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Dong X, Ma X, Zhao Z, Ma M. Exogenous betaine enhances salt tolerance of Glycyrrhiza uralensis through multiple pathways. BMC PLANT BIOLOGY 2024; 24:165. [PMID: 38431542 PMCID: PMC10908008 DOI: 10.1186/s12870-024-04851-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/22/2024] [Indexed: 03/05/2024]
Abstract
BACKGROUND Glycyrrhiza uralensis Fisch., a valuable medicinal plant, shows contrasting salt tolerance between seedlings and perennial individuals, and salt tolerance at seedling stage is very weak. Understanding this difference is crucial for optimizing cultivation practices and maximizing the plant's economic potential. Salt stress resistance at the seedling stage is the key to the cultivation of the plant using salinized land. This study investigated the physiological mechanism of the application of glycine betaine (0, 10, 20, 40, 80 mM) to seedling stages of G. uralensis under salt stress (160 mM NaCl). RESULTS G. uralensis seedlings' growth was severely inhibited under NaCl stress conditions, but the addition of GB effectively mitigated its effects, with 20 mM GB had showing most significant alleviating effect. The application of 20 mM GB under NaCl stress conditions significantly increased total root length (80.38%), total root surface area (93.28%), and total root volume (175.61%), and significantly increased the GB content in its roots, stems, and leaves by 36.88%, 107.05%, and 21.63%, respectively. The activity of betaine aldehyde dehydrogenase 2 (BADH2) was increased by 74.10%, 249.38%, and 150.60%, respectively. The 20 mM GB-addition treatment significantly increased content of osmoregulatory substances (the contents of soluble protein, soluble sugar and proline increased by 7.05%, 70.52% and 661.06% in roots, and also increased by 30.74%, 47.11% and 26.88% in leaves, respectively.). Furthermore, it markedly enhanced the activity of antioxidant enzymes and the content of antioxidants (SOD, CAT, POD, APX and activities and ASA contents were elevated by 59.55%, 413.07%, 225.91%, 300.00% and 73.33% in the root, and increased by 877.51%, 359.89%, 199.15%, 144.35%, and 108.11% in leaves, respectively.), and obviously promoted salt secretion capacity of the leaves, which especially promoted the secretion of Na+ (1.37 times). CONCLUSIONS In summary, the exogenous addition of GB significantly enhances the salt tolerance of G. uralensis seedlings, promoting osmoregulatory substances, antioxidant enzyme activities, excess salt discharge especially the significant promotion of the secretion of Na+Future studies should aim to elucidate the molecular mechanisms that operate when GB regulates saline stress tolerance.
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Affiliation(s)
- Xinping Dong
- College of Life Sciences, Shihezi University, Shihezi, 832003, China
- Ministry of Education Key Laboratory of Xinjiang Phytomedicine Resource Utilization, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Xiaomei Ma
- College of Life Sciences, Shihezi University, Shihezi, 832003, China
- Ministry of Education Key Laboratory of Xinjiang Phytomedicine Resource Utilization, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Zhilong Zhao
- College of Life Sciences, Shihezi University, Shihezi, 832003, China
- Ministry of Education Key Laboratory of Xinjiang Phytomedicine Resource Utilization, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Miao Ma
- College of Life Sciences, Shihezi University, Shihezi, 832003, China.
- Ministry of Education Key Laboratory of Xinjiang Phytomedicine Resource Utilization, College of Life Sciences, Shihezi University, Shihezi, 832003, China.
