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Tran TTT, Le LHM, Nguyen TT, Nguyen TC, Hoang TTH, Do PT, To HTM. QTL-seq identifies genomic region associated with the crown root development under Jasmonic acid response. Funct Integr Genomics 2024; 24:141. [PMID: 39160350 DOI: 10.1007/s10142-024-01422-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 08/06/2024] [Accepted: 08/09/2024] [Indexed: 08/21/2024]
Abstract
Rice root system plays a crucial role in plant adaptation under adverse conditions, particularly drought stress. However, the regulatory gene networks that govern rice root development during stress exposure remain largely unexplored. In this study, we applied a QTL sequencing method to identify QTL/gene controlling the crown root development under Jasmonic acid simulation using the Bulk-segregant analysis. Two rice cultivars with contrasting phenotypes from the Vietnamese traditional rice collection were used as parent pairs for crossing. The single-seed descent method was employed to generate an F2 population of progenies. This F2/3 population was further segregated based on root count under JA stress. Pooled DNA from the two extreme groups in this population was sequenced, and SNP indexes across all loci in these pools were calculated. We detected a significant genomic region on chromosome 10, spanned from 20.39-20.50 Mb, where two rice RLKs were located, OsPUB54 and OsPUB58. Receptor-like kinases (RLKs) are pivotal in regulating various aspects of root development in plants, and the U-box E3 ubiquitination ligase class was generally known for its degradation of some protein complexes. Notably, OsPUB54 was strongly induced by JA treatment, suggesting its involvement in the degradation of the Aux/IAA protein complex, thereby influencing crown root initiation. Besides, the Eukaryotic translation initiation of factor 3 subunit L (eIF3l) and the Mitogen-activated protein kinase kinase kinase 37 (MAPKKK 37) proteins identified from SNPs with high score index which suggests their significant roles in the translation initiation process and cellular signaling pathways, respectively. This information suggests several clues of how these candidates are involved in modifying the rice root system under stress conditions.
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Affiliation(s)
- Tam Thi Thanh Tran
- University of Science and Technology of Hanoi, Academy of Science and Technology, Hanoi, Vietnam
| | - Liem Huu Minh Le
- University of Science and Technology of Hanoi, Academy of Science and Technology, Hanoi, Vietnam
| | - Trang Thi Nguyen
- University of Science and Technology of Hanoi, Academy of Science and Technology, Hanoi, Vietnam
| | - Thanh Chi Nguyen
- University of Science and Technology of Hanoi, Academy of Science and Technology, Hanoi, Vietnam
| | | | - Phat Tien Do
- Institute of Biotechnology, Academy of Science and Technology, Hanoi, Vietnam
| | - Huong Thi Mai To
- University of Science and Technology of Hanoi, Academy of Science and Technology, Hanoi, Vietnam.
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2
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Lyu Y, Dong X, Niu S, Cao R, Shao G, Sheng Z, Jiao G, Xie L, Hu S, Tang S, Wei X, Hu P. An orchestrated ethylene-gibberellin signaling cascade contributes to mesocotyl elongation and emergence of rice direct seeding. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1427-1439. [PMID: 38751025 DOI: 10.1111/jipb.13671] [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: 02/13/2024] [Accepted: 04/18/2024] [Indexed: 07/12/2024]
Abstract
A mechanized direct seeding of rice with less labor and water usage, has been widely adopted. However, this approach requires varieties that exhibit uniform seedling emergence. Mesocotyl elongation (ME) offers the main drive of fast emergence of rice seedlings from soils; nevertheless, its genetic basis remains unknown. Here, we identify a major rice quantitative trait locus Mesocotyl Elongation1 (qME1), an allele of the Green Revolution gene Semi-Dwarf1 (SD1), encoding GA20-oxidase for gibberellin (GA) biosynthesis. ME1 expression is strongly induced by soil depth and ethylene. When rice grains are direct-seeded in soils, the ethylene core signaling factor OsEIL1 directly promotes ME1 transcription, accelerating bioactive GA biosynthesis. The GAs further degrade the DELLA protein SLENDER RICE 1 (SLR1), alleviating its inhibition of rice PHYTOCHROME-INTERACTING FACTOR-LIKE13 (OsPIL13) to activate the downstream expansion gene OsEXPA4 and ultimately promote rice seedling ME and emergence. The ancient traits of long mesocotyl and strong emergence ability in wild rice and landrace were gradually lost in company with the Green Revolution dwarf breeding process, and an elite ME1-R allele (D349H) is found in some modern Geng varieties (long mesocotyl lengths) in northern China, which can be used in the direct seeding and dwarf breeding of Geng varieties. Furthermore, the ectopic and high expression of ME1 driven by mesocotyl-specific promoters resulted in rice plants that could be direct-seeded without obvious plant architecture or yield penalties. Collectively, we reveal the molecular mechanism of rice ME, and provide useful information for breeding new Green Revolution varieties with long mesocotyl suitable for direct-seeding practice.
