1
|
Wang Q, Chen X, Meng Y, Niu M, Jia Y, Huang L, Ma W, Liang C, Li Z, Zhao L, Dang Z. The Potential Role of Genic-SSRs in Driving Ecological Adaptation Diversity in Caragana Plants. Int J Mol Sci 2024; 25:2084. [PMID: 38396759 PMCID: PMC10888960 DOI: 10.3390/ijms25042084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Caragana, a xerophytic shrub genus widely distributed in northern China, exhibits distinctive geographical substitution patterns and ecological adaptation diversity. This study employed transcriptome sequencing technology to investigate 12 Caragana species, aiming to explore genic-SSR variations in the Caragana transcriptome and identify their role as a driving force for environmental adaptation within the genus. A total of 3666 polymorphic genic-SSRs were identified across different species. The impact of these variations on the expression of related genes was analyzed, revealing a significant linear correlation (p < 0.05) between the length variation of 264 polymorphic genic-SSRs and the expression of associated genes. Additionally, 2424 polymorphic genic-SSRs were located in differentially expressed genes among Caragana species. Through weighted gene co-expression network analysis, the expressions of these genes were correlated with 19 climatic factors and 16 plant functional traits in various habitats. This approach facilitated the identification of biological processes associated with habitat adaptations in the studied Caragana species. Fifty-five core genes related to functional traits and climatic factors were identified, including various transcription factors such as MYB, TCP, ARF, and structural proteins like HSP90, elongation factor TS, and HECT. The roles of these genes in the ecological adaptation diversity of Caragana were discussed. Our study identified specific genomic components and genes in Caragana plants responsive to heterogeneous habitats. The results contribute to advancements in the molecular understanding of their ecological adaptation, lay a foundation for the conservation and development of Caragana germplasm resources, and provide a scientific basis for plant adaptation to global climate change.
Collapse
Affiliation(s)
- Qinglang Wang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Xing’er Chen
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Yue Meng
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Miaomiao Niu
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Yuanyuan Jia
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Lei Huang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Wenhong Ma
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Cunzhu Liang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Zhiyong Li
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Liqing Zhao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Zhenhua Dang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| |
Collapse
|
2
|
Ren D, Liu H, Sun X, Zhang F, Jiang L, Wang Y, Jiang N, Yan P, Cui J, Yang J, Li Z, Lu P, Luo X. Post-transcriptional regulation of grain weight and shape by the RBP-A-J-K complex in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:66-85. [PMID: 37970747 DOI: 10.1111/jipb.13583] [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: 06/03/2023] [Revised: 09/29/2023] [Accepted: 11/12/2023] [Indexed: 11/17/2023]
Abstract
RNA-binding proteins (RBPs) are components of the post-transcriptional regulatory system, but their regulatory effects on complex traits remain unknown. Using an integrated strategy involving map-based cloning, functional characterizations, and transcriptomic and population genomic analyses, we revealed that RBP-K (LOC_Os08g23120), RBP-A (LOC_Os11g41890), and RBP-J (LOC_Os10g33230) encode proteins that form an RBP-A-J-K complex that negatively regulates rice yield-related traits. Examinations of the RBP-A-J-K complex indicated RBP-K functions as a relatively non-specific RBP chaperone that enables RBP-A and RBP-J to function normally. Additionally, RBP-J most likely affects GA pathways, resulting in considerable increases in grain and panicle lengths, but decreases in grain width and thickness. In contrast, RBP-A negatively regulates the expression of genes most likely involved in auxin-regulated pathways controlling cell wall elongation and carbohydrate transport, with substantial effects on the rice grain filling process as well as grain length and weight. Evolutionarily, RBP-K is relatively ancient and highly conserved, whereas RBP-J and RBP-A are more diverse. Thus, the RBP-A-J-K complex may represent a typical functional model for many RBPs and protein complexes that function at transcriptional and post-transcriptional levels in plants and animals for increased functional consistency, efficiency, and versatility, as well as increased evolutionary potential. Our results clearly demonstrate the importance of RBP-mediated post-transcriptional regulation for the diversity of complex traits. Furthermore, rice grain yield and quality may be enhanced by introducing various complete or partial loss-of-function mutations to specific RBP genes using clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 technology and by exploiting desirable natural tri-genic allelic combinations at the loci encoding the components of the RBP-A-J-K complex through marker-assisted selection.
