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Khunsanit P, Jitsamai N, Thongsima N, Chadchawan S, Pongpanich M, Henry IM, Comai L, Suriya-Arunroj D, Budjun I, Buaboocha T. QTL-Seq identified a genomic region on chromosome 1 for soil-salinity tolerance in F 2 progeny of Thai salt-tolerant rice donor line "Jao Khao". FRONTIERS IN PLANT SCIENCE 2024; 15:1424689. [PMID: 39258300 PMCID: PMC11385611 DOI: 10.3389/fpls.2024.1424689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 07/22/2024] [Indexed: 09/12/2024]
Abstract
Introduction Owing to advances in high-throughput genome sequencing, QTL-Seq mapping of salt tolerance traits is a major platform for identifying soil-salinity tolerance QTLs to accelerate marker-assisted selection for salt-tolerant rice varieties. We performed QTL-BSA-Seq in the seedling stage of rice from a genetic cross of the extreme salt-sensitive variety, IR29, and "Jao Khao" (JK), a Thai salt-tolerant variety. Methods A total of 462 F2 progeny grown in soil and treated with 160 mM NaCl were used as the QTL mapping population. Two high- and low-bulk sets, based on cell membrane stability (CMS) and tiller number at the recovery stage (TN), were equally sampled. The genomes of each pool were sequenced, and statistical significance of QTL was calculated using QTLseq and G prime (G') analysis, which is based on calculating the allele frequency differences or Δ(SNP index). Results Both methods detected the overlapping interval region, wherein CMS-bulk was mapped at two loci in the 38.41-38.85 Mb region with 336 SNPs on chromosome 1 (qCMS1) and the 26.13-26.80 Mb region with 1,011 SNPs on chromosome 3 (qCMS3); the Δ(SNP index) peaks were -0.2709 and 0.3127, respectively. TN-bulk was mapped at only one locus in the overlapping 38.26-38.95 Mb region on chromosome 1 with 575 SNPs (qTN1) and a Δ(SNP index) peak of -0.3544. These identified QTLs in two different genetic backgrounds of segregating populations derived from JK were validated. The results confirmed the colocalization of the qCMS1 and qTN1 traits on chromosome 1. Based on the CMS trait, qCMS1/qTN1 stably expressed 6%-18% of the phenotypic variance in the two validation populations, while qCMS1/qTN1 accounted for 16%-20% of the phenotypic variance in one validation population based on the TN trait. Conclusion The findings confirm that the CMS and TN traits are tightly linked to the long arm of chromosome 1 rather than to chromosome 3. The validated qCMS-TN1 QTL can be used for gene/QTL pyramiding in marker-assisted selection to expedite breeding for salt resistance in rice at the seedling stage.
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Affiliation(s)
- Prasit Khunsanit
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Navarit Jitsamai
- Center of Excellence in Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Nattana Thongsima
- Center of Excellence in Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Supachitra Chadchawan
- Center of Excellence 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
| | - Monnat Pongpanich
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Isabelle M Henry
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, United States
| | - Luca Comai
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, United States
| | | | - Itsarapong Budjun
- Rice Department, Ministry of Agriculture and Cooperation, Bangkok, Thailand
| | - Teerapong Buaboocha
- Center of Excellence in Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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Zheng X, Peng Y, Qiao J, Henry R, Qian Q. Wild rice: unlocking the future of rice breeding. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 39150344 DOI: 10.1111/pbi.14443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 07/16/2024] [Accepted: 07/17/2024] [Indexed: 08/17/2024]
Abstract
Germplasm resources serve as the foundations of advancements in breeding and are crucial for maintaining food security. Wild rice species of the genus Oryza include rich sources of genetic diversity and high adaptability, making them a substantial resource for rice breeding. The discovery of wild-type cytoplasmic male sterility resources enabled the achievement of the 'three lines' goal in hybrid rice, significantly increasing rice yields. The application of resistance alleles from wild rice enables rice production to withstand losses caused by stress. Reduced genetic diversity due to rice breeding poses a significant limitation to further advances and can be alleviated through a systematic use of wild genetic resources that integrate geographic, climatic and environmental data of the original habitat, along with extensive germplasm collection and identification using advanced methods. Leveraging technological advancements in plant genomics, the understanding of genetic mechanisms and the application of artificial intelligence and gene editing can further enhance the efficiency and accuracy of this process. These advancements facilitate rapid isolation and functional studies of genes, and precise genome manipulation. This review systematically summarizes the utilization of superior genes and germplasm resources derived from wild rice sources, while also exploring the collection, conservation, identification and utilization of further wild rice germplasm resources. A focus on genome sequencing and biotechnology developments is leading to new breeding and biotechnology opportunities. These new opportunities will not only promote the development of rice varieties that exhibit high yields, superior stress resistance and high quality but also expand the genetic diversity among rice cultivars.