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Somsri A, Chu SH, Nawade B, Lee CY, Park YJ. Harnessing γ-TMT Genetic Variations and Haplotypes for Vitamin E Diversity in the Korean Rice Collection. Antioxidants (Basel) 2024; 13:234. [PMID: 38397832 PMCID: PMC10886147 DOI: 10.3390/antiox13020234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/31/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
Gamma-tocopherol methyltransferase (γ-TMT), a key gene in the vitamin E biosynthesis pathway, significantly influences the accumulation of tocochromanols, thereby determining rice nutritional quality. In our study, we analyzed the γ-TMT gene in 475 Korean rice accessions, uncovering 177 genetic variants, including 138 SNPs and 39 InDels. Notably, two functional SNPs, tmt-E2-28,895,665-G/A and tmt-E4-28,896,689-A/G, were identified, causing substitutions from valine to isoleucine and arginine to glycine, respectively, across 93 accessions. A positive Tajima's D value in the indica group suggests a signature of balancing selection. Haplotype analysis revealed 27 haplotypes, with two shared between cultivated and wild accessions, seven specific to cultivated accessions, and 18 unique to wild types. Further, profiling of vitamin E isomers in 240 accessions and their association with haplotypes revealed that Hap_2, distinguished by an SNP in the 3' UTR (tmt-3UTR-28,897,360-T/A) exhibited significantly lower α-tocopherol (AT), α-tocotrienol (AT3), total tocopherol, and total tocotrienol, but higher γ-tocopherol (GT) in the japonica group. Additionally, in the indica group, Hap_2 showed significantly higher AT, AT3, and total tocopherol, along with lower GT and γ-tocotrienol, compared to Hap_19, Hap_20, and Hap_21. Overall, this study highlights the genetic landscape of γ-TMT and provides a valuable genetic resource for haplotype-based breeding programs aimed at enhancing nutritional profiles.
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Affiliation(s)
- Aueangporn Somsri
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea; (A.S.); (S.-H.C.); (B.N.)
| | - Sang-Ho Chu
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea; (A.S.); (S.-H.C.); (B.N.)
| | - Bhagwat Nawade
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea; (A.S.); (S.-H.C.); (B.N.)
| | - Chang-Yong Lee
- Department of Industrial and Systems Engineering, College of Engineering, Kongju National University, Cheonan 31080, Republic of Korea;
| | - Yong-Jin Park
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea; (A.S.); (S.-H.C.); (B.N.)
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Yu Z, Niu L, Cai Q, Wei J, Shang L, Yang X, Ma R. Improved salt-tolerance of transgenic soybean by stable over-expression of AhBADH gene from Atriplex hortensis. PLANT CELL REPORTS 2023:10.1007/s00299-023-03031-8. [PMID: 37195504 DOI: 10.1007/s00299-023-03031-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/29/2023] [Accepted: 05/04/2023] [Indexed: 05/18/2023]
Abstract
KEY MESSAGE The salt-tolerance of transgenic soybean cleared for environmental release was improved by stable over-expression of AhBADH gene from Atriplex hortensis, which was demonstrated through molecular analysis and field experiments. An effective strategy for increasing the productivity of major crops under salt stress conditions is the development of transgenics that harbor genes responsible for salinity tolerance. Betaine aldehyde dehydrogenase (BADH) is a key enzyme involved in the biosynthesis of the osmoprotectant, glycine betaine (GB), and osmotic balance in plants, and several plants transformed with BADH gene have shown significant improvements in salt tolerance. However, very few field-tested transgenic cultivars have been reported, as most of the transgenic studies are limited to laboratory or green house experiments. In this study, we demonstrated through field experiments that AhBADH from Atriplex hortensis confers salt tolerance when transformed into soybean (Glycine max L.). AhBADH was successfully introduced into soybean by Agrobacterium mediated transformation. A total of 256 transgenic plants were obtained, out of which 47 lines showed significant enhancement of salt tolerance compared to non-transgenic control plants. Molecular analyses of the transgenic line TL2 and TL7 with the highest salt tolerance exhibited stable inheritance and expression of AhBADH in progenies with a single copy insertion. TL1, TL2 and TL7 exhibited stable enhanced salt tolerance and improved agronomic traits when subjected to 300mM NaCl treatment. Currently, the transgenic line TL2 and TL7 with stable enhanced salt tolerance, which have been cleared for environmental release, are under biosafety assessment. TL 2 and TL7 stably expressing AhBADH could then be applied in commercial breeding experiments to genetically improve salt tolerance in soybean.
