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      Genome-wide association study of seedling stage salinity tolerance in temperate japonica rice germplasm

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          Abstract

          Background

          Salinity has a significant impact on rice production in coastal, arid and semi-arid areas in many countries, including countries growing temperate rice, such as Kazakhstan. Recently, the complete genomes of 3000 rice accessions were sequenced through the 3 K rice genome project, and this set included 203 temperate japonica rice accessions. To identify salinity-tolerant germplasm and related genes for developing new salinity-tolerant breeding lines for the temperate japonica rice growing regions, we evaluated the seedling stage salinity tolerance of these sequenced temperate japonica rice accessions, and conducted genome-wide association studies (GWAS) for a series of salinity tolerance related traits.

          Results

          There were 27 accessions performed well (SES < 5.0) under moderate salinity stress (EC12), and 5 accessions were tolerant under both EC12 and EC18. A total of 26 QTLs were identified for 9 measured traits. Eleven of these QTLs were co-located with known salinity tolerance genes. QTL/gene clusters were observed on chromosome 1, 2, 3, 6, 8 and 9. Six candidate genes were identified for five promising QTLs. The alleles of major QTL Saltol and gene O S HKT1;5 ( SKC1) for Na +/K + ratio identified in indica rice accessions were different from those in the temperate japonica rice accessions used in this study.

          Conclusion

          Salinity tolerant temperate japonica rice accessions were identified in this study, these accessions are important resources for breeding programs. SNPs located in the promising QTLs and candidate genes could be used for future gene validation and marker assisted selection. This study provided useful information for future studies on genetics and breeding of salinity tolerance in temperate japonica rice.

          Electronic supplementary material

          The online version of this article (10.1186/s12863-017-0590-7) contains supplementary material, which is available to authorized users.

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          Most cited references44

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          Galactinol and raffinose constitute a novel function to protect plants from oxidative damage.

          Ayako Nishizawa, Yukinori Yabuta, Shigeru Shigeoka (2008)
          Galactinol synthase (GolS) is a key enzyme in the synthesis of raffinose family oligosaccharides that function as osmoprotectants in plant cells. In leaves of Arabidopsis (Arabidopsis thaliana) plants overexpressing heat shock transcription factor A2 (HsfA2), the transcription of GolS1, -2, and -4 and raffinose synthase 2 (RS2) was highly induced; thus, levels of galactinol and raffinose increased compared with those in wild-type plants under control growth conditions. In leaves of the wild-type plants, treatment with 50 mum methylviologen (MV) increased the transcript levels of not only HsfA2, but also GolS1, -2, -3, -4, and -8 and RS2, -4, -5, and -6, the total activities of GolS isoenzymes, and the levels of galactinol and raffinose. GolS1- or GolS2-overexpressing Arabidopsis plants (Ox-GolS1-11, Ox-GolS2-8, and Ox-GolS2-29) had increased levels of galactinol and raffinose in the leaves compared with wild-type plants under control growth conditions. High intracellular levels of galactinol and raffinose in the transgenic plants were correlated with increased tolerance to MV treatment and salinity or chilling stress. Galactinol and raffinose effectively protected salicylate from attack by hydroxyl radicals in vitro. These findings suggest the possibility that galactinol and raffinose scavenge hydroxyl radicals as a novel function to protect plant cells from oxidative damage caused by MV treatment, salinity, or chilling.
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            Shrinkage Estimation of the Realized Relationship Matrix

            Jeffrey Endelman, Jean-Luc Jannink (2012)
            The additive relationship matrix plays an important role in mixed model prediction of breeding values. For genotype matrix X (loci in columns), the product XX′ is widely used as a realized relationship matrix, but the scaling of this matrix is ambiguous. Our first objective was to derive a proper scaling such that the mean diagonal element equals 1+f, where f is the inbreeding coefficient of the current population. The result is a formula involving the covariance matrix for sampling genomic loci, which must be estimated with markers. Our second objective was to investigate whether shrinkage estimation of this covariance matrix can improve the accuracy of breeding value (GEBV) predictions with low-density markers. Using an analytical formula for shrinkage intensity that is optimal with respect to mean-squared error, simulations revealed that shrinkage can significantly increase GEBV accuracy in unstructured populations, but only for phenotyped lines; there was no benefit for unphenotyped lines. The accuracy gain from shrinkage increased with heritability, but at high heritability (> 0.6) this benefit was irrelevant because phenotypic accuracy was comparable. These trends were confirmed in a commercial pig population with progeny-test-estimated breeding values. For an anonymous trait where phenotypic accuracy was 0.58, shrinkage increased the average GEBV accuracy from 0.56 to 0.62 (SE < 0.00) when using random sets of 384 markers from a 60K array. We conclude that when moderate-accuracy phenotypes and low-density markers are available for the candidates of genomic selection, shrinkage estimation of the relationship matrix can improve genetic gain.
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              SNP-Seek database of SNPs derived from 3000 rice genomes

