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Liu S, Zheng Y, Zhao L, Gulam M, Ullah A, Xie G. CALMODULIN-LIKE16 and PIN-LIKES7a cooperatively regulate rice seedling primary root elongation under chilling. PLANT PHYSIOLOGY 2024; 195:1660-1680. [PMID: 38445796 DOI: 10.1093/plphys/kiae130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 11/29/2023] [Accepted: 12/21/2023] [Indexed: 03/07/2024]
Abstract
Low-temperature sensitivity at the germination stage is a challenge for direct seeding of rice in Asian countries. How Ca2+ and auxin (IAA) signaling regulate primary root growth under chilling remains unexplored. Here, we showed that OsCML16 interacted specifically with OsPILS7a to improve primary root elongation of early rice seedlings under chilling. OsCML16, a subgroup 6c member of the OsCML family, interacted with multiple cytosolic loop regions of OsPILS7a in a Ca2+-dependent manner. OsPILS7a localized to the endoplasmic reticulum membranes and functioned as an auxin efflux carrier in a yeast growth assay. Transgenics showed that presence of OsCML16 enhanced primary root elongation under chilling, whereas the ospils7a knockout mutant lines showed the opposite phenotype. Moreover, under chilling conditions, OsCML16 and OsPILS7a-mediated Ca2+ and IAA signaling and regulated the transcription of IAA signaling-associated genes (OsIAA11, OsIAA23, and OsARF16) and cell division marker genes (OsRAN1, OsRAN2, and OsLTG1) in primary roots. These results show that OsCML16 and OsPILS7a cooperatively regulate primary root elongation of early rice seedlings under chilling. These findings enhance our understanding of the crosstalk between Ca2+ and IAA signaling and reveal insights into the mechanisms underlying cold-stress response during rice germination.
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Affiliation(s)
- Shuang Liu
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuying Zheng
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Liyan Zhao
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Mihray Gulam
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Aman Ullah
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Guosheng Xie
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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Sandhu N, Singh J, Ankush AP, Augustine G, Raigar OP, Verma VK, Pruthi G, Kumar A. Development of Novel KASP Markers for Improved Germination in Deep-Sown Direct Seeded Rice. RICE (NEW YORK, N.Y.) 2024; 17:33. [PMID: 38727876 PMCID: PMC11087395 DOI: 10.1186/s12284-024-00711-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024]
Abstract
BACKGROUND The lack of stable-high yielding and direct-seeded adapted varieties with better germination ability from deeper soil depth and availability of molecular markers are major limitation in achieving the maximum yield potential of rice under water and resource limited conditions. Development of high-throughput and trait-linked markers are of great interest in genomics-assisted breeding. The aim of present study was to develop and validate novel KASP (Kompetitive Allele-Specific PCR) markers associated with traits improving germination and seedling vigor of deep sown direct seeded rice (DSR). RESULTS Out of 58 designed KASP assays, four KASP assays did not show any polymorphism in any of the eleven genetic backgrounds considered in the present study. The 54 polymorphic KASP assays were then validated for their robustness and reliability on the F1s plants developed from eight different crosses considered in the present study. The third next validation was carried out on 256 F3:F4 and 713 BC3F2:3 progenies. Finally, the reliability of the KASP assays was accessed on a set of random 50 samples from F3:F4 and 80-100 samples from BC3F2:3 progenies using the 10 random markers. From the 54 polymorphic KASP, based on the false positive rate, false negative rate, KASP utility in different genetic backgrounds and significant differences in the phenotypic values of the positive (desirable) and negative (undesirable) traits, a total of 12 KASP assays have been selected. These 12 KASP include 5 KASP on chromosome 3, 1 on chromosome 4, 3 on chromosome 7 and 3 on chromosome 8. The two SNPs lying in the exon regions of LOC_Os04g34290 and LOC_Os08g32100 led to non-synonymous mutations indicating a possible deleterious effect of the SNP variants on the protein structure. CONCLUSION The present research work will provide trait-linked KASP assays, improved breeding material possessing favourable alleles and breeding material in form of expected pre-direct-seeded adapted rice varieties. The marker can be utilized in introgression program during pyramiding of valuable QTLs/genes providing adaptation to rice under DSR. The functional studies of the genes LOC_Os04g34290 and LOC_Os08g32100 possessing two validated SNPs may provide valuable information about these genes.
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Affiliation(s)
- Nitika Sandhu
- Punjab Agricultural University, Ludhiana, Punjab, 141004, India.
| | - Jasneet Singh
- Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | | | | | | | | | - Gomsie Pruthi
- Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Arvind Kumar
- Delta Agrigenetics, Plot No. 99 & 100 Green Park Avenue, Village, Jeedimetla, Secunderabad, Telangana, 500055, India
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Gong W, Proud C, Vinarao R, Fukai S, Mitchell J. Genome-Wide Association Study of Early Vigour-Related Traits for a Rice ( Oryza sativa L.) japonica Diversity Set Grown in Aerobic Conditions. BIOLOGY 2024; 13:261. [PMID: 38666873 PMCID: PMC11048181 DOI: 10.3390/biology13040261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/02/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024]
Abstract
Aerobic rice production is a relatively new system in which rice is direct-seeded and grown in non-flooded but well-watered conditions to improve water productivity. Early vigour-related traits are likely to be important in aerobic conditions. This study aimed to identify quantitative trait loci (QTL) and candidate genes associated with early vigour-related traits in aerobic conditions using a japonica rice diversity set. Field experiments and glasshouse experiments conducted under aerobic conditions revealed significant genotypic variation in early vigour-related traits. Genome-wide association analysis identified 32 QTL associated with early vigour-related traits. Notably, two QTL, qAEV1.5 and qAEV8, associated with both early vigour score and mesocotyl length, explained up to 22.1% of the phenotypic variance. In total, 23 candidate genes related to plant growth development and abiotic stress response were identified in the two regions. This study provides novel insights into the genetic basis of early vigour under aerobic conditions. Validation of identified QTL and candidate genes in different genetic backgrounds is crucial for future studies. Moreover, testing the effect of QTL on yield under different environments would be valuable. After validation, these QTL and genes can be considered for developing markers in marker-assisted selection for aerobic rice production.
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Affiliation(s)
- Wenliu Gong
- School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, QLD 4072, Australia (J.M.)
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Aloryi KD, Okpala NE, Guo H, Karikari B, Amo A, Bello SF, Saini DK, Akaba S, Tian X. Integrated meta-analysis and transcriptomics pinpoint genomic loci and novel candidate genes associated with submergence tolerance in rice. BMC Genomics 2024; 25:338. [PMID: 38575927 PMCID: PMC10993490 DOI: 10.1186/s12864-024-10219-z] [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: 11/13/2023] [Accepted: 03/13/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Due to rising costs, water shortages, and labour shortages, farmers across the globe now prefer a direct seeding approach. However, submergence stress remains a major bottleneck limiting the success of this approach in rice cultivation. The merger of accumulated rice genetic resources provides an opportunity to detect key genomic loci and candidate genes that influence the flooding tolerance of rice. RESULTS In the present study, a whole-genome meta-analysis was conducted on 120 quantitative trait loci (QTL) obtained from 16 independent QTL studies reported from 2004 to 2023. These QTL were confined to 18 meta-QTL (MQTL), and ten MQTL were successfully validated by independent genome-wide association studies from diverse natural populations. The mean confidence interval (CI) of the identified MQTL was 3.44 times narrower than the mean CI of the initial QTL. Moreover, four core MQTL loci with genetic distance less than 2 cM were obtained. By combining differentially expressed genes (DEG) from two transcriptome datasets with 858 candidate genes identified in the core MQTL regions, we found 38 common differentially expressed candidate genes (DECGs). In silico expression analysis of these DECGs led to the identification of 21 genes with high expression in embryo and coleoptile under submerged conditions. These DECGs encode proteins with known functions involved in submergence tolerance including WRKY, F-box, zinc fingers, glycosyltransferase, protein kinase, cytochrome P450, PP2C, hypoxia-responsive family, and DUF domain. By haplotype analysis, the 21 DECGs demonstrated distinct genetic differentiation and substantial genetic distance mainly between indica and japonica subspecies. Further, the MQTL7.1 was successfully validated using flanked marker S2329 on a set of genotypes with phenotypic variation. CONCLUSION This study provides a new perspective on understanding the genetic basis of submergence tolerance in rice. The identified MQTL and novel candidate genes lay the foundation for marker-assisted breeding/engineering of flooding-tolerant cultivars conducive to direct seeding.
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Grants
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- Key R&D Project in Hubei Province, China
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Affiliation(s)
- Kelvin Dodzi Aloryi
- Hubei Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| | - Nnaemeka Emmanuel Okpala
- Hubei Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| | - Hong Guo
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Benjamin Karikari
- Département de phytologie, Université Laval, Québec, QC, Canada
- Department of Agricultural Biotechnology, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, Tamale, Ghana
| | - Aduragbemi Amo
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, USA
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, USA
| | - Semiu Folaniyi Bello
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, USA
| | - Selorm Akaba
- School of Agriculture, University of Cape Coast, Cape Coast, Ghana
| | - Xiaohai Tian
- Hubei Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China.
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Dong J, Ma Y, Hu H, Wang J, Yang W, Fu H, Zhang L, Chen J, Zhou L, Li W, Nie S, Liu Z, Zhao J, Liu B, Yang T, Zhang S. The Function of SD1 on Shoot Length and its Pyramiding Effect on Shoot Length and Plant Height in Rice (Oryza sativa L.). RICE (NEW YORK, N.Y.) 2024; 17:21. [PMID: 38526756 DOI: 10.1186/s12284-024-00699-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 03/08/2024] [Indexed: 03/27/2024]
Abstract
Strong seedling vigor is imperative to achieve stable seedling establishment and enhance the competitiveness against weeds in rice direct seeding. Shoot length (SL) is one of the important traits associated with seedling vigor in rice, but few genes for SL have been cloned so far. In the previous study, we identified two tightly linked and stably expressed QTLs for SL, qSL-1f and qSL-1d by genome-wide association study, and cloned the causal gene (LOC_Os01g68500) underlying qSL-1f. In the present study, we identify LOC_Os01g66100 (i.e. the semidwarf gene SD1), a well-known gene controlling plant height (PH) at the adult-plant stage, as the causal gene underlying qSL-1d through gene-based haplotype analysis and knockout transgenic verification. By measuring the phenotypes (SL and PH) of various haplotypes of the two genes and their knockout lines, we found SD1 and LOC_ Os01g68500 controlled both SL and PH, and worked in the same direction, which provided the directly genetic evidence for a positive correlation between SL and PH combined with the analysis of SL and PH in the diverse natural population. Moreover, the knockout transgenic experiments suggested that SD1 had a greater effect on PH compared with LOC_ Os01g68500, but no significant difference in the effect on SL. Further investigation of the pyramiding effects of SD1 and LOC_Os01g68500 based on their haplotype combinations suggested that SD1 may play a dominant role in controlling SL and PH when the two genes coexist. In this study, the effect of SD1 on SL at the seedling stage is validated. In total, two causal genes, SD1 and LOC_ Os01g68500, for SL are cloned in our studies, which controlled both SL and PH, and the suitable haplotypes of SD1 and LOC_ Os01g68500 are beneficial to achieve the desired SL and PH in different rice breeding objectives. These results provide a new clue to develop rice varieties for direct seeding and provide new genetic resources for molecular breeding of rice with suitable PH and strong seedling vigor.
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Affiliation(s)
- Jingfang Dong
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Yamei Ma
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Haifei Hu
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Jian Wang
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Wu Yang
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Hua Fu
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Longting Zhang
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
- College of Agriculture, South China Agricultural University, 510642, Guangzhou, China
| | - Jiansong Chen
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Lian Zhou
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Wenhui Li
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Shuai Nie
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Ziqiang Liu
- College of Agriculture, South China Agricultural University, 510642, Guangzhou, China
| | - Junliang Zhao
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Bin Liu
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Tifeng Yang
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China.
| | - Shaohong Zhang
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China.
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Danial AW, Basset RA. Amelioration of NaCl stress on germination, growth, and nitrogen fixation of Vicia faba at isosmotic Na-Ca combinations and Rhizobium. PLANTA 2024; 259:69. [PMID: 38340188 PMCID: PMC10858841 DOI: 10.1007/s00425-024-04343-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: 12/26/2023] [Accepted: 01/12/2024] [Indexed: 02/12/2024]
Abstract
MAIN CONCLUSION The Na+/Ca2+ ratio of 1/5 ameliorated the inhibitory action of NaCl and improved the germination and growth of Vicia faba. Addition of Rhizobium also enhanced nodulation and nitrogen fixation. Casting light upon the impact of salinity stress on growth and nitrogen fixation of Vicia faba supplemented with Rhizobium has been traced in this work. How Ca2+ antagonizes Na+ toxicity and osmotic stress of NaCl was also targeted in isosmotic combinations of NaCl and CaCl2 having various Na+:Ca2+ ratios. Growth of Vicia faba (cultivar Giza 3) was studied at two stages: germination and seedling. At both experiments, seeds or seedlings were exposed to successively increasing salinity levels (0, 50, 100, 150, and 200 mM NaCl) as well as isosmotic combinations of NaCl and CaCl2 (Na+:Ca2+ of 1:1, 1:5, 1:10, 1:15, 1:18, and 1: 20), equivalent to 150 mM NaCl. Inocula of the local nitrogen-fixing bacteria, Rhizobium leguminosarum (OP715892) were supplemented at both stages. NaCl salinity exerted a negative impact on growth and metabolism of Vicia faba; inhibition was proportional with increasing salinity level up to the highest level of 200 mM. Seed germination, shoot and root lengths, fresh and dry weights, chlorophyll content, and nodules (number, weight, leghemoglobin, respiration, and nitrogenase activity) were inhibited by salinity. Ca2+ substitution for Na+, particularly at a Na/Ca ratio of 1:5, was stimulatory to almost all parameters at both stages. Statistical correlations between salinity levels and Na/Ca combinations proved one of the four levels (strong- or weak positive, strong- or weak negative) with most of the investigated parameters, depending on the parameter.