Collapse
Affiliation(s)
- Ding Ren
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Hui Liu
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Xuejun Sun
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- MOE Key Laboratory of Crop Physiology, Ecology and Genetic Breeding College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Fan Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Ling Jiang
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ying Wang
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ning Jiang
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Peiwen Yan
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jinhao Cui
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jinshui Yang
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Zhikang Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Pingli Lu
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Xiaojin Luo
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- MOE Key Laboratory of Crop Physiology, Ecology and Genetic Breeding College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| |
Collapse
|
3
|
Ma L, Tao X, Wang W, Jiao J, Pu Y, Yang G, Liu L, Fang Y, Wu J, Sun W. Genome-wide identification of RNA recognition motif (RRM1) in Brassica rapa and functional analysis of RNA-binding protein (BrRBP) under low-temperature stress. BMC PLANT BIOLOGY 2023; 23:621. [PMID: 38057714 DOI: 10.1186/s12870-023-04639-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/29/2023] [Indexed: 12/08/2023]
Abstract
BACKGROUND The RNA recognition motif (RRM) is primarily engaged in the processing of mRNA and rRNA following gene transcription as well as the regulation of RNA transport; it is critical in preserving RNA stability. RESULTS In this study, we identified 102 members of the RRM1 gene family in Brassica rapa, which were dispersed across 10 chromosomes with the ninth chromosome being the most extensively distributed. The RRM1 gene family members of Brassica rapa and Arabidopsis thaliana were grouped into 14 subclades (I-XIV) using phylogenetic analysis. Moreover, the results of transcriptome analysis and RT-qPCR indicated that the expression of Brapa05T000840 was upregulated in the cultivars 'Longyou 7' and 'Longyou 99' following exposure to cold stress at a temperature of 4 °C for 24 h. The levels of expression in the leaves and growth cones of the 'Longyou 7' variety were found to be significantly higher than those observed in the 'Longyou 99' variety under conditions of low temperature and NaCl stress. It illustrates the involvement of the RRM1 gene in the physiological response to both low temperature and salt stress. In addition, it was observed that the survival rate of transgenic BrRBP (Brapa05T000840) Arabidopsis thaliana plants was notably higher compared to that of wild-type plants when subjected to varying durations of low temperature treatment. Furthermore, the expression of the BrRBP gene in transgenic plants exhibited an upward trend as the duration of low temperature treatment increased, reaching its peak at 24 h. The in-vivo enzymatic activity of reactive oxygen species-scavenging enzymes were found to be significantly elevated in comparison to wild-type plants, suggesting that the BrRBP gene may enhance the cold tolerance of Arabidopsis thaliana. CONCLUSIONS This study offers a significant foundation for comprehending the regulation mechanism of the RRM1 gene family in winter Brassica rapa subjected to cold stress, as well as for finding key genes associated with cold resistance.
Collapse
Affiliation(s)
- Li Ma
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xiaolei Tao
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Wangtian Wang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Jintang Jiao
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yuanyuan Pu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Gang Yang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Lijun Liu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yan Fang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Junyan Wu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China.
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Wancang Sun
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China.
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China.
| |
Collapse
|
4
|
Karamat U, Sun X, Li N, Zhao J. Genetic regulators of leaf size in Brassica crops. HORTICULTURE RESEARCH 2021; 8:91. [PMID: 33931619 PMCID: PMC8087820 DOI: 10.1038/s41438-021-00526-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 01/03/2021] [Accepted: 02/24/2021] [Indexed: 05/06/2023]
Abstract
Leaf size influences plant development and biomass and is also an important agricultural trait in Brassica crops, in which leaves are the main organ produced for consumption. Leaf size is determined by the coordinated regulation of cell proliferation and cell expansion during leaf development, and these processes are strictly controlled by various integrated signals from the intrinsic regulatory network and the growth environment. Understanding the molecular mechanism of leaf size control is a prerequisite for molecular breeding for crop improvement purposes. Although research on leaf size control is just beginning in Brassica, recent studies have identified several genes and QTLs that are important in leaf size regulation. These genes have been proposed to influence leaf growth through different pathways and mechanisms, including phytohormone biosynthesis and signaling, transcription regulation, small RNAs, and others. In this review, we summarize the current findings regarding the genetic regulators of leaf size in Brassica and discuss future prospects for this research.
