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Kim KD, Kang Y, Kim C. Application of Genomic Big Data in Plant Breeding:Past, Present, and Future. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1454. [PMID: 33126607 PMCID: PMC7694055 DOI: 10.3390/plants9111454] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/26/2020] [Accepted: 10/26/2020] [Indexed: 01/11/2023]
Abstract
Plant breeding has a long history of developing new varieties that have ensured the food security of the human population. During this long journey together with humanity, plant breeders have successfully integrated the latest innovations in science and technologies to accelerate the increase in crop production and quality. For the past two decades, since the completion of human genome sequencing, genomic tools and sequencing technologies have advanced remarkably, and adopting these innovations has enabled us to cost down and/or speed up the plant breeding process. Currently, with the growing mass of genomic data and digitalized biological data, interdisciplinary approaches using new technologies could lead to a new paradigm of plant breeding. In this review, we summarize the overall history and advances of plant breeding, which have been aided by plant genomic research. We highlight the key advances in the field of plant genomics that have impacted plant breeding over the past decades and introduce the current status of innovative approaches such as genomic selection, which could overcome limitations of conventional breeding and enhance the rate of genetic gain.
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Affiliation(s)
- Kyung Do Kim
- Department of Bioscience and Bioinformatics, Myongji University, Yongin 17058, Korea;
| | - Yuna Kang
- Department of Crop Science, Chungnam National University, Daejeon 34134, Korea;
| | - Changsoo Kim
- Department of Crop Science, Chungnam National University, Daejeon 34134, Korea;
- Department of Smart Agriculture Systems, Chungnam National University, Daejeon 34134, Korea
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Kumar A, Kumar S, Singh KB, Prasad M, Thakur JK. Designing a Mini-Core Collection Effectively Representing 3004 Diverse Rice Accessions. PLANT COMMUNICATIONS 2020; 1:100049. [PMID: 33367255 PMCID: PMC7748012 DOI: 10.1016/j.xplc.2020.100049] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/13/2019] [Accepted: 04/21/2020] [Indexed: 05/14/2023]
Abstract
Genetic diversity provides the foundation for plant breeding and genetic research. Over 3000 rice genomes were recently sequenced as part of the 3K Rice Genome (3KRG) Project. We added four additional Indian rice accessions to create a panel of 3004 accessions. However, such a large collection of germplasm is difficult to preserve and evaluate. The construction of core and mini-core collections is an efficient method for the management of genetic resources. In this study, we developed a mini-core comprising 520 accessions that captured most of the SNPs and represented all of the phenotypes and geographic regions from the original panel. The mini-core was validated using different statistical analyses and contained representatives from all major rice groups, including japonica, indica, aus/boro, and aromatic/basmati. Genome-wide association analyses of the mini-core panel efficiently reproduced the marker-trait associations identified in the original panel. Haplotype analysis validated the utility of the mini-core panel. In the current era with many ongoing large-scale sequencing projects, such a strategy for mini-core design should be useful in many crops. The rice mini-core collection developed in this study would be valuable for agronomic trait evaluation and useful for rice improvement via marker-assisted molecular breeding.
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Affiliation(s)
- Angad Kumar
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shivendra Kumar
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Kajol B.M. Singh
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Manoj Prasad
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Jitendra K. Thakur
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
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Ueda Y, Ohtsuki N, Kadota K, Tezuka A, Nagano AJ, Kadowaki T, Kim Y, Miyao M, Yanagisawa S. Gene regulatory network and its constituent transcription factors that control nitrogen-deficiency responses in rice. THE NEW PHYTOLOGIST 2020; 227:1434-1452. [PMID: 32343414 DOI: 10.1111/nph.16627] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 04/15/2020] [Indexed: 05/07/2023]
Abstract
Increase in the nitrogen (N)-use efficiency and optimization of N response in crop species are urgently needed. Although transcription factor-based genetic engineering is a promising approach for achieving these goals, transcription factors that play key roles in the response to N deficiency have not been studied extensively. Here, we performed RNA-seq analysis of root samples of 20 Asian rice (Oryza sativa) accessions with differential nutrient uptake. Data obtained from plants exposed to N-replete and N-deficient conditions were subjected to coexpression analysis and machine learning-based pathway inference to dissect the gene regulatory network required for the response to N deficiency. Four transcription factors, including members of the G2-like and bZIP families, were predicted to function as key regulators of gene transcription within the network in response to N deficiency. Cotransfection assays validated inferred novel regulatory pathways, and further analyses using genome-edited knockout lines suggested that these transcription factors are important for N-deficiency responses in planta. Many of the N deficiency-responsive genes, including those encoding key regulators within the network, were coordinately regulated by transcription factors belonging to different families. Transcription factors identified in this study could be valuable for the modification of N response and metabolism.
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Affiliation(s)
- Yoshiaki Ueda
- Biotechnology Research Center, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Namie Ohtsuki
- Biotechnology Research Center, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Koji Kadota
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Ayumi Tezuka
- Faculty of Agriculture, Ryukoku University, Yokotani 1-5, Seta Oe-cho, Otsu, Shiga, 520-2194, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Yokotani 1-5, Seta Oe-cho, Otsu, Shiga, 520-2194, Japan
| | - Taro Kadowaki
- Graduate School of Agricultural Science, Tohoku University, Aoba 468-1, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8572, Japan
| | - Yonghyun Kim
- Graduate School of Agricultural Science, Tohoku University, Aoba 468-1, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8572, Japan
| | - Mitsue Miyao
- Graduate School of Agricultural Science, Tohoku University, Aoba 468-1, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8572, Japan
| | - Shuichi Yanagisawa
- Biotechnology Research Center, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
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Li CX, Yan JY, Ren JY, Sun L, Xu C, Li GX, Ding ZJ, Zheng SJ. A WRKY transcription factor confers aluminum tolerance via regulation of cell wall modifying genes. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:1176-1192. [PMID: 31729146 DOI: 10.1111/jipb.12888] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/14/2019] [Indexed: 05/06/2023]
Abstract
Modification of cell wall properties has been considered as one of the determinants that confer aluminum (Al) tolerance in plants, while how cell wall modifying processes are regulated remains elusive. Here, we present a WRKY transcription factor WRKY47 involved in Al tolerance and root growth. Lack of WRKY47 significantly reduces, while overexpression of it increases Al tolerance. We show that lack of WRKY47 substantially affects subcellular Al distribution in the root, with Al content decreased in apoplast and increased in symplast, which is attributed to the reduced cell wall Al-binding capacity conferred by the decreased content of hemicellulose I in the wrky47-1 mutant. Based on microarray, real time-quantitative polymerase chain reaction and chromatin immunoprecipitation assays, we further show that WRKY47 directly regulates the expression of EXTENSIN-LIKE PROTEIN (ELP) and XYLOGLUCAN ENDOTRANSGLUCOSYLASE-HYDROLASES17 (XTH17) responsible for cell wall modification. Increasing the expression of ELP and XTH17 rescued Al tolerance as well as root growth in wrky47-1 mutant. In summary, our results demonstrate that WRKY47 is required for root growth under both normal and Al stress conditions via direct regulation of cell wall modification genes, and that the balance of Al distribution between root apoplast and symplast conferred by WRKY47 is important for Al tolerance.
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Affiliation(s)
- Chun Xiao Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jing Ying Yan
- Agricultural Experiment Station, Zhejiang University, Hangzhou, 310058, China
| | - Jiang Yuan Ren
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Li Sun
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chen Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Gui Xin Li
- College of Agronomy and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Zhong Jie Ding
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Shao Jian Zheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
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QTL mapping and candidate gene analysis of cadmium accumulation in polished rice by genome-wide association study. Sci Rep 2020; 10:11791. [PMID: 32678216 PMCID: PMC7366680 DOI: 10.1038/s41598-020-68742-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 06/26/2020] [Indexed: 11/09/2022] Open
Abstract
Cadmium (Cd) accumulation in rice is a serious threat to food safety and human health. Breeding rice varieties with low Cd accumulation is one of the most effective approaches to reducing health risks from Cd-polluted rice. However, the genetic basis of Cd accumulation in grains, especially in indica rice varieties, has not been fully elucidated. The evaluation of Cd-accumulation capacity was conducted among 338 diverse rice accessions grown in Cd-contaminated soils with different Cd contents. Thirteen rice lines with relatively low Cd accumulation, including six indica rice lines, were identified. Then, 35 QTLs significantly associated with Cd accumulation were identified through sequencing-based SNP discovery and a genome-wide association study (GWAS) in the two experimental years, and only qCd8-1 was detected in both years. Among of them, nine QTLs were co-localized with identified genes or QTLs. A novel QTL, qCd1-3, with the lowest P value was selected for further LD decay analysis and candidate gene prediction. We found differential expression of OsABCB24 between high-Cd-accumulative and low-Cd-accumulative accessions, suggesting it may be a candidate gene for qCd1-3 associated with low Cd accumulation. These results may be helpful for further exploiting novel functional genes related to Cd accumulation and developing rice variety with low Cd accumulation through marker-assisted breeding.
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Li X, Zheng H, Wu W, Liu H, Wang J, Jia Y, Li J, Yang L, Lei L, Zou D, Zhao H. QTL Mapping and Candidate Gene Analysis for Alkali Tolerance in Japonica Rice at the bud Stage Based on Linkage Mapping and Genome-Wide Association Study. RICE (NEW YORK, N.Y.) 2020; 13:48. [PMID: 32676742 PMCID: PMC7364718 DOI: 10.1186/s12284-020-00412-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 07/08/2020] [Indexed: 05/18/2023]
Abstract
BACKGROUND Salinity-alkalinity stress is one of the major factors limiting rice production. Damage caused by alkaline salt stress is more severe than that caused by neutral salt stress. Alkali tolerance at the bud stage in rice directly affects seedling survival and final yield when using the direct seeding cultivation model. However, genetic resources (QTLs and genes) for rice breeders to improve alkali tolerance are limited. In this study, we combined linkage mapping and a genome-wide association study (GWAS) to analyze the genetic structure of this trait in japonica rice at the bud stage. RESULTS A population of 184 recombinant inbred lines (RILs) was utilized to map quantitative trait loci (QTLs) for the root length under control condition (RL), alkaline stress (ARL) and relative root length (RRL) at the bud stage. A major QTL related to alkali tolerance at the rice bud stage, qAT11, was detected on chromosome 11. Interestingly, a GWAS identified a lead SNP (Chr_21,999,659) in qAT11 that was significantly associated with alkaline tolerance. After filtering by linkage disequilibrium (LD), haplotype analysis, quantitative real-time PCR, we obtained three candidate genes (LOC_Os11g37300, LOC_Os11g37320 and LOC_Os11g37390). In addition, we performed phenotype verification on the CRISPR/Cas9 mutant of LOC_Os11g37390. CONCLUSION Based on these results, LOC_Os11g37300, LOC_Os11g37320 and LOC_Os11g37390 were the candidate genes contributing to alkaline tolerance in japonica rice. This study provides resources for breeding aimed at improving rice responses to alkalinity stress.
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Affiliation(s)
- Xianwei Li
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Hongliang Zheng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Wenshen Wu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Hualong Liu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Jingguo Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Yan Jia
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Jiaming Li
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Luomiao Yang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Lei Lei
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Detang Zou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China.
| | - Hongwei Zhao
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China.
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Low Additive Genetic Variation in a Trait Under Selection in Domesticated Rice. G3-GENES GENOMES GENETICS 2020; 10:2435-2443. [PMID: 32439738 PMCID: PMC7341149 DOI: 10.1534/g3.120.401194] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Quantitative traits are important targets of both natural and artificial selection. The genetic architecture of these traits and its change during the adaptive process is thus of fundamental interest. The fate of the additive effects of variants underlying a trait receives particular attention because they constitute the genetic variation component that is transferred from parents to offspring and thus governs the response to selection. While estimation of this component of phenotypic variation is challenging, the increasing availability of dense molecular markers puts it within reach. Inbred plant species offer an additional advantage because phenotypes of genetically identical individuals can be measured in replicate. This makes it possible to estimate marker effects separately from the contribution of the genetic background not captured by genotyped loci. We focused on root growth in domesticated rice, Oryza sativa, under normal and aluminum (Al) stress conditions, a trait under recent selection because it correlates with survival under drought. A dense single nucleotide polymorphism (SNP) map is available for all accessions studied. Taking advantage of this map and a set of Bayesian models, we assessed additive marker effects. While total genetic variation accounted for a large proportion of phenotypic variance, marker effects contributed little information, particularly in the Al-tolerant tropical japonica population of rice. We were unable to identify any loci associated with root growth in this population. Models estimating the aggregate effects of all measured genotypes likewise produced low estimates of marker heritability and were unable to predict total genetic values accurately. Our results support the long-standing conjecture that additive genetic variation is depleted in traits under selection. We further provide evidence that this depletion is due to the prevalence of low-frequency alleles that underlie the trait.
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58
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Diop B, Wang DR, Drame KN, Gracen V, Tongoona P, Dzidzienyo D, Nartey E, Greenberg AJ, Djiba S, Danquah EY, McCouch SR. Bridging old and new: diversity and evaluation of high iron-associated stress response of rice cultivated in West Africa. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4188-4200. [PMID: 32277700 DOI: 10.1093/jxb/eraa182] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 04/09/2020] [Indexed: 05/20/2023]
Abstract
Adoption of rice varieties that perform well under high iron-associated (HIA) stress environments can enhance rice production in West Africa. This study reports the genetic characterization of 323 rice accessions and breeding lines cultivated in West Africa using genotyping-by-sequencing and their phenotypic response to HIA treatments in hydroponic solution (1500 mg l-1 FeSO4·7H2O) and hot-spot fields. The germplasm consisted of four genetic subpopulations: Oryza glaberrima (14%), O. sativa-japonica (7%), O. sativa-indica Group 1 (45%), and O. sativa-indica Group 2 (25%). Severe versus mild stress in the field was associated with a reduced SPAD value (12%), biomass (56%), and grain yield (57%), with leaf bronzing explaining 30% and 21% of the variation for biomass and grain yield, respectively. Association mapping using 175 indica genotypes identified 23 significant single nucleotide polymorphism (SNP) markers that mapped to 14 genomic regions. Genome-wide association study (GWAS) signals associated with leaf bronzing, a routinely used indicator of HIA stress, differed in hydroponic compared with field conditions. Contrastingly, six significant SNPs on chromosomes 8 and 9 were associated with the SPAD value under HIA stress in both field and hydroponic experiments, and a candidate potassium transporter gene mapped under the peak on chromosome 8. This study helps define criteria for assessing rice performance under HIA environments.
