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Phetluan W, Wanchana S, Aesomnuk W, Adams J, Pitaloka MK, Ruanjaichon V, Vanavichit A, Toojinda T, Gray JE, Arikit S. Candidate genes affecting stomatal density in rice (Oryza sativa L.) identified by genome-wide association. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 330:111624. [PMID: 36737006 DOI: 10.1016/j.plantsci.2023.111624] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/18/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Stomata regulate photosynthesis and water loss. They have been an active subject of research for centuries, but our knowledge of the genetic components that regulate stomatal development in crops remains very limited in comparison to the model plant Arabidopsis thaliana. Leaf stomatal density was found to vary by over 2.5-fold across a panel of 235 rice accessions. Using GWAS, we successfully identified five different QTLs associated with stomatal density on chromosomes 2, 3, 9, and 12. Forty-two genes were identified within the haplotype blocks corresponding to these QTLs. Of these, nine genes contained haplotypes that were associated with different stomatal densities. These include a gene encoding a trehalose-6-phosphate synthase, an enzyme that has previously been associated with altered stomatal density in Arabidopsis, and genes encoding a B-BOX zinc finger family protein, a leucine-rich repeat family protein, and the 40 S ribosomal protein S3a, none of which have previously been linked to stomatal traits. We investigated further and show that a closely related B-BOX protein regulates stomatal development in Arabidopsis. The results of this study provide information on genetic associations with stomatal density in rice. The QTLs and candidate genes may be useful in future breeding programs for low or high stomatal density and, consequently, improved photosynthetic capacity, water use efficiency, or drought tolerance.
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Affiliation(s)
- Watchara Phetluan
- Center for Agricultural Biotechnology, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand; Center of Excellence on Agricultural Biotechnology: (AG-BIO/MHESI), Bangkok 10900, Thailand.
| | - Samart Wanchana
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Pahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand.
| | - Wanchana Aesomnuk
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Pahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand.
| | - Julian Adams
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield S102TN, United Kingdom.
| | - Mutiara K Pitaloka
- Rice Science Center, Kasetsart University, Kamphaeng Saen, Nakhon Pathom 73140, Thailand.
| | - Vinitchan Ruanjaichon
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Pahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand.
| | - Apichart Vanavichit
- Rice Science Center, Kasetsart University, Kamphaeng Saen, Nakhon Pathom 73140, Thailand; Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom 73140, Thailand.
| | - Theerayut Toojinda
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Pahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand.
| | - Julie E Gray
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield S102TN, United Kingdom.
| | - Siwaret Arikit
- Rice Science Center, Kasetsart University, Kamphaeng Saen, Nakhon Pathom 73140, Thailand; Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom 73140, Thailand.
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Chen Y, Niu S, Deng X, Song Q, He L, Bai D, He Y. Genome-wide association study of leaf-related traits in tea plant in Guizhou based on genotyping-by-sequencing. BMC PLANT BIOLOGY 2023; 23:196. [PMID: 37046207 PMCID: PMC10091845 DOI: 10.1186/s12870-023-04192-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Studying the genetic characteristics of tea plant (Camellia spp.) leaf traits is essential for improving yield and quality through breeding and selection. Guizhou Plateau, an important part of the original center of tea plants, has rich genetic resources. However, few studies have explored the associations between tea plant leaf traits and single nucleotide polymorphism (SNP) markers in Guizhou. RESULTS In this study, we used the genotyping-by-sequencing (GBS) method to identify 100,829 SNP markers from 338 accessions of tea germplasm in Guizhou Plateau, a region with rich genetic resources. We assessed population structure based on high-quality SNPs, constructed phylogenetic relationships, and performed genome-wide association studies (GWASs). Four inferred pure groups (G-I, G-II, G-III, and G-IV) and one inferred admixture group (G-V), were identified by a population structure analysis, and verified by principal component analyses and phylogenetic analyses. Through GWAS, we identified six candidate genes associated with four leaf traits, including mature leaf size, texture, color and shape. Specifically, two candidate genes, located on chromosomes 1 and 9, were significantly associated with mature leaf size, while two genes, located on chromosomes 8 and 11, were significantly associated with mature leaf texture. Additionally, two candidate genes, located on chromosomes 1 and 2 were identified as being associated with mature leaf color and mature leaf shape, respectively. We verified the expression level of two candidate genes was verified using reverse transcription quantitative polymerase chain reaction (RT-qPCR) and designed a derived cleaved amplified polymorphism (dCAPS) marker that co-segregated with mature leaf size, which could be used for marker-assisted selection (MAS) breeding in Camellia sinensis. CONCLUSIONS In the present study, by using GWAS approaches with the 338 tea accessions population in Guizhou, we revealed a list of SNPs markers and candidate genes that were significantly associated with four leaf traits. This work provides theoretical and practical basis for the genetic breeding of related traits in tea plant leaves.