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Affiliation(s)
- Yusong Lyu
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Xinli Dong
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Shipeng Niu
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Ruijie Cao
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Gaoneng Shao
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Zhonghua Sheng
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Guiai Jiao
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Lihong Xie
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Shikai Hu
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Shaoqing Tang
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Xiangjin Wei
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Peisong Hu
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
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3
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Kabange NR, Alibu S, Kwon Y, Lee SM, Oh KW, Lee JH. Genome-wide association study (GWAS) with high-throughput SNP chip DNA markers identified novel genetic factors for mesocotyl elongation and seedling emergence in rice ( Oryza sativa L.) using multiple GAPIT models. Front Genet 2023; 14:1282620. [PMID: 38054028 PMCID: PMC10694456 DOI: 10.3389/fgene.2023.1282620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/08/2023] [Indexed: 12/07/2023] Open
Abstract
This study employed a joint strategy high-density SNP Chip DNA markers and multiple Genome Association and Prediction Integrated Tool (GAPIT) models [(Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK), Fixed and random model Circulating Probability Uniform (FarmCPU), General Linear Model (GLM), and Settlement of Mixed Linear Model (MLM) Under Progressively Exclusive Relationship (SUPER)], to investigate novel genetic factors controlling mesocotyl elongation and seedling emergence for direct-seeded rice. Genotype data (230,526 SNP Chip DNA makers) of 117 doubled haploid lines (derived from a cross between 93-11 (Oryza sativa L. ssp. indica) and Milyang352 (O. sativa L. ssp. japonica) were used to perform a Genome-Wide Association Study (GWAS). Results revealed the association between five (5) topmost significant SNP markers, of which number two [AX-155741269, Chr2: 15422406 bp, and AX-155200917, Chr7: 23814085 bp, explaining 37.5% and 13.8% of the phenotypic variance explained (PVE)] are linked to the mesocotyl elongation loci, while three (AX-282097034 and AX-283652873, Chr9: 9882817 bp and 1023383 bp, PVE 64.5%, and 20.2%, respectively, and AX-154356231, Chr1: 17413989 bp, PVE 21.1%) are tightly linked to the loci controlling seedling emergence. The qMEL2-1 and qSEM9-1 are identified as major QTLs explaining 37.5% and 64.5% of the PVE for mesocotyl elongation and seedling emergence, respectively. The AX-282097034 (Chr9: 9882817 bp) was co-detected by four GAPIT models (BLINK, FarmCPU, SUPER, and GLM), while AX-155741269 was co-detected by BLINK and SUPER. Furthermore, a high estimated heritability (Mesocotyl elongation: h2 = 0.955; seedling emergence: h2 = 0.863; shoot length: h2 = 0.707) was observed. Genes harbored by qMEL2-1 and qSEM9-1 have interesting annotated molecular functions that could be investigated through functional studies to uncover their roles during mesocotyl elongation and seedling emergence events in rice. Furthermore, the presence of genes encoding transcription factors, growth- and stress response, or signaling-related genes would suggest that mesocotyl elongation and seedling emergence from deep direct-seeded rice might involve an active signaling cascade and transport of molecules, which could be elucidated through functional analysis. Likewise, genomic selection analysis suggested markers useful for downstream marker-assisted selection (MAS).
