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Yang X, Yu S, Yan S, Wang H, Fang W, Chen Y, Ma X, Han L. Progress in Rice Breeding Based on Genomic Research. Genes (Basel) 2024; 15:564. [PMID: 38790193 PMCID: PMC11121554 DOI: 10.3390/genes15050564] [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: 03/21/2024] [Revised: 04/18/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
The role of rice genomics in breeding progress is becoming increasingly important. Deeper research into the rice genome will contribute to the identification and utilization of outstanding functional genes, enriching the diversity and genetic basis of breeding materials and meeting the diverse demands for various improvements. Here, we review the significant contributions of rice genomics research to breeding progress over the last 25 years, discussing the profound impact of genomics on rice genome sequencing, functional gene exploration, and novel breeding methods, and we provide valuable insights for future research and breeding practices.
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Affiliation(s)
- Xingye Yang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.Y.); (S.Y.); (H.W.); (W.F.); (Y.C.)
| | - Shicong Yu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China;
| | - Shen Yan
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.Y.); (S.Y.); (H.W.); (W.F.); (Y.C.)
| | - Hao Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.Y.); (S.Y.); (H.W.); (W.F.); (Y.C.)
| | - Wei Fang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.Y.); (S.Y.); (H.W.); (W.F.); (Y.C.)
| | - Yanqing Chen
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.Y.); (S.Y.); (H.W.); (W.F.); (Y.C.)
| | - Xiaoding Ma
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.Y.); (S.Y.); (H.W.); (W.F.); (Y.C.)
| | - Longzhi Han
- National Crop Genebank, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Wang Q, Cao K, Cheng L, Li Y, Guo J, Yang X, Wang J, Khan IA, Zhu G, Fang W, Chen C, Wang X, Wu J, Xu Q, Wang L. Multi-omics approaches identify a key gene, PpTST1, for organic acid accumulation in peach. HORTICULTURE RESEARCH 2022; 9:uhac026. [PMID: 35184194 PMCID: PMC9171119 DOI: 10.1093/hr/uhac026] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 12/25/2021] [Indexed: 06/14/2023]
Abstract
Organic acid content in fruit is an important determinant of peach organoleptic quality, which undergoes considerable variations during development and maturation. However, its molecular mechanism remains largely unclear. In this study, an integrative approach of genome-wide association studies and comparative transcriptome analysis were applied to identify candidate genes involved in organic acid accumulation in peach. A key gene PpTST1, encoding tonoplast sugar transporter, was identified and the genotype of PpTST1 with a single-base transversion (G1584T) in the third exon which leads to a single amino acid substitution (Q528H) was associated with low level of organic acid content in peach. Overexpression of PpTST1His resulted in reduced organic acid content along with increased sugar content both in peach and tomato fruits, suggesting its dual function in sugar accumulation and organic acid content reduction. Two V-type proton ATPases interact with PpTST1 in yeast two-hybridization assay. In addition, the G1584T transversion appeared and gradually accumulated during domestication and improvement, which indicated that PpTST1 was under selection. The identification and characterization of PpTST1 would facilitate the improvement of peach fruit quality.
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Affiliation(s)
- Qi Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
- College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Ke Cao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Lailiang Cheng
- Horticulture Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Yong Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Jian Guo
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Xuanwen Yang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Jiao Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Irshad Ahmad Khan
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Gengrui Zhu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Weichao Fang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Changwen Chen
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Xinwei Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Jinlong Wu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Qiang Xu
- College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Lirong Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
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Yu H, Shahid MQ, Li Q, Li Y, Li C, Lu Z, Wu J, Zhang Z, Liu X. Production Assessment and Genome Comparison Revealed High Yield Potential and Novel Specific Alleles Associated with Fertility and Yield in Neo-Tetraploid Rice. RICE (NEW YORK, N.Y.) 2020; 13:32. [PMID: 32494867 PMCID: PMC7271338 DOI: 10.1186/s12284-020-00387-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/28/2020] [Indexed: 05/07/2023]
Abstract
BACKGROUND Neo-tetraploid rice (NTR) is a new tetraploid rice germplasm that developed from the crossing and directional selection of different autotetraploid rice lines, which showed high fertility and promising yield potential. However, systematic yield assessment, genome composition and functional variations associated with fertility and yield remain elusive. RESULTS Two season's field trials of 15 NTRs and 27 autotetraploid rice (ATR) lines revealed that the improvement of YPP (yield per plant, 4.45 g increase) were significantly associated with the increase of SS (seed setting, 29.44% increase), and yield and seed setting of NTRs improved significantly compared to parental lines. Whole genome resequencing of 13 NTR sister lines and their parents at about 48.63 depth were conducted and genome compositions were illustrated using inherited chromosomal blocks. Interestingly, 222 non-parental genes were detected between NTRs and their low fertility parental lines, which were conserved in 13 NTRs. These genes were overlapped with yield and fertility QTLs, and RNA-Seq analysis revealed that 81 of them were enriched in reproductive tissues. CRISPR/Cas9 gene knockout was conducted for 9 non-parental genes to validate their function. Knockout mutants showed on an average 25.63% and 4.88 g decrease in SS and YPP, respectively. Notably, some mutants showed interesting phenotypes, e.g., kin7l (kinesin motor gene) and kin14m (kinesin motor gene), bzr3 (BES1/BZR1 homolog) and nrfg4 (neo-tetraploid rice fertility related gene) exhibited 44.65%, 24.30%, 24.42% and 28.33% decrease in SS and 8.81 g, 4.71 g, 5.90 g, 6.22 g reduction in YPP, respectively. CONCLUSION Comparative genomics provides insights into genome composition of neo-tetraploid rice and the genes associated with fertility and yield will play important role to reveal molecular mechanisms for the improvement of tetraploid rice.