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Affiliation(s)
- Xiaoming Zheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Sanya National Research Institute of Breeding in Hainan, Chinese Academy of Agricultural Sciences, Beijing, China
- International Rice Research Institute, Metro Manila, Philippines
| | | | - Jiyue Qiao
- Yazhouwan National Laboratory, Sanya, China
| | - Robert Henry
- University of Queensland, Brisbane, Queensland, Australia
| | - Qian Qian
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Sanya National Research Institute of Breeding in Hainan, Chinese Academy of Agricultural Sciences, Beijing, China
- Yazhouwan National Laboratory, Sanya, China
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Padmavathi G, Bangale U, Rao K, Balakrishnan D, Arun M, Singh RK, Sundaram RM. Progress and prospects in harnessing wild relatives for genetic enhancement of salt tolerance in rice. FRONTIERS IN PLANT SCIENCE 2024; 14:1253726. [PMID: 38371332 PMCID: PMC10870985 DOI: 10.3389/fpls.2023.1253726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 12/13/2023] [Indexed: 02/20/2024]
Abstract
Salt stress is the second most devastating abiotic stress after drought and limits rice production globally. Genetic enhancement of salinity tolerance is a promising and cost-effective approach to achieve yield gains in salt-affected areas. Breeding for salinity tolerance is challenging because of the genetic complexity of the response of rice plants to salt stress, as it is governed by minor genes with low heritability and high G × E interactions. The involvement of numerous physiological and biochemical factors further complicates this complexity. The intensive selection and breeding efforts targeted towards the improvement of yield in the green-revolution era inadvertently resulted in the gradual disappearance of the loci governing salinity tolerance and a significant reduction in genetic variability among cultivars. The limited utilization of genetic resources and narrow genetic base of improved cultivars have resulted in a plateau in response to salinity tolerance in modern cultivars. Wild species are an excellent genetic resource for broadening the genetic base of domesticated rice. Exploiting novel genes of underutilized wild rice relatives to restore salinity tolerance loci eliminated during domestication can result in significant genetic gain in rice cultivars. Wild species of rice, Oryza rufipogon and Oryza nivara, have been harnessed in the development of a few improved rice varieties like Jarava and Chinsura Nona 2. Furthermore, increased access to sequence information and enhanced knowledge about the genomics of salinity tolerance in wild relatives has provided an opportunity for the deployment of wild rice accessions in breeding programs, while overcoming the cross-incompatibility and linkage drag barriers witnessed in wild hybridization. Pre-breeding is another avenue for building material that are ready for utilization in breeding programs. Efforts should be directed towards systematic collection, evaluation, characterization, and deciphering salt tolerance mechanisms in wild rice introgression lines and deploying untapped novel loci to improve salinity tolerance in rice cultivars. This review highlights the potential of wild relatives of Oryza to enhance tolerance to salinity, track the progress of work, and provide a perspective for future research.
