Chromosome-level genome assemblies of four wild peach species provide insights into genome evolution and genetic basis of stress resistance
Abstract Background Peach (Prunus persica) is an economically important stone fruit crop in Rosaceae and widely cultivated in temperate and subtropical regions, emerging as an excellent material to study the interaction between plant and environment. During its genus, there are four wild species of...
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| Format: | Article |
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BMC
2022-06-01
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| Series: | BMC Biology |
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| Online Access: | https://doi.org/10.1186/s12915-022-01342-y |
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| author | Ke Cao Zhen Peng Xing Zhao Yong Li Kuozhan Liu Pere Arus Weichao Fang Changwen Chen Xinwei Wang Jinlong Wu Zhangjun Fei Lirong Wang |
| author_facet | Ke Cao Zhen Peng Xing Zhao Yong Li Kuozhan Liu Pere Arus Weichao Fang Changwen Chen Xinwei Wang Jinlong Wu Zhangjun Fei Lirong Wang |
| author_sort | Ke Cao |
| collection | DOAJ |
| description | Abstract Background Peach (Prunus persica) is an economically important stone fruit crop in Rosaceae and widely cultivated in temperate and subtropical regions, emerging as an excellent material to study the interaction between plant and environment. During its genus, there are four wild species of peach, all living in harsh environments. For example, one of the wild species, P. mira, originates from the Qinghai-Tibet Plateau (QTP) and exhibits strong cold/ultraviolet ray environmental adaptations. Although remarkable progresses in the gene discovery of fruit quality-related traits in peach using previous assembled genome were obtained, genomic basis of the response of these wild species to different geographical environments remains unclear. Results To uncover key genes regulating adaptability in different species and analyze the role of genetic variations in resistance formation, we performed de novo genome assembling of four wild relatives of peach (P. persica), P. mira, P. davidiana, P. kansuensis, and P. ferganensis and resequenced 175 peach varieties. The phylogenetic tree showed that the divergence time of P. mira and other wild relatives of peach was 11.5 million years ago, which was consistent with the drastic crustal movement of QTP. Abundant genetic variations were identified in four wild species when compared to P. persica, and the results showed that plant-pathogen interaction pathways were enriched in genes containing small insertions and deletions and copy number variations in all four wild relatives of peach. Then, the data were used to identify new genes and variations regulating resistance. For example, presence/absence variations which result from a hybridization event that occurred between P. mira and P. dulcis enhanced the resistance of their putative hybrid, P. davidiana. Using bulked segregant analysis, we located the nematode resistance locus of P. kansuensis in chromosome 2. Within the mapping region, a deletion in the promoter of one NBS-LRR gene was found to involve the resistance by regulating gene expression. Furthermore, combined with RNA-seq and selective sweeps analysis, we proposed that a deletion in the promoter of one CBF gene was essential for high-altitude adaptation of P. mira through increasing its resistance to low temperature. Conclusions In general, the reference genomes assembled in the study facilitate our understanding of resistance mechanism of perennial fruit crops, and provide valuable resources for future breeding and improvement. |
| first_indexed | 2024-04-13T19:19:16Z |
| format | Article |
| id | doaj.art-8fc6715c42664eca8e8a832b77592363 |
| institution | Directory Open Access Journal |
| issn | 1741-7007 |
| language | English |
| last_indexed | 2024-04-13T19:19:16Z |
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| spelling | doaj.art-8fc6715c42664eca8e8a832b775923632022-12-22T02:33:36ZengBMCBMC Biology1741-70072022-06-0120111710.1186/s12915-022-01342-yChromosome-level genome assemblies of four wild peach species provide insights into genome evolution and genetic basis of stress resistanceKe Cao0Zhen Peng1Xing Zhao2Yong Li3Kuozhan Liu4Pere Arus5Weichao Fang6Changwen Chen7Xinwei Wang8Jinlong Wu9Zhangjun Fei10Lirong Wang11The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural SciencesNovogene Bioinformatics InstituteNovogene Bioinformatics InstituteThe Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural SciencesThe Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural SciencesIRTA, Centre de Recerca en Agrigenòmica, CSIC-IRTA-UAB-UB, Campus UAB – Edifici CRAG, Cerdanyola del Vallès (Bellaterra)The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural SciencesThe Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural SciencesThe Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural SciencesThe Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural SciencesBoyce Thompson Institute for Plant Research, Cornell UniversityThe Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural SciencesAbstract Background Peach (Prunus persica) is an economically important stone fruit crop in Rosaceae and widely cultivated in temperate and subtropical regions, emerging as an excellent material to study the interaction between plant and environment. During its genus, there are four wild species of peach, all living in harsh environments. For example, one of the wild species, P. mira, originates from the Qinghai-Tibet Plateau (QTP) and exhibits strong cold/ultraviolet ray environmental adaptations. Although remarkable progresses in the gene discovery of fruit quality-related traits in peach using previous assembled genome were obtained, genomic basis of the response of these wild species to different geographical environments remains unclear. Results To uncover key genes regulating adaptability in different species and analyze the role of genetic variations in resistance formation, we performed de novo genome assembling of four wild relatives of peach (P. persica), P. mira, P. davidiana, P. kansuensis, and P. ferganensis and resequenced 175 peach varieties. The phylogenetic tree showed that the divergence time of P. mira and other wild relatives of peach was 11.5 million years ago, which was consistent with the drastic crustal movement of QTP. Abundant genetic variations were identified in four wild species when compared to P. persica, and the results showed that plant-pathogen interaction pathways were enriched in genes containing small insertions and deletions and copy number variations in all four wild relatives of peach. Then, the data were used to identify new genes and variations regulating resistance. For example, presence/absence variations which result from a hybridization event that occurred between P. mira and P. dulcis enhanced the resistance of their putative hybrid, P. davidiana. Using bulked segregant analysis, we located the nematode resistance locus of P. kansuensis in chromosome 2. Within the mapping region, a deletion in the promoter of one NBS-LRR gene was found to involve the resistance by regulating gene expression. Furthermore, combined with RNA-seq and selective sweeps analysis, we proposed that a deletion in the promoter of one CBF gene was essential for high-altitude adaptation of P. mira through increasing its resistance to low temperature. Conclusions In general, the reference genomes assembled in the study facilitate our understanding of resistance mechanism of perennial fruit crops, and provide valuable resources for future breeding and improvement.https://doi.org/10.1186/s12915-022-01342-yComparative genomicsStress resistanceHigh-altitude adaptationPeach |
| spellingShingle | Ke Cao Zhen Peng Xing Zhao Yong Li Kuozhan Liu Pere Arus Weichao Fang Changwen Chen Xinwei Wang Jinlong Wu Zhangjun Fei Lirong Wang Chromosome-level genome assemblies of four wild peach species provide insights into genome evolution and genetic basis of stress resistance BMC Biology Comparative genomics Stress resistance High-altitude adaptation Peach |
| title | Chromosome-level genome assemblies of four wild peach species provide insights into genome evolution and genetic basis of stress resistance |
| title_full | Chromosome-level genome assemblies of four wild peach species provide insights into genome evolution and genetic basis of stress resistance |
| title_fullStr | Chromosome-level genome assemblies of four wild peach species provide insights into genome evolution and genetic basis of stress resistance |
| title_full_unstemmed | Chromosome-level genome assemblies of four wild peach species provide insights into genome evolution and genetic basis of stress resistance |
| title_short | Chromosome-level genome assemblies of four wild peach species provide insights into genome evolution and genetic basis of stress resistance |
| title_sort | chromosome level genome assemblies of four wild peach species provide insights into genome evolution and genetic basis of stress resistance |
| topic | Comparative genomics Stress resistance High-altitude adaptation Peach |
| url | https://doi.org/10.1186/s12915-022-01342-y |
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