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Affiliation(s)
- Amal W Danial
- Botany and Microbiology Department, Faculty of Science, Assiut University, Assiut, 71516, Egypt.
| | - Refat Abdel Basset
- Botany and Microbiology Department, Faculty of Science, Assiut University, Assiut, 71516, Egypt
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Zhao X, Li J, Niu Y, Hossain Z, Gao X, Bai X, Mao T, Qi G, He F. Exogenous Serotonin (5-HT) Promotes Mesocotyl and Coleoptile Elongation in Maize Seedlings under Deep-Seeding Stress through Enhancing Auxin Accumulation and Inhibiting Lignin Formation. Int J Mol Sci 2023; 24:17061. [PMID: 38069387 PMCID: PMC10707020 DOI: 10.3390/ijms242317061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
Serotonin (5-HT), an indoleamine compound, has been known to mediate many physiological responses of plants under environmental stress. The deep-seeding (≥20 cm) of maize seeds is an important cultivation strategy to ensure seedling emergence and survival under drought stress. However, the role of 5-HT in maize deep-seeding tolerance remains unexplored. Understanding the mechanisms and evaluating the optimal concentration of 5-HT in alleviating deep-seeding stress could benefit maize production. In this study, two maize inbred lines were treated with or without 5-HT at both sowing depths of 20 cm and 3 cm, respectively. The effects of different concentrations of 5-HT on the growth phenotypes, physiological metabolism, and gene expression of two maize inbred lines were examined at the sowing depths of 20 cm and 3 cm. Compared to the normal seedling depth of 3 cm, the elongation of the mesocotyl (average elongation 3.70 cm) and coleoptile (average elongation 0.58 cm), secretion of indole-3-acetic acid (IAA; average increased 3.73 and 0.63 ng g-1 FW), and hydrogen peroxide (H2O2; average increased 1.95 and 0.63 μM g-1 FW) in the mesocotyl and coleoptile were increased under 20 cm stress, with a concomitant decrease in lignin synthesis (average decreased 0.48 and 0.53 A280 g-1). Under 20 cm deep-seeding stress, the addition of 5-HT activated the expression of multiple genes of IAA biosynthesis and signal transduction, including Zm00001d049601, Zm00001d039346, Zm00001d026530, and Zm00001d049659, and it also stimulated IAA production in both the mesocotyl and coleoptile of maize seedlings. On the contrary, 5-HT suppressed the expression of genes for lignin biosynthesis (Zm00001d016471, Zm00001d005998, Zm00001d032152, and Zm00001d053554) and retarded the accumulation of H2O2 and lignin, resulting in the elongation of the mesocotyl and coleoptile of maize seedlings. A comprehensive evaluation analysis showed that the optimum concentration of 5-HT in relieving deep-seeding stress was 2.5 mg/L for both inbred lines, and 5-HT therefore could improve the seedling emergence rate and alleviate deep-seeding stress in maize seedlings. These findings could provide a novel strategy for improving maize deep-seeding tolerance, thus enhancing yield potential under drought and water stress.
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Affiliation(s)
- Xiaoqiang Zhao
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (X.Z.); (J.L.); (X.B.); (T.M.); (G.Q.); (F.H.)
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiayao Li
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (X.Z.); (J.L.); (X.B.); (T.M.); (G.Q.); (F.H.)
| | - Yining Niu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (X.Z.); (J.L.); (X.B.); (T.M.); (G.Q.); (F.H.)
| | - Zakir Hossain
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK S9H 3X2, Canada;
| | - Xiquan Gao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaodong Bai
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (X.Z.); (J.L.); (X.B.); (T.M.); (G.Q.); (F.H.)
| | - Taotao Mao
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (X.Z.); (J.L.); (X.B.); (T.M.); (G.Q.); (F.H.)
| | - Guoxiang Qi
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (X.Z.); (J.L.); (X.B.); (T.M.); (G.Q.); (F.H.)
| | - Fuqiang He
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (X.Z.); (J.L.); (X.B.); (T.M.); (G.Q.); (F.H.)
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8
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Yang T, Dong J, Zhao J, Zhang L, Zhou L, Yang W, Ma Y, Wang J, Fu H, Chen J, Li W, Hu H, Jiang X, Liu Z, Liu B, Zhang S. Genome-wide association mapping combined with gene-based haplotype analysis identify a novel gene for shoot length in rice (Oryza sativa L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:251. [PMID: 37985474 PMCID: PMC10661777 DOI: 10.1007/s00122-023-04497-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 10/27/2023] [Indexed: 11/22/2023]
Abstract
KEY MESSAGE Genome-wide association mapping revealed a novel QTL for shoot length across multiple environments. Its causal gene, LOC_Os01g68500, was identified firstly through gene-based haplotype analysis, gene expression and knockout transgenic verification. Strong seedling vigor is an important breeding target for rice varieties used in direct seeding. Shoot length (SL) is one of the important traits associated with seedling vigor characterized by rapid growth of seedling, which enhance seedling emergence. Therefore, mining genes for SL and conducting molecular breeding help to develop varieties for direct seeding. However, few QTLs for SL have been fine mapped or cloned so far. In this study, a genome-wide association study of SL was performed in a diverse rice collection consisting of 391 accessions in two years, using phenotypes generated by different cultivation methods according to the production practice, and a total of twenty-four QTLs for SL were identified. Among them, the novel QTL qSL-1f on chromosome 1 could be stably detected across all three cultivation methods in the whole population and indica subpopulation. Through gene-based haplotype analysis of the annotated genes within the putative region of qSL-1f, and validated by gene expression and knockout transgenic experiments, LOC_Os01g68500 (i.e., Os01g0913100 in RAP-DB) was identified as the causal gene for SL, which has a single-base variation (C-to-A transversion) in its CDS region, resulting in the significant difference in SL of rice. LOC_Os01g68500 encodes a DUF538 (Domain of unknown function) containing protein, and the function of DUF538 protein gene on rice seedling growth is firstly reported in this study. These results provide a new clue for exploring the molecular mechanism regulating SL, and promising gene source for the molecular breeding in rice.
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Affiliation(s)
- Tifeng Yang
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jingfang Dong
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Junliang Zhao
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Longting Zhang
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Lian Zhou
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Wu Yang
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Yamei Ma
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jian Wang
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Hua Fu
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jiansong Chen
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Wenhui Li
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Haifei Hu
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Xianya Jiang
- Yangjiang Institute of Agricultural Science, Yangjiang, 529500, China
| | - Ziqiang Liu
- College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Bin Liu
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Shaohong Zhang
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
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9
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Yang J, Miao J, Li N, Zhou Z, Dai K, Ji F, Yang M, Tan C, Liu J, Wang H, Tang W. Genetic dissection of cold tolerance at the budding stage of rice in an indica-japonica recombination inbred line population. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 204:108086. [PMID: 37890228 DOI: 10.1016/j.plaphy.2023.108086] [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: 05/27/2023] [Revised: 09/07/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023]
Abstract
Rice is highly cold-sensitive, and thus, the promotion of cold resistance in buds is essential. In this study, we conducted a mapping analysis to identify quantitative trait loci (QTLs) associated with cold tolerance in buds. The analysis was performed using a recombinant inbred line (RIL) population consisting of 192 lines derived from the cold-tolerant strain 02428 and the cold-sensitive strain YZX. Seven additive loci on chromosomes 1, 4, 5, and 6 were identified, of which loci 3 and 7 were found in two crop seasons, indicating stability. Three epistatic interactions, one present over two seasons, were found. Loci 3 and 7 pyramided with two main-effect QTLs observed to control the rate of low-temperature germination in our previous study. Two materials with good cold resistance at the germination and bud stages were obtained, namely, G93 and G146. Transcriptome sequencing analysis of the two parent buds after cold treatment found that genes expressed differentially between the two parents were related to photosynthesis, energy metabolism, and reactive oxygen scavenging. Five candidate genes, namely, Os01g0385400, Os01g0388000, Os06g0287700, Os06g0289200, and Os06g0291100, were selected in the two stable intervals based on gene expression profiles and annotations. These genetic loci exhibit strong potential as targets for breeding cold tolerance in buds and require additional investigation. In conclusion, this work provides valuable genetic resources that can be utilized to improve the cold tolerance of rice.
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Affiliation(s)
- Jing Yang
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
| | - Jiahao Miao
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
| | - Nan Li
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
| | - Zixian Zhou
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
| | - Kunyan Dai
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
| | - Faru Ji
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
| | - Min Yang
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
| | - Chen Tan
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
| | - Jing Liu
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China.
| | - Hongyang Wang
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China.
| | - Wei Tang
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China.
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10
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Chen L, Liu R, Tan Q, Luo H, Chen Y, Jin Y, Zheng Z, Zhang B, Guo D. Improving the Herbicide Resistance of Rice 4-Hydroxyphenylpyruvate Dioxygenase by DNA Shuffling Basis-Directed Evolution. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:15186-15193. [PMID: 37788677 DOI: 10.1021/acs.jafc.3c04079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
4-Hydroxyphenylpyruvate dioxygenase (HPPD) is an ideal target for herbicide resistance genetic engineering. In this study, a mutant MFRR-2 with mesotrione resistance was screened from an Oryza sativa HPPD and mutant-Zea mays HPPD DNA shuffling library. The enzyme properties showed that although the stability of the mutant decreased in vitro, the enzyme activity of MFRR-2 at the optimum temperature of 25 °C was still equivalent to that of OsHPPD. Under 50 μM mesotrione treatment, MFRR-2 enzyme activity remained at approximately 90%, while the enzyme activity of OsHPPD decreased by approximately 50%. Surprisingly, Fe2+ was found to have an inhibitory effect on the enzyme activity. Then, the transgenic rice of the MFRR-2 gene showed approximately 1.5 times mesotrione resistance compared to OsHPPD transgenic rice. In conclusion, this study has conducted a beneficial exploration on the use of DNA shuffling for HPPD-directed evolution, and the mutant has potential application value for herbicide resistance genetic engineering.
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Affiliation(s)
- Le Chen
- College of Tropical Crops, Hainan University, Haikou 570228, P. R. China
- Key Laboratory of Jiangsu Province for Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, P. R. China
| | - Rui Liu
- College of Tropical Crops, Hainan University, Haikou 570228, P. R. China
| | - Qing Tan
- College of Tropical Crops, Hainan University, Haikou 570228, P. R. China
| | - Hongmei Luo
- College of Tropical Crops, Hainan University, Haikou 570228, P. R. China
| | - Yuyu Chen
- College of Tropical Crops, Hainan University, Haikou 570228, P. R. China
| | - Yaru Jin
- College of Tropical Crops, Hainan University, Haikou 570228, P. R. China
| | - Zhongbing Zheng
- College of Tropical Crops, Hainan University, Haikou 570228, P. R. China
| | - Baolong Zhang
- College of Tropical Crops, Hainan University, Haikou 570228, P. R. China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, P. R. China
- Key Laboratory of Jiangsu Province for Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, P. R. China
| | - Dongshu Guo
- Key Laboratory of Jiangsu Province for Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, P. R. China
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11
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Liang C, Li Y, Zhang K, Wu Z, Liu J, Liu J, Zhou C, Wang S, Li F, Sui G. Selection and Yield Formation Characteristics of Dry Direct Seeding Rice in Northeast China. PLANTS (BASEL, SWITZERLAND) 2023; 12:3496. [PMID: 37836236 PMCID: PMC10575160 DOI: 10.3390/plants12193496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/23/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023]
Abstract
Dry direct seeding rice (DSR) is an emerging production system because of increasing labor and water scarcity in rice cultivation. The limited availability of rice cultivars suitable for dry direct seeding hampers the widespread adoption of this cultivation method in Northeast China. This study aimed to investigate grain production and plant characteristics associated with dry direct seeding rice. We conducted a field experiment on 79 japonica rice cultivars in Shenyang City, Liaoning Province, Northeast China, in 2020 and 2021. This study found that the grain yield of the tested rice cultivars ranged from 5.75-11.00 t ha-1, with a growth duration lasting between 144-161 days across the cultivars. These cultivars were then categorized into high yielding (HY), medium yielding (MY), and low yielding (LY) based on daily yield by using Ward's hierarchical clustering method. The higher grain yield for HY compared to MY and LY was attributed to more spikelets per unit area. The HY alleviated the conflict between higher panicle density and larger panicle size by improving the seedling emergence rate and productive stem rate. It also significantly increased shoot biomass at maturity. The HY reduced the period between seeding and beginning of heading (BBCH 51) and the proportion of dry matter partitioned to the leaf at the heading stage. However, it also increased the accumulation of dry matter in the grain and the proportion of dry matter partitioned to the grain at maturity. Furthermore, the HY markedly increased the harvest index and grain-leaf ratio, which are beneficial to coordinate the source-sink relationship. A quadratic function predicted that 98 days is the optimum growth duration before heading (BBCH 51) for achieving maximum yield. In conclusion, for dry direct seeding rice, it is appropriate to select high-yielding japonica inbred rice cultivars with shorter growth duration before heading (about 93-102 day), higher panicle number (about 450-500 × 104 ha-1), more spikelet number per panicle (about 110-130), higher seedling emergence rate (about 70-75%), higher productive stem rate (about 60-70%), and greater harvest index (about 50-55%).