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Affiliation(s)
- Bathe Diop
- Institut Sénégalais de Recherches Agricoles/Centre de Recherches Agricoles de Djibélor, Ziguinchor, Senegal
- West Africa Centre for Crop Improvement, University of Ghana, Legon, Ghana
| | - Diane R Wang
- Purdue University, Department of Agronomy, West Lafayette, IN, USA
- Plant Breeding & Genetics, School of Integrated Plant Sciences, Cornell University, Ithaca, NY, USA
| | - Khady N Drame
- Africa Rice Center (AfricaRice), Abidjan 01, Cote d'Ivoire
| | - Vernon Gracen
- West Africa Centre for Crop Improvement, University of Ghana, Legon, Ghana
- Plant Breeding & Genetics, School of Integrated Plant Sciences, Cornell University, Ithaca, NY, USA
| | - Pangirayi Tongoona
- West Africa Centre for Crop Improvement, University of Ghana, Legon, Ghana
| | - Daniel Dzidzienyo
- West Africa Centre for Crop Improvement, University of Ghana, Legon, Ghana
| | - Eric Nartey
- University of Ghana, Department of Soil Science, School of Agriculture, Legon, Ghana
| | | | - Saliou Djiba
- Institut Sénégalais de Recherches Agricoles/Centre de Recherches Agricoles de Djibélor, Ziguinchor, Senegal
| | - Eric Y Danquah
- West Africa Centre for Crop Improvement, University of Ghana, Legon, Ghana
| | - Susan R McCouch
- Plant Breeding & Genetics, School of Integrated Plant Sciences, Cornell University, Ithaca, NY, USA
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Zhao L, Cui J, Cai Y, Yang S, Liu J, Wang W, Gai J, Hu Z, Li Y. Comparative Transcriptome Analysis of Two Contrasting Soybean Varieties in Response to Aluminum Toxicity. Int J Mol Sci 2020; 21:E4316. [PMID: 32560405 PMCID: PMC7352676 DOI: 10.3390/ijms21124316] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/09/2020] [Accepted: 06/12/2020] [Indexed: 01/02/2023] Open
Abstract
: Aluminum (Al) toxicity is a major factor limiting crop productivity on acid soils. Soybean (Glycine max) is an important oil crop and there is great variation in Al tolerance in soybean germplasms. However, only a few Al-tolerance genes have been reported in soybean. Therefore, the purpose of this study was to identify candidate Al tolerance genes by comparative transcriptome analysis of two contrasting soybean varieties in response to Al stress. Two soybean varieties, M90-24 (M) and Pella (P), which showed significant difference in Al tolerance, were used for RNA-seq analysis. We identified a total of 354 Al-tolerance related genes, which showed up-regulated expression by Al in the Al-tolerant soybean variety M and higher transcript levels in M than P under Al stress. These genes were enriched in the Gene Ontology (GO) terms of cellular glucan metabolic process and regulation of transcription. Five out of 11 genes in the enriched GO term of cellular glucan metabolic process encode cellulose synthases, and one cellulose synthase gene (Glyma.02G205800) was identified as the key hub gene by co-expression network analysis. Furthermore, treatment of soybean roots with a cellulose biosynthesis inhibitor decreased the Al tolerance, indicating an important role of cellulose production in soybean tolerance to Al toxicity. This study provides a list of candidate genes for further investigation on Al tolerance mechanisms in soybean.
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Affiliation(s)
- Lijuan Zhao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China; (L.Z.); (J.C.); (Y.C.); (S.Y.); (J.L.); (W.W.); (J.G.)
| | - Jingjing Cui
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China; (L.Z.); (J.C.); (Y.C.); (S.Y.); (J.L.); (W.W.); (J.G.)
| | - Yuanyuan Cai
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China; (L.Z.); (J.C.); (Y.C.); (S.Y.); (J.L.); (W.W.); (J.G.)
| | - Songnan Yang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China; (L.Z.); (J.C.); (Y.C.); (S.Y.); (J.L.); (W.W.); (J.G.)
| | - Juge Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China; (L.Z.); (J.C.); (Y.C.); (S.Y.); (J.L.); (W.W.); (J.G.)
| | - Wei Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China; (L.Z.); (J.C.); (Y.C.); (S.Y.); (J.L.); (W.W.); (J.G.)
| | - Junyi Gai
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China; (L.Z.); (J.C.); (Y.C.); (S.Y.); (J.L.); (W.W.); (J.G.)
| | - Zhubing Hu
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China;
| | - Yan Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China; (L.Z.); (J.C.); (Y.C.); (S.Y.); (J.L.); (W.W.); (J.G.)
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60
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Campbell MT, Du Q, Liu K, Sharma S, Zhang C, Walia H. Characterization of the transcriptional divergence between the subspecies of cultivated rice (Oryza sativa). BMC Genomics 2020; 21:394. [PMID: 32513103 PMCID: PMC7278148 DOI: 10.1186/s12864-020-06786-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 05/19/2020] [Indexed: 01/24/2023] Open
Abstract
Background Cultivated rice consists of two subspecies, Indica and Japonica, that exhibit well-characterized differences at the morphological and genetic levels. However, the differences between these subspecies at the transcriptome level remains largely unexamined. Here, we provide a comprehensive characterization of transcriptome divergence and cis-regulatory variation within rice using transcriptome data from 91 accessions from a rice diversity panel (RDP1). Results The transcriptomes of the two subspecies of rice are highly divergent. Japonica have significantly lower expression and genetic diversity relative to Indica, which is likely a consequence of a population bottleneck during Japonica domestication. We leveraged high-density genotypic data and transcript levels to identify cis-regulatory variants that may explain the genetic divergence between the subspecies. We identified significantly more eQTL that were specific to the Indica subspecies compared to Japonica, suggesting that the observed differences in expression and genetic variability also extends to cis-regulatory variation. Conclusions Using RNA sequencing data for 91diverse rice accessions and high-density genotypic data, we show that the two species are highly divergent with respect to gene expression levels, as well as the genetic regulation of expression. The data generated by this study provide, to date, the largest collection of genome-wide transcriptional levels for rice, and provides a community resource to accelerate functional genomic studies in rice.
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Affiliation(s)
- Malachy T Campbell
- Department of Agronomy and Horticulture, University of Nebraska Lincoln, 1825 N 38th St., Lincoln, 68583, NE, USA. .,Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, 175 West Campus Drive, Blacksburg, 24060, VA, USA.
| | - Qian Du
- School of Biological Sciences, University of Nebraska Lincoln, 1901 Vine St., Lincoln, 68503, NE, USA
| | - Kan Liu
- School of Biological Sciences, University of Nebraska Lincoln, 1901 Vine St., Lincoln, 68503, NE, USA
| | - Sandeep Sharma
- Department of Agronomy and Horticulture, University of Nebraska Lincoln, 1825 N 38th St., Lincoln, 68583, NE, USA.,Marine Biotechnology and Ecology Division, CSIR-CSMCRI, Bhavnagar, Gujarat, India
| | - Chi Zhang
- School of Biological Sciences, University of Nebraska Lincoln, 1901 Vine St., Lincoln, 68503, NE, USA
| | - Harkamal Walia
- Department of Agronomy and Horticulture, University of Nebraska Lincoln, 1825 N 38th St., Lincoln, 68583, NE, USA.
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Meng J, Wang W, Shi R, Song K, Li L, Que H, Zhang G. Identification of SNPs involved in Zn and Cu accumulation in the Pacific oyster (Crassostrea gigas) by genome-wide association analysis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 192:110208. [PMID: 32044602 DOI: 10.1016/j.ecoenv.2020.110208] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 01/07/2020] [Accepted: 01/11/2020] [Indexed: 06/10/2023]
Abstract
Oysters accumulate high concentrations of zinc (Zn) and copper (Cu), which can be transferred to human due to sea food consumption. Breeding new oyster varieties with low Zn and Cu accumulations is one important way to improve food safety. However, the genetic basis for metal accumulation in mollusks is not well understood. To address this issue, oysters collected in the field were used for genome-wide association study (GWAS) and then the identified genes were used for mRNA expressions analysis in laboratory. First, GWAS were conducted for Zn and Cu accumulation in 288 wild Pacific oysters (Crassostrea gigas) farmed in the same ocean environment. The oysters did not show obvious population structure or kinship but exhibited 8.43- and 10.0- fold changes of Zn and Cu contents respectively. GWAS have identified 11 and 12 single nucleotide polymorphisms (SNPs) associated with Zn and Cu, respectively, as well as 16 genes, which were Zn-containing proteins or participated in caveolae-dependent endocytosis. Second, the mRNA expressions of these 16 genes were observed under Zn and Cu exposure. After 9 days of Zn exposure, Zn contents increased 3.1-fold, while the mRNA expression of cell number regulator 3 increased 1.65-fold. Under 9 days of Cu exposure, Cu contents increased 1.97-fold, while the mRNA expression of caveolin-1 decreased 0.61-fold. These provide the evidence for their roles in regulating physiological levels of these two metals. The findings advance our understanding of the genetic basis of Zn and Cu accumulation in mollusks, which can be useful for breeding new, less toxic varieties of oysters.
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Affiliation(s)
- Jie Meng
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; National & Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Wenxiong Wang
- Marine Environmental Laboratory, HKUST Shenzhen Research Institute, Shenzhen, 518057, China
| | - Ruihui Shi
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; National & Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Kai Song
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Li Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China; National & Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
| | - Huayong Que
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; National & Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Guofan Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; National & Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
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Ram H, Gandass N, Sharma A, Singh A, Sonah H, Deshmukh R, Pandey AK, Sharma TR. Spatio-temporal distribution of micronutrients in rice grains and its regulation. Crit Rev Biotechnol 2020; 40:490-507. [DOI: 10.1080/07388551.2020.1742647] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Hasthi Ram
- Department of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Nishu Gandass
- Department of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Ankita Sharma
- Department of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Anmol Singh
- Department of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Humira Sonah
- Department of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Rupesh Deshmukh
- Department of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Ajay Kumar Pandey
- Department of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Tilak Raj Sharma
- Department of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
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Root transcriptome reveals efficient cell signaling and energy conservation key to aluminum toxicity tolerance in acidic soil adapted rice genotype. Sci Rep 2020; 10:4580. [PMID: 32165659 PMCID: PMC7067865 DOI: 10.1038/s41598-020-61305-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 02/25/2020] [Indexed: 11/24/2022] Open
Abstract
Aluminium (Al) toxicity is the single most important contributing factor constraining crop productivity in acidic soils. Hydroponics based screening of three rice genotypes, a tolerant (ARR09, AR), a susceptible (IR 1552, IR) and an acid soil adapted landrace (Theruvii, TH) revealed that AR accumulates less Al and shows minimum decrease in shoot and root biomass under Al toxicity conditions when compared with IR. Transcriptome data generated on roots (grown in presence or absence of Al) led to identification of ~1500 transcripts per genotype with percentage annotation ranging from 21.94% (AR) to 29.94% (TH). A total of 511, 804 and 912 DEGs were identified in genotypes AR, IR and TH, respectively. IR showed upregulation of transcripts involved in exergonic processes. AR appears to conserve energy by downregulating key genes of glycolysis pathway and maintaining transcript levels of key exergonic step enzymes under Al stress. The tolerance in AR appears to be as a result of novel mechanism as none of the reported Al toxicity genes or QTLs overlap with significant DEGs. Components of signal transduction and regulatory machinery like transcripts encoding zinc finger protein, calcieurin binding protein and cell wall associated transcripts are among the highly upregulated DEGs in AR, suggesting increased and better signal transduction in response to Al stress in tolerant rice. Sequencing of NRAT1 and glycine-rich protein A3 revealed distinct haplotype for indica type AR. The newly identified components of Al tolerance will help in designing molecular breeding tools to enhance rice productivity in acidic soils.
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64
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Luo T, Xia W, Gong S, Mason AS, Li Z, Liu R, Dou Y, Tang W, Fan H, Zhang C, Xiao Y. Identifying Vitamin E Biosynthesis Genes in Elaeis guineensis by Genome-Wide Association Study. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:678-685. [PMID: 31858793 DOI: 10.1021/acs.jafc.9b03832] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Elaeis guineensis is a tropical oil crop and has the highest oil yield per unit area. Palm oil has high palmitic acid content and is also rich in vitamins, including vitamin E. We conducted genome-wide association studies in a diversity panel of 161 E. guineensis accessions to identify single-nucleotide polymorphisms (SNPs) linked with vitamin E and validated candidate genes in these marker-associated intervals. Based on the SNPs reported in our previous research, 47 SNP markers were detected to be significantly associated with the variation of tocopherol and tocotrienol content at a cutoff P value of 6.3 × 10-7. A total of 656 candidate genes in the flanking regions of the 47 SNPs were identified, followed by pathway enrichment analysis. Of these candidate genes, EgHGGT (homogentisate geranylgeranyl transferase) involved in the biosynthesis of tocotrienols had a higher expression level in the mesocarp compared to other tissues. Expression of the EgHGGT gene was positively correlated with the variation in α-tocotrienol content. Induced overexpression of the gene in Arabidopsis caused a significant increase in vitamin E content and production of α-tocotrienols compared to wild Arabidopsis.