Collapse
Affiliation(s)
- Umer Karamat
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Xiaoxue Sun
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Na Li
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China.
| | - Jianjun Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China.
| |
Collapse
|
5
|
Hong WJ, Jiang X, Ahn HR, Choi J, Kim SR, Jung KH. Systematic Analysis of Cold Stress Response and Diurnal Rhythm Using Transcriptome Data in Rice Reveals the Molecular Networks Related to Various Biological Processes. Int J Mol Sci 2020; 21:E6872. [PMID: 32961678 PMCID: PMC7554834 DOI: 10.3390/ijms21186872] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/14/2020] [Accepted: 09/17/2020] [Indexed: 11/16/2022] Open
Abstract
Rice (Oryza sativa L.), a staple crop plant that is a major source of calories for approximately 50% of the human population, exhibits various physiological responses against temperature stress. These responses are known mechanisms of flexible adaptation through crosstalk with the intrinsic circadian clock. However, the molecular regulatory network underlining this crosstalk remains poorly understood. Therefore, we performed systematic transcriptome data analyses to identify the genes involved in both cold stress responses and diurnal rhythmic patterns. Here, we first identified cold-regulated genes and then identified diurnal rhythmic genes from those (119 cold-upregulated and 346 cold-downregulated genes). We defined cold-responsive diurnal rhythmic genes as CD genes. We further analyzed the functional features of these CD genes through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses and performed a literature search to identify functionally characterized CD genes. Subsequently, we found that light-harvesting complex proteins involved in photosynthesis strongly associate with the crosstalk. Furthermore, we constructed a protein-protein interaction network encompassing four hub genes and analyzed the roles of the Stay-Green (SGR) gene in regulating crosstalk with sgr mutants. We predict that these findings will provide new insights in understanding the environmental stress response of crop plants against climate change.
Collapse
Affiliation(s)
- Woo-Jong Hong
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea; (W.-J.H.); (X.J.); (H.R.A.)
| | - Xu Jiang
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea; (W.-J.H.); (X.J.); (H.R.A.)
| | - Hye Ryun Ahn
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea; (W.-J.H.); (X.J.); (H.R.A.)
| | - Juyoung Choi
- Department of Life Science, Sogang University, Seoul 04107, Korea;
| | - Seong-Ryong Kim
- Department of Life Science, Sogang University, Seoul 04107, Korea;
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea; (W.-J.H.); (X.J.); (H.R.A.)
| |
Collapse
|
6
|
Hu D, Zhang H, Du Q, Hu Z, Yang Z, Li X, Wang J, Huang F, Yu D, Wang H, Kan G. Genetic dissection of yield-related traits via genome-wide association analysis across multiple environments in wild soybean (Glycine soja Sieb. and Zucc.). PLANTA 2020; 251:39. [PMID: 31907621 DOI: 10.1007/s00425-019-03329-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 12/10/2019] [Indexed: 06/10/2023]
Abstract
MAIN CONCLUSION A total of 41 SNPs were identified as significantly associated with five yield-related traits in wild soybean populations across multiple environments, and the candidate gene GsCID1 was found to be associated with seed weight. These results may facilitate improvements in cultivated soybean. Crop-related wild species contain new sources of genetic diversity for crop improvement. Wild soybean (Glycine soja Sieb. and Zucc.) is the progenitor of cultivated soybean [Glycine max (L.) Merr.] and can be used as an essential genetic resource for yield improvements. In this research, using genome-wide association study (GWAS) in 96 out of 113 wild soybean accessions with 114,090 single nucleotide polymorphisms (SNPs) (with minor allele frequencies ≤ 0.05), SNPs associated with five yield-related traits were identified across multiple environments. In total, 41 SNPs were significantly associated with the traits in two or more environments (significance threshold P ≤ 8.76 × 10-6), with 29, 7, 3, and 2 SNPs detected for 100-seed weight (SW), maturity time (MT), seed yield per plant (SY) and flowering time (FT), respectively. BLAST search against the Glycine soja W05 reference genome was performed, 20 candidate genes were identified based on these 41 significant SNPs. One candidate gene, GsCID1 (Glysoja.04g010563), harbored two significant SNPs-AX-93713187, with a non-synonymous mutation, and AX-93713188, with a synonymous mutation. GsCID1 was highly expressed during seed development based on public information resources. The polymorphisms in this gene were associated with SW. We developed a derived cleaved amplified polymorphic sequence (dCAPS) marker for GsCID1 that was highly associated with SW and was validated as a functional marker. In summary, the revealed SNPs/genes are useful for understanding the genetic architecture of yield-related traits in wild soybean, which could be used as a potential exotic resource to improve cultivated soybean yields.