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Affiliation(s)
- Chao Liang
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; (C.L.); (Y.L.); (K.Z.); (Z.W.); (J.L.); (J.L.); (F.L.)
| | - Yimeng Li
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; (C.L.); (Y.L.); (K.Z.); (Z.W.); (J.L.); (J.L.); (F.L.)
| | - Kunhao Zhang
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; (C.L.); (Y.L.); (K.Z.); (Z.W.); (J.L.); (J.L.); (F.L.)
| | - Zhouzhou Wu
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; (C.L.); (Y.L.); (K.Z.); (Z.W.); (J.L.); (J.L.); (F.L.)
| | - Jiaxin Liu
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; (C.L.); (Y.L.); (K.Z.); (Z.W.); (J.L.); (J.L.); (F.L.)
| | - Junfeng Liu
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; (C.L.); (Y.L.); (K.Z.); (Z.W.); (J.L.); (J.L.); (F.L.)
| | - Chanchan Zhou
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; (C.L.); (Y.L.); (K.Z.); (Z.W.); (J.L.); (J.L.); (F.L.)
| | - Shu Wang
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; (C.L.); (Y.L.); (K.Z.); (Z.W.); (J.L.); (J.L.); (F.L.)
| | - Fenghai Li
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; (C.L.); (Y.L.); (K.Z.); (Z.W.); (J.L.); (J.L.); (F.L.)
| | - Guomin Sui
- Liaoning Academy of Agricultural Sciences, Shenyang 110161, China;
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12
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Yamasani MR, Pandu VR, Kalluru S, Bommaka RR, Bandela R, Duddu B, Komeri S, Kumbha D, Vemireddy LR. Haplotype analysis of QTLs governing early seedling vigor-related traits under dry-direct-seeded rice (Oryza sativa L.) conditions. Mol Biol Rep 2023; 50:8177-8188. [PMID: 37555871 DOI: 10.1007/s11033-023-08714-9] [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: 04/03/2023] [Accepted: 07/26/2023] [Indexed: 08/10/2023]
Abstract
BACKGROUND The eventual shifting of cultivation method from puddle transplanted rice to direct-seeded rice (DSR) to save water prompted researchers to develop DSR-suitable varieties. To achieve this, identification of molecular markers associated with must-have traits for DSR, especially early seedling vigour related traits is crucial. METHODS AND RESULTS In the present investigation, the haplotype analysis using flanking markers of three important quantitative trait loci (QTLs) for early seedling vigour-related traits viz., qSV-6a (RM204 and RM402) for root length; qVI (RM20429 and RM3) for seedling vigour index; qGP-6 (RM528 and RM400) for germination percentage revealed that the marker alleles were found to show significant associations with qVI and qGP-6 QTLs. The majority of genotypes with high early seedling vigour are with qVIHap-1 (220 and 160 bp) and qGPHap-1 (290 and 290 bp). The rice genotypes with superior haplotypes for early seedling vigour are BMF536, BMF540, BMF525, MM129 and MDP2. CONCLUSIONS In conclusion, here we demonstrated that the markers RM20429 and RM3 are associated with seedling vigour index whereas RM528 and RM400 are associated with germination percentage. Therefore, these markers can be utilized to develop varieties suitable for DSR conditions through haplotype-based breeding. In addition, the rice genotypes with superior haplotypes can be of immense value to use as donors or can be released as varieties also under DSR conditions.
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Affiliation(s)
- Mounika Reddy Yamasani
- Department of Genetics and Plant Breeding, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Vasanthi Raguru Pandu
- Department of Genetics and Plant Breeding, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Sudhamani Kalluru
- Department of Genetics and Plant Breeding, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Rupeshkumar Reddy Bommaka
- Department of Genetics and Plant Breeding, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Ramanamurthy Bandela
- Department of Statistics and Computer Applications, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Bharathi Duddu
- Department of Genetics and Plant Breeding, Regional Agricultural Research Station, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Srikanth Komeri
- Department of Molecular Biology and Biotechnology, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Dineshkumar Kumbha
- Department of Genetics and Plant Breeding, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Lakshminarayana R Vemireddy
- Department of Molecular Biology and Biotechnology, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India.
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13
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Padmashree R, Barbadikar KM, Honnappa, Magar ND, Balakrishnan D, Lokesha R, Gireesh C, Siddaiah AM, Madhav MS, Ramesha YM, Bharamappanavara M, Phule AS, Senguttuvel P, Diwan JR, Subrahmanyam D, Sundaram RM. Genome-wide association studies in rice germplasm reveal significant genomic regions for root and yield-related traits under aerobic and irrigated conditions. FRONTIERS IN PLANT SCIENCE 2023; 14:1143853. [PMID: 37538056 PMCID: PMC10395336 DOI: 10.3389/fpls.2023.1143853] [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: 01/13/2023] [Accepted: 04/19/2023] [Indexed: 08/05/2023]
Abstract
The development of nutrient-use efficient rice lines is a priority amidst the changing climate and depleting resources viz., water, land, and labor for achieving sustainability in rice cultivation. Along with the traditional transplanted irrigated system of cultivation, the dry direct-seeded aerobic system is gaining ground nationwide. The root-related traits play a crucial role in nutrient acquisition, adaptation and need to be concentrated along with the yield-attributing traits. We phenotyped an association panel of 118 rice lines for seedling vigour index (SVI) traits at 14 and 21 days after sowing (DAS), root-related traits at panicle initiation (PI) stage in polythene bags under controlled aerobic condition, yield and yield-related traits under the irrigated condition at ICAR-IIRR, Hyderabad, Telangana; irrigated and aerobic conditions at ARS, Dhadesugur, Raichur, Karnataka. The panel was genotyped using simple sequence repeats (SSR) markers and genome-wide association studies were conducted for identifying marker-trait associations (MTAs). Significant correlations were recorded for root length, root dry weight with SVI, root volume at the PI stage, number of productive tillers per plant, spikelet fertility, the total number of grains per panicle with grain yield per plant under irrigated conditions, and the total number of grains per panicle with grain yield per plant under aerobic condition. The panel was divided into three sub-groups (K = 3) and correlated with the principal component analysis. The maximum number of MTAs were found on chromosomes 2, 3, and 12 with considerable phenotypic variability. Consistent MTAs were recorded for SVI traits at 14 and 21 DAS (RM25310, RM80, RM22961, RM1385), yield traits under irrigated conditions (RM2584, RM5179, RM410, RM20698, RM14753) across years at ICAR-IIRR, grain yield per plant (RM22961, RM1146) under the aerobic condition, grain yield per plant at irrigated ICAR-IIRR and SVI (RM5501), root traits at PI stage (RM2584, RM80, RM410, RM1146, RM18472). Functionally relevant genes near the MTAs through in-silico expression analysis in root and panicle tissues viz., HBF2 bZIP transcription factor, WD40 repeat-like domain, OsPILS6a auxin efflux carrier, WRKY108, OsSCP42, OsMADS80, nodulin-like domain-containing protein, amino acid transporter using various rice expression databases were identified. The identified MTAs and rice lines having high SVI traits (Langphou, TI-128, Mouli, TI-124, JBB-631-1), high yield under aerobic (Phouren, NPK-43, JBB-684, Ratnamudi, TI-112), irrigated conditions (KR-209, KR-262, Phouren, Keibi-Phou, TI-17), robust root traits like root length (MoirangPhou-Angouba, Wangoo-Phou, JBB-661, Dissi, NPK-45), root volume (Ratnachudi, KJ-221, Mow, Heimang-Phou, PUP-229) can be further employed in breeding programs for the targeted environments aimed at improving seedling vigour, yield-related traits under irrigated condition, aerobic condition as adaptability to water-saving technology.
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Affiliation(s)
- Revadi Padmashree
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
- University of Agricultural Sciences (UAS), Raichur, India
| | - Kalyani M. Barbadikar
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Honnappa
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
- University of Agricultural Sciences (UAS), Raichur, India
| | - Nakul D. Magar
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
- Chaudhary Charan Singh University, Meerut, India
| | - Divya Balakrishnan
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - R. Lokesha
- University of Agricultural Sciences (UAS), Raichur, India
| | - C. Gireesh
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Anantha M. Siddaiah
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Maganti Sheshu Madhav
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Y. M Ramesha
- Agricultural Research Station (ARS) Dhadesugur, University of Agricultural Sciences (UAS), Raichur, India
| | | | - Amol S. Phule
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - P. Senguttuvel
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - J. R. Diwan
- University of Agricultural Sciences (UAS), Raichur, India
| | - D. Subrahmanyam
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Raman Menakshi Sundaram
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
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14
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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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15
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Prasad C T M, Kodde J, Angenent GC, Hay FR, McNally KL, Groot SPC. Identification of the rice Rc gene as a main regulator of seed survival under dry storage conditions. PLANT, CELL & ENVIRONMENT 2023; 46:1962-1980. [PMID: 36891587 DOI: 10.1111/pce.14581] [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: 12/17/2022] [Revised: 02/27/2023] [Accepted: 03/06/2023] [Indexed: 05/04/2023]
Abstract
Seed deterioration during storage results in poor germination, reduced vigour, and non-uniform seedling emergence. The aging rate depends on storage conditions and genetic factors. This study aims to identify these genetic factors determining the longevity of rice (Oryza sativa L.) seeds stored under experimental aging conditions mimicking long-term dry storage. Genetic variation for tolerance to aging was studied in 300 Indica rice accessions by storing dry seeds under an elevated partial pressure of oxygen (EPPO) condition. A genome-wide association analysis identified 11 unique genomic regions for all measured germination parameters after aging, differing from those previously identified in rice under humid experimental aging conditions. The significant single nucleotide polymorphism in the most prominent region was located within the Rc gene, encoding a basic helix-loop-helix transcription factor. Storage experiments using near-isogenic rice lines (SD7-1D (Rc) and SD7-1d (rc) with the same allelic variation confirmed the role of the wildtype Rc gene, providing stronger tolerance to dry EPPO aging. In the seed pericarp, a functional Rc gene results in accumulation of proanthocyanidins, an important sub-class of flavonoids having strong antioxidant activity, which may explain the variation in tolerance to dry EPPO aging.
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Affiliation(s)
- Manjunath Prasad C T
- Wageningen Plant Research, Wageningen University & Research, Wageningen, The Netherlands
- Laboratory of Molecular Biology, Wageningen University & Research, Wageningen, The Netherlands
- Department of Seed Science and Technology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Jan Kodde
- Wageningen Plant Research, Wageningen University & Research, Wageningen, The Netherlands
| | - Gerco C Angenent
- Wageningen Plant Research, Wageningen University & Research, Wageningen, The Netherlands
- Laboratory of Molecular Biology, Wageningen University & Research, Wageningen, The Netherlands
| | - Fiona R Hay
- Department of Agroecology, Aarhus University, Slagelse, Denmark
| | | | - Steven P C Groot
- Wageningen Plant Research, Wageningen University & Research, Wageningen, The Netherlands
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16
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Li X, Dong J, Zhu W, Zhao J, Zhou L. Progress in the study of functional genes related to direct seeding of rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:46. [PMID: 37309311 PMCID: PMC10248684 DOI: 10.1007/s11032-023-01388-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 04/20/2023] [Indexed: 06/14/2023]
Abstract
Rice is a major food crop in the world. Owing to the shortage of rural labor and the development of agricultural mechanization, direct seeding has become the main method of rice cultivation. At present, the main problems faced by direct seeding of rice are low whole seedling rate, serious weeds, and easy lodging of rice in the middle and late stages of growth. Along with the rapid development of functional genomics, the functions of a large number of genes have been confirmed, including seed vigor, low-temperature tolerance germination, low oxygen tolerance growth, early seedling vigor, early root vigor, resistance to lodging, and other functional genes related to the direct seeding of rice. A review of the related functional genes has not yet been reported. In this study, the genes related to direct seeding of rice are summarized to comprehensively understand the genetic basis and mechanism of action in direct seeding of rice and to lay the foundation for further basic theoretical research and breeding application research in direct seeding of rice.
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Affiliation(s)
- Xuezhong Li
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225 Guangdong China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
| | - Jingfang Dong
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
| | - Wen Zhu
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225 Guangdong China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
| | - Junliang Zhao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
| | - Lingyan Zhou
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225 Guangdong China
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17
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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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18
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Zhang H, Chen G, Xu H, Jing S, Jiang Y, Liu Z, Zhang H, Wang F, Hu X, Zhu Y. Transcriptome Analysis of Rice Embryo and Endosperm during Seed Germination. Int J Mol Sci 2023; 24:ijms24108710. [PMID: 37240056 DOI: 10.3390/ijms24108710] [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: 03/16/2023] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
Seed germination is a complex, multistage developmental process that is an important step in plant development. In this study, RNA-Seq was conducted in the embryo and endosperm of unshelled germinating rice seeds. A total of 14,391 differentially expressed genes (DEGs) were identified between the dry seeds and the germinating seeds. Of these DEGs, 7109 were identified in both the embryo and endosperm, 3953 were embryo specific, and 3329 were endosperm specific. The embryo-specific DEGs were enriched in the plant-hormone signal-transduction pathway, while the endosperm-specific DEGs were enriched in phenylalanine, tyrosine, and tryptophan biosynthesis. We categorized these DEGs into early-, intermediate-, and late-stage genes, as well as consistently responsive genes, which can be enriched in various pathways related to seed germination. Transcription-factor (TF) analysis showed that 643 TFs from 48 families were differentially expressed during seed germination. Moreover, 12 unfolded protein response (UPR) pathway genes were induced by seed germination, and the knockout of OsBiP2 resulted in reduced germination rates compared to the wild type. This study enhances our understanding of gene responses in the embryo and endosperm during seed germination and provides insight into the effects of UPR on seed germination in rice.
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Affiliation(s)
- Heng Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Guang Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Heng Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Sasa Jing
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Shanghai Key Laboratory of Bio-Energy Crops, Research Center for Natural Products, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Yingying Jiang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Ziwen Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Hua Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Fulin Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiangyang Hu
- Shanghai Key Laboratory of Bio-Energy Crops, Research Center for Natural Products, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Ying Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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19
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Mohanty SP, Nayak DK, Sanghamitra P, Barik SR, Pandit E, Behera A, Pani DR, Mohapatra S, Raj K R R, Pradhan KC, Sahoo CR, Mohanty MR, Behera C, Panda AK, Jena BK, Behera L, Dash PK, Pradhan SK. Mapping the Genomic Regions Controlling Germination Rate and Early Seedling Growth Parameters in Rice. Genes (Basel) 2023; 14:genes14040902. [PMID: 37107660 PMCID: PMC10138111 DOI: 10.3390/genes14040902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/24/2023] [Accepted: 03/31/2023] [Indexed: 04/29/2023] Open
Abstract
Seed vigor is the key performance parameter of good quality seed. A panel was prepared by shortlisting genotypes from all the phenotypic groups representing seedling growth parameters from a total of 278 germplasm lines. A wide variation was observed for the traits in the population. The panel was classified into four genetic structure groups. Fixation indices indicated the existence of linkage disequilibrium in the population. A moderate to high level of diversity parameters was assessed using 143 SSR markers. Principal component, coordinate, neighbor-joining tree and cluster analyses showed subpopulations with a fair degree of correspondence with the growth parameters. Marker-trait association analysis detected eight novel QTLs, namely qAGR4.1, qAGR6.1, qAGR6.2 and qAGR8.1 for absolute growth rate (AGR); qRSG6.1, qRSG7.1 and qRSG8.1 for relative shoot growth (RSG); and qRGR11.1 for relative growth rate (RGR), as analyzed by GLM and MLM. The reported QTL for germination rate (GR), qGR4-1, was validated in this population. Additionally, QTLs present on chromosome 6 controlling RSG and AGR at 221 cM and RSG and AGR on chromosome 8 at 27 cM were detected as genetic hotspots for the parameters. The QTLs identified in the study will be useful for improvement of the seed vigor trait in rice.
