Abstract
Key message
This study identified 333 genomic regions associated to 28 traits related to nitrogen use efficiency in European winter wheat using genome-wide association in a 214-varieties panel experimented in eight environments.
Abstract
Improving nitrogen use efficiency is a key factor to sustainably ensure global production increase. However, while high-throughput screening methods remain at a developmental stage, genetic progress may be mainly driven by marker-assisted selection. The objective of this study was to identify chromosomal regions associated with nitrogen use efficiency-related traits in bread wheat (Triticum aestivum L.) using a genome-wide association approach. Two hundred and fourteen European elite varieties were characterised for 28 traits related to nitrogen use efficiency in eight environments in which two different nitrogen fertilisation levels were tested. The genome-wide association study was carried out using 23,603 SNP with a mixed model for taking into account parentage relationships among varieties. We identified 1,010 significantly associated SNP which defined 333 chromosomal regions associated with at least one trait and found colocalisations for 39 % of these chromosomal regions. A method based on linkage disequilibrium to define the associated region was suggested and discussed with reference to false positive rate. Through a network approach, colocalisations were analysed and highlighted the impact of genomic regions controlling nitrogen status at flowering, precocity, and nitrogen utilisation on global agronomic performance. We were able to explain 40 ± 10 % of the total genetic variation. Numerous colocalisations with previously published genomic regions were observed with such candidate genes as Ppd-D1, Rht-D1, NADH-Gogat, and GSe. We highlighted selection pressure on yield and nitrogen utilisation discussing allele frequencies in associated regions.
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Abbreviations
- ADM_S:
-
Straw dry matter at maturity
- DArT:
-
Diversity array technology
- LD:
-
Linkage disequilibrium
- FLO:
-
Flowering date
- G:
-
Genotype
- G × E:
-
Genotype × environment
- GNY:
-
Grain nitrogen yield
- GPC:
-
Grain protein content
- GPD:
-
Grain protein deviation
- GY:
-
Grain dry matter yield
- HI:
-
Harvest index
- KS:
-
Kernel per spike
- N:
-
Nitrogen
- %N_S:
-
Straw nitrogen content at maturity
- NHI:
-
Nitrogen harvest index
- NSA:
-
Straw nitrogen per area
- NTA:
-
Total nitrogen in plant at maturity
- NUE:
-
Nitrogen use efficiency
- NUE_Prot:
-
Nitrogen use to protein efficiency
- NupE:
-
Nitrogen uptake
- NutE:
-
Nitrogen utilisation efficiency
- NutE_Prot:
-
Nitrogen utilisation to protein efficiency
- P :
-
P value
- PH:
-
Plant height
- QTL:
-
Quantitative trait locus
- QTN:
-
Quantitative trait nucleotide
- SA:
-
Spike per area
- SNP:
-
Small nucleotide polymorphism
- SSR:
-
Single sequence repeat
- TKW:
-
Thousand kernel weight
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Acknowledgments
These analyses were a part of a PhD thesis (129/2012) supported by the ANRT (Association Nationale de la Recherche et de la Technologie). Data were obtained thanks to the support of the ANR ProtNBle project (06 GPLA016). The authors are also grateful to experimental units staff at Estrées-Mons experimental unit (INRA) and at Villiers-le-Bâclea and Vraux (Arvalis), and to Quang Hien Le for English style proofing. Sincere thanks to Ian Mackay for his involvement in the reviewing process.
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The authors declare that they have no conflict of interest.
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The authors declare that the experiments comply with the current laws of the country in which they were performed.
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Communicated by Ian Mackay.
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Cormier, F., Le Gouis, J., Dubreuil, P. et al. A genome-wide identification of chromosomal regions determining nitrogen use efficiency components in wheat (Triticum aestivum L.). Theor Appl Genet 127, 2679–2693 (2014). https://doi.org/10.1007/s00122-014-2407-7
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DOI: https://doi.org/10.1007/s00122-014-2407-7