A Genome-Wide Association Study Reveals Candidate Genes Related to Salt Tolerance in Rice ( Oryza sativa ) at the Germination Stage

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Abstract

Salt toxicity is the major factor limiting crop productivity in saline soils. In this paper, 295 accessions including a heuristic core set (137 accessions) and 158 bred varieties were re-sequenced and ~1.65 million SNPs/indels were used to perform a genome-wide association study (GWAS) of salt-tolerance-related phenotypes in rice during the germination stage. A total of 12 associated peaks distributed on seven chromosomes using a compressed mixed linear model were detected. Determined by linkage disequilibrium (LD) blocks analysis, we finally obtained a total of 79 candidate genes. By detecting the highly associated variations located inside the genic region that overlapped with the results of LD block analysis, we characterized 17 genes that may contribute to salt tolerance during the seed germination stage. At the same time, we conducted a haplotype analysis of the genes with functional variations together with phenotypic correlation and orthologous sequence analyses. Among these genes, OsMADS31, which is a MADS-box family transcription factor, had a down-regulated expression under the salt condition and it was predicted to be involved in the salt tolerance at the rice germination stage. Our study revealed some novel candidate genes and their substantial natural variations in the rice genome at the germination stage. The GWAS in rice at the germination stage would provide important resources for molecular breeding and functional analysis of the salt tolerance during rice germination.

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Variation in NRT1.1B contributes to nitrate-use divergence between rice subspecies.

Bin Hu, Wei-wei Wang, Shujun Ou … (2015)

Asian cultivated rice (Oryza sativa L.) consists of two main subspecies, indica and japonica. Indica has higher nitrate-absorption activity than japonica, but the molecular mechanisms underlying that activity remain elusive. Here we show that variation in a nitrate-transporter gene, NRT1.1B (OsNPF6.5), may contribute to this divergence in nitrate use. Phylogenetic analysis revealed that NRT1.1B diverges between indica and japonica. NRT1.1B-indica variation was associated with enhanced nitrate uptake and root-to-shoot transport and upregulated expression of nitrate-responsive genes. The selection signature of NRT1.1B-indica suggests that nitrate-use divergence occurred during rice domestication. Notably, field tests with near-isogenic and transgenic lines confirmed that the japonica variety carrying the NRT1.1B-indica allele had significantly improved grain yield and nitrogen-use efficiency (NUE) compared to the variety without that allele. Our results show that variation in NRT1.1B largely explains nitrate-use divergence between indica and japonica and that NRT1.1B-indica can potentially improve the NUE of japonica.

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MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress

Rita Arora, Pinky Agarwal, Swatismita Ray … (2007)

Background MADS-box transcription factors, besides being involved in floral organ specification, have also been implicated in several aspects of plant growth and development. In recent years, there have been reports on genomic localization, protein motif structure, phylogenetic relationships, gene structure and expression of the entire MADS-box family in the model plant system, Arabidopsis. Though there have been some studies in rice as well, an analysis of the complete MADS-box family along with a comprehensive expression profiling was still awaited after the completion of rice genome sequencing. Furthermore, owing to the role of MADS-box family in flower development, an analysis involving structure, expression and functional aspects of MADS-box genes in rice and Arabidopsis was required to understand the role of this gene family in reproductive development. Results A genome-wide molecular characterization and microarray-based expression profiling of the genes encoding MADS-box transcription factor family in rice is presented. Using a thorough annotation exercise, 75 MADS-box genes have been identified in rice and categorized into MIKCc, MIKC*, Mα, Mβ and Mγ groups based on phylogeny. Chromosomal localization of these genes reveals that 16 MADS-box genes, mostly MIKCc-type, are located within the duplicated segments of the rice genome, whereas most of the M-type genes, 20 in all, seem to have resulted from tandem duplications. Nine members belonging to the Mβ group, which was considered absent in monocots, have also been identified. The expression profiles of all the MADS-box genes have been analyzed under 11 temporal stages of panicle and seed development, three abiotic stress conditions, along with three stages of vegetative development. Transcripts for 31 genes accumulate preferentially in the reproductive phase, of which, 12 genes are specifically expressed in seeds, and six genes show expression specific to panicle development. Differential expression of seven genes under stress conditions is also evident. An attempt has been made to gain insight into plausible functions of rice MADS-box genes by collating the expression data of functionally validated genes in rice and Arabidopsis. Conclusion Only a limited number of MADS genes have been functionally validated in rice. A comprehensive annotation and transcriptome profiling undertaken in this investigation adds to our understanding of the involvement of MADS-box family genes during reproductive development and stress in rice and also provides the basis for selection of candidate genes for functional validation studies.

