Landscape genomics reveals genetic evidence of local adaptation in a widespread tree, the Chinese wingnut (<i>Pterocarya stenoptera</i>)

Li, Linfeng; Cushman, Samuel A.; He, Yong; Ma, Xiaofei; Ge, Xue‐Jun; Li, Jiaxin; Qian, Zhi-Hao; Li, Yong

doi:10.1111/jse.12699

Cited by 12 publications

(6 citation statements)

References 79 publications

(101 reference statements)

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“…To search candidate DAGs, we reanalyzed previously published data [20]. According to previous landscape genomics study, precipitations of the driest month (Bio14) and quarter (Bio17) were strongly associated with PC1 axis [20]. Therefore, the genes related to PC1 axis can be regarded as the candidate DAGs.…”

Section: Reanalysis Of the Results Of Landscape Genomicsmentioning

confidence: 99%

“…Compared with a large amount of DRGs introduced by transient drought stress, a small amount of DAGs was produced in the natural population under the longterm differential drought stress. A total of 14 candidate DAGs were obtained on the basis of the annotated results from the SNPs identified by LFMM analysis using KEGG database [20]. The most identified DAGs did not overlap with DRGs, and only three DAGs were DRGs.…”

Section: Discussionmentioning

confidence: 99%

“…To date, no published studies have reported the molecular adaptation mechanism in P. stenoptera under drought stress. The landscape genomics study on P. stenoptera, which provides insight into EAGs, has been recently conducted [20].…”

Section: Introductionmentioning

confidence: 99%

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Comparative analysis of drought-responsive and -adaptive genes in Chinese wingnut (Pterocarya stenoptera C. DC)

et al. 2021

BMC Genomics

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Background Drought is the main stress factor for the cultivation of Pterocarya stenoptera in urban areas, and this factor will cause its dehydration and affect its growth. Identifying drought-related genes will be useful for understanding the drought adaptation mechanism of P. stenoptera. Results We used physiological indicator detection, comparative transcriptome sequencing, and reanalysis on the results of previous landscape genomics studies to investigate the drought adaptation mechanism in P. stenoptera. The changes in malondialdehyde content showed that P. stenoptera was remarkably affected by drought stress, and the increase in soluble sugar content suggested its important role in response to drought stress. Results of comparative transcriptome sequencing showed that P. stenoptera initiated a series of programs, such as increasing the gene expression of unsaturated fatty acids, tyrosine, and plant pathogen resistance, to deal with the transient drought stress. According to the annotated results in a previous study, P. stenoptera adapts to the long-term differential drought stress by regulating the thickness of cell walls and expressing upper or lower limits of the downstream genes in the hormone signaling pathway. Through the comparative analysis of drought-responsive and -adaptive genes in P. stenoptera, this study supports the hypothesis that the environment-responsive genes (ERGs) introduced by the transient environmental stresses will be substantially more than the environment-adaptive genes (EAGs) in response to long-term differential environmental stresses, and the EAGs are not necessarily ERGs. Conclusions Our study identified drought-responsive and -adaptive genes in P. stenoptera and revealed that P. stenoptera increased the gene expression of unsaturated fatty acids, tyrosine, and plant pathogen resistance in response to transient drought stress. This study reveals the different adaptation mechanism of P. stenoptera under the transient and long-term differential drought stresses.

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Section: Reanalysis Of the Results Of Landscape Genomicsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Comparative analysis of drought-responsive and -adaptive genes in Chinese wingnut (Pterocarya stenoptera C. DC)

et al. 2021

BMC Genomics

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“…Recently, there have been several examples of studies that successfully explored the mechanisms of local adaptation in a few species. For example, the natural populations of Pterocarya stenoptera are strongly differentiated in genes related to temperature, water, and light adaptation [ 7 ]. In addition, in the natural populations of Corymbia calophylla, adaptive differentiation occurs in the genes of temperature and precipitation [ 8 ].…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic responses to drought stress among natural populations provide insights into local adaptation of weeping forsythia