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Affiliation(s)
- Zhijing Yu
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Lu Niu
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Qinan Cai
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Jia Wei
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Lixia Shang
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Xiangdong Yang
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China.
| | - Rui Ma
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China.
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Myint NNA, Korinsak S, Chutteang C, Laosatit K, Thunnom B, Toojinda T, Siangliw JL. Identification of Pathogenicity Loci in Magnaporthe oryzae Using GWAS with Neck Blast Phenotypic Data. Genes (Basel) 2022; 13:916. [PMID: 35627301 PMCID: PMC9141631 DOI: 10.3390/genes13050916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [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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Affiliation(s)
- Nyein Nyein Aye Myint
- Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen, Nakhon Pathom 73140, Thailand;
| | - Siripar Korinsak
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (S.K.); (B.T.); (T.T.)
| | - Cattleya Chutteang
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen, Nakhon Pathom 73140, Thailand; (C.C.); (K.L.)
| | - Kularb Laosatit
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen, Nakhon Pathom 73140, Thailand; (C.C.); (K.L.)
| | - Burin Thunnom
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (S.K.); (B.T.); (T.T.)
| | - Theerayut Toojinda
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (S.K.); (B.T.); (T.T.)
| | - Jonaliza L. Siangliw
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (S.K.); (B.T.); (T.T.)
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Plant Responses and Tolerance to Salt Stress: Physiological and Molecular Interventions. Int J Mol Sci 2022; 23:ijms23094810. [PMID: 35563198 PMCID: PMC9103774 DOI: 10.3390/ijms23094810] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 04/17/2022] [Indexed: 02/05/2023] Open
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Lv Y, Ma J, Wei H, Xiao F, Wang Y, Jahan N, Hazman M, Qian Q, Shang L, Guo L. Combining GWAS, Genome-Wide Domestication and a Transcriptomic Analysis Reveals the Loci and Natural Alleles of Salt Tolerance in Rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2022; 13:912637. [PMID: 35783926 PMCID: PMC9248812 DOI: 10.3389/fpls.2022.912637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/23/2022] [Indexed: 05/12/2023]
Abstract
Soil salinity poses a serious threat to the sustainable production of rice (Oryza sativa L.) throughout the world. Thus, the detection of loci and alleles responsible for salt tolerance is fundamental to accelerating the improvement of rice and producing the resilient varieties that will ensure future harvests. In this study, we collected a set of 191 mini-core rice populations from around the world, evaluated their salt tolerance based on plant growth and development phenotypes at the seedling stage, and divided a standard evaluation score (SES) of visual salt injury into five different grades. We used ∼3.82 million single nucleotide polymorphisms (SNPs) to identify 155 significant SNPs and 275 genes associated with salt sensitivity based on a genome-wide association study (GWAS) of SES. In particular, two candidate genes, ZFP179 and OsDSR2, were associated with salt tolerance, and OsHKT1;1 was co-detected in the entire GWAS of all the panels and indica. Additionally, we investigated the transcriptional changes in cultivars 93-11 and PA64s under normal and salinity stress conditions and found 517 co-upregulated and 223 co-downregulated genes. These differentially expressed genes (DEGs) were highly enriched in "response to chemical" and "stress" based on the gene ontology enrichment analysis. Notably, 30 candidate genes that were associated with the salt tolerance analysis were obtained by integrating GWAS and transcriptomic DEG analyses, including 13 cloned genes that had no reports of tolerance to salt and 17 candidate genes whose functions were unknown. To further explore these genes and their alleles, we performed haplotype analysis, genome-wide domestication detection, and transcriptome analysis to breed improved varieties. This data and the genetic resources provided will be valuable for the development of salt tolerant rice varieties.