Collapse
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, 210095, China
| | - Huairen Zhang
- 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, 210095, China
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qing Du
- 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, 210095, China
| | - Zhenbin Hu
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - 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, 210095, 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, 210095, China
| | - Jiao Wang
- 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, 210095, 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, 210095, 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, 210095, China
- School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Hui Wang
- 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, 210095, 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, 210095, China.
| |
Collapse
|
7
|
Transcriptomic data-driven discovery of global regulatory features of rice seeds developing under heat stress. Comput Struct Biotechnol J 2020; 18:2556-2567. [PMID: 33033578 PMCID: PMC7522763 DOI: 10.1016/j.csbj.2020.09.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 11/30/2022] Open
Abstract
Plants respond to abiotic stressors through a suite of strategies including differential regulation of stress-responsive genes. Hence, characterizing the influences of the relevant global regulators or on stress-related transcription factors is critical to understand plant stress response. Rice seed development is highly sensitive to elevated temperatures. To elucidate the extent and directional hierarchy of gene regulation in rice seeds under heat stress, we developed and implemented a robust multi-level optimization-based algorithm called Minimal Regulatory Network identifier (MiReN). MiReN could predict the minimal regulatory relationship between a gene and its potential regulators from our temporal transcriptomic dataset. MiReN predictions for global regulators including stress-responsive gene Slender Rice 1 (SLR1) and disease resistance gene XA21 were validated with published literature. It also predicted novel regulatory influences of other major regulators such as Kinesin-like proteins KIN12C and STD1, and WD repeat-containing protein WD40. Out of the 228 stress-responsive transcription factors identified, we predicted de novo regulatory influences on three major groups (MADS-box M-type, MYB, and bZIP) and investigated their physiological impacts during stress. Overall, MiReN results can facilitate new experimental studies to enhance our understanding of global regulatory mechanisms triggered during heat stress, which can potentially accelerate the development of stress-tolerant cultivars.
Collapse
|
8
|
Liu Y, Zhu Y, Xu X, Sun F, Yang J, Cao L, Luo X. OstMAPKKK5, a truncated mitogen-activated protein kinase kinase kinase 5, positively regulates plant height and yield in rice. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.cj.2019.03.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
|
9
|
Chen S, Lin Z, Zhou D, Wang C, Li H, Yu R, Deng H, Tang X, Zhou S, Wang Deng X, He H. Genome-wide study of an elite rice pedigree reveals a complex history of genetic architecture for breeding improvement. Sci Rep 2017; 7:45685. [PMID: 28374863 PMCID: PMC5379486 DOI: 10.1038/srep45685] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 03/01/2017] [Indexed: 01/19/2023] Open
Abstract
Improving breeding has been widely utilized in crop breeding and contributed to yield and quality improvement, yet few researches have been done to analyze genetic architecture underlying breeding improvement comprehensively. Here, we collected genotype and phenotype data of 99 cultivars from the complete pedigree including Huanghuazhan, an elite, high-quality, conventional indica rice that has been grown over 4.5 million hectares in southern China and from which more than 20 excellent cultivars have been derived. We identified 1,313 selective sweeps (SSWs) revealing four stage-specific selection patterns corresponding to improvement preference during 65 years, and 1113 conserved Huanghuazhan traceable blocks (cHTBs) introduced from different donors and conserved in >3 breeding generations were the core genomic regions for superior performance of Huanghuazhan. Based on 151 quantitative trait loci (QTLs) identified for 13 improved traits in the pedigree, we reproduced their improvement process in silico, highlighting improving breeding works well for traits controlled by major/major + minor effect QTLs, but was inefficient for traits controlled by QTLs with complex interactions or explaining low levels of phenotypic variation. These results indicate long-term breeding improvement is efficient to construct superior genetic architecture for elite performance, yet molecular breeding with designed genotype of QTLs can facilitate complex traits improvement.