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Affiliation(s)
- Nkulu Rolly Kabange
- Department of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang, Republic of Korea
| | - Simon Alibu
- National Crops Resources Research Institute (NaCRRI), National Agricultural Research Organisation (NARO), Entebbe, Uganda
| | - Youngho Kwon
- Department of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang, Republic of Korea
| | - So-Myeong Lee
- Department of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang, Republic of Korea
| | - Ki-Won Oh
- Department of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang, Republic of Korea
| | - Jong-Hee Lee
- Department of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang, Republic of Korea
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Meng Y, Zhan J, Liu H, Liu J, Wang Y, Guo Z, He S, Nie L, Kohli A, Ye G. Natural variation of OsML1, a mitochondrial transcription termination factor, contributes to mesocotyl length variation in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:910-925. [PMID: 37133286 DOI: 10.1111/tpj.16267] [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: 12/24/2022] [Revised: 04/04/2023] [Accepted: 04/27/2023] [Indexed: 05/04/2023]
Abstract
Mesocotyl length (ML) is a crucial factor in determining the establishment and yield of rice planted through dry direct seeding, a practice that is increasingly popular in rice production worldwide. ML is determined by the endogenous and external environments, and inherits as a complex trait. To date, only a few genes have been cloned, and the mechanisms underlying mesocotyl elongation remain largely unknown. Here, through a genome-wide association study using sequenced germplasm, we reveal that natural allelic variations in a mitochondrial transcription termination factor, OsML1, predominantly determined the natural variation of ML in rice. Natural variants in the coding regions of OsML1 resulted in five major haplotypes with a clear differentiation between subspecies and subpopulations in cultivated rice. The much-reduced genetic diversity of cultivated rice compared to the common wild rice suggested that OsML1 underwent selection during domestication. Transgenic experiments and molecular analysis demonstrated that OsML1 contributes to ML by influencing cell elongation primarily determined by H2 O2 homeostasis. Overexpression of OsML1 promoted mesocotyl elongation and thus improved the emergence rate under deep direct seeding. Taken together, our results suggested that OsML1 is a key positive regulator of ML, and is useful in developing varieties for deep direct seeding by conventional and transgenic approaches.
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Affiliation(s)
- Yun Meng
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, 572025, China
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Junhui Zhan
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Hongyan Liu
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, 572025, China
| | - Jindong Liu
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yamei Wang
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Zhan Guo
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Sang He
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Lixiao Nie
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, 572025, China
| | - Ajay Kohli
- Rice Breeding Innovations Platform, International Rice Research Institute (IRRI), Metro Manila, 1301, Philippines
| | - Guoyou Ye
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- Rice Breeding Innovations Platform, International Rice Research Institute (IRRI), Metro Manila, 1301, Philippines
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Feng F, Ma X, Yan M, Zhang H, Mei D, Fan P, Xu X, Wei C, Lou Q, Li T, Liu H, Luo L, Mei H. Identification of Genetic Loci for Rice Seedling Mesocotyl Elongation in Both Natural and Artificial Segregating Populations. PLANTS (BASEL, SWITZERLAND) 2023; 12:2743. [PMID: 37514357 PMCID: PMC10385686 DOI: 10.3390/plants12142743] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023]
Abstract
Mesocotyl elongation of rice seedlings is a key trait for deep sowing tolerance and well seedling establishment in dry direct sowing rice (DDSR) production. Subsets of the Rice Diversity Panel 1 (RDP1, 294 accessions) and Hanyou 73 (HY73) recombinant inbred line (RIL) population (312 lines) were screened for mesocotyl length (ML) via dark germination. Six RDP1 accessions (Phudugey, Kasalath, CA902B21, Surjamkuhi, Djimoron, and Goria) had an ML longer than 10 cm, with the other 19 accessions being over 4 cm. A GWAS in RDP1 detected 118 associated SNPs on all 12 chromosomes using a threshold of FDR-adjusted p < 0.05, including 11 SNPs on chromosomes 1, 4, 5, 7, 10, and 12 declared by -log10(P) > 5.868 as the Bonferroni-corrected threshold. Using phenotypic data of three successive trials and a high-density bin map from resequencing genotypic data, four to six QTLs were detected on chromosomes 1, 2, 5, 6, and 10, including three loci repeatedly mapped for ML from two or three replicated trials. Candidate genes were predicted from the chromosomal regions covered by the associated LD blocks and the confidence intervals (CIs) of QTLs and partially validated by the dynamic RNA-seq data in the mesocotyl along different periods of light exposure. Potential strategies of donor parent selection for seedling establishment in DDSR breeding were discussed.