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Affiliation(s)
| | | | | | | | - Elssa Pandit
- Department of Biosciences and Biotechnology, Fakir Mohan University, Balasore 756020, India
| | | | - Dipti Ranjan Pani
- ICAR-National Bureau of Plant Genetic Resources, Base Center, Cuttack 753006, India
| | - Shibani Mohapatra
- ICAR-National Rice Research Institute, Cuttack 753006, India
- Environmental Science Laboratory, School of Applied Sciences, KIIT Deemed to be University, Bhubaneswar 751024, India
| | - Reshmi Raj K R
- ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Kartik Chandra Pradhan
- College of Agriculture, Odisha University of Agriculture & Technology, Bhubaneswar 751003, India
| | - Chita Ranjan Sahoo
- Directorate of Research, Odisha University of Agriculture & Technology, Bhubaneswar 751003, India
| | - Mihir Ranjan Mohanty
- Regional Research and Technology Transfer Station (RRTTS), Odisha University of Agriculture & Technology, Jeypore 764001, India
| | - Chinmayee Behera
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, SOA University, Bhubaneswar 753001, India
| | - Alok Kumar Panda
- Environmental Science Laboratory, School of Applied Sciences, KIIT Deemed to be University, Bhubaneswar 751024, India
| | - Binod Kumar Jena
- Krishi Vigyan Kendra, Odisha University of Agriculture & Technology, Rayagada 765022, India
| | - Lambodar Behera
- ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Prasanta K Dash
- ICAR-National Institute for Plant Biotechnology, Pusa, New Delhi 110012, India
| | - Sharat Kumar Pradhan
- ICAR-National Rice Research Institute, Cuttack 753006, India
- Indian Council of Agricultural Research, Krishi Bhavan, New Delhi 110001, India
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20
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Niu Y, Wang C, Suo W, Wang G, Zhao J, Wang Z, Zheng Y. Isopropylmalate synthase NtIPMS as a potential molecular marker for seed vigor in tobacco. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2023; 40:43-49. [PMID: 38213928 PMCID: PMC10777126 DOI: 10.5511/plantbiotechnology.23.0118a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/18/2023] [Indexed: 01/13/2024]
Abstract
Seed vigor is an important trait for tobacco production. However, the evaluation of seed vigor using molecular biomarkers is scarcely reported in tobacco. In this study, the development of molecular marker isopropylmalate synthase NtIPMS was conducted to detect seed ageing degree and seed priming effect in tobacco. Quantitative real-time PCR (qRT-PCR) analysis showed that the expression of NtIPMS was significantly induced at the initial imbibition stage during seed germination. The NtIPMS expression was positively correlated with the degree of seed ageing in non-pelleted and pelleted seeds. The mRNA level of NtIPMS was gradually increased with the increasing degree of seed ageing. The early best effect of gibberellin priming was observed in 30-h primed seeds, and the highest expression of NtIPMS was observed in 12-h primed seeds. The best stop time-point of seed priming is likely at the time 18 h after the relatively higher NtIPMS expression occurred during seed priming process. The NtIPMS mRNA detection has the potential usage as a potential molecular marker for the evaluation of seed vigor in tobacco.
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Affiliation(s)
- Yongzhi Niu
- Yuxi Zhongyan Seed Company Ltd., Seed Engineering Technology Center of Yunnan Province, Yuxi 653100, China
| | - Chengjing Wang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Wenlong Suo
- Yuxi Zhongyan Seed Company Ltd., Seed Engineering Technology Center of Yunnan Province, Yuxi 653100, China
| | - Guoping Wang
- Yuxi Zhongyan Seed Company Ltd., Seed Engineering Technology Center of Yunnan Province, Yuxi 653100, China
| | - Jia Zhao
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Zhoufei Wang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Yunye Zheng
- Yuxi Zhongyan Seed Company Ltd., Seed Engineering Technology Center of Yunnan Province, Yuxi 653100, China
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21
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Liu C, Yao Z, Jiang B, Yu W, Wang Y, Dong W, Li Y, Shi X, Liu C, Zhou Y. Effects of Exogenous Auxin on Mesocotyl Elongation of Sorghum. PLANTS (BASEL, SWITZERLAND) 2023; 12:944. [PMID: 36840291 PMCID: PMC9959298 DOI: 10.3390/plants12040944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
The length of sorghum mesocotyl plays a vital role in seed emergence from the soil, which is the foundation of healthy growth. In this study, we aimed to understand how exogenous auxin (IAA) promoted mesocotyl elongation of sorghum and its physiology mechanism. The results presented that exogenous IAA significantly promoted mesocotyl elongation in MS24B (short mesocotyl inbred line) by increasing the cell length, while with extra exogenous NPA (IAA inhibitor) application, the mesocotyl length presented a significant short phenotype. In Z210 (long mesocotyl inbred line), exogenous IAA had a slight effect on mesocotyl length elongation, while the NPA treatment decreased the mesocotyl length considerably. In MS24B, IAA treatment increased the activity of amylase to degrade starch to soluble sugar, and the activity of hexokinase was improved to consume the increased soluble sugar to offer more energy. The energy will help to increase the activity of PM H+-ATPase and the expression of expansin-related genes, which ultimately will promote the acidification of the plasma membrane in MS24B for cell elongation. Overall, the exogenous IAA functioned on the activation of energy metabolism, which in turn, inducted the acidification of the plasma membrane for mesocotyl elongation.
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Affiliation(s)
- Chang Liu
- College of Agronomy, Shenyang Agriculture University, Shenyang 110866, China
| | - Ziqing Yao
- College of Agronomy, Shenyang Agriculture University, Shenyang 110866, China
| | - Bing Jiang
- Jinzhou Academy of Agricultural Sciences, Jinzhou 121006, China
| | - Wenbo Yu
- College of Agronomy, Shenyang Agriculture University, Shenyang 110866, China
| | - Yu Wang
- College of Agronomy, Shenyang Agriculture University, Shenyang 110866, China
| | - Wenhui Dong
- College of Agronomy, Shenyang Agriculture University, Shenyang 110866, China
| | - Yutong Li
- College of Agronomy, Shenyang Agriculture University, Shenyang 110866, China
| | - Xiaolong Shi
- College of Agronomy, Shenyang Agriculture University, Shenyang 110866, China
| | - Chunjuan Liu
- College of Agronomy, Shenyang Agriculture University, Shenyang 110866, China
| | - Yufei Zhou
- College of Agronomy, Shenyang Agriculture University, Shenyang 110866, China
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22
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Nayak DK, Sahoo S, Barik SR, Sanghamitra P, Sangeeta S, Pandit E, Reshmi Raj KR, Basak N, Pradhan SK. Association mapping for protein, total soluble sugars, starch, amylose and chlorophyll content in rice. BMC PLANT BIOLOGY 2022; 22:620. [PMID: 36581797 PMCID: PMC9801606 DOI: 10.1186/s12870-022-04015-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 12/21/2022] [Indexed: 05/13/2023]
Abstract
BACKGROUND Protein, starch, amylose and total soluble sugars are basic metabolites of seed that influence the eating, cooking and nutritional qualities of rice. Chlorophyll is responsible for the absorption and utilization of the light energy influencing photosynthetic efficiency in rice plant. Mapping of these traits are very important for detection of more number of robust markers for improvement of these traits through molecular breeding approaches. RESULTS A representative panel population was developed by including 120 germplasm lines from the initial shortlisted 274 lines for mapping of the six biochemical traits using 136 microsatellite markers through association mapping. A wide genetic variation was detected for the traits, total protein, starch, amylose, total soluble sugars, chlorophyll a, and chlorophyll b content in the population. Specific allele frequency, gene diversity, informative markers and other diversity parameters obtained from the population indicated the effectiveness of utilization of the population and markers for mapping of these traits. The fixation indices values estimated from the population indicated the existence of linkage disequilibrium for the six traits. The population genetic structure at K = 3 showed correspondence with majority of the members in each group for the six traits. The reported QTL, qProt1, qPC6.2, and qPC8.2 for protein content; qTSS8.1 for total soluble sugar; qAC1.2 for amylose content; qCH2 and qSLCHH for chlorophyll a (Chl. a) while qChl5D for chlorophyll b (Chl. b) were validated in this population. The QTL controlling total protein content qPC1.2; qTSS7.1, qTSS8.2 and qTSS12.1 for total soluble sugars; qSC2.1, qSC2.2, qSC6.1 and qSC11.1 for starch content; qAC11.1, qAC11.2 and qAC11.3 for amylose content; qChla8.1 for Chl. a content and qChlb7.1 and qChlb8.1 for Chl. b identified by both Generalized Linear Model and Mixed Linear Model were detected as novel QTL. The chromosomal regions on chromosome 8 at 234 cM for grain protein content and total soluble sugars and at 363 cM for Chl. a and Chl. b along with the position at 48 cM on chromosome 11 for starch and amylose content are genetic hot spots for these traits. CONCLUSION The validated, co-localized and the novel QTL detected in this study will be useful for improvement of protein, starch, amylose, total soluble sugars and chlorophyll content in rice.
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Affiliation(s)
- D K Nayak
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - S Sahoo
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
- College of Agriculture, OUAT, Bhabaneswar, Odisha, 751003, India
| | - S R Barik
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - P Sanghamitra
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - S Sangeeta
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - E Pandit
- Fakir Mohan University, Balasore, Odisha, 756020, India
| | - K R Reshmi Raj
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - N Basak
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - S K Pradhan
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India.
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Liang W, Du H, Pang B, Cheng J, He B, Hu F, Lv Y, Zhang Y. High-density genetic mapping identified QTLs for anaerobic germination tolerance in rice. FRONTIERS IN PLANT SCIENCE 2022; 13:1076600. [PMID: 36618635 PMCID: PMC9822775 DOI: 10.3389/fpls.2022.1076600] [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: 10/21/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
The tolerance of rice anaerobic germination (AG) is the main limiting factor for direct seeding application, yet the genetics mechanism is still in its infancy. In the study, recombinant inbred lines population of TD70 Japonica cultivar and Kasalath Indica cultivar, was employed to construct a high-density genetic map by whole genome re-sequencing. As a result, a genetic map containing 12,328 bin-markers was constructed and a total of 50 QTLs were then detected for CL(coleoptile length), CD (coleoptile diameter), CSA (coleoptile surface area) and CV (coleoptile volume) related traits in the two stages of anaerobic treatment using complete interval mapping method (inclusive composite interval mapping, ICIM). Among the four traits associated with coleoptile, coleoptile volume had the largest number of QTLs (17), followed by coleoptile diameter (16), and coleoptile length had 5 QTLs. These QTLs could explain phenotypic contribution rates ranging from 0.34% to 11.17% and LOD values ranging from 2.52 to 11.57. Combined with transcriptome analysis, 31 candidate genes were identified. Furthermore, 12 stable QTLs were used to detect the aggregation effect analysis. Besides, It was found that individuals with more aggregation synergistic alleles had higher phenotypic values in different environments. Totally, high-density genetic map, QTL mapping and aggregation effect analysis of different loci related to the anaerobic germination of rice seeds were conducted to lay a foundation for the fine mapping of related genes in subsequent assisted breeding.
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Affiliation(s)
- Wenhua Liang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Hongyang Du
- Excellence and Innovation Center, Jiangsu Academy of Agricultural, Sciences, Nanjing, China
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Science, Hefei, China
| | - Bingwen Pang
- Excellence and Innovation Center, Jiangsu Academy of Agricultural, Sciences, Nanjing, China
| | - Junjie Cheng
- Excellence and Innovation Center, Jiangsu Academy of Agricultural, Sciences, Nanjing, China
| | - Bing He
- Excellence and Innovation Center, Jiangsu Academy of Agricultural, Sciences, Nanjing, China
| | - Fengqin Hu
- Excellence and Innovation Center, Jiangsu Academy of Agricultural, Sciences, Nanjing, China
| | - Yuanda Lv
- Excellence and Innovation Center, Jiangsu Academy of Agricultural, Sciences, Nanjing, China
| | - Yadong Zhang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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24
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He Y, Chen W, Tan J, Luo X, Zhou Y, Gong X, Yao J, Zhuang C, Jiang D. Rice CENTRORADIALIS 2 regulates seed germination and salt tolerance via ABA-mediated pathway. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4245-4259. [PMID: 36181524 DOI: 10.1007/s00122-022-04215-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 09/05/2022] [Indexed: 06/16/2023]
Abstract
A FT/TFL1 subfamily gene, rice CENTRORADIALIS 2, also known as RCN1, regulates seed germination and increase salt tolerance via ABA-mediated pathway. The ABA synthesis and metabolism related genes were changed relative expression levels. Seed germination is a complex biological process that is affected by many factors. Although a number of germination-related genes have been reported, the molecular mechanism of germination regulation has not yet been fully elucidated. Here, we reported that the rice OsCEN2 gene can negatively regulate seed germination. The germination speed of OsCEN2-RNAi seeds was significantly faster while that of OsCEN2-overexpression (OE) seeds was slower than that of the wild type (WT). The results of qRT-PCR showed that the OsCEN2 expression was increased in the early stage of seed germination. Exogenous application of abscisic acid (ABA) on seeds and seedlings showed that OsCEN2-OE seeds and seedlings were highly sensitive to ABA during germination and post-germination growth, respectively. The determination of endogenous ABA content in seeds also showed that the ABA content of OsCEN2-RNAi seeds was lower, while that of OsCEN2-OE seeds was higher. Moreover, the transgenic plants changed salt tolerance because of the altered ABA level. In addition, differences were also observed in the expression of genes related to ABA synthesis and metabolism in the seeds of OsCEN2-transgenic lines. This study reveals that OsCEN2 regulates the germination speed by affecting the content of ABA during seed germination and provides a theoretical basis for research on rice direct seeding.
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Affiliation(s)
- Ying He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Weiting Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Juhong Tan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xixiu Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yanjin Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaoting Gong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Juan Yao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Chuxiong Zhuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China.
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
| | - Dagang Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China.