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Affiliation(s)
- Guntupalli Padmavathi
- Crop Improvement Section, Plant Breeding, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Hyderabad, India
| | - Umakanth Bangale
- Crop Improvement Section, Plant Breeding, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Hyderabad, India
| | - K. Nagendra Rao
- Genetics and Plant Breeding, Sugarcane Research Station, Vuyyuru, India
| | - Divya Balakrishnan
- Crop Improvement Section, Plant Breeding, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Hyderabad, India
| | - Melekote Nagabhushan Arun
- Crop Production Section, Agronomy, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Hyderabad, India
| | - Rakesh Kumar Singh
- Crop Diversification and Genetics Section, International Center for Biosaline Agriculture (ICBA), Dubai, United Arab Emirates
| | - Raman Meenakshi Sundaram
- Crop Improvement Section, Plant Breeding, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Hyderabad, India
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Li S, Xu S, Zheng J, Du H, Li C, Shen S, Liang S, Wang J, Liu H, Yang L, Xin W, Jia Y, Zou D, Zheng H. Joint QTL Mapping and Transcriptome Sequencing Analysis Reveal Candidate Genes for Salinity Tolerance in Oryza sativa L. ssp. Japonica Seedlings. Int J Mol Sci 2023; 24:17591. [PMID: 38139418 PMCID: PMC10743832 DOI: 10.3390/ijms242417591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/13/2023] [Accepted: 12/16/2023] [Indexed: 12/24/2023] Open
Abstract
Salinity stress is one of the major abiotic stresses affecting crop growth and production. Rice is an important food crop in the world, but also a salt-sensitive crop, and the rice seedling stage is the most sensitive to salt stress, which directly affects the final yield formation. In this study, two RIL populations derived from the crosses of CD (salt-sensitive)/WD (salt-tolerant) and KY131 (salt-sensitive)/XBJZ (salt-tolerant) were used as experimental materials, and the score of salinity toxicity (SST), the relative shoot length (RSL), the relative shoot fresh weight (RSFW), and the relative shoot dry weight (RSDW) were used for evaluating the degree of tolerance under salt stress in different lines. The genetic linkage map containing 978 and 527 bin markers were constructed in two RIL populations. A total of 14 QTLs were detected on chromosomes 1, 2, 3, 4, 7, 9, 10, 11, and 12. Among them, qSST12-1, qSST12-2, and qRSL12 were co-localized in a 140-kb overlap interval on chromosome 12, which containing 16 candidate genes. Furthermore, transcriptome sequencing and qRT-PCR were analyzed in CD and WD under normal and 120 mM NaCl stress. LOC_Os12g29330, LOC_Os12g29350, LOC_Os12g29390, and LOC_Os12g29400 were significantly induced by salt stress in both CD and WD. Sequence analysis showed that LOC_Os12g29400 in the salt-sensitive parents CD and KY131 was consistent with the reference sequence (Nipponbare), whereas the salt-tolerant parents WD and XBJZ differed significantly from the reference sequence both in the promoter and exon regions. The salt-tolerant phenotype was identified by using two T3 homozygous mutant plants of LOC_Os12g29400; the results showed that the score of salinity toxicity (SST) of the mutant plants (CR-3 and CR-5) was significantly lower than that of the wild type, and the seedling survival rate (SSR) was significantly higher than that of the wild type, which indicated that LOC_Os12g29400 could negatively regulate the salinity tolerance of rice at the seedling stage. The results lay a foundation for the analysis of the molecular mechanism of rice salinity tolerance and the cultivation of new rice varieties.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Hongliang Zheng
- Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of Education/College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.L.); (S.X.); (J.Z.); (H.D.); (C.L.); (S.S.); (S.L.); (J.W.); (H.L.); (L.Y.); (W.X.); (Y.J.); (D.Z.)