Collapse
Affiliation(s)
- Shaoxia Chen
- School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, and School of Advanced Agriculture Sciences, Peking University, Beijing 100871, China.,Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program (PTN), Peking University, China
| | - Zechuan Lin
- School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, and School of Advanced Agriculture Sciences, Peking University, Beijing 100871, China
| | - Degui Zhou
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Chongrong Wang
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Hong Li
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Renbo Yu
- School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, and School of Advanced Agriculture Sciences, Peking University, Beijing 100871, China
| | - Hanchao Deng
- Shenzhen Institute of Molecular Crop Design, Shenzhen 518107, China
| | - Xiaoyan Tang
- Shenzhen Institute of Molecular Crop Design, Shenzhen 518107, China.,Guangdong Key Lab of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Shaochuan Zhou
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Xing Wang Deng
- School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, and School of Advanced Agriculture Sciences, Peking University, Beijing 100871, China.,Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program (PTN), Peking University, China
| | - Hang He
- School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, and School of Advanced Agriculture Sciences, Peking University, Beijing 100871, China.,Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program (PTN), Peking University, China
| |
Collapse
|
10
|
Liu D, Cai X. OsRRMh, a Spen-like gene, plays an important role during the vegetative to reproductive transition in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2013; 55:876-87. [PMID: 23621499 DOI: 10.1111/jipb.12056] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 04/02/2013] [Indexed: 05/11/2023]
Abstract
OsRRMh, a homologue of OsRRM, encodes a Spen-like protein, and is composed of two N-terminal RNA recognition motifs (RRM) and one C-terminal Spen paralogue and an orthologue C-terminal domain (SPOC). The gene has been found to be constitutively expressed in the root, stem, leaf, spikelet, and immature seed, and alternative splicing patterns were confirmed in different tissues, which may indicate diverse functions for OsRRMh. The OsRRMh dsRNAi lines exhibited late-flowering and a larger panicle phenotype. When full-length OsRRMh and/or its SPOC domain were overexpressed, the fertility rate and number of spikelets per panicle were both markedly reduced. Also, overexpression of OsRRMh in the Arabidopsis fpa mutant did not restore the normal flowering time, and it delayed flowering in Col plants. Therefore, we propose that OsRRMh may confer one of its functions in the vegetative-to-reproductive transition in rice (Oryza sativa L. subsp. japonica cv. Zhonghua No. 11 (ZH11)).
Collapse
Affiliation(s)
- Derui Liu
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, the Chinese Academy of Sciences, Shanghai, 200032, China; University of Chinese Academy of Sciences, the Chinese Academy of Sciences, Beijing, 100049, China
| | | |
Collapse
|
11
|
Park HY, Kang IS, Han JS, Lee CH, An G, Moon YH. OsDEG10 encoding a small RNA-binding protein is involved in abiotic stress signaling. Biochem Biophys Res Commun 2009; 380:597-602. [PMID: 19285007 DOI: 10.1016/j.bbrc.2009.01.131] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2009] [Accepted: 01/23/2009] [Indexed: 01/26/2023]
Abstract
Excessive light can be harmful to photosynthetic apparatus since it causes photoinhibition and photooxidation, and plants often encounter hypoxic or anoxic environments when they become submerged by heavy rain or an ensuing flood. In this study, Oryza sativa Differentially Expressed Genes (OsDEGs) from rice under photooxidation and anoxia conditions were isolated using DD-PCR. Among them, OsDEG10 is predicted to encode a small RNA-binding protein (RBP) and the transcript levels of OsDEG10 strongly increased under most of abiotic stress treatments such as high light, anoxia, NaCl, ABA, MV and cold. However, the transcript levels of two rice OsDEG10 homologs were not changed under those treatments. OsDEG10 RNAi transgenic plants were more sensitive to high light and cold stresses compared to wild-type plants. Our results suggest that OsDEG10 is a small RBP involved in the response to various abiotic stresses.
Collapse
Affiliation(s)
- Hee-Yeon Park
- Department of Biological Sciences, Pusan National University, San 30, Jangjeon-dong, Geumjeong-gu, Busan 609-735, Republic of Korea
| | | | | | | | | | | |
Collapse
|