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Liu C, Duan N, Chen X, Li X, Zhao N, Cao W, Li H, Liu B, Tan F, Zhao X, Li Q. Transcriptome Profiling and Chlorophyll Metabolic Pathway Analysis Reveal the Response of Nitraria tangutorum to Increased Nitrogen. PLANTS (BASEL, SWITZERLAND) 2023; 12:895. [PMID: 36840241 PMCID: PMC9962214 DOI: 10.3390/plants12040895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/04/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
To identify genes that respond to increased nitrogen and assess the involvement of the chlorophyll metabolic pathway and associated regulatory mechanisms in these responses, Nitraria tangutorum seedlings were subjected to four nitrogen concentrations (N0, N6, N36, and N60: 0, 6, 36, and 60 mmol·L-1 nitrogen, respectively). The N. tangutorum seedling leaf transcriptome was analyzed by high-throughput sequencing (Illumina HiSeq 4000), and 332,420 transcripts and 276,423 unigenes were identified. The numbers of differentially expressed genes (DEGs) were 4052 in N0 vs. N6, 6181 in N0 vs. N36, and 3937 in N0 vs. N60. Comparing N0 and N6, N0 and N36, and N0 and N60, we found 1101, 2222, and 1234 annotated DEGs in 113, 121, and 114 metabolic pathways, respectively, classified in the Kyoto Encyclopedia of Genes and Genomes database. Metabolic pathways with considerable accumulation were involved mainly in anthocyanin biosynthesis, carotenoid biosynthesis, porphyrin and chlorophyll metabolism, flavonoid biosynthesis, and amino acid metabolism. N36 increased δ-amino levulinic acid synthesis and upregulated expression of the magnesium chelatase H subunit, which promoted chlorophyll a synthesis. Hence, N36 stimulated chlorophyll synthesis rather than heme synthesis. These findings enrich our understanding of the N. tangutorum transcriptome and help us to research desert xerophytes' responses to increased nitrogen in the future.
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Affiliation(s)
- Chenggong Liu
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing 100091, China
| | - Na Duan
- Experimental Center of Desert Forestry, Chinese Academy of Forestry, Dengkou 015200, China
- National Long-Term Scientific Research Base of Ulan Buh Desert Comprehensive Control, National Forestry and Grassland Administration, Dengkou 015200, China
| | - Xiaona Chen
- Experimental Center of Desert Forestry, Chinese Academy of Forestry, Dengkou 015200, China
- National Long-Term Scientific Research Base of Ulan Buh Desert Comprehensive Control, National Forestry and Grassland Administration, Dengkou 015200, China
| | - Xu Li
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing 100091, China
| | - Naqi Zhao
- Experimental Center of Desert Forestry, Chinese Academy of Forestry, Dengkou 015200, China
- National Long-Term Scientific Research Base of Ulan Buh Desert Comprehensive Control, National Forestry and Grassland Administration, Dengkou 015200, China
| | - Wenxu Cao
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing 100091, China
| | - Huiqing Li
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing 100091, China
| | - Bo Liu
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing 100091, China
| | - Fengsen Tan
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing 100091, China
| | - Xiulian Zhao
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing 100091, China
| | - Qinghe Li
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing 100091, China
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Fu MJ, Wu HY, Jia DR, Tian B. Evolutionary history of a desert perennial Arnebia szechenyi (Boraginaceae): Intraspecific divergence, regional expansion and asymmetric gene flow. PLANT DIVERSITY 2021; 43:462-471. [PMID: 35024515 PMCID: PMC8720688 DOI: 10.1016/j.pld.2021.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 04/07/2021] [Accepted: 04/09/2021] [Indexed: 05/20/2023]
Abstract
The complex interactions of historical, geological and climatic events on plant evolution have been an important research focus for many years. However, the role of desert formation and expansion in shaping the genetic structures and demographic histories of plants occurring in arid areas has not been well explored. In the present study, we investigated the phylogeography of Arnebia szechenyi, a desert herb showing a near-circular distribution surrounding the Tengger Desert in Northwest China. We measured genetic diversity of populations using three maternally inherited chloroplast DNA (cpDNA) fragments and seven bi-paternally inherited nuclear DNA (nDNA) loci that were sequenced from individuals collected from 16 natural populations across its range and modelled current and historical potential habitats of the species. Our data indicated a considerably high level of genetic variation within A. szechenyi and noteworthy asymmetry in historical migration from the east to the west. Moreover, two nuclear genetic groups of populations were revealed, corresponding to the two geographic regions separated by the Tengger Desert. However, analysis of cpDNA data did not show significant geographic structure. The most plausible explanation for the discrepancy between our findings based on cpDNA and nDNA data is that A. szechenyi populations experienced long periods of geographic isolation followed by range expansion, which would have promoted generalized recombination of the nuclear genome. Our findings further highlight the important role that the Tengger Desert, together with the Helan Mountains, has played in the evolution of desert plants and the preservation of biodiversity in arid Northwest China.
