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Thummala SR, Guttikonda H, Tiwari S, Ramanan R, Baisakh N, Neelamraju S, Mangrauthia SK. Whole-Genome Sequencing of KMR3 and Oryza rufipogon-Derived Introgression Line IL50-13 (Chinsurah Nona 2/Gosaba 6) Identifies Candidate Genes for High Yield and Salinity Tolerance in Rice. Front Plant Sci 2022; 13:810373. [PMID: 35712577 PMCID: PMC9197125 DOI: 10.3389/fpls.2022.810373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 04/04/2022] [Indexed: 06/15/2023]
Abstract
The genomes of an elite rice restorer line KMR3 (salinity-sensitive) and its salinity-tolerant introgression line IL50-13, a popular variety of coastal West Bengal, India, were sequenced. High-quality paired-end reads were obtained for KMR3 (147.6 million) and IL50-13 (131.4 million) with a sequencing coverage of 30X-39X. Scaffolds generated from the pre-assembled contigs of each sequenced genome were mapped separately onto the reference genome of Oryza sativa ssp. japonica cultivar Nipponbare to identify genomic variants in terms of SNPs and InDels. The SNPs and InDels identified for KMR3 and IL50-13 were then compared with each other to identify polymorphic SNPs and InDels unique and common to both the genomes. Functional enrichment analysis of the protein-coding genes with unique InDels identified GO terms involved in protein modification, ubiquitination, deubiquitination, peroxidase activity, and antioxidant activity in IL50-13. Linoleic acid metabolism, circadian rhythm, and alpha-linolenic acid metabolism pathways were enriched in IL50-13. These GO terms and pathways are involved in reducing oxidative damage, thus suggesting their role in stress responses. Sequence analysis of QTL markers or genes known to be associated with grain yield and salinity tolerance showed polymorphism in 20 genes, out of which nine were not previously reported. These candidate genes encoded Nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4 (NB-ARC) domain-containing protein, cyclase, receptor-like kinase, topoisomerase II-associated protein PAT1 domain-containing protein, ion channel regulatory protein, UNC-93 domain-containing protein, subunit A of the heteromeric ATP-citrate lyase, and three conserved hypothetical genes. Polymorphism was observed in the coding, intron, and untranslated regions of the genes on chromosomes 1, 2, 4, 7, 11, and 12. Genes showing polymorphism between the two genomes were considered as sequence-based new candidates derived from Oryza rufipogon for conferring high yield and salinity tolerance in IL50-13 for further functional studies.
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Affiliation(s)
| | | | - Shrish Tiwari
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
| | | | - Niranjan Baisakh
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
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Sun Y, Zhang Y, Jia S, Lin C, Zhang J, Yan H, Peng B, Zhao L, Zhang W, Zhang C. Identification of a Candidate restorer-of-fertility Gene Rf3 Encoding a Pentatricopeptide Repeat Protein for the Cytoplasmic Male Sterility in Soybean. Int J Mol Sci 2022; 23:5388. [PMID: 35628200 PMCID: PMC9140608 DOI: 10.3390/ijms23105388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 12/04/2022] Open
Abstract
The cytoplasmic male sterility/restorer-of-fertility (CMS/Rf) system plays a vital role in high-efficiency hybrid seed production in crops, including soybean (Glycine max (L.) Merr.). The markers linked to fertility restoration and the restorer-of-fertility (Rf) genes are essential because they can facilitate the breeding of new CMS lines and production of commercial hybrid soybean seeds. To date, several soybean Rf genes have been mapped to various genetic loci in diverse genetic populations. However, the mapping range of restorer genes remains narrow, with relatively limited practical applicability. Therefore, in the present study, F2 and F3 segregating populations derived from the CMS line JLCMS5A crossed with the restorer line JLR2 were developed and used for Rf3 gene fine mapping. Genetic investigation indicated that the restorer line JLR2 was controlled by a single dominant gene, Rf3. By integrating bulk-segregant analysis and next-generation sequencing, a 4 Mb region on chromosome 9 was identified, which was most likely the target region harboring the candidate gene responsible for fertility restoration. This region was further narrowed down to 86.44 Kb via fine mapping in F2 and F3 populations using SSR, InDel, and dCAPS markers. This region contained 10 putative genes (Glyma.09G171100-Glyma.09G172000). Finally, Glyma.09G171200, which encodes a mitochondria-targeted pentatricopeptide repeat protein, was proposed as the potential candidate for Rf3 using sequence alignment and expression analysis in restorer and CMS lines. Based on single-nucleotide polymorphisms in Glyma.09G171200, a CAPS marker co-segregated with Rf3 named CAPS1712 was developed. Our results will be fundamental in the assisted selection and creation of potent lines for the production and rapid selection of novel restorer lines.
