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Hang Y, Yue L, Bingrui S, Qing L, Xingxue M, Liqun J, Shuwei L, Jing Z, Pingli C, Dajian P, Wenfeng C, Zhilan F, Chen L. Genetic Diversity and Breeding Signatures for Regional Indica Rice Improvement in Guangdong of Southern China. RICE (NEW YORK, N.Y.) 2023; 16:25. [PMID: 37191779 DOI: 10.1186/s12284-023-00642-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/14/2023] [Indexed: 05/17/2023]
Abstract
As the pioneer of the Green Revolution in China, Guangdong province witnessed the improvement and spread of semi-dwarf Xian/Indica rice cultivars and possessed diverse rice germplasm of landrace and cultivars. A total of 517 accessions containing a core germplasm of 479 newly sequenced landraces and modern cultivars were used to reveal breeding signatures and key variations for regional genetic improvement of indica rice from Guangdong. Four subpopulations were identified in the collection, which including Ind IV as a novel subpopulation that not covered by previously released accessions. Modern cultivars of subpopulation Ind II were inferred to have less deleterious variations, especially in yield related genes. About 15 Mb genomic segments were identified as potential breeding signatures by cross-population likelihood method (XP-CLR) of modern cultivars and landraces. The selected regions spanning multiple yield related QTLs (quantitative trait locus) which identified by GWAS (genome-wide association studies) of the same population, and specific variations that fixed in modern cultivars of Ind II were characterized. This study highlights genetic differences between traditional landraces and modern cultivars, which revealed the potential molecular basis of regional genetic improvement for Guangdong indica rice from southern China.
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Affiliation(s)
- Yu Hang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
- 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, Guangzhou, 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Liu Yue
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
- 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, Guangzhou, 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Sun Bingrui
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
- 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, Guangzhou, 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Liu Qing
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
- 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, Guangzhou, 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Mao Xingxue
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
- 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, Guangzhou, 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Jiang Liqun
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
- 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, Guangzhou, 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Lyu Shuwei
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
- 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, Guangzhou, 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Zhang Jing
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
- 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, Guangzhou, 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Chen Pingli
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
- 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, Guangzhou, 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Pan Dajian
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
- 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, Guangzhou, 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Chen Wenfeng
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
- 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, Guangzhou, 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Fan Zhilan
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
- 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, Guangzhou, 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Li Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
- 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, Guangzhou, 510640, China.
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China.
- Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China.
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Srikakulam N, Sridevi G, Pandi G. High-quality reference transcriptome construction improves RNA-seq quantification in Oryza sativa indica. Front Genet 2022; 13:995072. [PMID: 36246658 PMCID: PMC9558114 DOI: 10.3389/fgene.2022.995072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
Abstract
The Reference Transcriptomic Dataset (RTD) is an accurate and comprehensive collection of transcripts originating from a given organism. It holds the key to precise transcript quantification and downstream analysis of differential expressions and regulations. Currently, transcriptome annotations for most crop plants are far from complete. For example, Oryza sativa indica (O. sativa indica) is reported to have 40,759 transcripts in the Ensembl database without alternative transcript isoforms and alternative splicing (AS) events. To generate a high-quality RTD, we conducted RNA sequencing of rice leaf samples collected at various time points during Rhizoctonia solani infection. The obtained reads were analyzed by adopting the recently developed computational analysis pipeline to assemble the RTD with increased transcript and AS diversity for O. sativa indica (IndicaRTD). After stringent quality filtering, the newly constructed transcriptome annotation was comprised of 122,968 non-redundant transcripts from 53,695 genes. This study identified many novel transcripts compared to Ensembl deposited data that are important for regulating molecular and physiological processes in the plant system. Currently, the assembled IndicaRTD must allow fast quantification of transcript and gene expression with high precision.
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Affiliation(s)
- Nagesh Srikakulam
- Laboratory of RNA Biology and Epigenomics, Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, India
- *Correspondence: Nagesh Srikakulam, ; Gopal Pandi,
| | - Ganapathi Sridevi
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | - Gopal Pandi
- Laboratory of RNA Biology and Epigenomics, Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, India
- *Correspondence: Nagesh Srikakulam, ; Gopal Pandi,
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