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Affiliation(s)
- Tingting Luo
- National Research Center of Rapeseed Engineering and Technology, College of Plant Science and Technology , Huazhong Agricultural University , Wuhan 430070 , China
| | - Wei Xia
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops , Hainan University , Haikou 570228 , P.R China
| | - Shufang Gong
- Coconut Research Institute , Chinese Academy of Tropical Agricultural Sciences , Wenchang 571339 , P.R. China
| | - Annaliese S Mason
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition , Justus Liebig University Giessen , Heinrich-Buff-Ring 26-32 , Giessen 35392i , Germany
| | - Zhiying Li
- Coconut Research Institute , Chinese Academy of Tropical Agricultural Sciences , Wenchang 571339 , P.R. China
- Hainan Key Laboratory for Biosafe Monitoring and Molecular Breeding in Off-Season Reproduction Region , Institute of Tropical Bioscience and Biotechnology Chinese Academy of Tropical Agricultural Sciences , Haikou 571101 , China
| | - Rui Liu
- Coconut Research Institute , Chinese Academy of Tropical Agricultural Sciences , Wenchang 571339 , P.R. China
| | - Yajing Dou
- Coconut Research Institute , Chinese Academy of Tropical Agricultural Sciences , Wenchang 571339 , P.R. China
| | - Wenqi Tang
- Coconut Research Institute , Chinese Academy of Tropical Agricultural Sciences , Wenchang 571339 , P.R. China
| | - Haikuo Fan
- Coconut Research Institute , Chinese Academy of Tropical Agricultural Sciences , Wenchang 571339 , P.R. China
| | - Chunyu Zhang
- National Research Center of Rapeseed Engineering and Technology, College of Plant Science and Technology , Huazhong Agricultural University , Wuhan 430070 , China
| | - Yong Xiao
- Coconut Research Institute , Chinese Academy of Tropical Agricultural Sciences , Wenchang 571339 , P.R. China
- Hainan Key Laboratory for Biosafe Monitoring and Molecular Breeding in Off-Season Reproduction Region , Institute of Tropical Bioscience and Biotechnology Chinese Academy of Tropical Agricultural Sciences , Haikou 571101 , China
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Pariasca-Tanaka J, Baertschi C, Wissuwa M. Identification of Loci Through Genome-Wide Association Studies to Improve Tolerance to Sulfur Deficiency in Rice. FRONTIERS IN PLANT SCIENCE 2020; 10:1668. [PMID: 32010158 PMCID: PMC6975283 DOI: 10.3389/fpls.2019.01668] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 11/27/2019] [Indexed: 06/01/2023]
Abstract
Sulfur (S) is an essential nutrient for plant growth and development; however, S supply for crop production is decreasing due to reduced inputs from atmospheric deposition and reduced application of S-containing fertilizers. Sulfur deficiency in soil is therefore becoming a widespread cause of reduced grain yield and quality in rice (Oryza sativa L). We therefore assessed the genotypic variation for tolerance to S deficiency in rice and identified loci associated with improved tolerance. Plants were grown in nutrient solution with either low (0.01 mM) or high (1.0 mM) supply of S. Plants grown under low-S treatment showed a reduction in total biomass, mainly due to a marked reduction in shoot biomass, while root biomass and root-to-shoot ratio increased, relative to plants under high-S treatment. Genome-wide association studies (GWAS) identified loci associated with root length (qSUE2-3, qSUE4, and qSUE9), and root (qSUE1, qSUE2-1, and qSUE3-1 and qSUE3-2) or total dry matter (qSUE2, qSUE3-1, and qSUE11). Candidate genes identified at associated loci coded for enzymes involved in secondary S metabolic pathways (sulfotransferases), wherein the sulfated compounds play several roles in plant responses to abiotic stress; cell wall metabolism including wall loosening and modification (carbohydrate hydrolases: beta-glucosidase and beta-gluconase) important for root growth; and cell detoxification (glutathione S-transferase). This study confirmed the existence of genetic variation conferring tolerance to S deficiency among traditional aus rice varieties. The advantageous haplotypes identified could be exploited through marker assisted breeding to improve tolerance to S-deficiency in modern cultivars in order to achieve sustainable crop production and food security.
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66
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Hartley TN, Thomas AS, Maathuis FJM. A role for the OsHKT 2;1 sodium transporter in potassium use efficiency in rice. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:699-706. [PMID: 30854552 PMCID: PMC6946003 DOI: 10.1093/jxb/erz113] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 02/25/2019] [Indexed: 05/20/2023]
Abstract
Increasing the potassium use efficiency (KUE) of crops is important for agricultural sustainability. However, a greater understanding of this complex trait is required to develop new, high-KUE cultivars. To this end, a genome-wide association study (GWAS) was applied to diverse rice (Oryza sativa L.) genotypes grown under potassium-stressed and -replete conditions. Using high-stringency criteria, the genetic architecture of KUE was uncovered, together with the breadth of physiological responses to low-potassium stress. Specifically, three quantitative trait loci (QTLs) were identified, which contained >90 candidate genes. Of these, the sodium transporter gene OsHKT2;1 emerged as a key factor that impacts on KUE based on (i) the correlation between shoot Na+ and KUE, and (ii) higher levels of HKT2;1 expression in high-KUE lines.
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Seck W, Torkamaneh D, Belzile F. Comprehensive Genome-Wide Association Analysis Reveals the Genetic Basis of Root System Architecture in Soybean. FRONTIERS IN PLANT SCIENCE 2020; 11:590740. [PMID: 33391303 PMCID: PMC7772222 DOI: 10.3389/fpls.2020.590740] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 11/16/2020] [Indexed: 05/17/2023]
Abstract
Increasing the understanding genetic basis of the variability in root system architecture (RSA) is essential to improve resource-use efficiency in agriculture systems and to develop climate-resilient crop cultivars. Roots being underground, their direct observation and detailed characterization are challenging. Here, were characterized twelve RSA-related traits in a panel of 137 early maturing soybean lines (Canadian soybean core collection) using rhizoboxes and two-dimensional imaging. Significant phenotypic variation (P < 0.001) was observed among these lines for different RSA-related traits. This panel was genotyped with 2.18 million genome-wide single-nucleotide polymorphisms (SNPs) using a combination of genotyping-by-sequencing and whole-genome sequencing. A total of 10 quantitative trait locus (QTL) regions were detected for root total length and primary root diameter through a comprehensive genome-wide association study. These QTL regions explained from 15 to 25% of the phenotypic variation and contained two putative candidate genes with homology to genes previously reported to play a role in RSA in other species. These genes can serve to accelerate future efforts aimed to dissect genetic architecture of RSA and breed more resilient varieties.
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Affiliation(s)
- Waldiodio Seck
- Département de phytologie, Faculté des sciences de l’agriculture et de l’alimentation (FSAA), Université Laval, Quebec, QC, Canada
- Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Quebec, QC, Canada
| | - Davoud Torkamaneh
- Département de phytologie, Faculté des sciences de l’agriculture et de l’alimentation (FSAA), Université Laval, Quebec, QC, Canada
- Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Quebec, QC, Canada
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - François Belzile
- Département de phytologie, Faculté des sciences de l’agriculture et de l’alimentation (FSAA), Université Laval, Quebec, QC, Canada
- Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Quebec, QC, Canada
- *Correspondence: François Belzile,
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68
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Gallo-Franco JJ, Sosa CC, Ghneim-Herrera T, Quimbaya M. Epigenetic Control of Plant Response to Heavy Metal Stress: A New View on Aluminum Tolerance. FRONTIERS IN PLANT SCIENCE 2020; 11:602625. [PMID: 33391313 PMCID: PMC7772216 DOI: 10.3389/fpls.2020.602625] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/23/2020] [Indexed: 05/05/2023]
Abstract
High concentrations of heavy metal (HM) ions impact agronomic staple crop production in acid soils (pH ≤ 5) due to their cytotoxic, genotoxic, and mutagenic effects. Among cytotoxic ions, the trivalent aluminum cation (Al3+) formed by solubilization of aluminum (Al) into acid soils, is one of the most abundant and toxic elements under acidic conditions. In recent years, several studies have elucidated the different signal transduction pathways involved in HM responses, identifying complementary genetic mechanisms conferring tolerance to plants. Although epigenetics has become more relevant in abiotic stress studies, epigenetic mechanisms underlying plant responses to HM stress remain poorly understood. This review describes the main epigenetic mechanisms related to crop responses during stress conditions, specifically, the molecular evidence showing how epigenetics is at the core of plant adaptation responses to HM ions. We highlight the epigenetic mechanisms that induce Al tolerance. Likewise, we analyze the pivotal relationship between epigenetic and genetic factors associated with HM tolerance. Finally, using rice as a study case, we performed a general analysis over previously whole-genome bisulfite-seq published data. Specific genes related to Al tolerance, measured in contrasting tolerant and susceptible rice varieties, exhibited differences in DNA methylation frequency. The differential methylation patterns could be associated with epigenetic regulation of rice responses to Al stress, highlighting the major role of epigenetics over specific abiotic stress responses.
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Affiliation(s)
- Jenny Johana Gallo-Franco
- Departamento de Ciencias Naturales y Matemáticas, Pontificia Universidad Javeriana, Cali, Cali, Colombia
| | - Chrystian Camilo Sosa
- Departamento de Ciencias Naturales y Matemáticas, Pontificia Universidad Javeriana, Cali, Cali, Colombia
- Grupo de Investigación en Evolución, Ecología y Conservación EECO, Programa de Biología, Facultad de Ciencias Básicas y Tecnologías, Universidad del Quindío, Armenia, Colombia
| | | | - Mauricio Quimbaya
- Departamento de Ciencias Naturales y Matemáticas, Pontificia Universidad Javeriana, Cali, Cali, Colombia
- *Correspondence: Mauricio Quimbaya,
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Yang JL, Fan W, Zheng SJ. Mechanisms and regulation of aluminum-induced secretion of organic acid anions from plant roots. J Zhejiang Univ Sci B 2019; 20:513-527. [PMID: 31090277 DOI: 10.1631/jzus.b1900188] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Aluminum (Al) is the most abundant metal element in the earth's crust. On acid soils, at pH 5.5 or lower, part of insoluble Al-containing minerals become solubilized into soil solution, with resultant highly toxic effects on plant growth and development. Nevertheless, some plants have developed Al-tolerance mechanisms that enable them to counteract this Al toxicity. One such well-documented mechanism is the Al-induced secretion of organic acid anions, including citrate, malate, and oxalate, from plant roots. Once secreted, these anions chelate external Al ions, thus protecting the secreting plant from Al toxicity. Genes encoding the citrate and malate transporters responsible for secretion have been identified and characterized, and accumulating evidence indicates that regulation of the expression of these transporter genes is critical for plant Al tolerance. In this review, we outline the recent history of research into plant Al-tolerance mechanisms, with special emphasis on the physiology of Al-induced secretion of organic acid anions from plant roots. In particular, we summarize the identification of genes encoding organic acid transporters and review current understanding of genes regulating organic acid secretion. We also discuss the possible signaling pathways regulating the expression of organic acid transporter genes.
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Affiliation(s)
- Jian-Li Yang
- Institute of Plant Biology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wei Fan
- Laboratory of Agricultural Resources and Environment, College of Resources and Environment, Yunnan Agricultural University, Kunming 650201, China
| | - Shao-Jian Zheng
- Institute of Plant Biology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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Rana N, Rahim MS, Kaur G, Bansal R, Kumawat S, Roy J, Deshmukh R, Sonah H, Sharma TR. Applications and challenges for efficient exploration of omics interventions for the enhancement of nutritional quality in rice (Oryza sativa L.). Crit Rev Food Sci Nutr 2019; 60:3304-3320. [DOI: 10.1080/10408398.2019.1685454] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Nitika Rana
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | | | - Gazaldeep Kaur
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Ruchi Bansal
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Surbhi Kumawat
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Joy Roy
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Humira Sonah
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Tilak Raj Sharma
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
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71
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Zhang P, Zhong K, Zhong Z, Tong H. Mining candidate gene for rice aluminum tolerance through genome wide association study and transcriptomic analysis. BMC PLANT BIOLOGY 2019; 19:490. [PMID: 31718538 PMCID: PMC6852983 DOI: 10.1186/s12870-019-2036-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 09/12/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND The genetic mechanism of aluminum (Al) tolerance in rice is great complicated. Uncovering genetic mechanism of Al tolerance in rice is the premise for Al tolerance improvement. Mining elite genes within rice landrace is of importance for improvement of Al tolerance in rice. RESULTS Genome-wide association study (GWAS) performed in EMMAX for rice Al tolerance was carried out using 150 varieties of Ting's core collection constructed from 2262 Ting's collections with more than 3.8 million SNPs. Within Ting's core collection of clear population structure and kinship relatedness as well as high rate of linkage disequilibrium (LD) decay, 17 genes relating to rice Al tolerance including cloned genes like NRAT1, ART1 and STAR1 were identified in this study. Moreover, 13 new candidate regions with high LD and 69 new candidate genes were detected. Furthermore, 20 of 69 new candidate genes were detected with significant difference between Al treatment and without Al toxicity by transcriptome sequencing. Interestingly, both qRT-PCR and sequence analysis in CDS region demonstrated that the candidate genes in present study might play important roles in rice Al tolerance. CONCLUSIONS The present study provided important information for further using these elite genes existing in Ting's core collection for improvement of rice Al tolerance.