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Affiliation(s)
- Yanyan Sun
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 130033, China; (Y.S.); (Y.Z.); (S.J.); (C.L.); (J.Z.); (H.Y.); (B.P.); (L.Z.); (W.Z.)
- Key Laboratory of Hybrid Soybean Breeding of the Ministry of Agriculture and Rural Affairs, Changchun 130033, China
| | - Yan Zhang
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 130033, China; (Y.S.); (Y.Z.); (S.J.); (C.L.); (J.Z.); (H.Y.); (B.P.); (L.Z.); (W.Z.)
- Key Laboratory of Hybrid Soybean Breeding of the Ministry of Agriculture and Rural Affairs, Changchun 130033, China
| | - Shungeng Jia
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 130033, China; (Y.S.); (Y.Z.); (S.J.); (C.L.); (J.Z.); (H.Y.); (B.P.); (L.Z.); (W.Z.)
- Key Laboratory of Hybrid Soybean Breeding of the Ministry of Agriculture and Rural Affairs, Changchun 130033, China
| | - Chunjing Lin
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 130033, China; (Y.S.); (Y.Z.); (S.J.); (C.L.); (J.Z.); (H.Y.); (B.P.); (L.Z.); (W.Z.)
- Key Laboratory of Hybrid Soybean Breeding of the Ministry of Agriculture and Rural Affairs, Changchun 130033, China
| | - Jingyong Zhang
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 130033, China; (Y.S.); (Y.Z.); (S.J.); (C.L.); (J.Z.); (H.Y.); (B.P.); (L.Z.); (W.Z.)
- Key Laboratory of Hybrid Soybean Breeding of the Ministry of Agriculture and Rural Affairs, Changchun 130033, China
| | - Hao Yan
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 130033, China; (Y.S.); (Y.Z.); (S.J.); (C.L.); (J.Z.); (H.Y.); (B.P.); (L.Z.); (W.Z.)
- Key Laboratory of Hybrid Soybean Breeding of the Ministry of Agriculture and Rural Affairs, Changchun 130033, China
| | - Bao Peng
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 130033, China; (Y.S.); (Y.Z.); (S.J.); (C.L.); (J.Z.); (H.Y.); (B.P.); (L.Z.); (W.Z.)
- Key Laboratory of Hybrid Soybean Breeding of the Ministry of Agriculture and Rural Affairs, Changchun 130033, China
| | - Limei Zhao
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 130033, China; (Y.S.); (Y.Z.); (S.J.); (C.L.); (J.Z.); (H.Y.); (B.P.); (L.Z.); (W.Z.)
- Key Laboratory of Hybrid Soybean Breeding of the Ministry of Agriculture and Rural Affairs, Changchun 130033, China
| | - Wei Zhang
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 130033, China; (Y.S.); (Y.Z.); (S.J.); (C.L.); (J.Z.); (H.Y.); (B.P.); (L.Z.); (W.Z.)
- Key Laboratory of Hybrid Soybean Breeding of the Ministry of Agriculture and Rural Affairs, Changchun 130033, China
| | - Chunbao Zhang
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 130033, China; (Y.S.); (Y.Z.); (S.J.); (C.L.); (J.Z.); (H.Y.); (B.P.); (L.Z.); (W.Z.)