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Affiliation(s)
- Yang Lv
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jie Ma
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hua Wei
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Fang Xiao
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yueying Wang
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Noushin Jahan
- Department of Agronomy, Khulna Agricultural University, Khulna, Bangladesh
| | - Mohamed Hazman
- Agricultural Genetic Engineering Research Institute, Giza, Egypt
| | - Qian Qian
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Lianguang Shang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- *Correspondence: Longbiao Guo,
| | - Longbiao Guo
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- *Correspondence: Longbiao Guo,
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Phitaktansakul R, Kim KW, Aung KM, Maung TZ, Min MH, Somsri A, Lee W, Lee SB, Nam J, Kim SH, Lee J, Kwon SW, Nawade B, Chu SH, Park SW, Kang KK, Cho YH, Lee YS, Chung IM, Park YJ. Multi-omics analysis reveals the genetic basis of rice fragrance mediated by betaine aldehyde dehydrogenase 2. J Adv Res 2021; 42:303-314. [PMID: 36513420 PMCID: PMC9788947 DOI: 10.1016/j.jare.2021.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 11/15/2021] [Accepted: 12/11/2021] [Indexed: 02/08/2023] Open
Abstract
INTRODUCTION Fragrance is an important economic and quality trait in rice. The trait is controlled by the recessive gene betaine aldehyde dehydrogenase 2 (BADH2) via the production of 2-acetyl-1-pyrroline (2AP). OBJECTIVES Variation in BADH2 was evaluated at the population, genetic, transcriptional, and metabolic levels to obtain insights into fragrance regulation in rice. METHODS Whole-genome resequencing of the Korean World Rice Collection of 475 rice accessions, including 421 breeding lines and 54 wild accessions, was performed. Transcriptome analyses of a subset of 279 accessions, proteome analyses of 64 accessions, and volatile profiling of 421 breeding lines were also performed. RESULTS We identified over 3.1 million high-quality single nucleotide polymorphisms (SNPs) in Korean rice collection. Most SNPs were present in intergenic regions (79%), and 190,148 SNPs (6%) were located in the coding sequence, of which 53% were nonsynonymous. In total, 38 haplotypes were identified in the BADH2 coding region, including four novel haplotypes (one in cultivated and three in wild accessions). Tajima's D values suggested that BADH2 was under balancing selection in japonica rice. Furthermore, we identified 316 expression quantitative trait loci (eQTL), including 185 cis-eQTLs and 131 trans-eQTLs, involved in BADH2 regulation. A protein quantitative trait loci (pQTL) analysis revealed the presence of trans-pQTLs; 13 pQTLs were mapped 1 Mbp from the BADH2 region. Based on variable importance in projection (VIP) scores, 15 volatile compounds, including 2AP, discriminated haplotypes and were potential biomarkers for rice fragrance. CONCLUSION We generated a catalog of haplotypes based on a resequencing analysis of a large number of rice accessions. eQTLs and pQTLs associated with BADH2 gene expression and protein accumulation are likely involved in the regulation of 2AP variation in fragrant rice. These data improve our understanding of fragrance and provide valuable information for rice breeding.