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Genome-Wide Association Mapping of Root Traits in a Japonica Rice Panel

Brigitte Courtois, Alain Audebert, Audrey Dardou … (2013)

Rice is a crop prone to drought stress in upland and rainfed lowland ecosystems. A deep root system is recognized as the best drought avoidance mechanism. Genome-wide association mapping offers higher resolution for locating quantitative trait loci (QTLs) than QTL mapping in biparental populations. We performed an association mapping study for root traits using a panel of 167 japonica accessions, mostly of tropical origin. The panel was genotyped at an average density of one marker per 22.5 kb using genotyping by sequencing technology. The linkage disequilibrium in the panel was high (r2>0.6, on average, for 20 kb mean distances between markers). The plants were grown in transparent 50 cm × 20 cm × 2 cm Plexiglas nailboard sandwiches filled with 1.5 mm glass beads through which a nutrient solution was circulated. Root system architecture and biomass traits were measured in 30-day-old plants. The panel showed a moderate to high diversity in the various traits, particularly for deep (below 30 cm depth) root mass and the number of deep roots. Association analyses were conducted using a mixed model involving both population structure and kinship to control for false positives. Nineteen associations were significant at P<1e-05, and 78 were significant at P<1e-04. The greatest numbers of significant associations were detected for deep root mass and the number of deep roots, whereas no significant associations were found for total root biomass or deep root proportion. Because several QTLs for different traits were co-localized, 51 unique loci were detected; several co-localized with meta-QTLs for root traits, but none co-localized with rice genes known to be involved in root growth. Several likely candidate genes were found in close proximity to these loci. Additional work is necessary to assess whether these markers are relevant in other backgrounds and whether the genes identified are robust candidates.

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Author and article information

Journal

Journal ID (nlm-ta): Int J Mol Sci

Journal ID (iso-abbrev): Int J Mol Sci

Journal ID (publisher-id): ijms

Title: International Journal of Molecular Sciences

Publisher: MDPI

ISSN (Electronic): 1422-0067

Publication date (Electronic): 12 October 2018

Publication date Collection: October 2018

Volume: 19

Issue: 10

Electronic Location Identifier: 3145

Affiliations

[1 ]Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Korea; agnesyu121@ 123456ahau.edu.cn (J.Y.); wgzsri@ 123456126.com (W.Z.); wtong@ 123456ahau.edu.cn (W.T.); qiangh06@ 123456gmail.com (Q.H.); myyoon0721@ 123456gmail.com (M.-Y.Y.); lifengpeng2013@ 123456gmail.com (F.-P.L.); pckorea1587@ 123456gmail.com (B.C.); hueunbum@ 123456gmail.com (E.-B.H.)

[2 ]State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China

[3 ]School of Biotechnology, Jiangsu University of Science and Technology, Sibaidu, Zhenjiang, Jiangsu 212018, China

[4 ]National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China

[5 ]Leader of Eco. Energy & Bio (LEEBCOR), 190-26 Hwangyeonggongwon-ro, Asan-si, Chungcheongnam-do 31529, Korea

[6 ]Suzhou GENEWIZ Biotechnology Co. LTD, C3 218 Xinghu Road Suzhou Industrial Park, Suzhou 215123, China

[7 ]Chemical Safety Division, National Institute of Agricultural Sciences (NIAS), Wanju 55365, Korea

[8 ]Breeding & Research Institute, Koregon Co. LTD, Anseong Center 60-34, Gokcheon-gil, Bogae-Myeon, Anseong-Si, Gyeonggi-Do 17509, Korea

[9 ]Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan 32439, Korea

Author notes

[* ]Correspondence: sh.kyuwon@ 123456gmail.com (K.-W.K.); yjpark@ 123456kongju.ac.kr (Y.-J.P.); Tel.: +82-41-330-1200 (K.-W.K. & Y.-J.P.)

[†]

These authors contributed equally to this work.

Article

Publisher ID: ijms-19-03145

DOI: 10.3390/ijms19103145

PMC ID: 6213974

PubMed ID: 30322083

SO-VID: 5a6f1e8e-797a-4a39-a9bc-c00ef7504807

License:

Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

History

Date received : 21 September 2018

Date accepted : 09 October 2018

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A Genome-Wide Association Study Reveals Candidate Genes Related to Salt Tolerance in Rice ( Oryza sativa) at the Germination Stage

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Most cited references 51

Variation in NRT1.1B contributes to nitrate-use divergence between rice subspecies.

MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress

Genome-Wide Association Mapping of Root Traits in a Japonica Rice Panel

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