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Gao Q, Yin X, Wang F, Zhang C, Xiao F, Wang H, Hu S, Liu W, Zhou S, Chen L, Dai X, Liang M. Jacalin-related lectin 45 (OsJRL45) isolated from 'sea rice 86' enhances rice salt tolerance at the seedling and reproductive stages. BMC PLANT BIOLOGY 2023; 23:553. [PMID: 37940897 PMCID: PMC10634080 DOI: 10.1186/s12870-023-04533-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/17/2023] [Indexed: 11/10/2023]
Abstract
BACKGROUND Rice (Oryza sativa L.) is one of the most widely cultivated grain crops in the world that meets the caloric needs of more than half the world's population. Salt stress seriously affects rice production and threatens food security. Therefore, mining salt tolerance genes in salt-tolerant germplasm and elucidating their molecular mechanisms in rice are necessary for the breeding of salt tolerant cultivars. RESULTS In this study, a salt stress-responsive jacalin-related lectin (JRL) family gene, OsJRL45, was identified in the salt-tolerant rice variety 'sea rice 86' (SR86). OsJRL45 showed high expression level in leaves, and the corresponding protein mainly localized to the endoplasmic reticulum. The knockout mutant and overexpression lines of OsJRL45 revealed that OsJRL45 positively regulates the salt tolerance of rice plants at all growth stages. Compared with the wild type (WT), the OsJRL45 overexpression lines showed greater salt tolerance at the reproductive stage, and significantly higher seed setting rate and 1,000-grain weight. Moreover, OsJRL45 expression significantly improved the salt-resistant ability and yield of a salt-sensitive indica cultivar, L6-23. Furthermore, OsJRL45 enhanced the antioxidant capacity of rice plants and facilitated the maintenance of Na+-K+ homeostasis under salt stress conditions. Five proteins associated with OsJRL45 were screened by transcriptome and interaction network analysis, of which one, the transmembrane transporter Os10g0210500 affects the salt tolerance of rice by regulating ion transport-, salt stress-, and hormone-responsive proteins. CONCLUSIONS The OsJRL45 gene isolated from SR86 positively regulated the salt tolerance of rice plants at all growth stages, and significantly increased the yield of salt-sensitive rice cultivar under NaCl treatment. OsJRL45 increased the activity of antioxidant enzyme of rice and regulated Na+/K+ dynamic equilibrium under salinity conditions. Our data suggest that OsJRL45 may improve the salt tolerance of rice by mediating the expression of ion transport-, salt stress response-, and hormone response-related genes.
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Affiliation(s)
- Qinmei Gao
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, 410081, China
- College of Chemistry and Chemical Engineering, Jishou University, Hunan, 416000, China
| | - Xiaolin Yin
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Feng Wang
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Congzhi Zhang
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Feicui Xiao
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Hongyan Wang
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Shuchang Hu
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Weihao Liu
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Shiqi Zhou
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Liangbi Chen
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Xiaojun Dai
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, 410081, China.
| | - Manzhong Liang
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, 410081, China.
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Li P, Li Z, Liu X, Zhang H, Zhang S, Liu F, Li N, Yang Y, Xie K, Ding H, Yao F. Haplotype analysis and marker development of five salt-tolerant-related genes in rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1259462. [PMID: 37727858 PMCID: PMC10505798 DOI: 10.3389/fpls.2023.1259462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 08/10/2023] [Indexed: 09/21/2023]
Abstract
Salinity stress is a great threat to the growth and productivity of crops, and development of salt-tolerant crops is of great necessity to ensure food security. Although a few genes with natural variations that confer salt tolerance at germination and seedling stage in rice have been cloned, effective intragenic markers for these genes are awaited to be developed, which hinder the use of these genes in genetic improvement of salt tolerance in rice. In this study, we first performed haplotype analysis of five rice salt-tolerant-related genes using 38 rice accessions with reference genome and 4,726 rice germplasm accessions with imputed genotypes and classified main haplotype groups and haplotypes. Subsequently, we identified unique variations for elite haplotypes reported in previous studies and developed 11 effective intragenic makers. Finally, we conducted genotyping of 533 of the 4,726 rice accessions from worldwide and 70 approved temperate geng/japonica cultivars in China using the developed markers. These results could provide effective donors and markers of salt-tolerant-related genes and thus could be of great use in genetic improvement of salt tolerance in rice.