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Affiliation(s)
- Meng-Jiao Fu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China
| | - Hai-Yang Wu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China
| | - Dong-Rui Jia
- School of Ecology and Environmental Science & Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, Yunnan University, Kunming 650091, China
- Corresponding author.
| | - Bin Tian
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China
- CAS Key Laboratory for Plant Diversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
- Corresponding author. Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China.
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Qian C, Yan X, Fang T, Yin X, Zhou S, Fan X, Chang Y, Ma XF. Genomic Adaptive Evolution of Sand Rice ( Agriophyllum squarrosum) and Its Implications for Desert Ecosystem Restoration. Front Genet 2021; 12:656061. [PMID: 33995487 PMCID: PMC8120313 DOI: 10.3389/fgene.2021.656061] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 04/08/2021] [Indexed: 01/13/2023] Open
Abstract
Natural selection is a significant driver of population divergence and speciation of plants. Due to local adaptation to geographic regions with ecological gradients, plant populations harbored a wide range of adaptive genetic variation to enable them to survive the heterogeneous habitats. This is all the more necessary for desert plants, as they must tolerant more striking gradients of abiotic stresses. However, the genomic mechanism by which desert plants adapt to ecological heterogeneity remains unclear, which could help to guide the sustainability of desert ecosystems. Here, using restriction-site-associated DNA sequencing in 38 natural populations, we investigated the genomic divergence and environmental adaptation of sand rice, Agriophyllum squarrosum, an annual pioneer species that covers sand dunes in northern China. Population genetic structure analyses showed that sand rice could be divided into three geographically distinct lineages, namely, Northwest, Central, and East. Phylogeographic analyses revealed that the plant might originate locally in Bergen County and further differentiated into the East lineage and then the Central lineage. Ecological niche modeling found that different lineages occupied distinct ecological niches, suggesting that the ecological gradient would have triggered genomic differentiation among sand rice lineages. Ecological association study supported that the three SNPs under divergent selection were closely correlated with precipitation gradients, indicating that precipitation might be the most important stress trigger for lineage diversity in sand rice. These adaptive SNPs could be used to genotype suitable germplasms for the ecological restoration of specific desertified lands. Further analyses found that genetic structure could significantly overestimate the signals for balancing selection. Within the Central lineage, we still found that 175 SNPs could be subject to balancing selection, which could be the means by which sand rice maintains genetic diversity and adapts to multiple stresses across heterogeneous deserts and sandy lands. From a genomic point of view, this study highlighted the local and global adaptation patterns of a desert plant to extreme and heterogeneous habitats. Our data provide molecular guidance for the restoration of desertified lands in the arid and semi-arid regions of China and could facilitate the marker assistant breeding of this potential crop to mitigate climate change.
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Affiliation(s)
- Chaoju Qian
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Xia Yan
- School of Life Sciences, Nantong University, Nantong, China
- Key Laboratory of Eco-hydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Tingzhou Fang
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoyue Yin
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Shanshan Zhou
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Xingke Fan
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yuxiao Chang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiao-Fei Ma
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- School of Life Sciences, Nantong University, Nantong, China
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