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Affiliation(s)
- Peng Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Kaizhen Zhong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Zhengzheng Zhong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Hanhua Tong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
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Lee JS, Velasco-Punzalan M, Pacleb M, Valdez R, Kretzschmar T, McNally KL, Ismail AM, Cruz PCS, Sackville Hamilton NR, Hay FR. Variation in seed longevity among diverse Indica rice varieties. ANNALS OF BOTANY 2019; 124:447-460. [PMID: 31180503 PMCID: PMC6798842 DOI: 10.1093/aob/mcz093] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 05/24/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Understanding variation in seed longevity, especially within closely related germplasm, will lead to better understanding of the molecular basis of this trait, which is particularly important for seed genebanks, but is also relevant to anyone handling seeds. We therefore set out to determine the relative seed longevity of diverse Indica rice accessions through storage experiments. Since antioxidants are purported to play a role in seed storability, the antioxidant activity and phenolic content of caryopses were determined. METHODS Seeds of 299 Indica rice accessions harvested at 31, 38 and 45 d after heading (DAH) between March and May 2015 and differing in harvest moisture content (MC) were subsequently stored at 10.9 % MC and 45 °C. Samples were taken at regular intervals and sown for germination. Germination data were subjected to probit analysis and the resulting parameters that describe the loss of viability during storage were used for genome-wide association (GWA) analysis. KEY RESULTS The seed longevity parameters, Ki [initial viability in normal equivalent deviates (NED)], -σ-1 (σ is the time for viability to fall by 1 NED in experimental storage) and p50 [time for viability to fall to 50 % (0 NED)], varied considerably across the 299 Indica accessions. Seed longevity tended to increase as harvest MC decreased and to decrease as harvest MC increased. Eight major loci associated with seed longevity parameters were identified through GWA analysis. The favourable haplotypes on chromosomes 1, 3, 4, 9 and 11 enhanced p50 by ratios of 0.22-1.86. CONCLUSIONS This is the first study to describe the extent of variation in σ within a species' variety group. A priori candidate genes selected based on rice genome annotation and gene network ontology databases suggested that the mechanisms conferring high seed longevity might be related to DNA repair and transcription, sugar metabolism, reactive oxygen species scavenging and embryonic/root development.
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Affiliation(s)
- Jae-Sung Lee
- International Rice Research Institute, Los Baños, College, Laguna, Philippines
| | | | - Myrish Pacleb
- International Rice Research Institute, Los Baños, College, Laguna, Philippines
| | - Rocel Valdez
- International Rice Research Institute, Los Baños, College, Laguna, Philippines
- Institute of Crop Science, University of the Philippines Los Baños, College, Laguna, Philippines
| | - Tobias Kretzschmar
- International Rice Research Institute, Los Baños, College, Laguna, Philippines
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
| | - Kenneth L McNally
- International Rice Research Institute, Los Baños, College, Laguna, Philippines
| | - Abdel M Ismail
- International Rice Research Institute, Los Baños, College, Laguna, Philippines
| | - Pompe C Sta Cruz
- Institute of Crop Science, University of the Philippines Los Baños, College, Laguna, Philippines
| | | | - Fiona R Hay
- International Rice Research Institute, Los Baños, College, Laguna, Philippines
- Department of Agroecology, Aarhus University, Forsøgsvej, Slagelse, Denmark
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Yang H, Wang W, He Q, Xiang S, Tian D, Zhao T, Gai J. Identifying a wild allele conferring small seed size, high protein content and low oil content using chromosome segment substitution lines in soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2793-2807. [PMID: 31280342 DOI: 10.1007/s00122-019-03388-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 06/24/2019] [Indexed: 05/13/2023]
Abstract
KEY MESSAGE A wild soybean allele conferring 100-seed weight, protein content and oil content simultaneously was fine-mapped to a 329-kb region on Chromosome 15, in which Glyma.15g049200 was predicted a candidate gene. Annual wild soybean characterized with small 100-seed weight (100SW), high protein content (PRC), low oil content (OIC) may contain favourable alleles for broadening the genetic base of cultivated soybeans. To evaluate these alleles, a population composed of 195 chromosome segment substitution lines (SojaCSSLP4), with wild N24852 as donor and cultivated NN1138-2 as recurrent parent, was tested. In SojaCSSLP4, 10, 9 and 8 wild segments/QTL were detected for 100SW, PRC and OIC, respectively. Using a backcross-derived secondary population, one segment for the three traits (q100SW15, qPro15 and qOil15) and one for 100SW (q100SW18.2) were fine-mapped into a 329-kb region on chromosome 15 and a 286-kb region on chromosome 18, respectively. Integrated with the transcription data in SoyBase, 42 genes were predicted in the 329-kb region where Glyma.15g049200 showed significant expression differences at all seed development stages. Furthermore, the Glyma.15g049200 segments of the two parents were sequenced and compared, which showed two base insertions in CDS (coding sequence) in the wild N24852 comparing to the NN1138-2. Since only Glyma.15g049200 performed differential CDS between the two parents but related to the three traits, Glyma.15g049200 was predicted a pleiotropic candidate gene for 100SW, PRC and OIC. The functional annotation of Glyma.15g049200 indicated a bidirectional sucrose transporter belonging to MtN3/saliva family which might be the reason that this gene provides a same biochemical basis for 100SW, PRC and OIC, therefore, is responsible for the three traits. This result may facilitate isolation of the specific gene and provide prerequisite for understanding the other two pleiotropic QTL.
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Affiliation(s)
- Hongyan Yang
- Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- MARA National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Jiangsu Coastal Areas Institute of Agricultural Sciences, Yancheng, 224002, Jiangsu, China
| | - Wubin Wang
- Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- MARA National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General), Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Qingyuan He
- Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- MARA National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Shihua Xiang
- Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- MARA National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Dong Tian
- Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- MARA National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Tuanjie Zhao
- Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- MARA National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General), Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Junyi Gai
- Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
- MARA National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
- MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General), Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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Zhan C, Hu J, Pang Q, Yang B, Cheng Y, Xu E, Zhu P, Li Y, Zhang H, Cheng J. Genome-wide association analysis of panicle exsertion and uppermost internode in rice (Oryza sativa L.). RICE (NEW YORK, N.Y.) 2019; 12:72. [PMID: 31535313 PMCID: PMC6751241 DOI: 10.1186/s12284-019-0330-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 09/03/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Rice (Oryza sativa L.) yield is seriously influenced by panicle exsertion (PE) and the uppermost internode (UI) through panicle enclosure or energy transport during grain-filling stages. We evaluated the traits of PE and UI of 205 rice accessions in two independent environments and performed genome-wide association (GWAS) to explore the key genes controlling PE and UI, which could be used to improve panicle enclosure in rice breeding. RESULTS In this study, extensive genetic variation was found in both PE and UI among the 205 rice accessions, and 10.7% of accessions had panicle enclosure (PE/UI ≤ 0). Correlation analysis revealed that PE was significantly positively correlated with 1000-grain weight (1000-GW) but negatively correlated with heading date (HD), and UI was significantly positively correlated with HD but no significantly correlated with 1000-GW. A total of 22 and 24 quantitative trait loci (QTLs) were identified for PE and UI using GWAS, respectively. Eight loci for PE and nine loci for UI were simultaneously detected both in 2015 and in 2016, seven loci had adjacent physical positions between PE and UI, and ten loci for PE and seven loci for UI were located in previously reported QTLs. Further, we identified the CYP734A4 gene, encoding a cytochrome P450 monooxygenase, and the OsLIS-L1 gene, encoding a lissencephaly type-1-like protein, as causal genes for qPE14 and qUI14, and for qPE19, respectively. PE and UI were both significantly shorter in these two genes' mutants than in WT. Allelic Hap.1/2/4 of CYP734A4 and Hap.1/2/4 of OsLIS-L1 increased PE, UI, PE/UI, and 1000-GW, but Hap.3 of CYP734A4 and Hap.3 of OsLIS-L1 reduced them. In addition, six candidate genes were also detected for four key novel loci, qPE16, qPE21, qUI1, and qUI18, that seemed to be related to PE and UI. CONCLUSIONS Our results provide new information on the genetic architecture of PE and UI in rice, confirming that the CYP734A4 and OsLIS-L1 genes participate in PE and UI regulation, which could improve our understanding of the regulatory mechanism of PE and UI for rice breeding in the future.
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Affiliation(s)
- Chengfang Zhan
- Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Jiaxiao Hu
- Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Qiao Pang
- Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Bin Yang
- Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Yanhao Cheng
- Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Enshun Xu
- Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Peiwen Zhu
- Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Yingyi Li
- Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Hongsheng Zhang
- Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China.
| | - Jinping Cheng
- Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China.
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Du Q, Campbell M, Yu H, Liu K, Walia H, Zhang Q, Zhang C. Network-based feature selection reveals substructures of gene modules responding to salt stress in rice. PLANT DIRECT 2019; 3:e00154. [PMID: 31417977 PMCID: PMC6689793 DOI: 10.1002/pld3.154] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/18/2019] [Accepted: 07/19/2019] [Indexed: 05/27/2023]
Abstract
Rice, an important food resource, is highly sensitive to salt stress, which is directly related to food security. Although many studies have identified physiological mechanisms that confer tolerance to the osmotic effects of salinity, the link between rice genotype and salt tolerance is not very clear yet. Association of gene co-expression network and rice phenotypic data under stress has penitential to identify stress-responsive genes, but there is no standard method to associate stress phenotype with gene co-expression network. A novel method for integration of gene co-expression network and stress phenotype data was developed to conduct a system analysis to link genotype to phenotype. We applied a LASSO-based method to the gene co-expression network of rice with salt stress to discover key genes and their interactions for salt tolerance-related phenotypes. Submodules in gene modules identified from the co-expression network were selected by the LASSO regression, which establishes a linear relationship between gene expression profiles and physiological responses, that is, sodium/potassium condenses under salt stress. Genes in these submodules have functions related to ion transport, osmotic adjustment, and oxidative tolerance. We argued that these genes in submodules are biologically meaningful and useful for studies on rice salt tolerance. This method can be applied to other studies to efficiently and reliably integrate co-expression network and phenotypic data.
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Affiliation(s)
- Qian Du
- School of Biological SciencesCenter for Plant Science and InnovationUniversity of NebraskaLincolnNE
| | - Malachy Campbell
- Department of Agronomy and HorticultureCenter for Plant Science and InnovationUniversity of NebraskaLincolnNE
- Department of Animal and Poultry SciencesVirginia Polytechnic Institute and State UniversityBlacksburgVA
| | - Huihui Yu
- School of Biological SciencesCenter for Plant Science and InnovationUniversity of NebraskaLincolnNE
| | - Kan Liu
- School of Biological SciencesCenter for Plant Science and InnovationUniversity of NebraskaLincolnNE
| | - Harkamal Walia
- Department of Agronomy and HorticultureCenter for Plant Science and InnovationUniversity of NebraskaLincolnNE
| | - Qi Zhang
- Department of StatisticsUniversity of NebraskaLincolnNE
| | - Chi Zhang
- School of Biological SciencesCenter for Plant Science and InnovationUniversity of NebraskaLincolnNE
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Arbelaez JD, Dwiyanti MS, Tandayu E, Llantada K, Jarana A, Ignacio JC, Platten JD, Cobb J, Rutkoski JE, Thomson MJ, Kretzschmar T. 1k-RiCA (1K-Rice Custom Amplicon) a novel genotyping amplicon-based SNP assay for genetics and breeding applications in rice. RICE (NEW YORK, N.Y.) 2019; 12:55. [PMID: 31350673 PMCID: PMC6660535 DOI: 10.1186/s12284-019-0311-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/02/2019] [Indexed: 05/04/2023]
Abstract
BACKGROUND While a multitude of genotyping platforms have been developed for rice, the majority of them have not been optimized for breeding where cost, turnaround time, throughput and ease of use, relative to density and informativeness are critical parameters of their utility. With that in mind we report the development of the 1K-Rice Custom Amplicon, or 1k-RiCA, a robust custom sequencing-based amplicon panel of ~ 1000-SNPs that are uniformly distributed across the rice genome, designed to be highly informative within indica rice breeding pools, and tailored for genomic prediction in elite indica rice breeding programs. RESULTS Empirical validation tests performed on the 1k-RiCA showed average marker call rates of 95% with marker repeatability and concordance rates of 99%. These technical properties were not affected when two common DNA extraction protocols were used. The average distance between SNPs in the 1k-RiCA was 1.5 cM, similar to the theoretical distance which would be expected between 1,000 uniformly distributed markers across the rice genome. The average minor allele frequencies on a panel of indica lines was 0.36 and polymorphic SNPs estimated on pairwise comparisons between indica by indica accessions and indica by japonica accessions were on average 430 and 450 respectively. The specific design parameters of the 1k-RiCA allow for a detailed view of genetic relationships and unambiguous molecular IDs within indica accessions and good cost vs. marker-density balance for genomic prediction applications in elite indica germplasm. Predictive abilities of Genomic Selection models for flowering time, grain yield, and plant height were on average 0.71, 0.36, and 0.65 respectively based on cross-validation analysis. Furthermore the inclusion of important trait markers associated with 11 different genes and QTL adds value to parental selection in crossing schemes and marker-assisted selection in forward breeding applications. CONCLUSIONS This study validated the marker quality and robustness of the 1k-RiCA genotypic platform for genotyping populations derived from indica rice subpopulation for genetic and breeding purposes including MAS and genomic selection. The 1k-RiCA has proven to be an alternative cost-effective genotyping system for breeding applications.