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Affiliation(s)
- Fangjun Feng
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
| | - Xiaosong Ma
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Ming Yan
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
| | - Hong Zhang
- Anji Administrative Station of Water and Soil Conservation, Huzhou 313300, China
| | - Daoliang Mei
- Anji Administrative Station of Water and Soil Conservation, Huzhou 313300, China
| | - Peiqing Fan
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
| | - Xiaoyan Xu
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
| | - Chunlong Wei
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
| | - Qiaojun Lou
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
| | - Tianfei Li
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
| | - Hongyan Liu
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
| | - Lijun Luo
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Hanwei Mei
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
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Sakhale SA, Yadav S, Clark LV, Lipka AE, Kumar A, Sacks EJ. Genome-wide association analysis for emergence of deeply sown rice ( Oryza sativa) reveals novel aus-specific phytohormone candidate genes for adaptation to dry-direct seeding in the field. FRONTIERS IN PLANT SCIENCE 2023; 14:1172816. [PMID: 37377815 PMCID: PMC10291202 DOI: 10.3389/fpls.2023.1172816] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023]
Abstract
Dry direct-seeded rice (dry-DSR) is typically sown deeply to circumvent the need for irrigation, and thus seedling emergence is a crucial trait affecting plant stand and yield. To breed elite cultivars that use less water and are climate-resilient, an understanding of the genomic regions and underlying genes that confer emergence in deeply sown dry-DSR would be highly advantageous. A combined diversity panel of 470 rice accessions (RDP1 plus aus subset of 3K RGP) was evaluated with 2.9 million single nucleotide polymorphisms (SNPs) to identify associations with dry-DSR traits in the field and component traits in a controlled-environment experiment. Using genome-wide association study (GWAS) analyses, we identified 18 unique QTLs on chromosomes 1, 2, 4, 5, 6, 7, 9, 10, and 11, explaining phenotypic variance ranging from 2.6% to 17.8%. Three QTLs, namely, qSOE-1.1, qEMERG-AUS-1.2, and qEMERG-AUS-7.1, were co-located with previously reported QTLs for mesocotyl length. Among the identified QTLs, half were associated with the emergence of aus, and six were unique to the aus genetic group. Based on functional annotation, we identified eleven compelling candidate genes that primarily regulate phytohormone pathways such as cytokinin, auxin, gibberellic acid, and jasmonic acid. Prior studies indicated that these phytohormones play a critical role in mesocotyl length under deep sowing. This study provides new insight into the importance of aus and indica as desirable genetic resources to mine favorable alleles for deep-sowing tolerance in rice. The candidate genes and marker-tagged desirable alleles identified in this study should benefit rice breeding programs directly.