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Affiliation(s)
- Yanjun Chen
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
| | - Suzhen Niu
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Institute of Agro-Bioengineering, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
| | - Xinyue Deng
- School of Architecture, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
| | - Qinfei Song
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
| | - Limin He
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
| | - Dingchen Bai
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
| | - Yingqin He
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
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Identification of Pathogenicity Loci in Magnaporthe oryzae Using GWAS with Neck Blast Phenotypic Data. Genes (Basel) 2022; 13:genes13050916. [PMID: 35627301 PMCID: PMC9141631 DOI: 10.3390/genes13050916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/13/2022] [Accepted: 05/16/2022] [Indexed: 12/10/2022] Open
Abstract
Magnaporthae oryzae (M. oryzae) is the most destructive disease of rice worldwide. In this study, one hundred and two isolates of M. oryzae were collected from rice (Oryzae sativa L.) from 2001 to 2017, and six rice varieties with resistance genes Pizt, Pish, Pik, Pib, and Pi2 were used in a genome-wide association study to identify pathogenicity loci in M. oryzae. Genome-wide association analysis was performed using 5338 single nucleotide polymorphism (SNPs) and phenotypic data of neck blast screening by TASSEL software together with haplotype block and SNP effect analysis. Twenty-seven significant SNPs were identified on chromosomes 1, 2, 3, 4, 5, 6, and 7. Many predicted genes (820 genes) were found in the target regions of six rice varieties. Most of these genes are described as putative uncharacterized proteins, however, some genes were reported related to virulence in M. oryzae. Moreover, this study revealed that R genes, Pik, Pish, and Pi2, were broad-spectrum resistant against neck blast disease caused by Thai blast isolate. Haplotype analysis revealed that the combination of the favorable alleles causing reduced virulence of isolates against IRBLz5-CA carrying Pi2 gene contributes 69% of the phenotypic variation in pathogenicity. The target regions and information are useful to develop marker-specific genes to classify blast fungal isolates and select appropriate resistance genes for rice cultivation and improvement.
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Darwell CT, Wanchana S, Ruanjaichon V, Siangliw M, Thunnom B, Aesomnuk W, Toojinda T. riceExplorer: Uncovering the Hidden Potential of a National Genomic Resource Against a Global Database. FRONTIERS IN PLANT SCIENCE 2022; 13:781153. [PMID: 35574109 PMCID: PMC9100803 DOI: 10.3389/fpls.2022.781153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 04/06/2022] [Indexed: 06/15/2023]
Abstract
Agricultural crop breeding programs, particularly at the national level, typically consist of a core panel of elite breeding cultivars alongside a number of local landrace varieties (or other endemic cultivars) that provide additional sources of phenotypic and genomic variation or contribute as experimental materials (e.g., in GWAS studies). Three issues commonly arise. First, focusing primarily on core development accessions may mean that the potential contributions of landraces or other secondary accessions may be overlooked. Second, elite cultivars may accumulate deleterious alleles away from nontarget loci due to the strong effects of artificial selection. Finally, a tendency to focus solely on SNP-based methods may cause incomplete or erroneous identification of functional variants. In practice, integration of local breeding programs with findings from global database projects may be challenging. First, local GWAS experiments may only indicate useful functional variants according to the diversity of the experimental panel, while other potentially useful loci-identifiable at a global level-may remain undiscovered. Second, large-scale experiments such as GWAS may prove prohibitively costly or logistically challenging for some agencies. Here, we present a fully automated bioinformatics pipeline (riceExplorer) that can easily integrate local breeding program sequence data with international database resources, without relying on any phenotypic experimental procedure. It identifies associated functional haplotypes that may prove more robust in determining the genotypic determinants of desirable crop phenotypes. In brief, riceExplorer evaluates a global crop database (IRRI 3000 Rice Genomes) to identify haplotypes that are associated with extreme phenotypic variation at the global level and recorded in the database. It then examines which potentially useful variants are present in the local crop panel, before distinguishing between those that are already incorporated into the elite breeding accessions and those only found among secondary varieties (e.g., landraces). Results highlight the effectiveness of our pipeline, identifying potentially useful functional haplotypes across the genome that are absent from elite cultivars and found among landraces and other secondary varieties in our breeding program. riceExplorer can automatically conduct a full genome analysis and produces annotated graphical output of chromosomal maps, potential global diversity sources, and summary tables.
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Liu Z, Zhu Y, Shi H, Qiu J, Ding X, Kou Y. Recent Progress in Rice Broad-Spectrum Disease Resistance. Int J Mol Sci 2021; 22:11658. [PMID: 34769087 PMCID: PMC8584176 DOI: 10.3390/ijms222111658] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/25/2021] [Accepted: 10/25/2021] [Indexed: 11/25/2022] Open
Abstract
Rice is one of the most important food crops in the world. However, stable rice production is constrained by various diseases, in particular rice blast, sheath blight, bacterial blight, and virus diseases. Breeding and cultivation of resistant rice varieties is the most effective method to control the infection of pathogens. Exploitation and utilization of the genetic determinants of broad-spectrum resistance represent a desired way to improve the resistance of susceptible rice varieties. Recently, researchers have focused on the identification of rice broad-spectrum disease resistance genes, which include R genes, defense-regulator genes, and quantitative trait loci (QTL) against two or more pathogen species or many isolates of the same pathogen species. The cloning of broad-spectrum disease resistance genes and understanding their underlying mechanisms not only provide new genetic resources for breeding broad-spectrum rice varieties, but also promote the development of new disease resistance breeding strategies, such as editing susceptibility and executor R genes. In this review, the most recent advances in the identification of broad-spectrum disease resistance genes in rice and their application in crop improvement through biotechnology approaches during the past 10 years are summarized.
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Affiliation(s)
- Zhiquan Liu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (Z.L.); (Y.Z.); (H.S.); (J.Q.)
| | - Yujun Zhu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (Z.L.); (Y.Z.); (H.S.); (J.Q.)
| | - Huanbin Shi
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (Z.L.); (Y.Z.); (H.S.); (J.Q.)
| | - Jiehua Qiu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (Z.L.); (Y.Z.); (H.S.); (J.Q.)
| | - Xinhua Ding
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian 271018, China;
| | - Yanjun Kou
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (Z.L.); (Y.Z.); (H.S.); (J.Q.)
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