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Affiliation(s)
- Juan David Arbelaez
- International Rice Research Institute, DAPO Box 7777, 1301 Los Baños, Metro Manila Philippines
| | | | - Erwin Tandayu
- International Rice Research Institute, DAPO Box 7777, 1301 Los Baños, Metro Manila Philippines
| | - Krizzel Llantada
- International Rice Research Institute, DAPO Box 7777, 1301 Los Baños, Metro Manila Philippines
| | - Annalhea Jarana
- International Rice Research Institute, DAPO Box 7777, 1301 Los Baños, Metro Manila Philippines
| | - John Carlos Ignacio
- International Rice Research Institute, DAPO Box 7777, 1301 Los Baños, Metro Manila Philippines
| | - John Damien Platten
- International Rice Research Institute, DAPO Box 7777, 1301 Los Baños, Metro Manila Philippines
| | - Joshua Cobb
- International Rice Research Institute, DAPO Box 7777, 1301 Los Baños, Metro Manila Philippines
| | - Jessica Elaine Rutkoski
- International Rice Research Institute, DAPO Box 7777, 1301 Los Baños, Metro Manila Philippines
| | - Michael J. Thomson
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Houston, TX 77843 USA
| | - Tobias Kretzschmar
- Southern Cross Plant Sciences, Southern Cross University, PO Box 157, Lismore, NSW 2480 Australia
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Feng Z, Kang H, Li M, Zou L, Wang X, Zhao J, Wei L, Zhou N, Li Q, Lan Y, Zhang Y, Chen Z, Liu W, Pan X, Wang GL, Zuo S. Identification of new rice cultivars and resistance loci against rice black-streaked dwarf virus disease through genome-wide association study. RICE (NEW YORK, N.Y.) 2019; 12:49. [PMID: 31309320 PMCID: PMC6629753 DOI: 10.1186/s12284-019-0310-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/01/2019] [Indexed: 05/29/2023]
Abstract
BACKGROUND The rice black-streaked dwarf virus (RBSDV) disease causes severe rice yield losses in Eastern China and other East Asian countries. Breeding resistant cultivars is the most economical and effective strategy to control the disease. However, few varieties and QTLs for RBSDV resistance have been identified to date. RESULTS In this study, we conducted a genome-wide association study (GWAS) on RBSDV resistance using the rice diversity panel 1 (RDP1) cultivars that were genotyped by a 44,000 high-density single nucleotide polymorphism (SNP) markers array. We found that less than 15% of these cultivars displayed resistance to RBSDV when tested under natural infection conditions at two locations with serious RBSDV occurrence. The aus, indica and tropical japonica sub-populations displayed higher RBSDV resistance than the aromatic and temperate japonica sub-populations. In particular, we identified four varieties that displayed stable levels of RBSDV resistance at all testing locations. GWAS identified 84 non-redundant SNP loci significantly associated with RBSDV resistance at two locations, leading to the identification of 13 QTLs for RBSDV resistance. Among them, qRBSDV-4.2 and qRBSDV-6.3 were detected at both locations, suggesting their resistance stability against environmental influence. Field disease evaluations showed that qRBSDV-6.3 significantly reduces RBSDV disease severity by 20%. Furthermore, introgression of qRBSDV-6.3 into two susceptible rice cultivars by marker-assisted selection demonstrated the effectiveness of qRBSDV-6.3 in enhancing RBSDV resistance. CONCLUSIONS The new resistant cultivars and QTLs against RBSDV disease identified in this study provide important information and genetic materials for the cloning of RBSDV resistance genes as well as developing RBSDV resistant varieties through marker-assisted selection.
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Affiliation(s)
- Zhiming Feng
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Houxiang Kang
- State Key Laboratory for biology of plant diseases and insect pests/Institute of plant protection, Chinese academy of Agricultural Sciences, Beijing, 100093, China
| | - Mingyou Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Lihua Zou
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Xiaoqiu Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Jianhua Zhao
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Lang Wei
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Nana Zhou
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Qianqian Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Ying Lan
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Yafang Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Zongxiang Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Wende Liu
- State Key Laboratory for biology of plant diseases and insect pests/Institute of plant protection, Chinese academy of Agricultural Sciences, Beijing, 100093, China
| | - Xuebiao Pan
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Guo-Liang Wang
- State Key Laboratory for biology of plant diseases and insect pests/Institute of plant protection, Chinese academy of Agricultural Sciences, Beijing, 100093, China.
- Department of Plant Pathology, the Ohio State University, Columbus, OH, 43210, USA.
| | - Shimin Zuo
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China.
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Feng Z, Kang H, Li M, Zou L, Wang X, Zhao J, Wei L, Zhou N, Li Q, Lan Y, Zhang Y, Chen Z, Liu W, Pan X, Wang GL, Zuo S. Identification of new rice cultivars and resistance loci against rice black-streaked dwarf virus disease through genome-wide association study. RICE (NEW YORK, N.Y.) 2019; 12:49. [PMID: 31309320 DOI: 10.1016/j.rsci.2018.12.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/01/2019] [Indexed: 05/27/2023]
Abstract
BACKGROUND The rice black-streaked dwarf virus (RBSDV) disease causes severe rice yield losses in Eastern China and other East Asian countries. Breeding resistant cultivars is the most economical and effective strategy to control the disease. However, few varieties and QTLs for RBSDV resistance have been identified to date. RESULTS In this study, we conducted a genome-wide association study (GWAS) on RBSDV resistance using the rice diversity panel 1 (RDP1) cultivars that were genotyped by a 44,000 high-density single nucleotide polymorphism (SNP) markers array. We found that less than 15% of these cultivars displayed resistance to RBSDV when tested under natural infection conditions at two locations with serious RBSDV occurrence. The aus, indica and tropical japonica sub-populations displayed higher RBSDV resistance than the aromatic and temperate japonica sub-populations. In particular, we identified four varieties that displayed stable levels of RBSDV resistance at all testing locations. GWAS identified 84 non-redundant SNP loci significantly associated with RBSDV resistance at two locations, leading to the identification of 13 QTLs for RBSDV resistance. Among them, qRBSDV-4.2 and qRBSDV-6.3 were detected at both locations, suggesting their resistance stability against environmental influence. Field disease evaluations showed that qRBSDV-6.3 significantly reduces RBSDV disease severity by 20%. Furthermore, introgression of qRBSDV-6.3 into two susceptible rice cultivars by marker-assisted selection demonstrated the effectiveness of qRBSDV-6.3 in enhancing RBSDV resistance. CONCLUSIONS The new resistant cultivars and QTLs against RBSDV disease identified in this study provide important information and genetic materials for the cloning of RBSDV resistance genes as well as developing RBSDV resistant varieties through marker-assisted selection.
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Affiliation(s)
- Zhiming Feng
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Houxiang Kang
- State Key Laboratory for biology of plant diseases and insect pests/Institute of plant protection, Chinese academy of Agricultural Sciences, Beijing, 100093, China
| | - Mingyou Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Lihua Zou
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Xiaoqiu Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Jianhua Zhao
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Lang Wei
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Nana Zhou
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Qianqian Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Ying Lan
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Yafang Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Zongxiang Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Wende Liu
- State Key Laboratory for biology of plant diseases and insect pests/Institute of plant protection, Chinese academy of Agricultural Sciences, Beijing, 100093, China
| | - Xuebiao Pan
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Guo-Liang Wang
- State Key Laboratory for biology of plant diseases and insect pests/Institute of plant protection, Chinese academy of Agricultural Sciences, Beijing, 100093, China.
- Department of Plant Pathology, the Ohio State University, Columbus, OH, 43210, USA.
| | - Shimin Zuo
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China.
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Hu D, Kan G, Hu W, Li Y, Hao D, Li X, Yang H, Yang Z, He X, Huang F, Yu D. Identification of Loci and Candidate Genes Responsible for Pod Dehiscence in Soybean via Genome-Wide Association Analysis Across Multiple Environments. FRONTIERS IN PLANT SCIENCE 2019; 10:811. [PMID: 31293609 PMCID: PMC6598122 DOI: 10.3389/fpls.2019.00811] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 06/05/2019] [Indexed: 05/03/2023]
Abstract
Pod dehiscence (shattering) is the main cause of serious yield loss during the soybean mechanical harvesting process. A better understanding of the genetic architecture and molecular mechanisms of pod dehiscence is of great significance for soybean breeding. In this study, genome-wide association analysis (GWAS) with NJAU 355K SoySNP array was performed to detect single nucleotide polymorphisms (SNPs) associated with pod dehiscence in an association panel containing 211 accessions across five environments. A total of 163 SNPs were identified as significantly associated with pod dehiscence. Among these markers, 136 SNPs identified on chromosome 16 were located in the known QTL qPDH1. One, one, three, eleven, three, one, three, three and one SNPs were distributed on chromosome 1, 4, 6, 8, 9, 11, 17, 18, and 20, respectively. Favorable SNPs and six haplotypes were identified based on ten functional SNPs; among those Hap2 and Hap3 were considered as optimal haplotypes. In addition, based on GWAS results, the candidate gene Glyma09g06290 was identified. Quantitative real-time PCR (qRT-PCR) results and polymorphism analysis suggested that Glyma09g06290 might be involved in pod dehiscence. Furthermore, a derived cleaved amplified polymorphic sequences (dCAPS) marker for Glyma09g06290 was developed. Overall, the loci and genes identified in this study will be helpful in breeding soybean accessions resistant to pod dehiscence.
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Affiliation(s)
- Dezhou Hu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Guizhen Kan
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Wei Hu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Yali Li
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Derong Hao
- Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong, China
| | - Xiao Li
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Hui Yang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Zhongyi Yang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Xiaohong He
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Fang Huang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Deyue Yu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
- School of Life Sciences, Guangzhou University, Guangzhou, China
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80
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Zhang P, Zhong K, Zhong Z, Tong H. Genome-wide association study of important agronomic traits within a core collection of rice (Oryza sativa L.). BMC PLANT BIOLOGY 2019; 19:259. [PMID: 31208337 PMCID: PMC6580581 DOI: 10.1186/s12870-019-1842-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 05/21/2019] [Indexed: 05/15/2023]
Abstract
BACKGROUND Cultivated rice (Oryza sativa L.) is one of the staple food for over half of the world's population. Thus, improvement of cultivated rice is important for the development of the world. It has been shown that abundant elite genes exist in rice landraces in previous studies. RESULTS A genome-wide association study (GWAS) performed with EMMAX for 12 agronomic traits measured in both Guangzhou and Hangzhou was carried out using 150 accessions of Ting's core collection selected based on 48 phenotypic traits from 2262 accessions of Ting's collection, the GWAS included more than 3.8 million SNPs. Within Ting's core collection, which has a simple population structure, low relatedness, and rapid linkage disequilibrium (LD) decay, we found 32 peaks located closely to previously cloned genes such as Hd1, SD1, Ghd7, GW8, and GL7 or mapped QTL, and these loci might be natural variations in the cloned genes or QTL which influence potentially agronomic traits. Furthermore, we also detected 32 regions where new genes might be located, and some peaks of these new candidate genes such as the signal on chromosome 11 for heading days were even higher than that of Hd1. Detailed annotation of these significant loci were shown in this study. Moreover, according to the estimated LD decay distance of 100 to 350 kb on the 12 chromosomes in this study, we found 13 identical significant regions in the two locations. CONCLUSIONS This research provided important information for further mining these elite genes within Ting's core collection and using them for rice breeding.
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Affiliation(s)
- Peng Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Kaizhen Zhong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Zhengzheng Zhong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Hanhua Tong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
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81
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Assessing the genetic diversity and characterizing genomic regions conferring Tan Spot resistance in cultivated rye. PLoS One 2019; 14:e0214519. [PMID: 30921415 PMCID: PMC6438500 DOI: 10.1371/journal.pone.0214519] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 03/14/2019] [Indexed: 11/19/2022] Open
Abstract
Rye (Secale cereale L.) is known for its wide adaptation due to its ability to tolerate harsh environments in semiarid areas. To assess the diversity in rye we genotyped a panel of 178 geographically diverse accessions of four Secale sp. from U.S. National Small Grains Collection using 4,037 high-quality SNPs (single nucleotide polymorphisms) developed by genotyping-by-sequencing (GBS). PCA and STRUCTURE analysis revealed three major clusters that separate S. cereale L. from S. strictum and S. sylvestre, however, genetic clusters did not correlate with geographic origins and growth habit (spring/winter). The panel was evaluated for response to Pyrenophora tritici-repentis race 5 (PTR race 5) and nearly 59% accessions showed resistance or moderate resistance. Genome-wide association study (GWAS) was performed on S. cereale subsp. cereale using the 4,037 high-quality SNPs. Two QTLs (QTs.sdsu-5R and QTs.sdsu-2R) on chromosomes 5R and 2R were identified conferring resistance to PTR race 5 (p < 0.001) that explained 13.1% and 11.6% of the phenotypic variation, respectively. Comparative analysis showed a high degree of synteny between rye and wheat with known rearrangements as expected. QTs.sdsu-2R was mapped in the genomic region corresponding to wheat chromosome group 2 and QTs.sdsu-5R was mapped to a small terminal region on chromosome 4BL. Based on the genetic diversity, a set of 32 accessions was identified to represents more than 99% of the allelic diversity with polymorphic information content (PIC) of 0.25. This set can be utilized for genetic characterization of useful traits and genetic improvement of rye, triticale, and wheat.
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Cobb JN, Biswas PS, Platten JD. Back to the future: revisiting MAS as a tool for modern plant breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:647-667. [PMID: 30560465 PMCID: PMC6439155 DOI: 10.1007/s00122-018-3266-4] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 12/07/2018] [Indexed: 05/04/2023]
Abstract
KEY MESSAGE New models for integration of major gene MAS with modern breeding approaches stand to greatly enhance the reliability and efficiency of breeding, facilitating the leveraging of traditional genetic diversity. Genetic diversity is well recognised as contributing essential variation to crop breeding processes, and marker-assisted selection is cited as the primary tool to bring this diversity into breeding programs without the associated genetic drag from otherwise poor-quality genomes of donor varieties. However, implementation of marker-assisted selection techniques remains a challenge in many breeding programs worldwide. Many factors contribute to this lack of adoption, such as uncertainty in how to integrate MAS with traditional breeding processes, lack of confidence in MAS as a tool, and the expense of the process. However, developments in genomics tools, locus validation techniques, and new models for how to utilise QTLs in breeding programs stand to address these issues. Marker-assisted forward breeding needs to be enabled through the identification of robust QTLs, the design of reliable marker systems to select for these QTLs, and the delivery of these QTLs into elite genomic backgrounds to enable their use without associated genetic drag. To enhance the adoption and effectiveness of MAS, rice is used as an example of how to integrate new developments and processes into a coherent, efficient strategy for utilising genetic variation. When processes are instituted to address these issues, new genes can be rolled out into a breeding program rapidly and completely with a minimum of expense.
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Affiliation(s)
- Joshua N Cobb
- International Rice Research Institute, National Road, Los Banos, Laguna, Philippines
| | - Partha S Biswas
- International Rice Research Institute, National Road, Los Banos, Laguna, Philippines
- Bangladesh Rice Research Institute, Gazipur, 1701, Bangladesh
| | - J Damien Platten
- International Rice Research Institute, National Road, Los Banos, Laguna, Philippines.