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
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25
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Nowak B, Tomkowiak A, Bocianowski J, Sobiech A, Bobrowska R, Kowalczewski PŁ, Bocianowska M. The Use of DArTseq Technology to Identify Markers Linked to Genes Responsible for Seed Germination and Seed Vigor in Maize. Int J Mol Sci 2022; 23:ijms232314865. [PMID: 36499196 PMCID: PMC9736657 DOI: 10.3390/ijms232314865] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/20/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
Seed vigor and seed germination are very important traits, determined by several factors including genetic and physical purity, mechanical damage, and physiological condition, characterized by maintaining a high seed vigor and stable content after storage. The search for molecular markers related to improvement in seed vigor under adverse condition is an important issue in maize breeding currently. Higher sowing quality of seeds is necessary for the development of the agriculture production and better ability to resist all kinds of adversity in the seeds’ storage. Condition is a very important factor affecting the yield of plants, thanks to the construction of their vitality. Identification of molecular markers associated with seed germination and seed vigor may prove to be very important in the selection of high-yielding maize varieties. The aim of this study was to identify and select new markers for maize (SNP and SilicoDArT) linked to genes influencing the seed germination and seed vigor in inbred lines of maize (Zea mays L.). The plant material used for the research was 152 inbred maize lines. The seed germination and seed vigor were analyzed. For identification of SNP and SilicoDArT markers related to the seed germination and seed vigor, the SilicoDarT technique developed by Diversity Arrays Technology was used. The analysis of variance indicated a statistically significant differentiation between genotypes for both observed traits. Positive (r = 0.41) correlation (p < 0.001) between seed germination and seed vigor was observed. As a result of next-generation sequencing, the molecular markers SilicoDArT (53,031) and SNP (28,571) were obtained. Out of 81,602 identified SilicoDArT and SNP markers, 15,409 (1559 SilicoDArT and 13,850 SNP) were selected as a result of association mapping, which showed them to be significantly related to the analyzed traits. The 890 molecular markers were associated with seed vigor, and 1323 with seed germination. Fifty-six markers (47 SilicoDArT and nine SNP) were significant for both traits. Of these 56 markers, the 20 most significant were selected (five of these markers were significant at the level of 0.001 for seed vigor and at the level of 0.05 for seed germination, another five markers were significant at the level of 0.001 for seed germination and at the level of 0.05 for seed vigor, five markers significant at the level of 0.001 only for seed vigor and five significant at the level of 0.001 only for seed germination also selected). These markers were used for physical mapping to determine their location on the genetic map. Finally, it was found that six of these markers (five silicoDArT—2,435,784, 4,772,587, 4,776,334, 2,507,310, 25,981,291, and one SNP—2,386,217) are located inside genes, the action of which may affect both seed germination and seed vigor. These markers can be used to select genotypes with high vigor and good seed germination.
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Affiliation(s)
- Bartosz Nowak
- Smolice Plant Breeding Sp. z o. o. IHAR Group, Smolice 146, 63-740 Kobylin, Poland
| | - Agnieszka Tomkowiak
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland
- Correspondence:
| | - Jan Bocianowski
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, Wojska Polskiego 28, 60-637 Poznań, Poland
| | - Aleksandra Sobiech
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland
| | - Roksana Bobrowska
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland
| | - Przemysław Łukasz Kowalczewski
- Department of Food Technology of Plant Origin, Poznań University of Life Sciences, 31 Wojska Polskiego St., 60-624 Poznań, Poland
| | - Marianna Bocianowska
- Faculty of Chemical Technology, Poznań University of Technology, Piotrowo 3A, 60-965 Poznań, Poland
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26
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Abbas M, Abid MA, Meng Z, Abbas M, Wang P, Lu C, Askari M, Akram U, Ye Y, Wei Y, Wang Y, Guo S, Liang C, Zhang R. Integrating advancements in root phenotyping and genome-wide association studies to open the root genetics gateway. PHYSIOLOGIA PLANTARUM 2022; 174:e13787. [PMID: 36169590 DOI: 10.1111/ppl.13787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 09/12/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
Plant adaptation to challenging environmental conditions around the world has made root growth and development an important research area for plant breeders and scientists. Targeted manipulation of root system architecture (RSA) to increase water and nutrient use efficiency can minimize the adverse effects of climate change on crop production. However, phenotyping of RSA is a major bottleneck since the roots are hidden in the soil. Recently the development of 2- and 3D root imaging techniques combined with the genome-wide association studies (GWASs) have opened up new research tools to identify the genetic basis of RSA. These approaches provide a comprehensive understanding of the RSA, by accelerating the identification and characterization of genes involved in root growth and development. This review summarizes the latest developments in phenotyping techniques and GWAS for RSA, which are used to map important genes regulating various aspects of RSA under varying environmental conditions. Furthermore, we discussed about the state-of-the-art image analysis tools integrated with various phenotyping platforms for investigating and quantifying root traits with the highest phenotypic plasticity in both artificial and natural environments which were used for large scale association mapping studies, leading to the identification of RSA phenotypes and their underlying genetics with the greatest potential for RSA improvement. In addition, challenges in root phenotyping and GWAS are also highlighted, along with future research directions employing machine learning and pan-genomics approaches.
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Affiliation(s)
- Mubashir Abbas
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Ali Abid
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhigang Meng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Manzar Abbas
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Peilin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chao Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Askari
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Umar Akram
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yulu Ye
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunxiao Wei
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sandui Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chengzhen Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rui Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
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27
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Yang J, Wei J, Xu J, Xiong Y, Deng G, Liu J, Fahad S, Wang H. Mapping QTLs for anaerobic tolerance at germination and bud stages using new high density genetic map of rice. FRONTIERS IN PLANT SCIENCE 2022; 13:985080. [PMID: 36325568 PMCID: PMC9618957 DOI: 10.3389/fpls.2022.985080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Due to its low cost and convenience, direct seeding is an efficient technique for the production of rice in different rice growing areas. However, anaerobic conditions are a major obstacle to the direct seeding of rice and result in poor seedling establishment, which leads to yield losses. We constructed a collection of recombinant inbred lines (RIL) comprising 275 lines derived from the H335 and CHA-1 cross by the method of single seed descent. Via a genotyping-by-sequencing (GBS) strategy, a high-density genetic map containing 2498 recombination bin markers was constructed, the average physical distance between the markers was only 149.38 Kb. After anaerobic treatment, 12 phenotypes related to both the coleoptile at germination and seedling quality at budding were evaluated. There were no significant correlations between seedling and bud traits. Genetic mapping of quantitative traits was performed for these traits across two cropping seasons. A total of 20 loci were detected, named locus 1~20. Three of them were repeatedly detected across both seasons. Six loci overlapped with those in previous reports, and nine loci were associated with multiple traits at both stages. Notably, locus 3, which is located on chromosome 2 (26,713,837 to 27,333,897 bp), was detected for both the germination and bud traits. By focusing on the locus 3 interval and by combining gene annotation and expression analyses, we identified a promising candidate gene, trehalose-6-phosphate phosphatase (OsTPP1, LOC_Os02g44230). Furthermore, RILs (G289, G379, G403, G430 and G454) that have superior phenotypes and that pyramid elite alleles were recognized. The findings of present study provide new genetic resources for direct-seeding rice (DSR) varieties for molecular breeding strategies and expand our knowledge of genetic regulation of seedling establishment under anaerobic conditions.
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Affiliation(s)
- Jing Yang
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming, China
| | - Ji Wei
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming, China
| | - Jifen Xu
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming, China
| | - Yumeng Xiong
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming, China
| | - Gang Deng
- School of Agriculture, Yunnan University, Kunming, China
| | - Jing Liu
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming, China
| | - Shah Fahad
- Department of Agriculture, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
- Department of Agronomy, The University of Haripur, Haripur, Pakistan
| | - Hongyang Wang
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming, China
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28
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Ma Y, Wang J, Yang T, Dong J, Yang W, Chen L, Zhou L, Chen J, Liu B, Zhang S, Edwards D, Zhao J. Genome-wide association mapping and gene expression analysis identify OsCPS1 as a new candidate gene controlling early seedling length in rice. FRONTIERS IN PLANT SCIENCE 2022; 13:976669. [PMID: 36119573 PMCID: PMC9478204 DOI: 10.3389/fpls.2022.976669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/01/2022] [Indexed: 06/14/2023]
Abstract
High seedling vigor can improve the ability to compete against weeds and flooding at the seedling stage and is essential for the direct seeding of rice. Early shoot length is an important performance index in seedling vigor evaluation. However, information on the identity of rice germplasm with high seedling vigor, and the genetic basis of seedling vigor are not well understood. In this study, we have conducted a genome-wide association study using 302 international diverse rice accessions from the Rice Diversity Panel 2. Six quantitative trait loci (QTLs) were found to associate with shoot length (SL). The locus qSL2 was further analyzed for candidate gene characterization. We identified OsCPS1, which encodes CDP synthase and functions in GA (Gibberellins) biosynthesis in rice, exhibits differential expression between long and short SL accessions. Using the Nipponbare genome sequence as the reference, we identified a 36 bp deletion in the 5' UTR of OsCPS1 in long SL accessions, which is absent in short SL accessions. GA content analysis showed that the levels of bioactive GA1 and GA4 are considerably higher in long SL accessions than in short SL accessions. Genome-wide gene expression analysis indicated the expression of some photosynthesis genes is higher in long SL accessions than in short SL accessions. In contrast, genes involved in ABA (Abscisic Acid)-activated signal pathway showed lower expression in long SL accessions. Population analysis across wild rice, indica and japonica, suggested that OsCPS1 may be under selection in japonica during domestication. The results suggest that OsCPS1 is a candidate gene underlying qSL2. These data provide a promising source for candidate genetic variation associated with seedling vigor, with practical applications in rice breeding.
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Affiliation(s)
- Yamei Ma
- Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Jian Wang
- Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Tifeng Yang
- Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Jingfang Dong
- Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Wu Yang
- Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Luo Chen
- Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Lian Zhou
- Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Jiansong Chen
- Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Bin Liu
- Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Shaohong Zhang
- Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - David Edwards
- School of Biological Sciences and Centre for Applied Bioinformatics, The University of Western Australia, Perth, WA, Australia
| | - Junliang Zhao
- Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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29
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Veisi S, Sabouri A, Abedi A. Meta-analysis of QTLs and candidate genes associated with seed germination in rice ( Oryza sativa L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:1587-1605. [PMID: 36389095 PMCID: PMC9530108 DOI: 10.1007/s12298-022-01232-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 08/18/2022] [Accepted: 09/16/2022] [Indexed: 06/12/2023]
Abstract
Seed germination is one of the critical stages of plant life, and many quantitative trait loci (QTLs) control this complex trait. Meta-analysis of QTLs is a powerful computational technique for estimating the most stable QTLs regardless of the population's genetic background. Besides, this analysis effectively narrows down the confidence interval (CI) to identify candidate genes (CGs) and marker development. In the current study, a comprehensive genome-wide meta-analysis was performed on QTLs associated with germination in rice. This analysis was conducted based on the data reported over the last two decades. In this case, various analyses were performed, including seed germination rate, plumule length, radicle length, germination percentage, coleoptile length, coleorhiza length, radicle fresh weight, germination potential, and germination index. A total of 67 QTLs were projected onto a reference map for these traits and then integrated into 32 meta-QTLs (MQTLs) to provide a genetic framework for seed germination. The average CI of MQTLs was considerably reduced from 15.125 to 8.73 cM compared to the initial QTLs. This situation identified 728 well-known functionally characterized genes and novel putative CGs for investigated traits. The fold change calculation demonstrated that 155 CGs had significant changes in expression analysis. In this case, 112 and 43 CGs were up-regulated and down-regulated during germination, respectively. This study provides an overview and compares genetic loci controlling traits related to seed germination in rice. The findings can bridge the gap between QTLs and CGs for seed germination. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-022-01232-1.
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Affiliation(s)
- Sheida Veisi
- Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences, University of Guilan, P.O. Box: 41635-1314, Rasht, Iran
| | - Atefeh Sabouri
- Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences, University of Guilan, P.O. Box: 41635-1314, Rasht, Iran
| | - Amin Abedi
- Department of Plant Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
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30
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Unraveling the genomic regions controlling the seed vigour index, root growth parameters and germination per cent in rice. PLoS One 2022; 17:e0267303. [PMID: 35881571 PMCID: PMC9321372 DOI: 10.1371/journal.pone.0267303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 04/06/2022] [Indexed: 12/21/2022] Open
Abstract
High seed vigour ensures good quality seed and higher productivity. Early seedling growth parameters indicate seed vigour in rice. Seed vigour via physiological growth parameters is a complex trait controlled by many quantitative trait loci. A panel was prepared representing a population of 274 rice landraces by including genotypes from all the phenotypic groups of sixseedling stage physiological parameters including germination % for association mapping. Wide variations for the six studiedtraits were observed in the population. The population was classified into 3 genetic groups. Fixation indices indicated the presence of linkage disequilibrium in the population. The population was classified into subpopulations and each subpopulation showed correspondence with the 6 physiological traits. A total of 5 reported QTLs viz., qGP8.1 for germination % (GP); qSVII2.1, qSVII6.1 and qSVII6.2 for seed vigour index II (SVII), and qRSR11.1 for root-shoot ratio (RSR) were validated in this mapping population. In addition, 13 QTLs regulating the physiological parameters such as qSVI 11.1 for seed vigour index I; qSVI11.1 and qSVI12.1 for seed vigour index II; qRRG10.1, qRRG8.1, qRRG8.2, qRRG6.1 and qRRG4.1 for rate of root growth (RRG); qRSR2.1, qRSR3.1 and qRSR5.1 for root-shoot ratio (RSR) while qGP6.2 and qGP6.3 for germination %were identified. Additionally, co-localization or co-inheritance of QTLs, qGP8.1 and qSVI8.1 for GP and SVI-1; qGP6.2 and qRRG6.1 for GP and RRG, and qSVI11.1 and qRSR11.1 for SVI and RSR were detected. The QTLs identified in this study will be useful for improvement of seed vigour trait in rice.
