Genome-Wide Association Studies Reveal the Genetic Basis of Ionomic Variation in Rice

Yang, Meng; Lü, Kai; Zhao, Fang‐Jie; Xie, Weibo; Ramakrishna, Priya; Wang, Guangyuan; Du, Qingqing; Liang, Limin; Sun, Cuiju; Zhao, Hu; Zhang, Zhanyi; Liu, Zonghao; Tian, Jingjing; Huang, Xin‐Yuan; Wang, Wensheng; Dong, Huaxia; Jintao, Hu; Ming, Luchang; Xing, Yongzhong; Wang, Gongwei; Xiao, Jinghua; Salt, David E.; Lian, Xingming

doi:10.1105/tpc.18.00375

Cited by 176 publications

(183 citation statements)

References 97 publications

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“…Genome‐wide association study has been successfully used to uncover the molecular basis of ion accumulation in plants (Baxter et al , ; Chao et al , ; Yang et al , ; Kang et al , ). However, the genetic basis underlying natural variations in Na + and K + accumulation and salt tolerance in tomato remains to be identified.…”

Section: Resultsmentioning

confidence: 99%

“…GWAS is a powerful approach for uncovering the molecular basis of mineral composition in crops because more historical recombination, a larger number of alleles, and wider genetic variations can be investigated in an association study as compared to linkage analysis (Baxter et al , ; Chao et al , ; Yang et al , ; Kang et al , ). Tomato as a worldwide leading vegetable crop has publicly available sequences and an assembled genome (Sato et al , ; Lin et al , ).…”

Section: Introductionmentioning

confidence: 99%

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Loss of salt tolerance during tomato domestication conferred by variation in a Na ⁺ /K ⁺ transporter

et al. 2020

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Domestication has resulted in reduced salt tolerance in tomato. To identify the genetic components causing this deficiency, we performed a genome-wide association study (GWAS) for root Na + /K + ratio in a population consisting of 369 tomato accessions with large natural variations. The most significant variations associated with root Na + /K + ratio were identified within the gene SlHAK20 encoding a member of the clade IV HAK/KUP/KT transporters. We further found that SlHAK20 transports Na + and K + and regulates Na + and K + homeostasis under salt stress conditions. A variation in the coding sequence of SlHAK20 was found to be the causative variant associated with Na + /K + ratio and confer salt tolerance in tomato. Knockout mutations in tomato SlHAK20 and the rice homologous genes resulted in hypersensitivity to salt stress. Together, our study uncovered a previously unknown molecular mechanism of salt tolerance responsible for the deficiency in salt tolerance in cultivated tomato varieties. Our findings provide critical information for molecular breeding to improve salt tolerance in tomato and other crops.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Loss of salt tolerance during tomato domestication conferred by variation in a Na ⁺ /K ⁺ transporter

et al. 2020

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“…www.nature.com/scientificreports www.nature.com/scientificreports/ Leaf nitrogen content was determined in the method as described previously 60 . Leaf samples were inactivated at 105 °C for 30 min, then were dried at 80 °C until constant weight, and were ground to fine powders.…”

Section: Scientific Reports |mentioning

confidence: 99%

A xylan glucuronosyltransferase gene exhibits pleiotropic effects on cellular composition and leaf development in rice