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Transcriptomic Analysis for Indica and Japonica Rice Varieties under Aluminum Toxicity. Int J Mol Sci 2019; 20:ijms20040997. [PMID: 30823582 PMCID: PMC6412857 DOI: 10.3390/ijms20040997] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/21/2019] [Accepted: 02/21/2019] [Indexed: 12/18/2022] Open
Abstract
Aluminum (Al) at high concentrations inhibits root growth, damage root systems, and causes significant reductions in rice yields. Indica and Japonica rice have been cultivated in distinctly different ecological environments with different soil acidity levels; thus, they might have different mechanisms of Al-tolerance. In the present study, transcriptomic analysis in the root apex for Al-tolerance in the seedling stage was carried out within Al-tolerant and -sensitive varieties belonging to different subpopulations (i.e., Indica, Japonica, and mixed). We found that there were significant differences between the gene expression patterns of Indica Al-tolerant and Japonica Al-tolerant varieties, while the gene expression patterns of the Al-tolerant varieties in the mixed subgroup, which was inclined to Japonica, were similar to the Al-tolerant varieties in Japonica. Moreover, after further GO (gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses of the transcriptomic data, we found that eight pathways, i.e., “Terpenoid backbone biosynthesis”, “Ribosome”, “Amino sugar and nucleotide sugar metabolism”, “Plant hormone signal transduction”, “TCA cycle”, “Synthesis and degradation of ketone bodies”, and “Butanoate metabolism” were found uniquely for Indica Al-tolerant varieties, while only one pathway (i.e., “Sulfur metabolism”) was found uniquely for Japonica Al-tolerant varieties. For Al-sensitive varieties, one identical pathway was found, both in Indica and Japonica. Three pathways were found uniquely in “Starch and sucrose metabolism”, “Metabolic pathway”, and “Amino sugar and nucleotide sugar metabolism”.
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84
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Lekklar C, Pongpanich M, Suriya-arunroj D, Chinpongpanich A, Tsai H, Comai L, Chadchawan S, Buaboocha T. Genome-wide association study for salinity tolerance at the flowering stage in a panel of rice accessions from Thailand. BMC Genomics 2019; 20:76. [PMID: 30669971 PMCID: PMC6343365 DOI: 10.1186/s12864-018-5317-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 11/27/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Salt stress, a major plant environmental stress, is a critical constraint for rice productivity. Dissecting the genetic loci controlling salt tolerance in rice for improving productivity, especially at the flowering stage, remains challenging. Here, we conducted a genome-wide association study (GWAS) of salt tolerance based on exome sequencing of the Thai rice accessions. RESULTS Photosynthetic parameters and cell membrane stability under salt stress at the flowering stage; and yield-related traits of 104 Thai rice (Oryza sativa L.) accessions belonging to the indica subspecies were evaluated. The rice accessions were subjected to exome sequencing, resulting in 112,565 single nucleotide polymorphisms (SNPs) called with a minor allele frequency of at least 5%. LD decay analysis of the panel indicates that the average LD for SNPs at 20 kb distance from each other was 0.34 (r2), which decayed to its half value (~ 0.17) at around 80 kb. By GWAS performed using mixed linear model, two hundred loci containing 448 SNPs on exons were identified based on the salt susceptibility index of the net photosynthetic rate at day 6 after salt stress; and the number of panicles, filled grains and unfilled grains per plant. One hundred and forty six genes, which accounted for 73% of the identified loci, co-localized with the previously reported salt quantitative trait loci (QTLs). The top four regions that contained a high number of significant SNPs were found on chromosome 8, 12, 1 and 2. While many are novel, their annotation is consistent with potential involvement in plant salt tolerance and in related agronomic traits. These significant SNPs greatly help narrow down the region within these QTLs where the likely underlying candidate genes can be identified. CONCLUSIONS Insight into the contribution of potential genes controlling salt tolerance from this GWAS provides further understanding of salt tolerance mechanisms of rice at the flowering stage, which can help improve yield productivity under salinity via gene cloning and genomic selection.
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Affiliation(s)
- Chakkree Lekklar
- Biological Sciences Program, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Center of Excellent in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Monnat Pongpanich
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Duangjai Suriya-arunroj
- Nakhon Ratchasima Rice Research Center, Rice Department, Ministry of Agriculture and Cooperatives, Nakhon Ratchasima, Thailand
| | - Aumnart Chinpongpanich
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Helen Tsai
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA USA
| | - Luca Comai
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA USA
| | - Supachitra Chadchawan
- Center of Excellent in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Teerapong Buaboocha
- Center of Excellent in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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85
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Prince SJ, Valliyodan B, Ye H, Yang M, Tai S, Hu W, Murphy M, Durnell LA, Song L, Joshi T, Liu Y, Van de Velde J, Vandepoele K, Grover Shannon J, Nguyen HT. Understanding genetic control of root system architecture in soybean: Insights into the genetic basis of lateral root number. PLANT, CELL & ENVIRONMENT 2019; 42:212-229. [PMID: 29749073 DOI: 10.1111/pce.13333] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 03/26/2018] [Indexed: 05/04/2023]
Abstract
Developing crops with better root systems is a promising strategy to ensure productivity in both optimum and stress environments. Root system architectural traits in 397 soybean accessions were characterized and a high-density single nucleotide polymorphisms (SNPs)-based genome-wide association study was performed to identify the underlying genes associated with root structure. SNPs associated with root architectural traits specific to landraces and elite germplasm pools were detected. Four loci were detected in landraces for lateral root number (LRN) and distribution of root thickness in diameter Class I with a major locus on chromosome 16. This major loci was detected in the coding region of unknown protein, and subsequent analyses demonstrated that root traits are affected with mutated haplotypes of the gene. In elite germplasm pool, 3 significant SNPs in alanine-glyoxalate aminotransferase, Leucine-Rich Repeat receptor/No apical meristem, and unknown functional genes were found to govern multiple traits including root surface area and volume. However, no major loci were detected for LRN in elite germplasm. Nucleotide diversity analysis found evidence of selective sweeps around the landraces LRN gene. Soybean accessions with minor and mutated allelic variants of LRN gene were found to perform better in both water-limited and optimal field conditions.
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Affiliation(s)
- Silvas J Prince
- Division of Plant Sciences, University of Missouri, Columbia, 65211, MO, USA
- Noble Research Institute, Ardmore, 73401, OK, USA
| | - Babu Valliyodan
- Division of Plant Sciences, University of Missouri, Columbia, 65211, MO, USA
| | - Heng Ye
- Division of Plant Sciences, University of Missouri, Columbia, 65211, MO, USA
| | - Ming Yang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Wushu Hu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Mackensie Murphy
- Division of Plant Sciences, University of Missouri, Columbia, 65211, MO, USA
| | - Lorellin A Durnell
- Division of Plant Sciences, University of Missouri, Columbia, 65211, MO, USA
| | - Li Song
- Division of Plant Sciences, University of Missouri, Columbia, 65211, MO, USA
- Institutes of Agricultural Science and Technology Development, Joint International Research Laboratory of Agriculture and Agri-Product Safety, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Trupti Joshi
- Department of Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Department of Molecular Microbiology and Immunology and Office of Research, School of Medicine, University of Missouri, Columbia, MO, USA
| | - Yang Liu
- Department of Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Jan Van de Velde
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 927, 9052, Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 927, 9052, Ghent, Belgium
| | - J Grover Shannon
- Division of Plant Sciences, University of Missouri, Columbia, 65211, MO, USA
| | - Henry T Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, 65211, MO, USA
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Lin HA, Chen SY, Chang FY, Tung CW, Chen YC, Shen WC, Chen RS, Wu CW, Chung CL. Genome-wide association study of rice genes and loci conferring resistance to Magnaporthe oryzae isolates from Taiwan. BOTANICAL STUDIES 2018; 59:32. [PMID: 30578469 PMCID: PMC6303224 DOI: 10.1186/s40529-018-0248-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 12/12/2018] [Indexed: 05/10/2023]
Abstract
BACKGROUND Rice blast, caused by Magnaporthe oryzae, is an important rice disease occurring in all rice-growing areas. To manage blast disease effectively and in an environmentally friendly way, it is important to continually discover diverse resistant resources for breeding. In this study, genome-wide association study (GWAS) was used to map genes/loci resistant to rice blast in the open-access rice diversity panel 1 (RDP1), previously genotyped with a 44K single-nucleotide polymorphism array. Two geographically and genetically different M. oryzae isolates from Taiwan, D41-2 and 12YL-DL3-2, were used to challenge RDP1. Infected leaves were visually rated for lesion type (LT) and evaluated for proportion of diseased leaf area (%DLA) by image analysis software. RESULTS A total of 32 quantitative trait loci (QTLs) were identified, including 6 from LT, 30 from DLA, and 4 from both LT and DLA. In all, 22 regions co-localized with previously reported resistance (R) genes and/or QTLs, including two cloned R genes, Pita and Ptr; 19 mapped R loci, and 20 QTLs. We identified 100 candidate genes encoding leucine-rich repeat-containing proteins, transcription factors, ubiquitination-related proteins, and peroxidases, among others, in the QTL intervals. Putative resistance and susceptibility haplotypes of the 32 QTL regions for each tested rice accessions were also determined. CONCLUSIONS By using Taiwanese M. oryzae isolates and image-based phenotyping for detailed GWAS, this study offers insights into the genetics underlying the natural variation of blast resistance in RDP1. The results can help facilitate the selection of desirable donors for gene/QTL validation and blast resistance breeding.
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Affiliation(s)
- Heng-An Lin
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617 Taiwan
| | - Szu-Yu Chen
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617 Taiwan
| | - Fang-Yu Chang
- Kaohsiung District Agricultural Research and Extension Station, No. 2-6, Dehe Rd., Pingtung County, 90846 Taiwan
| | - Chih-Wei Tung
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617 Taiwan
| | - Yi-Chia Chen
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617 Taiwan
| | - Wei-Chiang Shen
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617 Taiwan
| | - Ruey-Shyang Chen
- Department of Biochemical Science and Technology, National Chiayi University, No. 300, Syuefu Rd., Chiayi City, 60004 Taiwan
| | - Chih-Wen Wu
- Kaohsiung District Agricultural Research and Extension Station, No. 2-6, Dehe Rd., Pingtung County, 90846 Taiwan
| | - Chia-Lin Chung
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617 Taiwan
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Zhao M, Song J, Wu A, Hu T, Li J. Mining Beneficial Genes for Aluminum Tolerance Within a Core Collection of Rice Landraces Through Genome-Wide Association Mapping With High Density SNPs From Specific-Locus Amplified Fragment Sequencing. FRONTIERS IN PLANT SCIENCE 2018; 9:1838. [PMID: 30619409 PMCID: PMC6305482 DOI: 10.3389/fpls.2018.01838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 11/27/2018] [Indexed: 06/09/2023]
Abstract
Trivalent Aluminum (Al3+) in acidic soils is harmful to root growth and significantly reduce crop yields. Therefore, mining beneficial genes for Al tolerance is valuable for rice production. The objective of this research is to identify some beneficial genes for Al tolerance from rice landraces with high density SNP set from SLAF-seq (Specific-Locus Amplified Fragment sequencing). A total of 67,511 SNPs were obtained from SLAF-seq and used for genome-wide association study (GWAS) for Al tolerance with the 150 accessions of rice landraces in the Ting's rice core collection. The results showed that rice landraces in the Ting's rice core collection possessed a wide-range of variation for Al tolerance, measured by relative root elongation (RRE). With the mixed linear models, GWAS identified a total of 25 associations between SNPs and Al tolerant trait with p < 0.001 and false discovery rate (FDR) <10%. The explained percentage by quantitative trait locus (QTL) to phenotypic variation was from 7.27 to 13.31%. Five of twenty five QTLs identified in this study were co-localized with the previously cloned genes or previously identified QTLs related to Al tolerance or root growth/development. These results indicated that landraces are important sources for Al tolerance in rice and the mapping results could provide important information to breed Al tolerant rice cultivars through marker-assisted selection.
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Affiliation(s)
- Minghui Zhao
- Rice Research Institute, Shenyang Agriculture University, Shenyang, China
| | - Jiayu Song
- Rice Research Institute, Shenyang Agriculture University, Shenyang, China
| | - Aiting Wu
- Rice Research Institute, Shenyang Agriculture University, Shenyang, China
| | - Tao Hu
- Rice Research Institute, Shenyang Agriculture University, Shenyang, China
| | - Jinquan Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
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TA KN, KHONG NG, HA TL, NGUYEN DT, MAI DC, HOANG TG, PHUNG TPN, BOURRIE I, COURTOIS B, TRAN TTH, DINH BY, LA TN, DO NV, LEBRUN M, GANTET P, JOUANNIC S. A genome-wide association study using a Vietnamese landrace panel of rice (Oryza sativa) reveals new QTLs controlling panicle morphological traits. BMC PLANT BIOLOGY 2018; 18:282. [PMID: 30428844 PMCID: PMC6234598 DOI: 10.1186/s12870-018-1504-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 10/26/2018] [Indexed: 05/20/2023]
Abstract
CONTEXT Yield improvement is an important issue for rice breeding. Panicle architecture is one of the key components of rice yield and exhibits a large diversity. To identify the morphological and genetic determinants of panicle architecture, we performed a detailed phenotypic analysis and a genome-wide association study (GWAS) using an original panel of Vietnamese landraces. RESULTS Using a newly developed image analysis tool, morphological traits of the panicles were scored over two years: rachis length; primary, secondary and tertiary branch number; average length of primary and secondary branches; average length of internode on rachis and primary branch. We observed a high contribution of spikelet number and secondary branch number per panicle to the overall phenotypic diversity in the dataset. Twenty-nine stable QTLs associated with seven traits were detected through GWAS over the two years. Some of these QTLs were associated with genes already implicated in panicle development. Importantly, the present study revealed the existence of new QTLs associated with the spikelet number, secondary branch number and primary branch number traits. CONCLUSIONS Our phenotypic analysis of panicle architecture variation suggests that with the panel of samples used, morphological diversity depends largely on the balance between indeterminate vs. determinate axillary meristem fate on primary branches, supporting the notion of differences in axillary meristem fate between rachis and primary branches. Our genome-wide association study led to the identification of numerous genomic sites covering all the traits studied and will be of interest for breeding programs aimed at improving yield. The new QTLs detected in this study provide a basis for the identification of new genes controlling panicle development and yield in rice.
