Quantitative trait locus mapping of deep rooting by linkage and association analysis in rice

Lou, Qiaojun; Chen, Liang; Mei, Hanwei; Wei, Haibin; Fěng, Fang; Wang, Pei; Xia, Hui; Li, Tiemei; Luo, Lijun

doi:10.1093/jxb/erv246

Cited by 103 publications

(87 citation statements)

References 58 publications

(71 reference statements)

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“…This population has previously been used in GWAS for mesocotyl elongation and ratio of deep rooting (Lou et al, 2015; Wu et al, 2015). All accessions were tested under two water regimes: well watered and drought stress, in a drought resistance screening facility (Luo, 2010) at the Baihe Experimental Station of the Shanghai Agrobiological Gene Center (31°15′N, 121°10′E, 4 m altitude) in 2011 and 2012.…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Association Study for Plant Height and Grain Yield in Rice under Contrasting Moisture Regimes

Fěng

Wei

et al. 2016

Front. Plant Sci.

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Drought is one of the vitally critical environmental stresses affecting both growth and yield potential in rice. Drought resistance is a complicated quantitative trait that is regulated by numerous small effect loci and hundreds of genes controlling various morphological and physiological responses to drought. For this study, 270 rice landraces and cultivars were analyzed for their drought resistance. This was done via determination of changes in plant height and grain yield under contrasting water regimes, followed by detailed identification of the underlying genetic architecture via genome-wide association study (GWAS). We controlled population structure by setting top two eigenvectors and combining kinship matrix for GWAS in this study. Eighteen, five, and six associated loci were identified for plant height, grain yield per plant, and drought resistant coefficient, respectively. Nine known functional genes were identified, including five for plant height (OsGA2ox3, OsGH3-2, sd-1, OsGNA1, and OsSAP11/OsDOG), two for grain yield per plant (OsCYP51G3 and OsRRMh) and two for drought resistant coefficient (OsPYL2 and OsGA2ox9), implying very reliable results. A previous study reported OsGNA1 to regulate root development, but this study reports additional controlling of both plant height and root length. Moreover, OsRLK5 is a new drought resistant candidate gene discovered in this study. OsRLK5 mutants showed faster water loss rates in detached leaves. This gene plays an important role in the positive regulation of yield-related traits under drought conditions. We furthermore discovered several new loci contributing to the three investigated traits (plant height, grain yield, and drought resistance). These associated loci and candidate genes significantly improve our knowledge of the genetic control of these traits in rice. In addition, many drought resistant cultivars screened in this study can be used as parental genotypes to improve drought resistance of rice by molecular breeding.

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Section: Methodsmentioning

confidence: 99%

Genome-Wide Association Study for Plant Height and Grain Yield in Rice under Contrasting Moisture Regimes

Fěng

Wei

et al. 2016

Front. Plant Sci.

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“…Recently, another QTL was identified (DRO3) that affects root growth angle in a DRO1-dependent manner (Uga et al, 2015). Additional QTL and genomewide association studies in rice revealed further QTLs for deeper root growth under water-deficit conditions (Courtois et al, 2009;Lou et al, 2015;Wade et al, 2015).…”

Section: Growth Direction Is Determined Locally By Water Availabilitymentioning

confidence: 99%

Growing Out of Stress: The Role of Cell- and Organ-Scale Growth Control in Plant Water-Stress Responses

et al. 2016

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Water is the most limiting resource on land for plant growth, and its uptake by plants is affected by many abiotic stresses, such as salinity, cold, heat, and drought. While much research has focused on exploring the molecular mechanisms underlying the cellular signaling events governing water-stress responses, it is also important to consider the role organismal structure plays as a context for such responses. The regulation of growth in plants occurs at two spatial scales: the cell and the organ. In this review, we focus on how the regulation of growth at these different spatial scales enables plants to acclimate to water-deficit stress. The cell wall is discussed with respect to how the physical properties of this structure affect water loss and how regulatory mechanisms that affect wall extensibility maintain growth under water deficit. At a higher spatial scale, the architecture of the root system represents a highly dynamic physical network that facilitates access of the plant to a heterogeneous distribution of water in soil. We discuss the role differential growth plays in shaping the structure of this system and the physiological implications of such changes.