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Affiliation(s)
- Pingbo Li
- Institute of Wetland Agriculture and Ecology, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Zhen Li
- Institute of Wetland Agriculture and Ecology, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xu Liu
- Institute of Wetland Agriculture and Ecology, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Hua Zhang
- Institute of Wetland Agriculture and Ecology, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Shuyong Zhang
- Agriculture and Rural Affairs Bureau of Yutai County, Jining, China
| | - Fang Liu
- Institute of Wetland Agriculture and Ecology, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Nana Li
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yongyi Yang
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Kun Xie
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Hanfeng Ding
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Fangyin Yao
- Institute of Wetland Agriculture and Ecology, Shandong Academy of Agricultural Sciences, Jinan, China
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Tong S, Ashikari M, Nagai K, Pedersen O. Can the Wild Perennial, Rhizomatous Rice Species Oryza longistaminata be a Candidate for De Novo Domestication? RICE (NEW YORK, N.Y.) 2023; 16:13. [PMID: 36928797 PMCID: PMC10020418 DOI: 10.1186/s12284-023-00630-7] [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: 01/05/2023] [Accepted: 03/05/2023] [Indexed: 06/18/2023]
Abstract
As climate change intensifies, the development of resilient rice that can tolerate abiotic stresses is urgently needed. In nature, many wild plants have evolved a variety of mechanisms to protect themselves from environmental stresses. Wild relatives of rice may have abundant and virtually untapped genetic diversity and are an essential source of germplasm for the improvement of abiotic stress tolerance in cultivated rice. Unfortunately, the barriers of traditional breeding approaches, such as backcrossing and transgenesis, make it challenging and complex to transfer the underlying resilience traits between plants. However, de novo domestication via genome editing is a quick approach to produce rice with high yields from orphans or wild relatives. African wild rice, Oryza longistaminata, which is part of the AA-genome Oryza species has two types of propagation strategies viz. vegetative propagation via rhizome and seed propagation. It also shows tolerance to multiple types of abiotic stress, and therefore O. longistaminata is considered a key candidate of wild rice for heat, drought, and salinity tolerance, and it is also resistant to lodging. Importantly, O. longistaminata is perennial and propagates also via rhizomes both of which are traits that are highly valuable for the sustainable production of rice. Therefore, O. longistaminata may be a good candidate for de novo domestication through genome editing to obtain rice that is more climate resilient than modern elite cultivars of O. sativa.
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Affiliation(s)
- Shuai Tong
- Department of Biology, University of Copenhagen, Universitetsparken 4, 3Rd Floor, 2100, Copenhagen, Denmark
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center of Nagoya University, Furo-Cho, Chikusa, Nagoya, Aichi, 464-8602, Japan
| | - Keisuke Nagai
- Bioscience and Biotechnology Center of Nagoya University, Furo-Cho, Chikusa, Nagoya, Aichi, 464-8602, Japan.
| | - Ole Pedersen
- Department of Biology, University of Copenhagen, Universitetsparken 4, 3Rd Floor, 2100, Copenhagen, Denmark.
- School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
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Lei L, Cao L, Ding G, Zhou J, Luo Y, Bai L, Xia T, Chen L, Wang J, Liu K, Lei Q, Xie T, Yang G, Wang X, Sun S, Lai Y. OsBBX11 on qSTS4 links to salt tolerance at the seeding stage in Oryza sativa L. ssp. Japonica. FRONTIERS IN PLANT SCIENCE 2023; 14:1139961. [PMID: 36968393 PMCID: PMC10030886 DOI: 10.3389/fpls.2023.1139961] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Rice has been reported to be highly sensitive to salt stress at the seedling stage. However, the lack of target genes that can be used for improving salt tolerance has resulted in several saline soils unsuitable for cultivation and planting. To characterize new salt-tolerant genes, we used 1,002 F2:3 populations derived from Teng-Xi144 and Long-Dao19 crosses as the phenotypic source to systematically characterize seedlings' survival days and ion concentration under salt stress. Utilizing QTL-seq resequencing technology and a high-density linkage map based on 4,326 SNP markers, we identified qSTS4 as a major QTL influencing seedling salt tolerance, which accounted for 33.14% of the phenotypic variation. Through functional annotation, variation detection and qRT-PCR analysis of genes within 46.9 Kb of qSTS4, it was revealed that there was one SNP in the promoter region of OsBBX11, which resulted in a significant response difference between the two parents to salt stress. Transgenic plants using knockout-based technology and demonstrated that Na+ and K+ in the roots of the functional-loss-type OsBBX11 were translocated largely to the leaves under 120 mmol/L NaCl compared with the wild-type, causing osbbx11 leaves to die after 12 days of salt stress due to an imbalance in osmotic pressure. In conclusion, this study identified OsBBX11 as a salt-tolerance gene, and one SNPs in the OsBBX11 promoter region can be used to identify its interacting transcription factors. This provides a theoretical basis for finding the molecular mechanism of OsBBX11 upstream and downstream regulation of salt tolerance and molecular design breeding in the future.
