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. 2019 Feb 19;20(4):900.
doi: 10.3390/ijms20040900.

Identification of Quantitative Trait Loci Associated with Nutrient Use Efficiency Traits, Using SNP Markers in an Early Backcross Population of Rice (Oryza sativa L.)

Zilhas Ahmed Jewel  1 , Jauhar Ali  2 , Anumalla Mahender  3 , Jose Hernandez  4 , Yunlong Pang  5   6 , Zhikang Li  7
Affiliations

Identification of Quantitative Trait Loci Associated with Nutrient Use Efficiency Traits, Using SNP Markers in an Early Backcross Population of Rice (Oryza sativa L.)

Zilhas Ahmed Jewel et al. Int J Mol Sci. .

Abstract

The development of rice cultivars with nutrient use efficiency (NuUE) is highly crucial for sustaining global rice production in Asia and Africa. However, this requires a better understanding of the genetics of NuUE-related traits and their relationship to grain yield. In this study, simultaneous efforts were made to develop nutrient use efficient rice cultivars and to map quantitative trait loci (QTLs) governing NuUE-related traits in rice. A total of 230 BC₁F₅ introgression lines (ILs) were developed from a single early backcross population involving Weed Tolerant Rice 1, as the recipient parent, and Hao-an-nong, as the donor parent. The ILs were cultivated in field conditions with a different combination of fertilizer schedule under six nutrient conditions: minus nitrogen (⁻N), minus phosphorus (⁻P), (⁻NP), minus nitrogen phosphorus and potassium (⁻NPK), 75% of recommended nitrogen (75N), and NPK. Analysis of variance revealed that significant differences (p < 0.01) were noted among ILs and treatments for all traits. A high-density linkage map was constructed by using 704 high-quality single nucleotide polymorphism (SNP) markers. A total of 49 main-effect QTLs were identified on all chromosomes, except on chromosome 7, 11 and 12, which are showing 20.25% to 34.68% of phenotypic variation. With further analysis of these QTLs, we refined them to four top hotspot QTLs (QTL harbor-I to IV) located on chromosomes 3, 5, 9, and 11. However, we identified four novel putative QTLs for agronomic efficiency (AE) and 22 QTLs for partial factor productivity (PFP) under ⁻P and 75N conditions. These interval regions of QTLs, several transporters and genes are located that were involved in nutrient uptake from soil to plant organs and tolerance to biotic and abiotic stresses. Further, the validation of these potential QTLs, genes may provide remarkable value for marker-aided selection and pyramiding of multiple QTLs, which would provide supporting evidence for the enhancement of grain yield and cloning of NuUE tolerance-responsive genes in rice.

Keywords: agronomic efficiency; nutrient use efficiency; partial factor productivity; quantitative trait loci (QTLs), molecular markers.

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Conflict of interest statement

The authors declare that the research review was conducted in the absence of any commercial or economic associations that could be construed as potential conflicts of interest.

Figures

Figure 1
Figure 1
Grain yield performances of introgression lines, parents and checks in all six nutrient conditions.
Figure 2
Figure 2
Distribution of trait-wise (a); and NPK combinations (b), associated with a total number of quantitative trait loci (QTLs) and hotspot QTLs in different nutrient conditions in rice.
Figure 3
Figure 3
Linkage map of 261 QTLs distributed on 12 chromosomes, with respective polymorphic markers and colors depicting the QTLs governing crucial different nutrient traits.
Figure 4
Figure 4
Application of fertilizers in six NuUE conditions with five splits.
See this image and copyright information in PMC

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References

    1. Godfray H.C., Beddington J.R., Crute I.R., Haddad L., Lawrence D., Muir J.F., Pretty J., Robinson S., Thomas S.M., Toulmin C. Food security: The challenge of feeding 9 billion people. Science. 2010;327:812–818. doi: 10.1126/science.1185383. - DOI - PubMed
    1. FAO The State of Food Insecurity in the World 2009. [(accessed on 30 October 2009)]; Available online: http://www.fao.org/tempref/docrep/fao/012/i0876e/i0876e_flyer.pdf.
    1. Tilman D., Balzer C., Hill J., Befort B.L. Global food demand and the sustainable intensification of agriculture. Proc. Natl. Acad. Sci. USA. 2011;108:20260–20264. doi: 10.1073/pnas.1116437108. - DOI - PMC - PubMed
    1. Edgerton M.D. Increasing crop productivity to meet global needs for feed, food, and fuel. Plant Physiol. 2009;149:7–13. doi: 10.1104/pp.108.130195. - DOI - PMC - PubMed
    1. Naresh R.K., Gupta R.K., Ashok K., Singh B., Prakash S., Kumar S., Rathi R.C. Direct-seeding and reduced-tillage options in the rice-wheat system of the Western Indo-Gangetic Plains. Int. J. Agric. Sci. 2011;7:197–208.