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31
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Anandan A, Panda S, Sabarinathan S, Travis AJ, Norton GJ, Price AH. Superior Haplotypes for Early Root Vigor Traits in Rice Under Dry Direct Seeded Low Nitrogen Condition Through Genome Wide Association Mapping. FRONTIERS IN PLANT SCIENCE 2022; 13:911775. [PMID: 35874029 PMCID: PMC9305665 DOI: 10.3389/fpls.2022.911775] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/13/2022] [Indexed: 06/14/2023]
Abstract
Water and land resources have been aggressively exploited in the recent decades to meet the growing demands for food. The changing climate has prompted rice scientists and farmers of the tropics and subtropics to adopt the direct seeded rice (DSR) system. DSR system of rice cultivation significantly reduces freshwater consumption and labor requirements, while increasing system productivity, resource use efficiency, and reducing greenhouse gas emissions. Early root vigor is an essential trait required in an ideal DSR system of rice cultivation to ensure a good crop stand, adequate uptake of water, nutrients and compete with weeds. The aus subpopulation which is adapted for DSR was evaluated to understand the biology of early root growth under limited nitrogen conditions over two seasons under two-time points (14 and 28 days). The correlation study identified a positive association between shoot dry weight and root dry weight. The genome-wide association study was conducted on root traits of 14 and 28 days with 2 million single-nucleotide polymorphisms (SNPs) using an efficient mixed model. QTLs over a significant threshold of p < 0.0001 and a 10% false discovery rate were selected to identify genes involved in root growth related to root architecture and nutrient acquisition from 97 QTLs. Candidate genes under these QTLs were explored. On chromosome 4, around 30 Mbp are two important peptide transporters (PTR5 and PTR6) involved in mobilizing nitrogen in the root during the early vegetative stage. In addition, several P transporters and expansin genes with superior haplotypes are discussed. A novel QTL from 21.12 to 21.46 Mb on chromosome 7 with two linkage disequilibrium (LD) blocks governing root length at 14 days were identified. The QTLs/candidate genes with superior haplotype for early root vigor reported here could be explored further to develop genotypes for DSR conditions.
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Affiliation(s)
- Annamalai Anandan
- Crop Improvement Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack, India
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Seed Science (IISS), Bengaluru, India
| | - Siddharth Panda
- Crop Improvement Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack, India
- Department of Plant Breeding and Genetics, Odisha University of Agriculture & Technology, Bhubaneswar, India
| | - S. Sabarinathan
- Crop Improvement Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack, India
| | - Anthony J. Travis
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Gareth J. Norton
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Adam H. Price
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
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He Y, Chen S, Liu K, Chen Y, Cheng Y, Zeng P, Zhu P, Xie T, Chen S, Zhang H, Cheng J. OsHIPL1, a hedgehog-interacting protein-like 1 protein, increases seed vigour in rice. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1346-1362. [PMID: 35315188 PMCID: PMC9241377 DOI: 10.1111/pbi.13812] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/19/2022] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
The cultivation of rice varieties with high seed vigour is vital for the direct seeding of rice, and the molecular basis of regulation of seed vigour remains elusive. Here, we cloned a new gene OsHIPL1, which encodes hedgehog-interacting protein-like 1 protein as a causal gene of the major QTL qSV3 for rice seed vigour. OsHIPL1 was mainly localized in the plasma membrane and nucleus. RNA sequencing (RNA-seq) revealed that the ABA-related genes were involved in the OsHIPL1 regulation of seed vigour in rice. The higher levels of endogenous ABA were measured in germinating seeds of OsHIPL1 mutants and NIL-qsv3 line compared to IR26 plants, with two up-regulated ABA biosynthesis genes (OsZEP and OsNCED4) and one down-regulated ABA catabolism gene OsABA8ox3. The expression of abscisic acid-insensitive 3 (OsABI3), OsABI4 and OsABI5 was significantly up-regulated in germinating seeds of OsHIPL1 mutants and NIL-qsv3 line compared to IR26 plants. These results indicate that the regulation of seed vigour of OsHIPL1 may be through modulating endogenous ABA levels and altering OsABIs expression during seed germination in rice. Meanwhile, we found that OsHIPL1 interacted with the aquaporin OsPIP1;1, then affected water uptake to promote rice seed germination. Based on analysis of single-nucleotide polymorphism data of rice accessions, we identified a Hap1 haplotype of OsHIPL1 that was positively correlated with seed germination. Our findings showed novel insights into the molecular mechanism of OsHIPL1 on seed vigour.
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Affiliation(s)
- Ying He
- State Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionJiangsu Province Engineering Research Center of Seed Industry Science and TechnologyCyrus Tang Innovation Center for Seed IndustryNanjing Agricultural UniversityNanjingChina
| | - Shanshan Chen
- State Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionJiangsu Province Engineering Research Center of Seed Industry Science and TechnologyCyrus Tang Innovation Center for Seed IndustryNanjing Agricultural UniversityNanjingChina
| | - Kexin Liu
- State Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionJiangsu Province Engineering Research Center of Seed Industry Science and TechnologyCyrus Tang Innovation Center for Seed IndustryNanjing Agricultural UniversityNanjingChina
| | - Yongji Chen
- State Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionJiangsu Province Engineering Research Center of Seed Industry Science and TechnologyCyrus Tang Innovation Center for Seed IndustryNanjing Agricultural UniversityNanjingChina
| | - Yanhao Cheng
- State Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionJiangsu Province Engineering Research Center of Seed Industry Science and TechnologyCyrus Tang Innovation Center for Seed IndustryNanjing Agricultural UniversityNanjingChina
| | - Peng Zeng
- State Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionJiangsu Province Engineering Research Center of Seed Industry Science and TechnologyCyrus Tang Innovation Center for Seed IndustryNanjing Agricultural UniversityNanjingChina
| | - Peiwen Zhu
- State Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionJiangsu Province Engineering Research Center of Seed Industry Science and TechnologyCyrus Tang Innovation Center for Seed IndustryNanjing Agricultural UniversityNanjingChina
| | - Ting Xie
- State Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionJiangsu Province Engineering Research Center of Seed Industry Science and TechnologyCyrus Tang Innovation Center for Seed IndustryNanjing Agricultural UniversityNanjingChina
| | - Sunlu Chen
- State Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionJiangsu Province Engineering Research Center of Seed Industry Science and TechnologyCyrus Tang Innovation Center for Seed IndustryNanjing Agricultural UniversityNanjingChina
| | - Hongsheng Zhang
- State Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionJiangsu Province Engineering Research Center of Seed Industry Science and TechnologyCyrus Tang Innovation Center for Seed IndustryNanjing Agricultural UniversityNanjingChina
| | - Jinping Cheng
- State Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionJiangsu Province Engineering Research Center of Seed Industry Science and TechnologyCyrus Tang Innovation Center for Seed IndustryNanjing Agricultural UniversityNanjingChina
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Yang B, Chen M, Zhan C, Liu K, Cheng Y, Xie T, Zhu P, He Y, Zeng P, Tang H, Tsugama D, Chen S, Zhang H, Cheng J. Identification of OsPK5 involved in rice glycolytic metabolism and GA/ABA balance for improving seed germination via genome-wide association study. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3446-3461. [PMID: 35191960 PMCID: PMC9162179 DOI: 10.1093/jxb/erac071] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 02/19/2022] [Indexed: 06/12/2023]
Abstract
Seed germination plays a pivotal role in the plant life cycle, and its precise regulatory mechanisms are not clear. In this study, 19 quantitative trait loci (QTLs) associated with rice seed germination were identified through genome-wide association studies (GWAS) of the following traits in 2016 and 2017: germination rate (GR) at 3, 5, and 7 days after imbibition (DAI) and germination index (GI). Two major stable QTLs, qSG4 and qSG11.1, were found to be associated with GR and GI over 2 continuous years. Furthermore, OsPK5, encoding a pyruvate kinase, was shown to be a crucial regulator of seed germination in rice, and might be a causal gene of the key QTL qSG11.1, on chromosome 11. Natural variation in OsPK5 function altered the activity of pyruvate kinase. The disruption of OsPK5 function resulted in slow germination and seedling growth during seed germination, blocked glycolytic metabolism, caused glucose accumulation, decreased energy levels, and affected the GA/ABA balance. Taken together, our results provide novel insights into the roles of OsPK5 in seed germination, and facilitate its application in rice breeding to improve seed vigour.
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Affiliation(s)
| | | | | | - Kexin Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Cyrus Tang Innovation Center for Seed Industry, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanhao Cheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Cyrus Tang Innovation Center for Seed Industry, Nanjing Agricultural University, Nanjing 210095, China
| | - Ting Xie
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Cyrus Tang Innovation Center for Seed Industry, Nanjing Agricultural University, Nanjing 210095, China
| | - Peiwen Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Cyrus Tang Innovation Center for Seed Industry, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying He
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Cyrus Tang Innovation Center for Seed Industry, Nanjing Agricultural University, Nanjing 210095, China
| | - Peng Zeng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Cyrus Tang Innovation Center for Seed Industry, Nanjing Agricultural University, Nanjing 210095, China
| | - Haijuan Tang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Cyrus Tang Innovation Center for Seed Industry, Nanjing Agricultural University, Nanjing 210095, China
| | - Daisuke Tsugama
- Asian Natural Environmental Science Center (ANESC), The University of Tokyo, 1-1-1 Midori-cho, Nishitokyo-shi, Tokyo 188-0002, Japan
| | - Sunlu Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Cyrus Tang Innovation Center for Seed Industry, Nanjing Agricultural University, Nanjing 210095, China
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Adhikary S, Biswas B, Chakraborty D, Timsina J, Pal S, Chandra Tarafdar J, Banerjee S, Hossain A, Roy S. Seed priming with selenium and zinc nanoparticles modifies germination, growth, and yield of direct-seeded rice (Oryza sativa L.). Sci Rep 2022; 12:7103. [PMID: 35501374 PMCID: PMC9061837 DOI: 10.1038/s41598-022-11307-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/14/2022] [Indexed: 11/09/2022] Open
Abstract
Direct-seeded rice (DSR) seeds are often exposed to multiple environmental stresses in the field, leading to poor emergence, growth and productivity. Appropriate seed priming agents may help to overcome these challenges by ensuring uniform seed germination, and better seedling stand establishment. To examine the effectiveness of sodium selenite (Na-selenite), sodium selenate (Na-selenate), zinc oxide nanoparticles (ZnO-NPs), and their combinations as priming agents for DSR seeds, a controlled pot experiment followed by a field experiment over two consecutive years was conducted on a sandy clay loam soil (Inceptisol) in West Bengal, India. Priming with combinations of all priming agents had advantages over the hydro-priming treatment (control). All the combinations of the three priming agents resulted in the early emergence of seedlings with improved vigour. In the field experiment, all the combinations increased the plant chlorophyll, phenol and protein contents, leaf area index and duration, crop growth rate, uptake of nutrients (N, P, K, B, Zn and Si), and yield of DSR over the control. Our findings suggest that seed priming with the combination of ZnO-NPs, Na-selenite, and Na-selenate could be a viable option for the risk mitigation in DSR.
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Affiliation(s)
- Saju Adhikary
- Department of Agronomy, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, Nadia, West Bengal, 741 252, India
| | - Benukar Biswas
- Department of Agronomy, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, Nadia, West Bengal, 741 252, India.
| | - Debashis Chakraborty
- Division of Agricultural Physics, Indian Agricultural Research Institute, New Delhi, 110 012, India.
| | - Jagadish Timsina
- Global Evergreening Alliance, 1 Vision Drive, East Burwood, Melbourne, VIC, 3151, Australia.
- Institute for Study and Development Worldwide, Sydney, NSW, Australia.
| | - Srikumar Pal
- Department of Agricultural Biochemistry, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, Nadia, West Bengal, 741 252, India
| | - Jagadish Chandra Tarafdar
- Ex-Scientist, Central Arid Zone Research Institute, 17E/361A, C. H. B., Jodhpur, 342008, India
- 32/E/2/1, BanamalipurBarasat, Kolkata, West Bengal, 700124, India
| | - Saon Banerjee
- Department of Agricultural Physics and Meteorology, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, Nadia, West Bengal, 741 252, India
| | - Akbar Hossain
- Bangladesh Wheat and Maize Research Institute, Dinajpur, 5200, Bangladesh
| | - Sovan Roy
- Department of Science & Technology and Biotechnology, Vigyan Chetana Bhavan, Kolkata, West Bengal, 700064, India
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Nie L, Song S, Yin Q, Zhao T, Liu H, He A, Wang W. Enhancement in Seed Priming-Induced Starch Degradation of Rice Seed Under Chilling Stress via GA-Mediated α-Amylase Expression. RICE (NEW YORK, N.Y.) 2022; 15:19. [PMID: 35344097 PMCID: PMC8960536 DOI: 10.1186/s12284-022-00567-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 03/21/2022] [Indexed: 05/20/2023]
Abstract
Chilling stress is the major abiotic stress that severely limited the seedling establishment of direct-seeded rice in temperate and sub-tropical rice production regions. While seed priming is an efficient pre-sowing seed treatment in enhancing crop establishment under abiotic stress. Our previous research has identified two seed priming treatments, selenium priming (Se) and salicylic priming (SA) that effectively improved the seed germination and seedling growth of rice under chilling stress. To further explore how seed priming enhance the starch degradation of rice seeds under chilling stress, the present study evaluated the effects of Se and SA priming on germination and seedling growth, α-amylase activity, total soluble sugar content, hormone content and associated gene relative expression under chilling stress. The results showed that both Se and SA priming significantly increased the seed germination and seedling growth attributes, and enhanced the starch degradation ability by increasing α-amylase activity and total soluble sugar content under chilling stress. Meanwhile, seed priming increased the transcription level of OsRamy1A, OsRamy3B that regulated by GA, and increased the transcription level of OsRamy3E that regulated by sugar signals. Furthermore, seed priming significantly improved the GA3 contents in rice seeds by up-regulating the expression of OsGA3ox1 and OsGA20ox1, and decreased the ABA content and the expression of OsNCED1, indicating that the improved starch degradation ability in primed rice seeds under chilling stress might be attributed to the increased GA3 and decreased ABA levels in primed rice seeds, which induced the expression of GA-mediated α-amylase. However, studies to explore how seed priming mediate hormonal metabolism and the expression of OsRamy3E are desperately needed.
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Affiliation(s)
- Lixiao Nie
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
| | - Shaokun Song
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
| | - Qi Yin
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
| | - Tingcheng Zhao
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
| | - Hongyan Liu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
| | - Aibin He
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Weiqin Wang
- College of Agronomy, Hunan Agricultural University, Changsha, China.