              Nickolai Alexandrov, Shuaishuai Tai, Wensheng Wang … (2014)
              We have identified about 20 million rice SNPs by aligning reads from the 3000 rice genomes project with the Nipponbare genome. The SNPs and allele information are organized into a SNP-Seek system (http://www.oryzasnp.org/iric-portal/), which consists of Oracle database having a total number of rows with SNP genotypes close to 60 billion (20 M SNPs × 3 K rice lines) and web interface for convenient querying. The database allows quick retrieving of SNP alleles for all varieties in a given genome region, finding different alleles from predefined varieties and querying basic passport and morphological phenotypic information about sequenced rice lines. SNPs can be visualized together with the gene structures in JBrowse genome browser. Evolutionary relationships between rice varieties can be explored using phylogenetic trees or multidimensional scaling plots.
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                Author and article information

                Contributors
                Dariga Batayeva: dariga.batayeva@gmail.com
                Benedick Labaco: b.labaco@irri.org
                Changrong Ye:
                ORCID: http://orcid.org/0000-0002-4095-1068
                yechr@hotmail.com
                Xiaolin Li: xiaolinli@163.com
                Bakdaulet Usenbekov: rubakdaulet7@mail.ru
                Aiman Rysbekova: rysbekova@gmail.com
                Gulzhamal Dyuskalieva: dyuskalieva47@mail.ru
                Georgina Vergara: g.vergara@irri.org
                Russell Reinke: r.reinke@irri.org
                Hei Leung: h.leung@irri.org
                Journal
                Journal ID (nlm-ta): BMC Genet
                Journal ID (iso-abbrev): BMC Genet
                Title: BMC Genetics
                Publisher: BioMed Central (London )
                ISSN (Electronic): 1471-2156
                Publication date (Electronic): 3 January 2018
                Publication date PMC-release: 3 January 2018
                Publication date Collection: 2018
                Volume: 19
                Electronic Location Identifier: 2
                Affiliations
                [1 ]Kazakh State Women’s Teacher Training University, Almaty, 050040 Kazakhstan
                [2 ]ISNI 0000 0001 0729 330X, GRID grid.419387.0, International Rice Research Institute, ; Laguna, 4031 Philippines
                [3 ]ISNI 0000 0004 1799 1111, GRID grid.410732.3, Institute of Food Crops, Yunnan Academy of Agricultural Sciences, ; Kunming, 650205 China
                [4 ]Institute of Plant Biology and Biotechnology, Ministry of Education and Science, Almaty, 050010 Kazakhstan
                Author information
                http://orcid.org/0000-0002-4095-1068
                Article
                Publisher ID: 590
                DOI: 10.1186/s12863-017-0590-7
                PMC ID: 5753436
                PubMed ID: 29298667
                SO-VID: a8497d71-ca0a-4c6f-98dc-6ca68435ed61
                Copyright © © The Author(s). 2018
                License:

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                Date received : 15 December 2016
                Date accepted : 20 December 2017
                Funding
                Funded by: Yunnan province, China
                Award ID: 2016HE006
                Award Recipient :
                Funded by: Kazakhstan government
                Award ID: 2113/GF4
                Award Recipient :
                Categories
                Subject: Research Article
                Custom metadata
                issue-copyright-statement © The Author(s) 2018

                ScienceOpen disciplines: Genetics
                Keywords: genome-wide association studies,seedling stage,salinity tolerance,candidate gene,temperate japonica
                Data availability:
                ScienceOpen disciplines: Genetics
                Keywords: genome-wide association studies, seedling stage, salinity tolerance, candidate gene, temperate japonica

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