Genetic Variation Analysis of Hsp101 Gene in Common Wild Rice and Asian Cultivated Rice Germplasm Resources
【Objective】The Hsp101 gene is a key gene that regulating rice heat tolerance, however, limited knowledge is available about its genetic variation and evolutionary patterns in rice germplasm resources. The study aims to investigate the genetic variation of the Hsp101 gene in common wild rice and Asia...
Saved in:
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Guangdong Academy of Agricultural Sciences
2024-11-01
|
| Series: | Guangdong nongye kexue |
| Subjects: | |
| Online Access: | http://gdnykx.cnjournals.org/gdnykx/ch/reader/view_abstract.aspx?file_no=202411004 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832595675045429248 |
|---|---|
| author | Yue LIU Liqun JIANG Shuwei LYU Bingrui SUN Chen LI Qing LIU Hang YU |
| author_facet | Yue LIU Liqun JIANG Shuwei LYU Bingrui SUN Chen LI Qing LIU Hang YU |
| author_sort | Yue LIU |
| collection | DOAJ |
| description | 【Objective】The Hsp101 gene is a key gene that regulating rice heat tolerance, however, limited knowledge is available about its genetic variation and evolutionary patterns in rice germplasm resources. The study aims to investigate the genetic variation of the Hsp101 gene in common wild rice and Asian cultivated rice, laying a foundation for the exploration of gene resources with excellent heat tolerance.【Methods】The rice germplasm resources of 3 325 genome sequencing data were obtained through retrieval and collation, and single nucleotide polymorphism (SNP) and small fragment insertion and deletion (InDel) variations were revealed by genome resequencing data analysis. Genetic diversity and gene variation haplotype analysis of the Hsp101 gene was conducted base on these genetic variations.【Results】A total of 471 genetic mutations were identified in the region of the Hsp101 gene, among which 94 non-synonymous variation sites resulted in amino acid coding changes. The analysis of genetic diversity and inter-population differentiation index showed that the genetic diversity of cultivated rice was significantly lower, and the genetic differentiation between common wild rice and Xian / Geng rice was obvious. Eight major haplotypes were identified, through haplotype analysis, with Hap1 being predominant in indica rice and Hap2 being predominant in japonica rice (7 haplotypes were found in common wild rice, except for Hap6). Further analyses including haplotype network analysis and phylogenetic analysis indicated that the wide rice haplotype Hap8 may be the oldest allele of the Hsp101 gene. In addition, three Xian or Geng rice specific variations were validated by using PCR amplification and Sanger sequencing. It was found that the specific variation of Hsp101 gene existed in Xian rice and Geng rice.【Conclusion】A total of 94 nonsynonymous variants and 8 major genetic variation haplotypes were identified in the Hsp101 gene. Hsp101 gene haplotypes of cultivated rice were evolved from those found in wild rice, and a lower degree of differentiation was observed between Xian and wild rice compared with Geng rice. It was speculated that the genetic differentiation time of Xian rice was earlier than that of Geng rice, and the genetic differences between Xian rice and Geng rice at the Hsp101 locus may be associated with the natural heat stress of their respective ecological environments. |
| format | Article |
| id | doaj-art-4369bfabecae41eea2b1a41590acd1dc |
| institution | Kabale University |
| issn | 1004-874X |
| language | English |
| publishDate | 2024-11-01 |
| publisher | Guangdong Academy of Agricultural Sciences |
| record_format | Article |
| series | Guangdong nongye kexue |
| spelling | doaj-art-4369bfabecae41eea2b1a41590acd1dc2025-01-18T06:57:00ZengGuangdong Academy of Agricultural SciencesGuangdong nongye kexue1004-874X2024-11-015111394710.16768/j.issn.1004-874X.2024.11.004202411004Genetic Variation Analysis of Hsp101 Gene in Common Wild Rice and Asian Cultivated Rice Germplasm ResourcesYue LIU0Liqun JIANG1Shuwei LYU2Bingrui SUN3Chen LI4Qing LIU5Hang YU6Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of Rice Science and Technology/Guangdong Rice Engineering Laboratory, Guangzhou 510640, ChinaRice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of Rice Science and Technology/Guangdong Rice Engineering Laboratory, Guangzhou 510640, ChinaRice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of Rice Science and Technology/Guangdong Rice Engineering Laboratory, Guangzhou 510640, ChinaRice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of Rice Science and Technology/Guangdong Rice Engineering Laboratory, Guangzhou 510640, ChinaRice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of Rice Science and Technology/Guangdong Rice Engineering Laboratory, Guangzhou 510640, ChinaRice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of Rice Science and Technology/Guangdong Rice Engineering Laboratory, Guangzhou 510640, ChinaRice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of Rice Science and Technology/Guangdong Rice Engineering Laboratory, Guangzhou 510640, China【Objective】The Hsp101 gene is a key gene that regulating rice heat tolerance, however, limited knowledge is available about its genetic variation and evolutionary patterns in rice germplasm resources. The study aims to investigate the genetic variation of the Hsp101 gene in common wild rice and Asian cultivated rice, laying a foundation for the exploration of gene resources with excellent heat tolerance.