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“…A plant with improved drought-avoidance might utilize more water via a well-developed root system, while a plant with improved drought-tolerance maintains its basic life activities even when dehydrated (Blum, 2005; Luo, 2010). Drought-avoidance via enlargement of the root system plays a primary role in plant responses to drought and the molecular basis for this has been studied and applied in the breeding of drought-resistant cultivars (Pietta, 2000; Uga et al, 2013; Lou et al, 2015). Drought-tolerance plays an important role during the later stage of drought and has great potential to enhance drought-resistance.…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic and Metabolomic Studies Disclose Key Metabolism Pathways Contributing to Well-maintained Photosynthesis under the Drought and the Consequent Drought-Tolerance in Rice

et al. 2016

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In contrast to wild species, drought-tolerance in crops requires a fully functional metabolism during drought (particularly photosynthetic processes). However, the link between drought-tolerance, photosynthetic regulation during drought, and the associated transcript and metabolic foundation, remains largely unknown. For this study, we used two rice cultivars with contrasting drought-tolerance (the drought-intolerant cultivar IRAT109 and the drought-tolerant cultivar IAC1246) to explore transcript and metabolic responses to long-term drought. The drought-tolerant cultivar represented higher osmotic adjustment and antioxidant capacity, as well as higher relative photosynthesis rate under a progressive drought stress occurred in a modified field with shallow soil-layers. A total of 4059 and 2677 differentially expressed genes (DEGs) were identified in IRAT109 and IAC1246 between the drought and well-watered conditions, respectively. A total of 69 and 47 differential metabolites (DMs) were identified between the two treatments in IRAT109 and IAC1246, respectively. Compared to IRAT109, the DEGs of IAC1246 displayed enhanced regulatory amplitude during drought. We found significant correlations between DEGs and the osmolality and total antioxidant capacity (AOC) of both cultivars. During the early stages of drought, we detected up-regulation of DEGs in IAC1246 related to photosynthesis, in accordance with its higher relative photosynthesis rate. The contents of six differential metabolites were correlated with the osmotic potential and AOC. Moreover, they were differently regulated between the two cultivars. Particularly, up-regulations of 4-hydroxycinnamic acid and ferulic acid were consistent with the performance of photosynthesis-related DEGs at the early stages of drought in IAC1246. Therefore, 4-hydroxycinnamic acid and ferulic acid were considered as key metabolites for rice drought-tolerance. DEGs involved in pathways of these metabolites are expected to be good candidate genes to improve drought-tolerance. In conclusion, well-maintained photosynthesis under drought should contribute to improved drought-tolerance in rice. Metabolites play vital roles in protecting photosynthesis under dehydration via osmotic adjustments and/or antioxidant mechanisms. A metabolite-based method was thus an effective way to explore drought candidate genes. Metabolic accompanied by transcript responses to drought stress should be further studied to find more useful metabolites, pathways, and genes.

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Quantitative trait locus mapping of deep rooting by linkage and association analysis in rice

Abstract: HighlightMajor quantitative trait loci (QTLs) of rice deep rooting were identified by combined linkage-based and linage disequilibrium-based QTL mapping in this study.

Cited by 103 publications

References 58 publications

Genome-Wide Association Study for Plant Height and Grain Yield in Rice under Contrasting Moisture Regimes

Genome-Wide Association Study for Plant Height and Grain Yield in Rice under Contrasting Moisture Regimes

Growing Out of Stress: The Role of Cell- and Organ-Scale Growth Control in Plant Water-Stress Responses

Transcriptomic and Metabolomic Studies Disclose Key Metabolism Pathways Contributing to Well-maintained Photosynthesis under the Drought and the Consequent Drought-Tolerance in Rice

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