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Affiliation(s)
- Lei Lei
- Postdoctoral Scientific Research Station of Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Heilongjiang Rice Quality Improvement and Genetic Breeding Engineering Research Center, Harbin, China
- Northeast of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Harbin, China
| | - Liangzi Cao
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Heilongjiang Rice Quality Improvement and Genetic Breeding Engineering Research Center, Harbin, China
- Northeast of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Harbin, China
| | - Guohua Ding
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Heilongjiang Rice Quality Improvement and Genetic Breeding Engineering Research Center, Harbin, China
- Northeast of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Harbin, China
| | - Jinsong Zhou
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Heilongjiang Rice Quality Improvement and Genetic Breeding Engineering Research Center, Harbin, China
- Northeast of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Harbin, China
| | - Yu Luo
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Liangming Bai
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Heilongjiang Rice Quality Improvement and Genetic Breeding Engineering Research Center, Harbin, China
| | - Tianshu Xia
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Lei Chen
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Jiangxu Wang
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Kai Liu
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Qingjun Lei
- Branch of Animal Husbandry and Veterinary of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Tingting Xie
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Guang Yang
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Xueyang Wang
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Shichen Sun
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Heilongjiang Rice Quality Improvement and Genetic Breeding Engineering Research Center, Harbin, China
- Northeast of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Harbin, China
| | - Yongcai Lai
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Northeast of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Harbin, China
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Rasheed A, Li H, Nawaz M, Mahmood A, Hassan MU, Shah AN, Hussain F, Azmat S, Gillani SFA, Majeed Y, Qari SH, Wu Z. Molecular tools, potential frontiers for enhancing salinity tolerance in rice: A critical review and future prospective. FRONTIERS IN PLANT SCIENCE 2022; 13:966749. [PMID: 35968147 PMCID: PMC9366114 DOI: 10.3389/fpls.2022.966749] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 06/28/2022] [Indexed: 05/08/2023]
Abstract
Improvement of salinity tolerance in rice can minimize the stress-induced yield losses. Rice (Oryza sativa) is one of Asia's most widely consumed crops, native to the subtropical regions, and is generally associated with sensitivity to salinity stress episodes. Salt-tolerant rice genotypes have been developed using conventional breeding methods; however, the success ratio is limited because of the complex nature of the trait and the high cost of development. The narrow genetic base of rice limited the success of conventional breeding methods. Hence, it is critical to launch the molecular tools for screening rice novel germplasm for salt-tolerant genes. In this regard, the latest molecular techniques like quantitative trait loci (QTL) mapping, genetic engineering (GE), transcription factors (TFs) analysis, and clustered regularly interspaced short palindromic repeats (CRISPR) are reliable for incorporating the salt tolerance in rice at the molecular level. Large-scale use of these potent genetic approaches leads to identifying and editing several genes/alleles, and QTL/genes are accountable for holding the genetic mechanism of salinity tolerance in rice. Continuous breeding practices resulted in a huge decline in rice genetic diversity, which is a great worry for global food security. However, molecular breeding tools are the only way to conserve genetic diversity by exploring wild germplasm for desired genes in salt tolerance breeding programs. In this review, we have compiled the logical evidences of successful applications of potent molecular tools for boosting salinity tolerance in rice, their limitations, and future prospects. This well-organized information would assist future researchers in understanding the genetic improvement of salinity tolerance in rice.