- Key Laboratory of Hybrid Soybean Breeding of the Ministry of Agriculture and Rural Affairs, Changchun 130033, China
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Ding G, Hu B, Zhou Y, Yang W, Zhao M, Xie J, Zhang F. Development and Characterization of Chromosome Segment Substitution Lines Derived from Oryza rufipogon in the Background of the Oryza sativa indica Restorer Line R974. Genes (Basel) 2022; 13:genes13050735. [PMID: 35627119 PMCID: PMC9140843 DOI: 10.3390/genes13050735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/12/2022] [Accepted: 04/19/2022] [Indexed: 12/04/2022] Open
Abstract
Dongxiang wild rice (DXWR) (O. rufipogon Griff.), which has the northernmost worldwide distribution of a wild rice species, is a valuable genetic resource with respect to improving stress tolerance in cultivated rice (Oryza sativa L.). In the three-line hybrid rice breeding system, restorer lines play important roles in enhancing the tolerance of hybrid rice. However, restorer lines have yet to be used as a genomic background for development of substitution lines carrying DXWR chromosome segments. We developed a set of 84 chromosome segment substitution lines (CSSLs) from a donor parent DXWR × recurrent parent restorer line R974 (Oryza sativa indica) cross. On average, each CSSL carried 6.27 introgressed homozygous segments, with 93.37% total genome coverage. Using these CSSLs, we identified a single QTL, qDYST-1, associated with salt stress tolerance on chromosome 3. Furthermore, five CSSLs showing strong salt stress tolerance were subjected to whole-genome single-nucleotide polymorphism chip analyses, during which we detected a common substitution segment containing qDYST-1 in all five CSSLs, thereby implying the validity and efficacy of qDYST-1. These novel CSSLs could make a significant contribution to detecting valuable DXWR QTLs, and provide important germplasm resources for breeding novel restorer lines for use in hybrid rice breeding systems.
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Affiliation(s)
- Gumu Ding
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; (G.D.); (Y.Z.); (M.Z.)
| | - Biaolin Hu
- Rice National Engineering Laboratory, Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330022, China;
| | - Yi Zhou
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; (G.D.); (Y.Z.); (M.Z.)
| | - Wanling Yang
- Jiangxi Provincial Key Laboratory of Protection and Utilization of Subtropical Plant Resources, Nanchang 330022, China;
| | - Minmin Zhao
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; (G.D.); (Y.Z.); (M.Z.)
| | - Jiankun Xie
- Jiangxi Provincial Key Laboratory of Protection and Utilization of Subtropical Plant Resources, Nanchang 330022, China;
- Correspondence: (J.X.); (F.Z.)
| | - Fantao Zhang
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; (G.D.); (Y.Z.); (M.Z.)
- Correspondence: (J.X.); (F.Z.)
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Shi J, Li D, Li Y, Li X, Guo X, Luo Y, Lu Y, Zhang Q, Xu Y, Fan J, Huang F, Wang W. Identification of rice blast resistance genes in the elite hybrid rice restorer line Yahui2115. Genome 2016; 58:91-7. [PMID: 26158382 DOI: 10.1139/gen-2015-0005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Rice blast, caused by the ascomycete fungus Magnaporthe oryzae, is one of the most serious rice diseases worldwide. We previously developed an elite hybrid rice restorer line with high resistance to rice blast, Yahui2115 (YH2115). To identify the blast resistance genes in YH2115, we first performed expression profiling on previously reported blast resistance genes and disease assay on monogenic lines, and we found that Pi2, Pi9, and Pikm were the most likely resistance candidates in YH2115. Furthermore, RNA interference and linkage analysis demonstrated that silencing of Pi2 reduced the blast resistance of YH2115 and a Pi2 linkage marker was closely associated with blast resistance in an F2 population generated from YH2115. These data suggest that the broad-spectrum blast resistance gene Pi2 contributes greatly to the blast resistance of YH2115. Thus, YH2115 could be used as a new germplasm to facilitate rice blast resistance breeding in hybrid rice breeding programs.
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Affiliation(s)
- Jun Shi
- a Department of Plant Pathology, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China.,b Mianyang Academy of Agricultural Sciences, Mianyang, Sichuan 621023, China.,c Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China.,d Provincial Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu 611130, China
| | - Deqiang Li
- a Department of Plant Pathology, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China.,d Provincial Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Li
- c Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China.,d Provincial Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoyan Li
- a Department of Plant Pathology, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China.,d Provincial Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoyi Guo
- c Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China.,d Provincial Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu 611130, China.,e Rice and Sorghum Institute, Sichuan Academy of Agricultural Sciences / Key Laboratory of Southwest Rice Biology and Genetic Breeding, Ministry of Agriculture, Deyang 618000, China
| | - Yiwan Luo
- a Department of Plant Pathology, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China.,d Provincial Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu 611130, China
| | - Yuangen Lu
- c Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China.,d Provincial Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu 611130, China
| | - Qin Zhang
- a Department of Plant Pathology, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China.,d Provincial Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu 611130, China
| | - Yongju Xu
- c Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China.,d Provincial Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu 611130, China
| | - Jing Fan
- c Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China.,d Provincial Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu 611130, China
| | - Fu Huang
- a Department of Plant Pathology, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China.,d Provincial Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu 611130, China
| | - Wenming Wang
- c Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China.,d Provincial Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu 611130, China
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