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Affiliation(s)
- Rungnapa Phitaktansakul
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea
| | - Kyu-Won Kim
- Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan 32439, Republic of Korea
| | - Kyaw Myo Aung
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea
| | - Thant Zin Maung
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea
| | - Myeong-Hyeon Min
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea
| | - Aueangporn Somsri
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea
| | - Wondo Lee
- Seedpia, 85 Maesil-ro, Kwonsun-ku, Suwon 16395, Republic of Korea
| | - Sang-Beom Lee
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea
| | - Jungrye Nam
- Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan 32439, Republic of Korea
| | - Seung-Hyun Kim
- Department of Applied Bioscience, Konkuk University, Seoul 05029, Republic of Korea
| | - Joohyun Lee
- Department of Applied Bioscience, Konkuk University, Seoul 05029, Republic of Korea
| | - Soon-Wook Kwon
- Department of Plant Bioscience, Pusan National University, Pusan 46241, Republic of Korea
| | - Bhagwat Nawade
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea
| | - Sang-Ho Chu
- Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan 32439, Republic of Korea
| | - Sang-Won Park
- Chemical Safety Division, National Institute of Agriculture Science (NIAS), Wanju 55365, Republic of Korea
| | - Kwon Kyoo Kang
- Department of Horticultural Life Science, Hankyong National University, Anseong 17579, Republic of Korea
| | - Yoo-Hyun Cho
- Seedpia, 85 Maesil-ro, Kwonsun-ku, Suwon 16395, Republic of Korea
| | - Young-Sang Lee
- Department of Medical Biotechnology, Soonchunhyang University, Asan 31538, Republic of Korea
| | - Ill-Min Chung
- Department of Applied Bioscience, Konkuk University, Seoul 05029, Republic of Korea,Corresponding authors at: Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Korea (Yong-Jin Park); Department of Applied Bioscience, Konkuk University, Seoul 05029, Korea (Ill-Min Chung).
| | - Yong-Jin Park
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea,Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan 32439, Republic of Korea,Corresponding authors at: Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Korea (Yong-Jin Park); Department of Applied Bioscience, Konkuk University, Seoul 05029, Korea (Ill-Min Chung).
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Maung TZ, Chu SH, Park YJ. Functional Haplotypes and Evolutionary Insight into the Granule-Bound Starch Synthase II ( GBSSII) Gene in Korean Rice Accessions (KRICE_CORE). Foods 2021; 10:2359. [PMID: 34681408 PMCID: PMC8535093 DOI: 10.3390/foods10102359] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/28/2021] [Accepted: 09/30/2021] [Indexed: 12/30/2022] Open
Abstract
Granule-bound starch synthase 2 (GBSSII), a paralogous isoform of GBSSI, carries out amylose biosynthesis in rice. Unlike GBSSI, it mainly functions in transient organs, such as leaves. Despite many reports on the starch gene family, little is known about the genetics and genomics of GBSSII. Haplotype analysis was conducted to unveil genetic variations (SNPs and InDels) of GBSSII (OS07G0412100) and it was also performed to gain evolutionary insight through genetic diversity, population genetic structure, and phylogenetic analyses using the KRICE_CORE set (475 rice accessions). Thirty nonsynonymous SNPs (nsSNPs) were detected across the diverse GBSSII coding regions, representing 38 haplotypes, including 13 cultivated, 21 wild, and 4 mixed (a combination of cultivated and wild) varieties. The cultivated haplotypes (C_1-C_13) contained more nsSNPs across the GBSSII genomic region than the wild varieties. Nucleotide diversity analysis highlighted the higher diversity values of the cultivated varieties (weedy = 0.0102, landrace = 0.0093, and bred = 0.0066) than the wild group (0.0045). The cultivated varieties exhibited no reduction in diversity during domestication. Diversity reduction in the japonica and the wild groups was evidenced by the negative Tajima's D values under purifying selection, suggesting the domestication signatures of GBSSII; however, balancing selection was indicated by positive Tajima's D values in indica. Principal component analysis and population genetics analyses estimated the ambiguous evolutionary relationships among the cultivated and wild rice groups, indicating highly diverse structural features of the rice accessions within the GBSSII genomic region. FST analysis differentiated most of the classified populations in a range of greater FST values. Our findings provide evolutionary insights into GBSSII and, consequently, a molecular breeding program can be implemented for select desired traits using these diverse nonsynonymous (functional) alleles.
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Affiliation(s)
- Thant Zin Maung
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan 32439, Korea;
| | - Sang-Ho Chu
- Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan 32439, Korea;
| | - Yong-Jin Park
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan 32439, Korea;
- Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan 32439, Korea;
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