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Affiliation(s)
- Sandeep A. Sakhale
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, IL, United States
- International Rice Research Institute (IRRI), Los Baños, Philippines
- International Rice Research Institute (IRRI), South Asia Regional Centre (ISARC), Varanasi, India
| | - Shailesh Yadav
- International Rice Research Institute (IRRI), Los Baños, Philippines
- Africa Rice Center (AfricaRice), Abidjan, Côte d’Ivoire
| | - Lindsay V. Clark
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, IL, United States
- Seattle Children’s Research Institute, Seattle, WA, United States
| | - Alexander E. Lipka
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, IL, United States
| | - Arvind Kumar
- International Rice Research Institute (IRRI), Los Baños, Philippines
- International Rice Research Institute (IRRI), South Asia Regional Centre (ISARC), Varanasi, India
| | - Erik J. Sacks
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, IL, United States
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Ju L, Lv N, Yin F, Niu H, Yan H, Wang Y, Fan F, Lv X, Chu J, Ping J. Identification of Key Genes Regulating Sorghum Mesocotyl Elongation through Transcriptome Analysis. Genes (Basel) 2023; 14:1215. [PMID: 37372395 DOI: 10.3390/genes14061215] [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: 05/03/2023] [Revised: 05/28/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Sorghum with longer mesocotyls is beneficialfor improving its deep tolerance, which is important for the seedling rates. Here, we perform transcriptome analysis between four different sorghum lines, with the aim of identifying the key genes regulating sorghum mesocotyl elongation. According to the mesocotyl length (ML) data, we constructed four comparison groups for the transcriptome analysis and detected 2705 common DEGs. GO and KEGG enrichment analysis showed that the most common category of DEGs were involved in cell wall, microtubule, cell cycle, phytohormone, and energy metabolism-related pathways. In the cell wall biological processes, the expression of SbEXPA9-1, SbEXPA9-2, SbXTH25, SbXTH8-1, and SbXTH27 are increased in the sorghum lines with long ML. In the plant hormone signaling pathway, five auxin-responsive genes and eight cytokinin/zeatin/abscisic acid/salicylic acid-related genes showed a higher expression level in the long ML sorghum lines. In addition, five ERF genes showed a higher expression level in the sorghum lines with long ML, whereas two ERF genes showed a lower expression level in these lines. Furthermore, the expression levels of these genes were further analyzed using real-time PCR (RT-qPCR), which showed similar results. This work identified the candidate gene regulating ML, which may provide additional evidence to understand the regulatory molecular mechanisms of sorghum mesocotyl elongation.
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Affiliation(s)
- Lan Ju
- Shanxi Key Laboratory of Sorghum Genetic and Germplasm Innovation, Sorghum Research Institute, Shanxi Agricultural University, Jinzhong 030600, China
| | - Na Lv
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030600, China
| | - Feng Yin
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030600, China
| | - Hao Niu
- Shanxi Key Laboratory of Sorghum Genetic and Germplasm Innovation, Sorghum Research Institute, Shanxi Agricultural University, Jinzhong 030600, China
| | - Haisheng Yan
- Shanxi Key Laboratory of Sorghum Genetic and Germplasm Innovation, Sorghum Research Institute, Shanxi Agricultural University, Jinzhong 030600, China
| | - Yubin Wang
- Shanxi Key Laboratory of Sorghum Genetic and Germplasm Innovation, Sorghum Research Institute, Shanxi Agricultural University, Jinzhong 030600, China
| | - Fangfang Fan
- Shanxi Key Laboratory of Sorghum Genetic and Germplasm Innovation, Sorghum Research Institute, Shanxi Agricultural University, Jinzhong 030600, China
| | - Xin Lv
- Shanxi Key Laboratory of Sorghum Genetic and Germplasm Innovation, Sorghum Research Institute, Shanxi Agricultural University, Jinzhong 030600, China
| | - Jianqiang Chu
- Shanxi Key Laboratory of Sorghum Genetic and Germplasm Innovation, Sorghum Research Institute, Shanxi Agricultural University, Jinzhong 030600, China
| | - Junai Ping
- Shanxi Key Laboratory of Sorghum Genetic and Germplasm Innovation, Sorghum Research Institute, Shanxi Agricultural University, Jinzhong 030600, China
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8
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Wang Y, Liu H, Meng Y, Liu J, Ye G. Validation of genes affecting rice mesocotyl length through candidate association analysis and identification of the superior haplotypes. FRONTIERS IN PLANT SCIENCE 2023; 14:1194119. [PMID: 37324692 PMCID: PMC10267709 DOI: 10.3389/fpls.2023.1194119] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 05/02/2023] [Indexed: 06/17/2023]
Abstract