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Affiliation(s)
- Adnan Rasheed
- Key Laboratory of Plant Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Huijie Li
- Key Laboratory of Plant Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, Jiangxi Agricultural University, Nanchang, China
- College of Humanity and Public Administration, Jiangxi Agricultural University, Nanchang, China
| | - Muhammad Nawaz
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Athar Mahmood
- Department of Agronomy, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Muhammad Umair Hassan
- Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang, China
| | - Adnan Noor Shah
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Fiaz Hussain
- Directorate of Agronomy, Ayub Agricultural Research Institute, Faisalabad, Pakistan
| | - Saira Azmat
- Department of Agriculture, Agriculture Extension and Adaptive Research, Government of the Punjab, Lahore, Pakistan
| | | | - Yasir Majeed
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Sameer H. Qari
- Department of Biology, Al-Jumum University College, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Ziming Wu
- Key Laboratory of Plant Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, Jiangxi Agricultural University, Nanchang, China
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Ding G, Hu B, Zhou Y, Yang W, Zhao M, Xie J, Zhang F. Development and Characterization of Chromosome Segment Substitution Lines Derived from Oryza rufipogon in the Background of the Oryza sativa indica Restorer Line R974. Genes (Basel) 2022; 13:genes13050735. [PMID: 35627119 PMCID: PMC9140843 DOI: 10.3390/genes13050735] [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: 03/30/2022] [Revised: 04/12/2022] [Accepted: 04/19/2022] [Indexed: 12/04/2022] Open
Abstract
Dongxiang wild rice (DXWR) (O. rufipogon Griff.), which has the northernmost worldwide distribution of a wild rice species, is a valuable genetic resource with respect to improving stress tolerance in cultivated rice (Oryza sativa L.). In the three-line hybrid rice breeding system, restorer lines play important roles in enhancing the tolerance of hybrid rice. However, restorer lines have yet to be used as a genomic background for development of substitution lines carrying DXWR chromosome segments. We developed a set of 84 chromosome segment substitution lines (CSSLs) from a donor parent DXWR × recurrent parent restorer line R974 (Oryza sativa indica) cross. On average, each CSSL carried 6.27 introgressed homozygous segments, with 93.37% total genome coverage. Using these CSSLs, we identified a single QTL, qDYST-1, associated with salt stress tolerance on chromosome 3. Furthermore, five CSSLs showing strong salt stress tolerance were subjected to whole-genome single-nucleotide polymorphism chip analyses, during which we detected a common substitution segment containing qDYST-1 in all five CSSLs, thereby implying the validity and efficacy of qDYST-1. These novel CSSLs could make a significant contribution to detecting valuable DXWR QTLs, and provide important germplasm resources for breeding novel restorer lines for use in hybrid rice breeding systems.
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Affiliation(s)
- Gumu Ding
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; (G.D.); (Y.Z.); (M.Z.)
| | - Biaolin Hu
- Rice National Engineering Laboratory, Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330022, China;
| | - Yi Zhou
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; (G.D.); (Y.Z.); (M.Z.)
| | - Wanling Yang
- Jiangxi Provincial Key Laboratory of Protection and Utilization of Subtropical Plant Resources, Nanchang 330022, China;
| | - Minmin Zhao
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; (G.D.); (Y.Z.); (M.Z.)
| | - Jiankun Xie
- Jiangxi Provincial Key Laboratory of Protection and Utilization of Subtropical Plant Resources, Nanchang 330022, China;
- Correspondence: (J.X.); (F.Z.)
| | - Fantao Zhang
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; (G.D.); (Y.Z.); (M.Z.)
- Correspondence: (J.X.); (F.Z.)
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