Genome-wide and pan-genomic analysis reveals rich variants of NBS-LRR genes in a newly developed wild rice line from Oryza alta Swallen
IntroductionOryza alta Swallen is an allotetraploid perennial wild rice and contains CCDD genome, which may harbor favorable genes for the enrichment of genetic resource.MethodsA new wild rice line, Huaye 5, was developed from Oryza alta Swallen in our lab. Whole genome re-sequencing and pan-genomic...
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Frontiers Media S.A.
2024-04-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2024.1345708/full |
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| author | Fimanekeni Ndaitavela Shivute Fimanekeni Ndaitavela Shivute Fimanekeni Ndaitavela Shivute Yi Zhong Yi Zhong Yi Zhong Jinwen Wu Jinwen Wu Jinwen Wu Yueming Bao Yueming Bao Yueming Bao Wei Wang Wei Wang Wei Wang Xiangdong Liu Xiangdong Liu Xiangdong Liu Zijun Lu Zijun Lu Zijun Lu Hang Yu |
| author_facet | Fimanekeni Ndaitavela Shivute Fimanekeni Ndaitavela Shivute Fimanekeni Ndaitavela Shivute Yi Zhong Yi Zhong Yi Zhong Jinwen Wu Jinwen Wu Jinwen Wu Yueming Bao Yueming Bao Yueming Bao Wei Wang Wei Wang Wei Wang Xiangdong Liu Xiangdong Liu Xiangdong Liu Zijun Lu Zijun Lu Zijun Lu Hang Yu |
| author_sort | Fimanekeni Ndaitavela Shivute |
| collection | DOAJ |
| description | IntroductionOryza alta Swallen is an allotetraploid perennial wild rice and contains CCDD genome, which may harbor favorable genes for the enrichment of genetic resource.MethodsA new wild rice line, Huaye 5, was developed from Oryza alta Swallen in our lab. Whole genome re-sequencing and pan-genomic analysis were employed to analyze its genomic variations and novel genes.Results and DiscussionMore than ten million genomic variations were detected when compared with Asian cultivar. Among the variational genes, 724, 197 and 710 genes coded protein kinase, synthetase and transcription factor, respectively. A total of 353, 131 and 135 variational genes were associated with morphological trait, physiological trait, resistance or tolerance, respectively. A total of 62 were NBS-LRR genes were detected, in which 11 NBS-LRR genes expressed in sheath and mature stem, and 26 expressed in young and mature roots expressed. The pan-genome sequences of wild rice species with CCDD genome were constructed by integrating 8 Oryza alta (OA), 2 Oryza grandiglumis (OG) and 18 Oryza latifolia (OL) accessions. A total of 28 non-reference NBS-LRR genes were revealed, and 7 of which were mainly expressed in mature roots. This research demonstrated rich DNA variation in the Oryza alta Swallen that may provide a new germplasm for rice resistance breeding. |
| first_indexed | 2024-04-24T12:30:41Z |
| format | Article |
| id | doaj.art-6a590ac4d0f242ee92a5ea984247e16a |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-24T12:30:41Z |
| publishDate | 2024-04-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Plant Science |
| spelling | doaj.art-6a590ac4d0f242ee92a5ea984247e16a2024-04-08T04:52:57ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2024-04-011510.3389/fpls.2024.13457081345708Genome-wide and pan-genomic analysis reveals rich variants of NBS-LRR genes in a newly developed wild rice line from Oryza alta SwallenFimanekeni Ndaitavela Shivute0Fimanekeni Ndaitavela Shivute1Fimanekeni Ndaitavela Shivute2Yi Zhong3Yi Zhong4Yi Zhong5Jinwen Wu6Jinwen Wu7Jinwen Wu8Yueming Bao9Yueming Bao10Yueming Bao11Wei Wang12Wei Wang13Wei Wang14Xiangdong Liu15Xiangdong Liu16Xiangdong Liu17Zijun Lu18Zijun Lu19Zijun Lu20Hang Yu21State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, ChinaGuangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, ChinaCollege of Agriculture, South China Agricultural University, Guangzhou, ChinaState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, ChinaGuangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, ChinaCollege of Agriculture, South China Agricultural University, Guangzhou, ChinaState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, ChinaGuangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, ChinaCollege