Mesocotyl is an essential organ of rice for pushing buds out of soil and plays a crucial role in seeding emergence and development in direct-seeding. Thus, identify the loci associated with mesocotyl length (ML) could accelerate breeding progresses for direct-seeding cultivation. Mesocotyl elongation was mainly regulated by plant hormones. Although several regions and candidate genes governing ML have been reported, the effects of them in diverse breeding populations were still indistinct. In this study, 281 genes related to plant hormones at the genomic regions associated with ML were selected and evaluated by single-locus mixed linear model (SL-MLM) and multi-locus random-SNP-effect mixed linear model (mr-MLM) in two breeding panels (Trop and Indx) originated from the 3K re-sequence project. Furthermore, superior haplotypes with longer mesocotyl were also identified for marker assisted selection (MAS) breeding. Totally, LOC_Os02g17680 (explained 7.1-8.9% phenotypic variations), LOC_Os04g56950 (8.0%), LOC_Os07g24190 (9.3%) and LOC_Os12g12720 (5.6-8.0%) were identified significantly associated with ML in Trop panel, whereas LOC_Os02g17680 (6.5-7.4%), LOC_Os04g56950 (5.5%), LOC_Os06g24850 (4.8%) and LOC_Os07g40240 (4.8-7.1%) were detected in Indx panel. Among these, LOC_Os02g17680 and LOC_Os04g56950 were identified in both panels. Haplotype analysis for the six significant genes indicated that haplotype distribution of the same gene varies at Trop and Indx panels. Totally, 8 (LOC_Os02g17680-Hap1 and Hap2, LOC_Os04g56950-Hap1, Hap2 and Hap8, LOC_Os07g24190-Hap3, LOC_Os12g12720-Hap3 and Hap6) and six superior haplotypes (LOC_Os02g17680-Hap2, Hap5 and Hap7, LOC_Os04g56950-Hap4, LOC_Os06g24850-Hap2 and LOC_Os07g40240-Hap3) with higher ML were identified in Trop and Indx panels, respectively. In addition, significant additive effects for ML with more superior haplotypes were identified in both panels. Overall, the 6 significantly associated genes and their superior haplotypes could be used to enhancing ML through MAS breeding and further promote direct-seedling cultivation.
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Affiliation(s)
- Yamei Wang
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- School of Agriculture, Sun Yat-sen University, Shenzhen, China
| | - Hongyan Liu
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, China
| | - Yun Meng
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, China
| | - Jindong Liu
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Guoyou Ye
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Strategic Innovation Platform, International Rice Research Institute, Manila, Philippines
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9
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Zhao X, Niu Y, Hossain Z, Shi J, Mao T, Bai X. Integrated QTL Mapping, Meta-Analysis, and RNA-Sequencing Reveal Candidate Genes for Maize Deep-Sowing Tolerance. Int J Mol Sci 2023; 24:ijms24076770. [PMID: 37047743 PMCID: PMC10094843 DOI: 10.3390/ijms24076770] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/24/2023] [Accepted: 03/30/2023] [Indexed: 04/08/2023] Open
Abstract
Synergetic elongation of mesocotyl and coleoptile are crucial in governing maize seedlings emergence, especially for the maize sown in deep soil. Studying the genomic regions controlling maize deep-sowing tolerance would aid the development of new varieties that are resistant to harsh conditions, such as drought and low temperature during seed germination. Using 346 F2:3 maize population families from W64A × K12 cross at three sowing depths, we identified 33 quantitative trait loci (QTLs) for the emergence rate, mesocotyl, coleoptile, and seedling lengths via composite interval mapping (CIM). These loci explained 2.89% to 14.17% of phenotypic variation in a single environment, while 12 of 13 major QTLs were identified at two or more sowing environments. Among those, four major QTLs in Bin 1.09, Bin 4.08, Bin 6.01, and Bin 7.02 supported pleiotropy for multiple deep-sowing tolerant traits. Meta-analysis identified 17 meta-QTLs (MQTLs) based on 130 original QTLs from present and previous studies. RNA-Sequencing of mesocotyl and coleoptile in both parents (W64A and K12) at 3 cm and 20 cm sowing environments identified 50 candidate genes expressed differentially in all major QTLs and MQTLs regions: six involved in the circadian clock, 27 associated with phytohormones biosynthesis and signal transduction, seven controlled lignin biosynthesis, five regulated cell wall organization formation and stabilization, three were responsible for sucrose and starch metabolism, and two in the antioxidant enzyme system. These genes with highly interconnected networks may form a complex molecular mechanism of maize deep-sowing tolerance. Findings of this study will facilitate the construction of molecular modules for deep-sowing tolerance in maize. The major QTLs and MQTLs identified could be used in marker-assisted breeding to develop elite maize varieties.