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Heredia MC, Kant J, Prodhan MA, Dixit S, Wissuwa M. Breeding rice for a changing climate by improving adaptations to water saving technologies. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:17-33. [PMID: 34218290 DOI: 10.1007/s00122-021-03899-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 06/25/2021] [Indexed: 06/13/2023]
Abstract
Climate change is expected to increasingly affect rice production through rising temperatures and decreasing water availability. Unlike other crops, rice is a main contributor to greenhouse gas emissions due to methane emissions from flooded paddy fields. Climate change can therefore be addressed in two ways in rice: through making the crop more climate resilient and through changes in management practices that reduce methane emissions and thereby slow global warming. In this review, we focus on two water saving technologies that reduce the periods lowland rice will be grown under fully flooded conditions, thereby improving water use efficiency and reducing methane emissions. Rice breeding over the past decades has mostly focused on developing high-yielding varieties adapted to continuously flooded conditions where seedlings were raised in a nursery and transplanted into a puddled flooded soil. Shifting cultivation to direct-seeded rice or to introducing non-flooded periods as in alternate wetting and drying gives rise to new challenges which need to be addressed in rice breeding. New adaptive traits such as rapid uniform germination even under anaerobic conditions, seedling vigor, weed competitiveness, root plasticity, and moderate drought tolerance need to be bred into the current elite germplasm and to what extent this is being addressed through trait discovery, marker-assisted selection and population improvement are reviewed.
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Affiliation(s)
| | | | - M Asaduzzaman Prodhan
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan
| | - Shalabh Dixit
- International Rice Research Institute (IRRI), Los Baños, The Philippines
| | - Matthias Wissuwa
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan.
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Pan Z, Tan B, Cao G, Zheng R, Liu M, Zeng R, Wang S, Zhu H, Ye H, Zhao G, Cao W, Liu G, Zhang G, Zhou Y. Integrative QTL Identification, Fine Mapping and Candidate Gene Analysis of a Major Locus qLTG3a for Seed Low-Temperature Germinability in Rice. RICE (NEW YORK, N.Y.) 2021; 14:103. [PMID: 34910270 PMCID: PMC8674402 DOI: 10.1186/s12284-021-00544-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 12/03/2021] [Indexed: 05/31/2023]
Abstract
Low-temperature germinability (LTG) is an important agronomic trait that can affect the planting time, planting area, and grain yield of staple crops, such as rice. However, the genetic mechanism of LTG is still unclear. In this study, a multi-parental permanent population with 208 single segment substitution lines (SSSLs) was used to conduct a genetic dissection for LTG across four cropping seasons. LTG was a typical quantitative trait with a high combined broad-sense heritability of 0.71. By comparison with the recipient parent, Huajingxian74, 24 SSSLs were identified as carrying LTG QTLs, which were further merged into integrated QTLs with shorter genetic distances by substitution mapping. Finally, 14 LTG QTLs were mapped on ten chromosomes, including seven positive-effect and seven negative-effect QTLs, with additive effect contributions ranging from 19.2 to 39.9%. qLTG3a, a main-effect and novel QTL, was confirmed by bulk segregant analysis using an F2 segregating population, and five key recombinants were selected to develop F3 populations for progeny testing. Marker-trait association analysis fine mapped qLTG3a to a 332.7-kb physical region between markers M6026 and M6341. Within this interval, 40 annotated genes were revealed, and three genes (Os03g0213300, Os03g0214400, and Os03g0214600) were considered as pivotal candidate genes for qLTG3a based on their sequence variations and expression patterns. Besides low temperature, qLTG3a can also enhance seed germination under standard temperature and osmotic stress. In summary, this study identified some genetic factors regulating LTG and opened a new window for breeding elite direct-seeded rice varieties. It will help reduce the climate risk in the production process of rice, which is of great significance to ensuring food security.
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Affiliation(s)
- Zhaoyuan Pan
- Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Bin Tan
- Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Guiyuan Cao
- Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Rongqi Zheng
- Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Meng Liu
- Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Ruizhen Zeng
- Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Shaokui Wang
- Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Haitao Zhu
- Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Heng Ye
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Guangmiao Zhao
- Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Wei Cao
- Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Guifu Liu
- Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Guiquan Zhang
- Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.
| | - Yuliang Zhou
- Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.
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Ye S, Huang Z, Zhao G, Zhai R, Ye J, Wu M, Yu F, Zhu G, Zhang X. Differential Physiological Responses to Salt Stress between Salt-Sensitive and Salt-Tolerant japonica Rice Cultivars at the Post-Germination and Seedling Stages. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112433. [PMID: 34834796 PMCID: PMC8696616 DOI: 10.3390/plants10112433] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/09/2021] [Accepted: 11/09/2021] [Indexed: 05/20/2023]
Abstract
Soil salinity is a key source of abiotic stress in the cultivation of rice. In this study, two currently cultivated japonica rice species-Zhegeng 78 (salt-tolerant) and Zhegeng 99 (salt-sensitive)-with similar backgrounds were identified and used to investigate their differential responses to salt stress at the post-germination and seedling stages. Quantitative RT-PCR analysis demonstrated that the expression of OsSOS1, OsHAK1, and OsHAK5 at the post-germination stage, and the expression of OsHKT1,1, OsHTK2,1, and OsHAK1 at the seedling stage, were significantly higher in the salt-tolerant Zhegeng 78 compared with those of the salt-sensitive Zhegeng 99 under salt stress. The significantly lower Na+ net uptake rate at the post-germination and higher K+ net uptake rates at the post-germination and seedling stages were observed in the salt-tolerant Zhegeng 78 compared with those of the salt-sensitive Zhegeng 99 under salt stress. Significantly higher activity of peroxidase (POD) and the lower hydrogen peroxide (H2O2) accumulation were observed in the salt-tolerant Zhegeng 78 compared with those of salt-sensitive Zhegeng 99 under salt stress at the seeding stage. The salt-tolerant Zhegeng 78 might be valuable in future cultivation in salinity soils.
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Affiliation(s)
- Shenghai Ye
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (S.Y.); (R.Z.); (J.Y.); (M.W.); (F.Y.); (G.Z.)
| | - Zhibo Huang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (Z.H.); (G.Z.)
| | - Guibin Zhao
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (Z.H.); (G.Z.)
| | - Rongrong Zhai
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (S.Y.); (R.Z.); (J.Y.); (M.W.); (F.Y.); (G.Z.)
| | - Jing Ye
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (S.Y.); (R.Z.); (J.Y.); (M.W.); (F.Y.); (G.Z.)
| | - Mingming Wu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (S.Y.); (R.Z.); (J.Y.); (M.W.); (F.Y.); (G.Z.)
| | - Faming Yu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (S.Y.); (R.Z.); (J.Y.); (M.W.); (F.Y.); (G.Z.)
| | - Guofu Zhu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (S.Y.); (R.Z.); (J.Y.); (M.W.); (F.Y.); (G.Z.)
| | - Xiaoming Zhang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (S.Y.); (R.Z.); (J.Y.); (M.W.); (F.Y.); (G.Z.)
- Correspondence:
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Laboratory phenomics predicts field performance and identifies superior indica haplotypes for early seedling vigour in dry direct-seeded rice. Genomics 2021; 113:4227-4236. [PMID: 34774680 DOI: 10.1016/j.ygeno.2021.11.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 10/22/2021] [Accepted: 11/07/2021] [Indexed: 11/22/2022]
Abstract
Seedling vigour is an important agronomic trait and is gaining attention in Asian rice (Oryza sativa) as cultivation practices shift from transplanting to forms of direct seeding. To understand the genetic control of rice seedling vigour in dry direct seeded (aerobic) conditions we measured multiple seedling traits in 684 accessions from the 3000 Rice Genomes (3K-RG) population in both the laboratory and field at three planting depths. Our data show that phenotyping of mesocotyl length in laboratory conditions is a good predictor of field performance. By performing a genome wide association study, we found that the main QTL for mesocotyl length, percentage seedling emergence and shoot biomass are co-located on the short arm of chromosome 7. We show that haplotypes in the indica subgroup from this region can be used to predict the seedling vigour of 3K-RG accessions. The selected accessions may serve as potential donors in genomics-assisted breeding programs.
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Kaur P, Sachan S, Sharma A. Weed competitive ability in wheat: a peek through in its functional significance, present status and future prospects. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2165-2179. [PMID: 34744359 PMCID: PMC8526637 DOI: 10.1007/s12298-021-01079-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/02/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
Weed competitive ability of a crop is one of the most widely explored aspects in the current scenario of aftermaths of synthetic herbicides such as herbicide resistant weeds emergence, residue accumulation in trophic levels; increased demands of organic produce, global climatic shifts, and other environmental issues. Further weed infestations are known to cause much more economic losses relative to crop attacks by pests. To understand the basic characteristics and underlying processes governing the competitive ability of a crop is therefore prudent, particularly in staples such as wheat. We discuss here an overview of the existing attributes of wheat-weed environment, the significance of crop competitiveness and various associated above-ground and below-ground traits (pertaining to early seed vigor and early seedling germination) discerned through biological, classical genetics and high throughput omics toolbox to provide numerous resources in terms of genome and transcriptome sequences, potential QTLs, genetic variation, molecular markers, association mapping studies, and others. Competitiveness is a cumulative response manifested as morphological, physiological, biochemical or allelochemical response ultimately driven through genetic architecture of a crop and its interaction with environment. Development of wheat competitive cultivar thus requires interdisciplinary approaches and germplasm screening to identify potential donors for competitiveness is an attractive and feasible alternative. For which utilization of landraces and other wild species, already proven to house sufficient genetic heterogeneity, thus poses a competitive advantage. Further, the availability of novel breeding techniques such as rapid generation advance could speed up the development of competitive wheat ideotype.
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Affiliation(s)
- Parampreet Kaur
- School of Organic Farming, Punjab Agricultural University, Ludhiana, Punjab India
| | - Shephali Sachan
- School of Organic Farming, Punjab Agricultural University, Ludhiana, Punjab India
| | - Achla Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab India
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Li W, Yang B, Xu J, Peng L, Sun S, Huang Z, Jiang X, He Y, Wang Z. A genome-wide association study reveals that the 2-oxoglutarate/malate translocator mediates seed vigor in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:478-491. [PMID: 34376020 DOI: 10.1111/tpj.15455] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 08/01/2021] [Accepted: 08/05/2021] [Indexed: 05/25/2023]
Abstract
Seed vigor is an important trait for the direct seeding of rice (Oryza sativa L.). In this study, we examined the genetic architecture of variation in the germination rate using a diverse panel of rice accessions. Four quantitative trait loci for germination rate were identified using a genome-wide association study during early germination. One candidate gene, encoding the 2-oxoglutarate/malate translocator (OsOMT), was validated for qGR11. Disruption of this gene (Osomt mutants) reduced seed vigor, including seed germination and seedling growth, in rice. Functional analysis revealed that OsOMT influences seed vigor mainly by modulating amino acid levels and glycolysis and tricarboxylic acid cycle processes. The levels of most amino acids, including the Glu family (Glu, Pro, Arg, and GABA), Asp family (Asp, Thr, Lys, Ile, and Met), Ser family (Ser, Gly, and Cys), and others (His, Ala, Leu, and Val), were significantly reduced in the mature grains and the early germinating seeds of Osomt mutants compared to wild type (WT). The glucose and soluble sugar contents, as well as adenosine triphosphate levels, were significantly decreased in germinating seeds of Osomt mutants compared to WT. These results provide important insights into the role of OsOMT in seed vigor in rice.
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Affiliation(s)
- Wenjun Li
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Bin Yang
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Jiangyu Xu
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Liling Peng
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Shan Sun
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Zhibo Huang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Xiuhua Jiang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Yongqi He
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Zhoufei Wang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
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42
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Wang Y, Liu J, Meng Y, Liu H, Liu C, Ye G. Rapid Identification of QTL for Mesocotyl Length in Rice Through Combining QTL-seq and Genome-Wide Association Analysis. Front Genet 2021; 12:713446. [PMID: 34349792 PMCID: PMC8326918 DOI: 10.3389/fgene.2021.713446] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 06/15/2021] [Indexed: 02/01/2023] Open
Abstract
Mesocotyl is a crucial organ for pushing buds out of soil, which plays a vital role in seedling emergence and establishment in direct-seeded rice. Thus, the identification of quantitative trait loci (QTL) associated with mesocotyl length (ML) could accelerate genetic improvement of rice for direct seeding cultivation. In this study, QTL sequencing (QTL-seq) applied to 12 F2 populations identified 14 QTL for ML, which were distributed on chromosomes 1, 3, 4, 5, 6, 7, and 9 based on the Δ(SNP-index) or G-value statistics. Besides, a genome-wide association study (GWAS) using two diverse panels identified five unique QTL on chromosomes 1, 8, 9, and 12 (2), respectively, explaining 5.3–14.6% of the phenotypic variations. Among these QTL, seven were in the regions harboring known genes or QTLs, whereas the other 10 were potentially novel. Six of the QTL were stable across two or more populations. Eight high-confidence candidate genes related to ML were identified for the stable loci based on annotation and expression analyses. Association analysis revealed that two PCR gel-based markers for the loci co-located by QTL-seq and GWAS, Indel-Chr1:18932318 and Indel-Chr7:15404166 for loci qML1.3 and qML7.2 respectively, were significantly associated with ML in a collection of 140 accessions and could be used as breeder-friendly markers in further breeding.