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Affiliation(s)
- Kim Nhung TA
- LMI RICE, University of Montpellier, IRD, CIRAD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
- Present address: Plant Genetics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Ngan Giang KHONG
- LMI RICE, University of Montpellier, IRD, CIRAD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
- Present address: Department of Molecular Biology, Palacký University, Olomouc, Czech Republic
| | - Thi Loan HA
- LMI RICE, University of Montpellier, IRD, CIRAD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
| | - Dieu Thu NGUYEN
- LMI RICE, University of Montpellier, IRD, CIRAD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
| | - Duc Chung MAI
- LMI RICE, University of Montpellier, IRD, CIRAD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
| | - Thi Giang HOANG
- LMI RICE, University of Montpellier, IRD, CIRAD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
| | - Thi Phuong Nhung PHUNG
- LMI RICE, University of Montpellier, IRD, CIRAD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
| | | | - Brigitte COURTOIS
- CIRAD, UMR AGAP, University of Montpellier, INRA, Montpellier, France
| | | | | | | | - Nang Vinh DO
- LMI RICE, University of Montpellier, IRD, CIRAD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
| | - Michel LEBRUN
- LMI RICE, University of Montpellier, IRD, CIRAD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
- UMR LSTM, University of Montpellier, CIRAD, IRD, Montpellier, France
| | - Pascal GANTET
- LMI RICE, University of Montpellier, IRD, CIRAD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
- UMR DIADE, University of Montpellier, IRD, Montpellier, France
| | - Stefan JOUANNIC
- LMI RICE, University of Montpellier, IRD, CIRAD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
- UMR DIADE, University of Montpellier, IRD, Montpellier, France
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Quero G, Gutiérrez L, Monteverde E, Blanco P, Pérez de Vida F, Rosas J, Fernández S, Garaycochea S, McCouch S, Berberian N, Simondi S, Bonnecarrère V. Genome-Wide Association Study Using Historical Breeding Populations Discovers Genomic Regions Involved in High-Quality Rice. THE PLANT GENOME 2018; 11:170076. [PMID: 30512035 DOI: 10.3835/plantgenome2017.08.0076] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Rice ( L.) is one of the most important staple food crops in the world; however, there has recently been a shift in consumer demand for higher grain quality. Therefore, understanding the genetic architecture of grain quality has become a key objective of rice breeding programs. Genome-wide association studies (GWAS) using large diversity panels have successfully identified genomic regions associated with complex traits in diverse crop species. Our main objective was to identify genomic regions associated with grain quality and to identify and characterize favorable haplotypes for selection. We used two locally adapted rice breeding populations and historical phenotypic data for three rice quality traits: yield after milling, percentage of head rice recovery, and percentage of chalky grain. We detected 22 putative quantitative trait loci (QTL) in the same genomic regions as starch synthesis, starch metabolism, and cell wall synthesis-related genes are found. Additionally, we found a genomic region on chromosome 6 in the population that was associated with all quality traits and we identified favorable haplotypes. Furthermore, this region is linked to the gene that codes for a starch branching enzyme I, which is implicated in starch granule formation. In , we also found two putative QTL linked to , , and . Our study provides an insight into the genetic basis of rice grain chalkiness, yield after milling, and head rice, identifying favorable haplotypes and molecular markers for selection in breeding programs.
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90
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Yang M, Lu K, Zhao FJ, Xie W, Ramakrishna P, Wang G, Du Q, Liang L, Sun C, Zhao H, Zhang Z, Liu Z, Tian J, Huang XY, Wang W, Dong H, Hu J, Ming L, Xing Y, Wang G, Xiao J, Salt DE, Lian X. Genome-Wide Association Studies Reveal the Genetic Basis of Ionomic Variation in Rice. THE PLANT CELL 2018; 30:2720-2740. [PMID: 30373760 PMCID: PMC6305983 DOI: 10.1105/tpc.18.00375] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 09/28/2018] [Accepted: 10/24/2018] [Indexed: 05/18/2023]
Abstract
Rice (Oryza sativa) is an important dietary source of both essential micronutrients and toxic trace elements for humans. The genetic basis underlying the variations in the mineral composition, the ionome, in rice remains largely unknown. Here, we describe a comprehensive study of the genetic architecture of the variation in the rice ionome performed using genome-wide association studies (GWAS) of the concentrations of 17 mineral elements in rice grain from a diverse panel of 529 accessions, each genotyped at ∼6.4 million single nucleotide polymorphism loci. We identified 72 loci associated with natural ionomic variations, 32 that are common across locations and 40 that are common within a single location. We identified candidate genes for 42 loci and provide evidence for the causal nature of three genes, the sodium transporter gene Os-HKT1;5 for sodium, Os-MOLYBDATE TRANSPORTER1;1 for molybdenum, and Grain number, plant height, and heading date7 for nitrogen. Comparison of GWAS data from rice versus Arabidopsis (Arabidopsis thaliana) also identified well-known as well as new candidates with potential for further characterization. Our study provides crucial insights into the genetic basis of ionomic variations in rice and serves as an important foundation for further studies on the genetic and molecular mechanisms controlling the rice ionome.
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Affiliation(s)
- Meng Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Kai Lu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Center of Applied Biotechnology, Wuhan Institute of Bioengineering, Wuhan 430415, China
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Weibo Xie
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Priya Ramakrishna
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom
| | - Guangyuan Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Qingqing Du
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Limin Liang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Cuiju Sun
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Hu Zhao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Zhanyi Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Zonghao Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Jingjing Tian
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Xin-Yuan Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Wensheng Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Huaxia Dong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Jintao Hu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Luchang Ming
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Gongwei Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Jinhua Xiao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - David E Salt
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom
| | - Xingming Lian
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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91
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Xiao N, Gao Y, Qian H, Gao Q, Wu Y, Zhang D, Zhang X, Yu L, Li Y, Pan C, Liu G, Zhou C, Jiang M, Huang N, Dai Z, Liang C, Chen Z, Chen J, Li A. Identification of Genes Related to Cold Tolerance and a Functional Allele That Confers Cold Tolerance. PLANT PHYSIOLOGY 2018; 177:1108-1123. [PMID: 29764927 PMCID: PMC6052991 DOI: 10.1104/pp.18.00209] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 05/05/2018] [Indexed: 05/22/2023]
Abstract
Cold stress is a major factor limiting rice (Oryza sativa) production worldwide, especially at the seedling and booting stages. The identification of genes associated with cold tolerance (CT) in rice is important for sustainable food production. Here, we report the results of a genome-wide association study to identify the genetic loci associated with CT by using a 1,033-accession diversity panel. We identified five CT-related genetic loci at the booting stage. Accessions carrying multiple cold-tolerant alleles displayed a higher seed-setting rate than did accessions that had no cold-tolerant alleles or carried a single allele. At the seedling stage, eight genetic loci related to CT have been identified. Among these, LOC_Os10g34840 was identified as the candidate gene for the qPSR10 genetic locus that is associated with CT in rice seedlings. A single-nucleotide polymorphism (SNP), SNP2G, at position 343 in LOC_Os10g34840 is responsible for conferring CT at the seedling stage in rice. Further analysis of the haplotype network revealed that SNP2G was present in 80.08% of the temperate japonica accessions but only 3.8% of the indica ones. We used marker-assisted selection to construct a series of BC4F3 near-isogenic lines possessing the cold-tolerant allele SNP2G When subjected to cold stress, plants carrying SNP2G survived better as seedlings and showed higher grain weight than plants carrying the SNP2A allele. The CT-related loci identified here and the functional verification of LOC_Os10g34840 will provide genetic resources for breeding cold-tolerant varieties and for studying the molecular basis of CT in rice.
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Affiliation(s)
- Ning Xiao
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou 225009, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing 210095, China
- National Rice Industry Technology System of Yangzhou Comprehensive Experimental Station, Yangzhou, Jiangsu Province, 225009, China
| | - Yong Gao
- Jiangsu Key Laboratories of Crop Genetics and Physiology and Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu, Yangzhou University, Yangzhou 225009, China
| | - Huangjun Qian
- Jiangsu Key Laboratories of Crop Genetics and Physiology and Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu, Yangzhou University, Yangzhou 225009, China
| | - Qiang Gao
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yunyu Wu
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou 225009, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing 210095, China
- National Rice Industry Technology System of Yangzhou Comprehensive Experimental Station, Yangzhou, Jiangsu Province, 225009, China
| | - Dongping Zhang
- Jiangsu Key Laboratories of Crop Genetics and Physiology and Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu, Yangzhou University, Yangzhou 225009, China
| | - Xiaoxiang Zhang
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou 225009, China
| | - Ling Yu
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou 225009, China
| | - Yuhong Li
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou 225009, China
| | - Cunhong Pan
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou 225009, China
| | - Guangqing Liu
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou 225009, China
| | - Changhai Zhou
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou 225009, China
| | - Min Jiang
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou 225009, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing 210095, China
- National Rice Industry Technology System of Yangzhou Comprehensive Experimental Station, Yangzhou, Jiangsu Province, 225009, China
| | - Niansheng Huang
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou 225009, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing 210095, China
- National Rice Industry Technology System of Yangzhou Comprehensive Experimental Station, Yangzhou, Jiangsu Province, 225009, China
| | - Zhengyuan Dai
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou 225009, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing 210095, China
- National Rice Industry Technology System of Yangzhou Comprehensive Experimental Station, Yangzhou, Jiangsu Province, 225009, China
| | - Chengzhi Liang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhou Chen
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianmin Chen
- Jiangsu Key Laboratories of Crop Genetics and Physiology and Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu, Yangzhou University, Yangzhou 225009, China
| | - Aihong Li
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou 225009, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing 210095, China
- National Rice Industry Technology System of Yangzhou Comprehensive Experimental Station, Yangzhou, Jiangsu Province, 225009, China
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92
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Tao Y, Niu Y, Wang Y, Chen T, Naveed SA, Zhang J, Xu J, Li Z. Genome-wide association mapping of aluminum toxicity tolerance and fine mapping of a candidate gene for Nrat1 in rice. PLoS One 2018; 13:e0198589. [PMID: 29894520 PMCID: PMC5997306 DOI: 10.1371/journal.pone.0198589] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 05/22/2018] [Indexed: 11/30/2022] Open
Abstract
Aluminum (Al) stress is becoming the major limiting factor in crop production in acidic soils. Rice has been reported as the most Al-tolerant crop and the capacity of Al toxicity tolerance is generally evaluated by comparing root growth under Al stress. Here, we performed an association mapping of Al toxicity tolerance using a core collection of 211 indica rice accessions with 700 K high quality SNP data. A total of 21 putative QTL affecting shoot height (SH), root length (RL), shoot fresh weight (SFW), shoot dry weight (SDW), root dry weight (RDW) and shoot water content (SWC) were identified at seedling stage, including three QTL detected only under control condition, eight detected only under Al stress condition, ten simultaneously detected in both control and Al stress conditions, and seven were identified by stress tolerance index of their corresponding traits. Total of 21 candidate genes for 7 important QTL regions associated with Al toxicity tolerance were identified based on combined haplotype analysis and functional annotation, and the most likely candidate gene(s) for each important QTL were also discussed. Also a candidate gene Nrat1 on chromosome 2 was further fine-mapped using BSA-seq and linkage analysis in the F2 population derived from the cross of Al tolerant accession CC105 and super susceptible accession CC180. A new non-synonymous SNP variation was observed at Nrat1 between CC105 and CC180, which resulted in an amino-acid substitution from Ala (A) in CC105 to Asp (D) in CC180. Haplotype analysis of Nrat1 using 327 3K RGP accessions indicated that minor allele variations in aus and indica subpopulations decreased Al toxicity tolerance in rice. The candidate genes identified in this study provide valuable information for improvement of Al toxicity tolerance in rice. Our research indicated that minor alleles are important for QTL mapping and its application in rice breeding when natural gene resources are used.
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Affiliation(s)
- Yonghong Tao
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanan Niu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yun Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tianxiao Chen
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shahzad Amir Naveed
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jian Zhang
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| | - Jianlong Xu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
- Shenzhen Institute of Breeding and Innovation, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhikang Li
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
- Shenzhen Institute of Breeding and Innovation, Chinese Academy of Agricultural Sciences, Shenzhen, China
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93
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Identification of quantitative trait loci for salinity tolerance in rice (Oryza sativa L.) using IR29/Hasawi mapping population. J Genet 2018; 96:571-582. [PMID: 28947705 DOI: 10.1007/s12041-017-0803-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Salinity is the second most important abiotic stress after drought that hampers rice production, especially in south and Southeast Asia. Breeding approach supplemented with molecularmarkers-assisted selection is the most promising approach in terms of efficiency to increase the productivity under salt-affected soils. Thirty-day-old rice seedlings of 300 F5:6 recombinant-inbred lines derived from a cross between the salt sensitive, IR29 (indica), and a salt tolerant, Hasawi (aus), were used to identify quantitative trait loci (QTLs) linked to salinity tolerance. One hundred and ninety four polymorphic SNP markers were used to construct a genetic linkage map involving 142 selected RILs that covered 1441.96 cM genome with an average distance of 7.88 cMbetween loci. Twenty new QTLs (LOD > 3) were identified on chromosomes 1, 2, 4, 6, 8, 9 and 12 using composite interval mapping with R2 as high as >20% with LODvalue of 7.21. Many earlier studies reported big qSaltol for seedling stage salinity tolerance in rice is on short arm of chromosome 1 but none of the QTL in our study was on qSaltol or nearby position, therefore, Hasawi conferred salinity tolerance in RILs due to novel QTLs. It is suggested to fine map the novel QTLs so that the level of salinity tolerance could be further enhanced by pyramiding of the different QTLs in one genetic background through marker-assisted selection.