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Affiliation(s)
- Xiaoqiang Zhao
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Yining Niu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Zakir Hossain
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK S9H 3X2, Canada
| | - Jing Shi
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Taotao Mao
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiaodong Bai
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
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10
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Edzesi WM, Dang X, Liu E, Bandoh WKN, Gakpetor PM, Ofori DA, Hong D. Screening germplasm and detecting QTLs for mesocotyl elongation trait in rice (Oryza sativa L.) by association mapping. BMC Genom Data 2023; 24:8. [PMID: 36792993 PMCID: PMC9930352 DOI: 10.1186/s12863-023-01107-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 01/23/2023] [Indexed: 02/17/2023] Open
Abstract
BACKGROUND Rice is one of the most important food crops in the world and mainly cultivated in paddy field by transplanting seedlings. However, increasing water scarcity due to climate change, labor cost for transplanting, and competition from urbanization is making this traditional method of rice production unsustainable in the long term. In the present study, we mined favorable alleles for mesocotyl elongation length (MEL) by combining the phenotypic data of 543 rice accessions with genotypic data of 262 SSR markers through association mapping method. RESULTS Among the 543 rice accessions studied, we found 130 accessions could elongate mesocotyl length under dark germination condition. A marker-trait association analysis based on a mixed linear model revealed eleven SSR markers were associated with MEL trait with p-value less than 0.01. Among the 11 association loci, seven were novel. In total, 30 favorable marker alleles for MEL were mined, and RM265-140 bp showed the highest phenotypic effect value of 1.8 cm with Yuedao46 as the carrier accession. The long MEL group of rice accessions had higher seedling emergence rate than the short MEL group in the field. The correlation coefficient (r GCC-FSC = 0.485**) between growth chamber condition (GCC) and field soil condition (FSC) showed positive relationship and highly significant (P < 0.01) indicating that the result obtained in GCC could basically represent that obtained under FSC. CONCLUSION Not every genotype of the rice possesses the ability to elongate its mesocotyl length under dark or deep sowing condition. Mesocotyl elongation length is a quantitative trait controlled by many gene loci, and can be improved by pyramiding favorable alleles dispersed at different loci in different germplasm into a single genotype.
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Affiliation(s)
- Wisdom Mawuli Edzesi
- grid.27871.3b0000 0000 9750 7019State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China ,grid.423756.10000 0004 1764 1672Council for Scientific and Industrial Research, Forestry Research Institute of Ghana, P. O. Box UP 63, KNUST, Fumesua, Kumasi, Ashanti Region Ghana
| | - Xiaojing Dang
- grid.27871.3b0000 0000 9750 7019State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China ,grid.469521.d0000 0004 1756 0127Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Erbao Liu
- grid.27871.3b0000 0000 9750 7019State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China ,grid.411389.60000 0004 1760 4804College of Agriculture, Anhui Agricultural University, Hefei, 230036 China
| | - William Kwame Nuako Bandoh
- grid.423756.10000 0004 1764 1672Council for Scientific and Industrial Research, Forestry Research Institute of Ghana, P. O. Box UP 63, KNUST, Fumesua, Kumasi, Ashanti Region Ghana
| | - Patience Mansa Gakpetor
- grid.423756.10000 0004 1764 1672Council for Scientific and Industrial Research, Forestry Research Institute of Ghana, P. O. Box UP 63, KNUST, Fumesua, Kumasi, Ashanti Region Ghana
| | - Daniel Aninagyei Ofori
- grid.423756.10000 0004 1764 1672Council for Scientific and Industrial Research, Forestry Research Institute of Ghana, P. O. Box UP 63, KNUST, Fumesua, Kumasi, Ashanti Region Ghana
| | - Delin Hong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
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