Shi

Pei

et al. 2021

BMC Plant Biol

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Background Understanding the genetic mechanisms of local adaptation is an important emerging topic in molecular ecology and evolutionary biology. Results Here, we identify the physiological changes and differential expression of genes among different weeping forsythia populations under drought stress in common garden experiments. Physiological results showed that HBWZ might have higher drought tolerance among four populations. RNA-seq results showed that significant differential expression in the genes responding to the synthesis of flavonoids, aromatic substances, aromatic amino acids, oxidation–reduction process, and transmembrane transport occured among four populations. By further reanalysis of results of previous studies, sequence differentiation was found in the genes related to the synthesis of aromatic substances among different weeping forsythia populations. Conclusions Overall, our study supports the hypothesis that the dual differentiation in gene efficiency and expression increases among populations in response to heterogeneous environments and is an important evolutionary process of local adaptation. Here, we proposed a new working model of local adaptation of weeping forsythia populations under different intensities of drought stress, which provides new insights for understanding the genetic mechanisms of local adaptation for non-model species.

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“…张宏祥等: 新疆野苹果种群遗传结构及其环境适应性 1105 DOI: 10.17521/cjpe.2022.0024表3 基于LFMM分析识别并比对到栽培苹果参考基因组上的15个适应性位点许多其他温带树种空间遗传变异格局的主要环境因子 , 诸如 Quercus lobata 和枫杨 (Pterocarya stenoptera)等(Browne et al, 2019;Li et al, 2022)。迫时发挥重要作用(Guerrero-Sánchez et al, 2021);而 12-氧代植二烯酸还原酶则在西洋梨 (Pyrus www.plant-ecology.com…”

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Population genetic structure of <i>Malus sieversii </i>and environmental adaptations

ZHANG¹,

WEN²,

Wang³

2022

Chinese Journal of Plant Ecology

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Aims Malus sieversii, being listed as a national second-class protected plant in China, is recognized as one of the wild ancestors for domesticated apple. It is fragmentally distributed in arid mountains of the Central Asian. Here, we aimed to investigate the main environment variables shaping population genetic variations and the genetic adaptation in response to these environment variables for this species. MethodsWe collected ten M. sieversii populations from Yili Prefecture of China, Kazakhstan and Kyrgyzstan. Single nucleotide polymorphism (SNP) dataset was generated by SLAF-seq. Population genetic structure was inferred using the ADMIXTURE software and principal component analysis. Main environment variables shaping population genetic variations were assessed by gradient forest analysis and redundancy analysis. Tests of associated outlier loci with environmental variations were carried out by latent factor mixed models, which was used to access genetic signatures of local adaptation.Important findings Ten populations were clustered into two lineages. Lineage A dominated eastern populations, while Lineage B mainly distributed in western populations. Two lineages were mixed in central populations, and an obvious pattern of geographical substitute along the longitude direction was found. The most important environment variables that influence the change of allele frequency for M. sieversii populations were temperature annual range (bio 07) and temperature seasonality (bio 04). Fifteen loci having a significant association with environmental variables were successfully annotated. Most of them were genes related to abiotic stress responses and stress-induced physiological adaptations, such as drought, salt and cold. In conclusion, temperature variation is the main factor that drives the adaptation of M. sieversii to environments. Physiological adaptations, as

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Landscape genomics reveals genetic evidence of local adaptation in a widespread tree, the Chinese wingnut (Pterocarya stenoptera)

Cited by 12 publications

References 79 publications

Comparative analysis of drought-responsive and -adaptive genes in Chinese wingnut (Pterocarya stenoptera C. DC)

Comparative analysis of drought-responsive and -adaptive genes in Chinese wingnut (Pterocarya stenoptera C. DC)

Transcriptomic responses to drought stress among natural populations provide insights into local adaptation of weeping forsythia

Population genetic structure of <i>Malus sieversii </i>and environmental adaptations

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