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94
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Patishtan J, Hartley TN, Fonseca de Carvalho R, Maathuis FJM. Genome-wide association studies to identify rice salt-tolerance markers. PLANT, CELL & ENVIRONMENT 2018; 41:970-982. [PMID: 28436093 DOI: 10.1111/pce.12975] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 04/03/2017] [Accepted: 04/03/2017] [Indexed: 05/17/2023]
Abstract
Salinity is an ever increasing menace that affects agriculture worldwide. Crops such as rice are salt sensitive, but its degree of susceptibility varies widely between cultivars pointing to extensive genetic diversity that can be exploited to identify genes and proteins that are relevant in the response of rice to salt stress. We used a diversity panel of 306 rice accessions and collected phenotypic data after short (6 h), medium (7 d) and long (30 d) salinity treatment (50 mm NaCl). A genome-wide association study (GWAS) was subsequently performed, which identified around 1200 candidate genes from many functional categories, but this was treatment period dependent. Further analysis showed the presence of cation transporters and transcription factors with a known role in salinity tolerance and those that hitherto were not known to be involved in salt stress. Localization analysis of single nucleotide polymorphisms (SNPs) showed the presence of several hundred non-synonymous SNPs (nsSNPs) in coding regions and earmarked specific genomic regions with increased numbers of nsSNPs. It points to components of the ubiquitination pathway as important sources of genetic diversity that could underpin phenotypic variation in stress tolerance.
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Affiliation(s)
- Juan Patishtan
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Tom N Hartley
- Department of Biology, University of York, York, YO10 5DD, UK
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95
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Genome-wide association study to identify candidate loci and genes for Mn toxicity tolerance in rice. PLoS One 2018; 13:e0192116. [PMID: 29425206 PMCID: PMC5806864 DOI: 10.1371/journal.pone.0192116] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 01/18/2018] [Indexed: 11/19/2022] Open
Abstract
Manganese (Mn) is an essential micro-nutrient for plants, but flooded rice fields can accumulate high levels of Mn2+ leading to Mn toxicity. Here, we present a genome-wide association study (GWAS) to identify candidate loci conferring Mn toxicity tolerance in rice (Oryza sativa L.). A diversity panel of 288 genotypes was grown in hydroponic solutions in a greenhouse under optimal and toxic Mn concentrations. We applied a Mn toxicity treatment (5 ppm Mn2+, 3 weeks) at twelve days after transplanting. Mn toxicity caused moderate damage in rice in terms of biomass loss and symptom formation despite extremely high shoot Mn concentrations ranging from 2.4 to 17.4 mg g-1. The tropical japonica subpopulation was more sensitive to Mn toxicity than other subpopulations. Leaf damage symptoms were significantly correlated with Mn uptake into shoots. Association mapping was conducted for seven traits using 416741 single nucleotide polymorphism (SNP) markers using a mixed linear model, and detected six significant associations for the traits shoot manganese concentration and relative shoot length. Candidate regions contained genes coding for a heavy metal transporter, peroxidase precursor and Mn2+ ion binding proteins. The significant marker SNP-2.22465867 caused an amino acid change in a gene (LOC_Os02g37170) with unknown function. This study demonstrated significant natural variation in rice for Mn toxicity tolerance and the possibility of using GWAS to unravel genetic factors responsible for such complex traits.
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96
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Wang X, Zou B, Shao Q, Cui Y, Lu S, Zhang Y, Huang Q, Huang J, Hua J. Natural variation reveals that OsSAP16 controls low-temperature germination in rice. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:413-421. [PMID: 29237030 PMCID: PMC5853544 DOI: 10.1093/jxb/erx413] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 10/25/2017] [Indexed: 05/06/2023]
Abstract
Low temperature affects seed germination in plants, and low-temperature germination (LTG) is an important agronomic trait. Natural variation of LTG has been reported in rice, but the molecular basis for this variation is largely unknown. Here we report the phenotypic analysis of LTG in 187 rice natural accessions and a genome-wide association study (GWAS) of LTG in this collection. A total of 53 quantitative trait loci (QTLs) were found to be associated with LTG, of which 20 were located in previously reported QTLs. We further identified Stress-Associated Protein 16 (OsSAP16), coding for a zinc-finger domain protein, as a causal gene for one of the major LTG QTLs. Loss of OsSAP16 function reduces germination while greater expression of OsSAP16 enhances germination at low temperature. In addition, accessions with extremely high and low LTG values have correspondingly high and low OsSAP16 expression at low temperatures, suggesting that variation in expression of the OsSAP16 gene contributes to LTG variation. As the first case of identification of an LTG gene through GWAS, this study indicates that GWAS of natural accessions is an effective strategy in genetically dissecting LTG processes and gaining molecular understanding of low-temperature response and germination.
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Affiliation(s)
- Xiang Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Baohong Zou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Qiaolin Shao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Yongmei Cui
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Shan Lu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Yan Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Quansheng Huang
- Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Ji Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Correspondence: ,
| | - Jian Hua
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Plant Biology Section, School of Integrated Plant Science, Cornell University, Ithaca, NY, USA
- Correspondence: ,
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97
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Wójcik-Jagła M, Fiust A, Kościelniak J, Rapacz M. Association mapping of drought tolerance-related traits in barley to complement a traditional biparental QTL mapping study. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:167-181. [PMID: 29071393 PMCID: PMC5750332 DOI: 10.1007/s00122-017-2994-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 09/27/2017] [Indexed: 05/04/2023]
Abstract
Association mapping of drought-related traits in barley was used to increase the density of existing QTL maps without recreating mapping populations. We used 109 spring barley genotypes exhibiting high or low drought tolerance to elucidate the associations between diversity array technology sequencing (DArTseq) and single nucleotide polymorphism (SNP) markers and various physiological parameters related to plant responses to drought conditions. The study was performed in controlled conditions (growth chambers), drought tolerance was phenotyped in the four-leaf seedlings. We identified 58 associations including 34 new markers (i.e., 16 DArTseq and 18 SNP markers). The results for three markers were consistent with the data obtained in an earlier traditional biparental QTL mapping study. The regions neighboring markers on linkage group 2H contained the highest number of significant marker-trait associations. Five markers related to the photosynthetic activity of photosystem II were detected on chromosome 4H. The lowest number of associations were observed for the sequences neighboring DArT markers on linkage group 6H. A chromosome 3H region related to water use efficiency and net photosynthesis rate in both biparental QTL, and association study, may be particularly valuable, as these parameters correspond to the ability of plants to remain highly productive under water deficit stress. Our findings confirm that association mapping can increase the density of existing QTL maps without recreating mapping populations.
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Affiliation(s)
- Magdalena Wójcik-Jagła
- Department of Plant Physiology, University of Agriculture in Krakow, Podłużna 3, 30-239, Kraków, Poland.
| | - Anna Fiust
- Department of Plant Physiology, University of Agriculture in Krakow, Podłużna 3, 30-239, Kraków, Poland
| | - Janusz Kościelniak
- Department of Plant Physiology, University of Agriculture in Krakow, Podłużna 3, 30-239, Kraków, Poland
| | - Marcin Rapacz
- Department of Plant Physiology, University of Agriculture in Krakow, Podłużna 3, 30-239, Kraków, Poland
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Dang X, Fang B, Chen X, Li D, Sowadan O, Dong Z, Liu E, She D, Wu G, Liang Y, Hong D. Favorable Marker Alleles for Panicle Exsertion Length in Rice ( Oryza sativa L.) Mined by Association Mapping and the RSTEP-LRT Method. FRONTIERS IN PLANT SCIENCE 2017; 8:2112. [PMID: 29312380 PMCID: PMC5732986 DOI: 10.3389/fpls.2017.02112] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/27/2017] [Indexed: 05/14/2023]
Abstract
The panicle exsertion length (PEL) in rice (Oryza sativa L.) is an important trait for hybrid seed production. We investigated the PEL in a chromosome segment substitution line (CSSL) population consisting of 66 lines and a natural population composed of 540 varieties. In the CSSL population, a total of seven QTLs for PEL were detected across two environments. The percentage of phenotypic variance explained (PVE) ranged from 10.22 to 50.18%, and the additive effect ranged from -1.77 to 6.47 cm. Among the seven QTLs, qPEL10.2 had the largest PVE, 44.05 and 50.18%, with an additive effect of 5.91 and 6.47 cm in 2015 and in 2016, respectively. In the natural population, 13 SSR marker loci were detected that were associated with PEL in all four environments, with the PVE ranging from 1.20 to 6.26%. Among the 13 loci, 7 were novel. The RM5746-170 bp allele had the largest phenotypic effect (5.11 cm), and the typical carrier variety was Qiaobinghuang. An RM5620-RM6100 region harboring the EUI2 locus on chromosome 10 was detected in both populations. The sequencing results showed that the accessions with a shorter PEL contained the A base, while the accessions with a longer PEL contained the G base at the 1,475 bp location of the EUI2 gene.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Delin Hong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
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Hori K, Yamamoto T, Yano M. Genetic dissection of agronomically important traits in closely related temperate japonica rice cultivars. BREEDING SCIENCE 2017; 67:427-434. [PMID: 29398936 PMCID: PMC5790047 DOI: 10.1270/jsbbs.17053] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 07/11/2017] [Indexed: 05/15/2023]
Abstract
Many quantitative trait loci (QTLs) for agronomically important traits such as grain yield, disease resistance, and stress tolerance of rice (Oryza sativa L.) have been detected by using segregating populations derived from crosses between indica and japonica subspecies or with wild relatives. However, the QTLs involved in the control of natural variation in agronomic traits among closely related cultivars are still unclear. Decoding the whole genome sequences of Nipponbare and other temperate japonica rice cultivars has accelerated the collection of a huge number of single nucleotide polymorphisms (SNPs). These SNPs are good resource for developing polymorphic DNA markers and for detecting QTLs distributed across all rice chromosomes. The temperate japonica rice cultivar Koshihikari has remained the top cultivar for about 40 years since 1979 in Japan. Unraveling the genetic factors in Koshihikari will provide important insights into improving agronomic traits in temperate japonica rice cultivars. Here we describe recent progress in our studies as an example of genetic analysis in closely related cultivars.
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100
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Volante A, Tondelli A, Aragona M, Valente MT, Biselli C, Desiderio F, Bagnaresi P, Matic S, Gullino ML, Infantino A, Spadaro D, Valè G. Identification of bakanae disease resistance loci in japonica rice through genome wide association study. RICE (NEW YORK, N.Y.) 2017; 10:29. [PMID: 28597326 PMCID: PMC5465229 DOI: 10.1186/s12284-017-0168-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 05/30/2017] [Indexed: 05/02/2023]
Abstract
BACKGROUND Bakanae disease, caused by seed-borne Fusarium species, mainly F. fujikuroi, is a rice disease whose importance is considerably increasing in several rice growing countries, leading to incremental production losses. RESULTS A germplasm collection of japonica rice was screened for F. fujikuroi resistance, allowing the identification of accessions with high-to-moderate levels of resistance to bakanae. A GWAS approach uncovered two genomic regions highly associated with the observed phenotypic variation for response to bakanae infection on the short arm of chromosome 1 (named as qBK1_628091) and on the long arm of chromosome 4 (named as qBK4_31750955). High levels of phenotypic resistance to bakanae were associated to the cumulated presence of the resistant alleles at the two resistance loci, suggesting that they can provide useful levels of disease protection in resistance breeding. A fine comparison with the genomic positions of qBK1_628091 and qBK4_31750955 with respect to the QTLs for bakanae resistance reported in the literature suggests that the resistant loci here described represent new genomic regions associated to F. fujikuroi resistance. A search for candidate genes with a putative role in bakanae resistance was conducted considering all the annotated genes and F. fujikuroi-related DEGs included in the two genomic regions highlighting several gene functions that could be involved in resistance, thus paving the way to the functional characterization of the resistance loci. CONCLUSIONS New effective sources for bakanae resistance were identified on rice chromosomes 1 and 4 and tools for resistance breeding are provided.
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Affiliation(s)
- Andrea Volante
- Council for Agricultural Research and Economics (CREA), Rice Research Unit, S.S. 11 to Torino, Km 2.5, 13100, Vercelli, Italy
| | - Alessandro Tondelli
- Council for Agricultural Research and Economics (CREA), Genomics Research Centre, Via S. Protaso, 302, 29017, Piacenza, Fiorenzuola d'Arda, Italy
| | - Maria Aragona
- Council for Agricultural Research and Economics (CREA), Plant Pathology Research Centre, Via C. G. Bertero 22, 00156, Roma, Italy
| | - Maria Teresa Valente
- Council for Agricultural Research and Economics (CREA), Plant Pathology Research Centre, Via C. G. Bertero 22, 00156, Roma, Italy
| | - Chiara Biselli
- Council for Agricultural Research and Economics (CREA), Genomics Research Centre, Via S. Protaso, 302, 29017, Piacenza, Fiorenzuola d'Arda, Italy
| | - Francesca Desiderio
- Council for Agricultural Research and Economics (CREA), Genomics Research Centre, Via S. Protaso, 302, 29017, Piacenza, Fiorenzuola d'Arda, Italy
| | - Paolo Bagnaresi
- Council for Agricultural Research and Economics (CREA), Genomics Research Centre, Via S. Protaso, 302, 29017, Piacenza, Fiorenzuola d'Arda, Italy
| | - Slavica Matic
- AGROINNOVA, Università di Torino, Largo P. Braccini 2, 10095, Torino, Grugliasco, Italy
| | - Maria Lodovica Gullino
- AGROINNOVA, Università di Torino, Largo P. Braccini 2, 10095, Torino, Grugliasco, Italy
- DISAFA, Università di Torino, Largo P. Braccini 2, 10095, Torino, Grugliasco, Italy
| | - Alessandro Infantino
- Council for Agricultural Research and Economics (CREA), Plant Pathology Research Centre, Via C. G. Bertero 22, 00156, Roma, Italy
| | - Davide Spadaro
- AGROINNOVA, Università di Torino, Largo P. Braccini 2, 10095, Torino, Grugliasco, Italy
- DISAFA, Università di Torino, Largo P. Braccini 2, 10095, Torino, Grugliasco, Italy
| | - Giampiero Valè
- Council for Agricultural Research and Economics (CREA), Rice Research Unit, S.S. 11 to Torino, Km 2.5, 13100, Vercelli, Italy.
- Council for Agricultural Research and Economics (CREA), Genomics Research Centre, Via S. Protaso, 302, 29017, Piacenza, Fiorenzuola d'Arda, Italy.
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