Gao

Sun

Wang

et al. 2020

Sci Rep

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Leaf chlorophyll content is an important physiological indicator of plant growth, metabolism and nutritional status, and it is highly correlated with leaf nitrogen content and photosynthesis. in this study, we report the cloning and identification of a xylan glucuronosyltransferase gene (OsGUX1) that affects relative chlorophyll content in rice leaf. Using a set of chromosomal segment substitution lines derived from a cross of wild rice accession ACC10 and indica variety Zhenshan 97 (ZS97), we identified numerous quantitative trait loci for relative chlorophyll content. one major locus of them for relative chlorophyll content was mapped to a 10.3-kb region that contains OsGUX1. the allele OsGUX1 AC from ACC10 significantly decreases nitrogen content and chlorophyll content of leaf compared with OsGUX1 ZS from ZS97. The overexpression of OsGUX1 reduced chlorophyll content, and the suppression of this gene increased chlorophyll content of rice leaf. OsGUX1 is located in Golgi apparatus, and highly expressed in seedling leaf and the tissues in which primary cell wall synthesis occurring. our experimental data indicate that OsGUX1 is responsible for addition of glucuronic acid residues onto xylan and participates in accumulation of cellulose and hemicellulose in the cell wall deposition, thus thickening the primary cell wall of mesophyll cells, which might lead to reduced chlorophyll content in rice leaf. These findings provide insights into the association of cell wall components with leaf nitrogen content in rice.Rice (Oryza sativa. L) providing a staple food for more than half of the population in the world, is a monocot model species for genetics, biology and functional genomics studies. Leaf photosynthesis has great potential for the improvement of rice yield, which will significantly contribute to addressing food demand challenge. The chloroplast of green tissue or leaf, as the most important supporter of carbon fixation and energy transformation, plays important roles in photosynthesis 1-3 . Both genetic and environmental factors have effect on the biochemical composition in chloroplast, thus affecting photosynthetic rate 4 .Previous studies have indicated that leaf color is a sensitive indicator of crop growth, metabolism and nutritional status, and it is closely related to the content of photosynthetic pigment, and positively correlated with leaf nitrogen (N) content 5-7 . Understanding the genetic and physiological bases of leaf nitrogen status is essential for efficient crop production and nitrogen management in intensive rice cropping systems. Leaf greenness is determined by specific properties, such as leaf chlorophyll content and chloroplast development, and leaf morphological characteristics (leaf thickness, surface structure and wall components). To study the genetic and molecular basis of leaf color, more than one hundred of rice mutants associated with leaf colors and chlorophyll content have been identified (http://archive.gramene.org/db/genes/). Several genes have been implicated in the chlorophyl...

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“…Similar to metabolomic approach, advances in the ionome technology, such as ICP-MS, has enabled us to profile the content of multiple minerals simultaneously. Yang et al, (2018) profiled 17 mineral nutrients, such as macro (e.g., N, P, and K), micro (e.g., Mo and Zn), and nonessential nutrients (e.g., As and Cd) for 529 rice accessions. Next, they identified several candidate genes associated with the natural variation of each mineral content by GWAS, that included previously reported mineral transporters involving the mineral uptake, such as HKT1;5 for K content and MOLYBDATE TRANSPORTER 1;1 (MOT1;1) for Mo content.…”

Section: Gwas For Mineral Contentmentioning

confidence: 99%

Genome-wide Association Studies of Agronomic Traits Consisting of Field- and Molecular-based Phenotypes

Nakano

Kobayashi

2020

RAS

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Genome-wide association study (GWAS) is a powerful approach to identify the genetic factors underlying the intraspecific phenotypic variations. Recent advances in DNA sequencing technology, including next generation sequencing has enabled us to easily genotype high density genome-wide SNPs. In addition, many accessions of various plant species have been widely collected in recent years. These genetic resources have made GWAS a markedly more popular approach for investigation of natural variations occurring in various traits using large populations. In addition to genotyping technology, advances in high-throughput phenotyping technologies have enabled us to acquire variation data on a large number of accessions characterized for various traits, including not only the field traits (e.g., yield and disease resistance) but also molecular traits (e.g., gene expression level and metabolite content). Thus, it is possible to expand the range of application of GWAS and enhance the detection power of genomic association. In this review, we summarize recent GWAS of various agronomic traits at field and molecular scale, following which we highlight the integration approach involving GWAS and high-throughput phenotyping technologies including transcriptome, ionome and metabolome.

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Genome-Wide Association Studies Reveal the Genetic Basis of Ionomic Variation in Rice

Cited by 176 publications

References 97 publications

Loss of salt tolerance during tomato domestication conferred by variation in a Na ⁺ /K ⁺ transporter

Loss of salt tolerance during tomato domestication conferred by variation in a Na ⁺ /K ⁺ transporter

A xylan glucuronosyltransferase gene exhibits pleiotropic effects on cellular composition and leaf development in rice

Genome-wide Association Studies of Agronomic Traits Consisting of Field- and Molecular-based Phenotypes

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Genome-Wide Association Studies Reveal the Genetic Basis of Ionomic Variation in Rice

Cited by 176 publications

References 97 publications

Loss of salt tolerance during tomato domestication conferred by variation in a Na + /K + transporter

Loss of salt tolerance during tomato domestication conferred by variation in a Na + /K + transporter

A xylan glucuronosyltransferase gene exhibits pleiotropic effects on cellular composition and leaf development in rice

Genome-wide Association Studies of Agronomic Traits Consisting of Field- and Molecular-based Phenotypes

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Loss of salt tolerance during tomato domestication conferred by variation in a Na ⁺ /K ⁺ transporter

Loss of salt tolerance during tomato domestication conferred by variation in a Na ⁺ /K ⁺ transporter