of Agriculture, South China Agricultural University, Guangzhou, ChinaState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, ChinaGuangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, ChinaCollege of Agriculture, South China Agricultural University, Guangzhou, ChinaState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, ChinaGuangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, ChinaCollege of Agriculture, South China Agricultural University, Guangzhou, ChinaState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, ChinaGuangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, ChinaCollege of Agriculture, South China Agricultural University, Guangzhou, ChinaState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, ChinaGuangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, ChinaCollege of Agriculture, South China Agricultural University, Guangzhou, ChinaRice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, ChinaIntroductionOryza alta Swallen is an allotetraploid perennial wild rice and contains CCDD genome, which may harbor favorable genes for the enrichment of genetic resource.MethodsA new wild rice line, Huaye 5, was developed from Oryza alta Swallen in our lab. Whole genome re-sequencing and pan-genomic analysis were employed to analyze its genomic variations and novel genes.Results and DiscussionMore than ten million genomic variations were detected when compared with Asian cultivar. Among the variational genes, 724, 197 and 710 genes coded protein kinase, synthetase and transcription factor, respectively. A total of 353, 131 and 135 variational genes were associated with morphological trait, physiological trait, resistance or tolerance, respectively. A total of 62 were NBS-LRR genes were detected, in which 11 NBS-LRR genes expressed in sheath and mature stem, and 26 expressed in young and mature roots expressed. The pan-genome sequences of wild rice species with CCDD genome were constructed by integrating 8 Oryza alta (OA), 2 Oryza grandiglumis (OG) and 18 Oryza latifolia (OL) accessions. A total of 28 non-reference NBS-LRR genes were revealed, and 7 of which were mainly expressed in mature roots. This research demonstrated rich DNA variation in the Oryza alta Swallen that may provide a new germplasm for rice resistance breeding.https://www.frontiersin.org/articles/10.3389/fpls.2024.1345708/fullgermplasmwild riceOryza alta swallengenome sequencingpan-genome |
| spellingShingle | Fimanekeni Ndaitavela Shivute Fimanekeni Ndaitavela Shivute Fimanekeni Ndaitavela Shivute Yi Zhong Yi Zhong Yi Zhong Jinwen Wu Jinwen Wu Jinwen Wu Yueming Bao Yueming Bao Yueming Bao Wei Wang Wei Wang Wei Wang Xiangdong Liu Xiangdong Liu Xiangdong Liu Zijun Lu Zijun Lu Zijun Lu Hang Yu Genome-wide and pan-genomic analysis reveals rich variants of NBS-LRR genes in a newly developed wild rice line from Oryza alta Swallen Frontiers in Plant Science germplasm wild rice Oryza alta swallen genome sequencing pan-genome |
| title | Genome-wide and pan-genomic analysis reveals rich variants of NBS-LRR genes in a newly developed wild rice line from Oryza alta Swallen |
| title_full | Genome-wide and pan-genomic analysis reveals rich variants of NBS-LRR genes in a newly developed wild rice line from Oryza alta Swallen |
| title_fullStr | Genome-wide and pan-genomic analysis reveals rich variants of NBS-LRR genes in a newly developed wild rice line from Oryza alta Swallen |
| title_full_unstemmed | Genome-wide and pan-genomic analysis reveals rich variants of NBS-LRR genes in a newly developed wild rice line from Oryza alta Swallen |
| title_short | Genome-wide and pan-genomic analysis reveals rich variants of NBS-LRR genes in a newly developed wild rice line from Oryza alta Swallen |
| title_sort | genome wide and pan genomic analysis reveals rich variants of nbs lrr genes in a newly developed wild rice line from oryza alta swallen |
| topic | germplasm wild rice Oryza alta swallen genome sequencing pan-genome |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2024.1345708/full |
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