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Affiliation(s)
- Hang Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
| | - Qihang Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
| | - Yudi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
| | - Cong Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
| | - Zijun Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
| | - Jinwen Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
| | - Zemin Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
| | - Xiangdong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642 China
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Melandri G, Sikirou M, Arbelaez JD, Shittu A, Semwal VK, Konaté KA, Maji AT, Ngaujah SA, Akintayo I, Govindaraj V, Shi Y, Agosto-Peréz FJ, Greenberg AJ, Atlin G, Ramaiah V, McCouch SR. Multiple Small-Effect Alleles of Indica Origin Enhance High Iron-Associated Stress Tolerance in Rice Under Field Conditions in West Africa. FRONTIERS IN PLANT SCIENCE 2020; 11:604938. [PMID: 33584748 PMCID: PMC7874229 DOI: 10.3389/fpls.2020.604938] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/15/2020] [Indexed: 05/03/2023]
Abstract
Understanding the genetics of field-based tolerance to high iron-associated (HIA) stress in rice can accelerate the development of new varieties with enhanced yield performance in West African lowland ecosystems. To date, few field-based studies have been undertaken to rigorously evaluate rice yield performance under HIA stress conditions. In this study, two NERICA × O. sativa bi-parental rice populations and one O.sativa diversity panel consisting of 296 rice accessions were evaluated for grain yield and leaf bronzing symptoms over multiple years in four West African HIA stress and control sites. Mapping of these traits identified a large number of QTLs and single nucleotide polymorphisms (SNPs) associated with stress tolerance in the field. Favorable alleles associated with tolerance to high levels of iron in anaerobic rice soils were rare and almost exclusively derived from the indica subpopulation, including the most favorable alleles identified in NERICA varieties. These findings highlight the complex genetic architecture underlying rice response to HIA stress and suggest that a recurrent selection program focusing on an expanded indica genepool could be productively used in combination with genomic selection to increase the efficiency of selection in breeding programs designed to enhance tolerance to this prevalent abiotic stress in West Africa.
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Affiliation(s)
- Giovanni Melandri
- Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
| | - Mouritala Sikirou
- Africa Rice Center, Ibadan, Nigeria
- School of Horticulture and Green Landscaping, Kétou, Bénin
| | - Juan D. Arbelaez
- Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
| | | | | | | | | | | | - Inoussa Akintayo
- Central Agricultural Research Institute, Suakoko, Liberia
- Africa Rice Center, Suakoko, Liberia
| | - Vishnu Govindaraj
- Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
| | - Yuxin Shi
- Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
| | | | | | - Gary Atlin
- Bill & Melinda Gates Foundation, Seattle, WA, United States
| | | | - Susan R. McCouch
- Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
- Venuprasad Ramaiah,
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Integrative transcriptome analysis discloses the molecular basis of a heterogeneous fungal phytopathogen complex, Rhizoctonia solani AG-1 subgroups. Sci Rep 2019; 9:19626. [PMID: 31873088 PMCID: PMC6928066 DOI: 10.1038/s41598-019-55734-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 11/26/2019] [Indexed: 02/06/2023] Open
Abstract
Rhizoctonia solani is a fungal species complex that causes necrotrophic crop diseases. It comprises several anastomosis groups, some of which include intra-subgroups, such as AG-1 IA and AG-1 IB, exhibiting varying pathogenicity. Owing to its heterozygous and multinucleate features, genomic analyses of R. solani are still challenging, and understanding of its genetic diversity and genic components is limited. In this study, in order to elucidate the molecular basis of this phytopathogen complex, an integrated transcriptome analysis was undertaken for three subgroups of AG-1, i.e. AG-1 IA, AG-1 IB, and AG-1 IC. Sequence variations suggested substantial evolutionary distances within AG-1. Transcript simple sequence repeats showed comparable characteristics among AG-1, but contained polymorphic sites. Intra-subgroup polymorphisms suggested varying genic heterozygosity within AG-1, suggesting their independent evolutionary trajectory. Sequences of pathogenic factors, phytotoxin biosynthesis pathway enzymes, secreted lignocellulosic enzymes, secreted reactive oxygen species detoxification enzymes, apoplastic/cytoplasmic effector candidates, were conserved among those subgroups. dN/dS ratios of a secretome subset suggested core secreted proteins in AG-1 and distinct evolution of Cys-rich small secreted proteins after differentiation of AG-1 subgroups. Identification of likely pathogenic factors including allergen protein homologues, oxidative phosphorylation and ethylene biosynthesis pathways, and diversification of polysaccharide monooxygenases provides molecular insight into key genomic components that play a role in R. solani pathogenesis.
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Rana N, Rahim MS, Kaur G, Bansal R, Kumawat S, Roy J, Deshmukh R, Sonah H, Sharma TR. Applications and challenges for efficient exploration of omics interventions for the enhancement of nutritional quality in rice (Oryza sativa L.). Crit Rev Food Sci Nutr 2019; 60:3304-3320. [DOI: 10.1080/10408398.2019.1685454] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Nitika Rana
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | | | - Gazaldeep Kaur
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Ruchi Bansal
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Surbhi Kumawat
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Joy Roy
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Humira Sonah
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Tilak Raj Sharma
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
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