【Methods】The rice germplasm resources of 3 325 genome sequencing data were obtained through retrieval and collation, and single nucleotide polymorphism (SNP) and small fragment insertion and deletion (InDel) variations were revealed by genome resequencing data analysis. Genetic diversity and gene variation haplotype analysis of the Hsp101 gene was conducted base on these genetic variations.【Results】A total of 471 genetic mutations were identified in the region of the Hsp101 gene, among which 94 non-synonymous variation sites resulted in amino acid coding changes. The analysis of genetic diversity and inter-population differentiation index showed that the genetic diversity of cultivated rice was significantly lower, and the genetic differentiation between common wild rice and Xian / Geng rice was obvious. Eight major haplotypes were identified, through haplotype analysis, with Hap1 being predominant in indica rice and Hap2 being predominant in japonica rice (7 haplotypes were found in common wild rice, except for Hap6). Further analyses including haplotype network analysis and phylogenetic analysis indicated that the wide rice haplotype Hap8 may be the oldest allele of the Hsp101 gene. In addition, three Xian or Geng rice specific variations were validated by using PCR amplification and Sanger sequencing. It was found that the specific variation of Hsp101 gene existed in Xian rice and Geng rice.【Conclusion】A total of 94 nonsynonymous variants and 8 major genetic variation haplotypes were identified in the Hsp101 gene. Hsp101 gene haplotypes of cultivated rice were evolved from those found in wild rice, and a lower degree of differentiation was observed between Xian and wild rice compared with Geng rice. It was speculated that the genetic differentiation time of Xian rice was earlier than that of Geng rice, and the genetic differences between Xian rice and Geng rice at the Hsp101 locus may be associated with the natural heat stress of their respective ecological environments.http://gdnykx.cnjournals.org/gdnykx/ch/reader/view_abstract.aspx?file_no=202411004riceasian cultivated ricecommon wild ricehsp101 genegermplasm resourcegenetic diversity |
| spellingShingle | Yue LIU Liqun JIANG Shuwei LYU Bingrui SUN Chen LI Qing LIU Hang YU Genetic Variation Analysis of Hsp101 Gene in Common Wild Rice and Asian Cultivated Rice Germplasm Resources Guangdong nongye kexue rice asian cultivated rice common wild rice hsp101 gene germplasm resource genetic diversity |
| title | Genetic Variation Analysis of Hsp101 Gene in Common Wild Rice and Asian Cultivated Rice Germplasm Resources |
| title_full | Genetic Variation Analysis of Hsp101 Gene in Common Wild Rice and Asian Cultivated Rice Germplasm Resources |
| title_fullStr | Genetic Variation Analysis of Hsp101 Gene in Common Wild Rice and Asian Cultivated Rice Germplasm Resources |
| title_full_unstemmed | Genetic Variation Analysis of Hsp101 Gene in Common Wild Rice and Asian Cultivated Rice Germplasm Resources |
| title_short | Genetic Variation Analysis of Hsp101 Gene in Common Wild Rice and Asian Cultivated Rice Germplasm Resources |
| title_sort | genetic variation analysis of hsp101 gene in common wild rice and asian cultivated rice germplasm resources |
| topic | rice asian cultivated rice common wild rice hsp101 gene germplasm resource genetic diversity |
| url | http://gdnykx.cnjournals.org/gdnykx/ch/reader/view_abstract.aspx?file_no=202411004 |
| work_keys_str_mv | AT yueliu geneticvariationanalysisofhsp101geneincommonwildriceandasiancultivatedricegermplasmresources AT liqunjiang geneticvariationanalysisofhsp101geneincommonwildriceandasiancultivatedricegermplasmresources AT shuweilyu geneticvariationanalysisofhsp101geneincommonwildriceandasiancultivatedricegermplasmresources AT bingruisun geneticvariationanalysisofhsp101geneincommonwildriceandasiancultivatedricegermplasmresources AT chenli geneticvariationanalysisofhsp101geneincommonwildriceandasiancultivatedricegermplasmresources AT qingliu geneticvariationanalysisofhsp101geneincommonwildriceandasiancultivatedricegermplasmresources AT hangyu geneticvariationanalysisofhsp101geneincommonwildriceandasiancultivatedricegermplasmresources |