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Affiliation(s)
- Yamei Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jindong Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yun Meng
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,College of Tropical Crops, Hainan University, Haikou, China
| | - Hongyan Liu
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,College of Tropical Crops, Hainan University, Haikou, China
| | - Chang Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Guoyou Ye
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,Rice Breeding Innovation Platform, International Rice Research Institute, Metro Manila, Philippines
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Anandan A, Parameswaran C, Mahender A, Nayak AK, Vellaikumar S, Balasubramaniasai C, Ali J. Trait variations and expression profiling of OsPHT1 gene family at the early growth-stages under phosphorus-limited conditions. Sci Rep 2021; 11:13563. [PMID: 34193908 PMCID: PMC8245478 DOI: 10.1038/s41598-021-92580-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/06/2021] [Indexed: 02/06/2023] Open
Abstract
To better understand the early response of genotypes to limited-phosphorus (P) conditions and the role of the phosphate transporter OsPHT1 gene family in the presence of PSTOL1, it is essential to characterize the level of tolerance in rice under limited-P conditions. In the present experiment, six rice genotypes were studied in three-way interactions [genotype (G) × phosphorus (P) × duration (D)] by comparing them at two instances (14 d and 28 d) under seven different concentrations of P (0.5‒10.0 ppm) in a hydroponic system. Trait differences and interactions of these traits were clearly distinguished among the various P rates. However, aboveground trait expression registered increased growth from 6.0 to 10.0 ppm of P. The major root-attributed traits in 0.5 ppm of P are significantly increased vis-à-vis 10 ppm of P. Analysis of variance displayed a significant difference between the genotypes for PSTOL1 and PHT1 expression. In low P, maximum root length with a shoot and root dry weight was observed in a new indigenous accession, IC459373, with higher expression of PSTOL1 than in Dular and IR64-Pup1 in 0.5 ppm of P at 14 d. Among the 13 PHT1 genes, OsPT1, OsPT2, OsPT6, and OsPT13 showed significant upregulation in IC459373, Dular, and IR64-Pup1. These results indicated that studying the expression levels of the PSTOL1 and PHT1 gene family at the early growth stages would be helpful in identifying superior donors to improve low-P tolerance and P-use efficiency in rice breeding programs.
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Affiliation(s)
- Annamalai Anandan
- grid.418371.80000 0001 2183 1039Crop Improvement Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack, Odisha 753006 India
| | - Chidambaranathan Parameswaran
- grid.418371.80000 0001 2183 1039Crop Improvement Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack, Odisha 753006 India
| | - Anumalla Mahender
- grid.419387.00000 0001 0729 330XRice Breeding Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, 4031 Philippines
| | - Amaresh Kumar Nayak
- grid.418371.80000 0001 2183 1039Crop Improvement Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack, Odisha 753006 India
| | - Sampthamprajan Vellaikumar
- grid.412906.80000 0001 2155 9899Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, 641003 India
| | - Cayalvizhi Balasubramaniasai
- grid.418371.80000 0001 2183 1039Crop Improvement Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack, Odisha 753006 India
| | - Jauhar Ali
- grid.419387.00000 0001 0729 330XRice Breeding Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, 4031 Philippines
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Proofing Direct-Seeded Rice with Better Root Plasticity and Architecture. Int J Mol Sci 2021; 22:ijms22116058. [PMID: 34199720 PMCID: PMC8199995 DOI: 10.3390/ijms22116058] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 05/30/2021] [Accepted: 06/01/2021] [Indexed: 11/16/2022] Open
Abstract
The underground reserve (root) has been an uncharted research territory with its untapped genetic variation yet to be exploited. Identifying ideal traits and breeding new rice varieties with efficient root system architecture (RSA) has great potential to increase resource-use efficiency and grain yield, especially under direct-seeded rice, by adapting to aerobic soil conditions. In this review, we tried to mine the available research information on the direct-seeded rice (DSR) root system to highlight the requirements of different root traits such as root architecture, length, number, density, thickness, diameter, and angle that play a pivotal role in determining the uptake of nutrients and moisture at different stages of plant growth. RSA also faces several stresses, due to excess or deficiency of moisture and nutrients, low or high temperature, or saline conditions. To counteract these hindrances, adaptation in response to stress becomes essential. Candidate genes such as early root growth enhancer PSTOL1, surface rooting QTL qSOR1, deep rooting gene DRO1, and numerous transporters for their respective nutrients and stress-responsive factors have been identified and validated under different circumstances. Identifying the desired QTLs and transporters underlying these traits and then designing an ideal root architecture can help in developing a suitable DSR cultivar and aid in further advancement in this direction.
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QTL Mapping and Phenotypic Variation for Seedling Vigour Traits in Barley ( Hordeum vulgare L.). PLANTS 2021; 10:plants10061149. [PMID: 34200109 PMCID: PMC8227620 DOI: 10.3390/plants10061149] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 11/26/2022]
Abstract
Seed vigour is considered a critical stage for barley production, and cultivars with early seedling vigour (ESV) facilitate rapid canopy formation. In this study, QTLs for 12 ESV-related traits were mapped using 185 RILs derived from a Xena x H94061120 evaluated across six independent environments. DArT markers were used to develop a genetic map (1075.1 cM; centimorgans) with an average adjacent-marker distance of 3.28 cM. In total, 46 significant QTLs for ESV-related traits were detected. Fourteen QTLs for biomass yield were found on all chromosomes, two of them co-localized with QTLs on 1H for grain yield. The related traits: length of the first and second leaves and dry weight of the second leaf, biomass yield and grain yield, had high heritability (>30%). Meanwhile, a significant correlation was observed between grain yield and biomass yield, which provided a clear image of these traits in the selection process. Our results demonstrate that a pleiotropic QTL related to the specific leaf area of the second leaf, biomass yield, and grain yield was linked to the DArT markers bPb-9280 and bPb-9108 on 1H, which could be used to significantly improve seed vigour by marker-assisted selection and facilitate future map-based cloning efforts.
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Panda D, Barik J, Sarkar RK. Recent Advances of Genetic Resources, Genes and Genetic Approaches for Flooding Tolerance in Rice. Curr Genomics 2021; 22:41-58. [PMID: 34045923 PMCID: PMC8142345 DOI: 10.2174/1389202922666210114104140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 12/16/2020] [Accepted: 12/26/2020] [Indexed: 12/16/2022] Open
Abstract
Flooding is one of the most hazardous natural disasters and a major stress constraint to rice production throughout the world, which results in huge economic losses. The frequency and duration of flooding is predicted to increase in near future as a result of global climate change. Breeding of flooding tolerance in rice is a challenging task because of the complexity of the component traits, screening technique, environmental factors and genetic interactions. A great progress has been made during last two decades to find out the flooding tolerance mechanism in rice. An important breakthrough in submergence research was achieved by the identification of major quantitative trait locus (QTL) SUB1 in rice chromosomes that acts as the primary contributor for tolerance. This enabled the use of marker-assisted backcrossing (MABC) to transfer SUB1 QTL into popular varieties which showed yield advantages in flood prone areas. However, SUB1 varieties are not always tolerant to stagnant flooding and flooding during germination stage. So, gene pyramiding approach can be used by combining several important traits to develop new breeding rice lines that confer tolerances to different types of flooding. This review highlights the important germplasm/genetic resources of rice to different types of flooding stress. A brief discussion on the genes and genetic mechanism in rice exhibited to different types of flooding tolerance was discussed for the development of flood tolerant rice variety. Further research on developing multiple stresses tolerant rice can be achieved by combining SUB1 with other tolerance traits/genes for wider adaptation in the rain-fed rice ecosystems.
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Affiliation(s)
- Debabrata Panda
- Department of Biodiversity and Conservation of Natural Resources, Central University of Odisha, Koraput-764 020, Odisha, India
| | - Jijnasa Barik
- Department of Biodiversity and Conservation of Natural Resources, Central University of Odisha, Koraput-764 020, Odisha, India
| | - Ramani K Sarkar
- ICAR-National Rice Research Institute, Cuttack-753 006, Odisha, India
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Zhao J, Yang B, Li W, Sun S, Peng L, Feng D, Li L, Di H, He Y, Wang Z. A genome-wide association study reveals that the glucosyltransferase OsIAGLU regulates root growth in rice. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1119-1134. [PMID: 33130882 DOI: 10.1093/jxb/eraa512] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/26/2020] [Indexed: 05/18/2023]
Abstract
Good root growth in the early post-germination stages is an important trait for direct seeding in rice, but its genetic control is poorly understood. In this study, we examined the genetic architecture of variation in primary root length using a diverse panel of 178 accessions. Four QTLs for root length (qRL3, qRL6, qRL7, and qRL11) were identified using genome-wide association studies. One candidate gene was validated for the major QTL qRL11, namely the glucosyltransferase OsIAGLU. Disruption of this gene in Osiaglu mutants reduced the primary root length and the numbers of lateral and crown roots. The natural allelic variations of OsIAGLU contributing to root growth were identified. Functional analysis revealed that OsIAGLU regulates root growth mainly via modulating multiple hormones in the roots, including levels of auxin, jasmonic acid, abscisic acid, and cytokinin. OsIAGLU also influences the expression of multiple hormone-related genes associated with root growth. The regulation of root growth through multiple hormone pathways by OsIAGLU makes it a potential target for future rice breeding for crop improvement.
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Affiliation(s)
- Jia Zhao
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, People's Republic of China
| | - Bin Yang
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, People's Republic of China
| | - Wenjun Li
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, People's Republic of China
| | - Shan Sun
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, People's Republic of China
| | - Liling Peng
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, People's Republic of China
| | - Defeng Feng
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, People's Republic of China
| | - Li Li
- Huzhou Agricultural Science and Technology Development Center, Huzhou, People's Republic of China
| | - Hong Di
- Northeast Agricultural University, Harbin, People's Republic of China
| | - Yongqi He
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, People's Republic of China
| | - Zhoufei Wang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, People's Republic of China
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Wei Z, Yuan Q, Lin H, Li X, Zhang C, Gao H, Zhang B, He H, Liu T, Jie Z, Gao X, Shi S, Wang B, Gao Z, Kong L, Qian Q, Shang L. Linkage analysis, GWAS, transcriptome analysis to identify candidate genes for rice seedlings in response to high temperature stress. BMC PLANT BIOLOGY 2021; 21:85. [PMID: 33563229 DOI: 10.1186/s12870-021-02857-2852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 01/26/2021] [Indexed: 05/26/2023]
Abstract
BACKGROUND Rice plants suffer from the rising temperature which is becoming more and more prominent. Mining heat-resistant genes and applying them to rice breeding is a feasible and effective way to solve the problem. RESULT Three main biomass traits, including shoot length, dry weight, and fresh weight, changed after abnormally high-temperature treatment in the rice seedling stage of a recombinant inbred lines and the natural indica germplasm population. Based on a comparison of the results of linkage analysis and genome-wide association analysis, two loci with lengths of 57 kb and 69 kb in qDW7 and qFW6, respectively, were associated with the rice response to abnormally high temperatures at the seedling stage. Meanwhile, based on integrated transcriptome analysis, some genes are considered as important candidate genes. Combining with known genes and analysis of homologous genes, it was found that there are eight genes in candidate intervals that need to be focused on in subsequent research. CONCLUSIONS The results indicated several relevant loci, which would help researchers to further discover beneficial heat-resistant genes that can be applied to rice heat-resistant breeding.
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Affiliation(s)
- Zhaoran Wei
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- State Key Laboratory of Crop Biology, College of Agriculture, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Qiaoling Yuan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hai Lin
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiaoxia Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Chao Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hongsheng Gao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Bin Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Huiying He
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Tianjiao Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhang Jie
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xu Gao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shandang Shi
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Bo Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Lingrang Kong
- State Key Laboratory of Crop Biology, College of Agriculture, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Qian Qian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China.
| | - Lianguang Shang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
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Wei Z, Yuan Q, Lin H, Li X, Zhang C, Gao H, Zhang B, He H, Liu T, Jie Z, Gao X, Shi S, Wang B, Gao Z, Kong L, Qian Q, Shang L. Linkage analysis, GWAS, transcriptome analysis to identify candidate genes for rice seedlings in response to high temperature stress. BMC PLANT BIOLOGY 2021; 21:85. [PMID: 33563229 PMCID: PMC7874481 DOI: 10.1186/s12870-021-02857-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 01/26/2021] [Indexed: 05/28/2023]
Abstract
BACKGROUND Rice plants suffer from the rising temperature which is becoming more and more prominent. Mining heat-resistant genes and applying them to rice breeding is a feasible and effective way to solve the problem. RESULT Three main biomass traits, including shoot length, dry weight, and fresh weight, changed after abnormally high-temperature treatment in the rice seedling stage of a recombinant inbred lines and the natural indica germplasm population. Based on a comparison of the results of linkage analysis and genome-wide association analysis, two loci with lengths of 57 kb and 69 kb in qDW7 and qFW6, respectively, were associated with the rice response to abnormally high temperatures at the seedling stage. Meanwhile, based on integrated transcriptome analysis, some genes are considered as important candidate genes. Combining with known genes and analysis of homologous genes, it was found that there are eight genes in candidate intervals that need to be focused on in subsequent research. CONCLUSIONS The results indicated several relevant loci, which would help researchers to further discover beneficial heat-resistant genes that can be applied to rice heat-resistant breeding.
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Affiliation(s)
- Zhaoran Wei
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- State Key Laboratory of Crop Biology, College of Agriculture, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Qiaoling Yuan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hai Lin
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiaoxia Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Chao Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hongsheng Gao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Bin Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Huiying He
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Tianjiao Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhang Jie
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xu Gao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shandang Shi
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Bo Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Lingrang Kong
- State Key Laboratory of Crop Biology, College of Agriculture, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Qian Qian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China.
| | - Lianguang Shang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
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50
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The Rice Small Auxin-Up RNA Gene OsSAUR33 Regulates Seed Vigor via Sugar Pathway during Early Seed Germination. Int J Mol Sci 2021; 22:ijms22041562. [PMID: 33557166 PMCID: PMC7913900 DOI: 10.3390/ijms22041562] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/28/2021] [Accepted: 02/01/2021] [Indexed: 11/16/2022] Open
Abstract
Seed vigor affects seed germination and seedling emergence, and therefore is an important agronomic trait in rice. Small auxin-up RNAs (SAURs) function in a range of developmental processes, but their role in seed vigor remains unclear. Here, we observed that disruption of OsSAUR33 resulted in reduced germination rates and low seed uniformity in early germination. Expression of OsSAUR33 was higher in mature grains and early germinating seeds. RNA-seq analysis revealed that OsSAUR33 modulated seed vigor by affecting the mobilization of stored reserves during germination. Disruption of OsSAUR33 increased the soluble sugar content in dry mature grains and seeds during early germination. OsSAUR33 interacted with the sucrose non-fermenting-1-related protein kinase OsSnRK1A, a regulator of the sugar signaling pathway, which influences the expression of sugar signaling-related genes during germination. Disruption of OsSAUR33 increased sugar-sensitive phenotypes in early germination, suggesting OsSAUR33 likely affects seed vigor through the sugar pathway. One elite haplotype of OsSAUR33 associated with higher seed vigor was identified mainly in indica accessions. This study provides insight into the effects of OsSAUR33 on seed vigor in rice.
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