham, NG8 1BB, UK
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Abstract  The root system architecture (RSA) of a crop has a profound effect on the uptake of nutrients and consequently the potential yield.  However, little is known about the genetic basis of RSA and resource adaptive responses in wheat (Triticum aestivum L.).  Here, a high-throughput germination paper-based plant phenotyping system was used to identify seedling traits in a wheat doubled haploid mapping population, Savannah×Rialto.  Significant genotypic and nitrate-N treatment variation was found across the population for seedling traits with distinct trait grouping for root size-related traits and root distribution-related traits.  Quantitative trait locus (QTL) analysis identified a total of 59 seedling trait QTLs.  Across two nitrate treatments, 27 root QTLs were specific to the nitrate treatment.  Transcriptomic analyses for one of the QTLs on chromosome 2D, which was found under low nitrate conditions, revealed gene enrichment in N-related biological processes and 28 differentially expressed genes with possible involvement in a root angle response.  Together, these findings provide genetic insight into root system architecture and plant adaptive responses to nitrate, as well as targets that could help improve N capture in wheat.
Keywords:  doubled-haploid population       nitrate        RNA-seq        quantitative trait loci        root system architecture        riticum aestivum L. (wheat)  
Received: 02 December 2020   Accepted: 02 April 2021
Fund: This work was supported by the Biotechnology and Biological Sciences Research Council, UK (BB/M001806/1, BB/L026848/1, BB/P026834/1, and BB/M019837/1)(MJB, DMW, and MPP); the Leverhulme Trust, UK (RPG-2016–409) (MJB and DMW); the European Research Council FUTUREROOTS Advanced Investigator Grant, UK (294729) to MG, JAA, DMW, and MJB; and the University of Nottingham Future Food Beacon of Excellence, UK.
About author:  Marcus GRIFFITHS, E-mail:; Correspondence Darren M. Wells, Tel: +44-115-9516373, E-mail:

Cite this article: 

Marcus GRIFFITHS, Jonathan A. ATKINSON, Laura-Jayne GARDINER, Ranjan SWARUP, Michael P. POUND, Michael H. WILSON, Malcolm J. BENNETT, Darren M. WELLS. 2022. Identification of QTL and underlying genes for root system architecture associated with nitrate nutrition in hexaploid wheat. Journal of Integrative Agriculture, 21(4): 917-932.

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