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      Prioritizing quantitative trait loci for root system architecture in tetraploid wheat

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          The genetic variation of root system architecture in the A and B wheat genomes is described, providing the necessary knowledge ultimately to fine-tune the expression of the root system architecture.

          Abstract

          Optimization of root system architecture (RSA) traits is an important objective for modern wheat breeding. Linkage and association mapping for RSA in two recombinant inbred line populations and one association mapping panel of 183 elite durum wheat ( Triticum turgidum L. var. durum Desf.) accessions evaluated as seedlings grown on filter paper/polycarbonate screening plates revealed 20 clusters of quantitative trait loci (QTLs) for root length and number, as well as 30 QTLs for root growth angle (RGA). Divergent RGA phenotypes observed by seminal root screening were validated by root phenotyping of field-grown adult plants. QTLs were mapped on a high-density tetraploid consensus map based on transcript-associated Illumina 90K single nucleotide polymorphisms (SNPs) developed for bread and durum wheat, thus allowing for an accurate cross-referencing of RSA QTLs between durum and bread wheat. Among the main QTL clusters for root length and number highlighted in this study, 15 overlapped with QTLs for multiple RSA traits reported in bread wheat, while out of 30 QTLs for RGA, only six showed co-location with previously reported QTLs in wheat. Based on their relative additive effects/significance, allelic distribution in the association mapping panel, and co-location with QTLs for grain weight and grain yield, the RSA QTLs have been prioritized in terms of breeding value. Three major QTL clusters for root length and number ( RSA_QTL_cluster_5#, RSA_QTL_cluster_6#, and RSA_QTL_cluster_12#) and nine RGA QTL clusters ( QRGA.ubo-2A.1, QRGA.ubo-2A.3, QRGA.ubo-2B.2/2B.3, QRGA.ubo-4B.4, QRGA.ubo-6A.1, QRGA.ubo-6A.2, QRGA.ubo-7A.1, QRGA.ubo-7A.2, and QRGA.ubo-7B) appear particularly valuable for further characterization towards a possible implementation of breeding applications in marker-assisted selection and/or cloning of the causal genes underlying the QTLs.

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          Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought conditions.

          Yusaku Uga, Kazuhiko Sugimoto, Satoshi Ogawa … (2013)
          The genetic improvement of drought resistance is essential for stable and adequate crop production in drought-prone areas. Here we demonstrate that alteration of root system architecture improves drought avoidance through the cloning and characterization of DEEPER ROOTING 1 (DRO1), a rice quantitative trait locus controlling root growth angle. DRO1 is negatively regulated by auxin and is involved in cell elongation in the root tip that causes asymmetric root growth and downward bending of the root in response to gravity. Higher expression of DRO1 increases the root growth angle, whereby roots grow in a more downward direction. Introducing DRO1 into a shallow-rooting rice cultivar by backcrossing enabled the resulting line to avoid drought by increasing deep rooting, which maintained high yield performance under drought conditions relative to the recipient cultivar. Our experiments suggest that control of root system architecture will contribute to drought avoidance in crops.
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            Steep, cheap and deep: an ideotype to optimize water and N acquisition by maize root systems.

            Jonathan Lynch (2013)
            A hypothetical ideotype is presented to optimize water and N acquisition by maize root systems. The overall premise is that soil resource acquisition is optimized by the coincidence of root foraging and resource availability in time and space. Since water and nitrate enter deeper soil strata over time and are initially depleted in surface soil strata, root systems with rapid exploitation of deep soil would optimize water and N capture in most maize production environments. • THE IDEOTYPE: Specific phenes that may contribute to rooting depth in maize include (a) a large diameter primary root with few but long laterals and tolerance of cold soil temperatures, (b) many seminal roots with shallow growth angles, small diameter, many laterals, and long root hairs, or as an alternative, an intermediate number of seminal roots with steep growth angles, large diameter, and few laterals coupled with abundant lateral branching of the initial crown roots, (c) an intermediate number of crown roots with steep growth angles, and few but long laterals, (d) one whorl of brace roots of high occupancy, having a growth angle that is slightly shallower than the growth angle for crown roots, with few but long laterals, (e) low cortical respiratory burden created by abundant cortical aerenchyma, large cortical cell size, an optimal number of cells per cortical file, and accelerated cortical senescence, (f) unresponsiveness of lateral branching to localized resource availability, and (g) low K(m) and high Vmax for nitrate uptake. Some elements of this ideotype have experimental support, others are hypothetical. Despite differences in N distribution between low-input and commercial maize production, this ideotype is applicable to low-input systems because of the importance of deep rooting for water acquisition. Many features of this ideotype are relevant to other cereal root systems and more generally to root systems of dicotyledonous crops.
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              Root system architecture: opportunities and constraints for genetic improvement of crops.

              Sophie De Dorlodot, Brian Peter Forster, Loïc Pagès … (2007)
              Abiotic stresses increasingly curtail crop yield as a result of global climate change and scarcity of water and nutrients. One way to minimize the negative impact of these factors on yield is to manipulate root system architecture (RSA) towards a distribution of roots in the soil that optimizes water and nutrient uptake. It is now established that most of the genetic variation for RSA is driven by a suite of quantitative trait loci. As we discuss here, marker-assisted selection and quantitative trait loci cloning for RSA are underway, exploiting genomic resources, candidate genes and the knowledge gained from Arabidopsis, rice and other crops. Nonetheless, efficient and accurate phenotyping, modelling and collaboration with breeders remain important challenges, particularly when defining ideal RSA for different crops and target environments.
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                Author and article information

                Journal
                Journal ID (nlm-ta): J Exp Bot
                Journal ID (iso-abbrev): J. Exp. Bot
                Journal ID (hwp): jexbot
                Journal ID (publisher-id): exbotj
                Title: Journal of Experimental Botany
                Publisher: Oxford University Press (UK )
                ISSN (Print): 0022-0957
                ISSN (Electronic): 1460-2431
                Publication date (Print): February 2016
                Publication date (Electronic): 13 February 2016
                Publication date PMC-release: 13 February 2016
                Volume: 67
                Issue: 4 , Special Issue: Plant Roots: New Challenges in a Changing World
                Pages: 1161-1178
                Affiliations
                1Department of Agricultural Sciences (DipSA), University of Bologna , 40127 Bologna, Italy
                2Department of Crop Sciences, Faculty of Agriculture, Alexandria University , 23714 Alexandria, Egypt
                3Department of Agriculture, Hajiabad Branch, Islamic Azad University , 21100 Hajiabad, Iran
                Author notes

                Editor: Adam Price, University of Aberdeen

                Article
                DOI: 10.1093/jxb/erw039
                PMC ID: 4753857
                PubMed ID: 26880749
                SO-VID: eb598821-5469-4f09-a6e3-0ed0ff53f357
                Copyright © © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Page count
                Pages: 18
                Categories
                Subject: Research Paper

                ScienceOpen disciplines: Plant science & Botany
                Keywords: association mapping,drought stress,germplasm collection,gwas,grain yield,meta-qtls,root growth angle,rooting depth,root system architecture,seminal root.
                Data availability:
                ScienceOpen disciplines: Plant science & Botany
                Keywords: association mapping, drought stress, germplasm collection, gwas, grain yield, meta-qtls, root growth angle, rooting depth, root system architecture, seminal root.

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