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Genomics-Based Tree Breeding to Improve Resilience in the Face of Global Climate Change

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (30 September 2023) | Viewed by 14414

Special Issue Editor

Dr. Hengfu Yin

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Guest Editor
Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
Interests: tree genetics and genomics; genus Camellia; non-coding RNA; genome evolution; plant domestication
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The increasing uncertainty of global climate change can lead to harsh environments, such as sudden changes of temperature, outbreaks of pests and pathogens, and limited water supply, which represent a threat to the survival and growth of trees. To sustain the effective ecological and economic functions of tree plants, the current molecular breeding paradigm calls for an enhanced breeding strategy to build resilience in economically and ecologically important trees. Recent advances in DNA sequencing provide an opportunity to reveal the genomic basis of adaptations in trees, which can aid the process of breeding climate-resilient trees. This Special Issue aims to provide an avenue for sharing recent progress and ideas around research that addresses issues of genetic and genomic mechanisms underlying tree adaptations. The main scope includes but is not limited to large-scale population genomics research on trees, comparative genomics analysis of biotic or abiotic responses, identification and characterization of natural variations in various traits related to environmental responses, and other relevant studies toward climate resilience.

Dr. Hengfu Yin
Guest Editor

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Keywords

  • tree breeding
  • biotic and abiotic stress response
  • genome characterization
  • comparative genomics
  • large-scale genomics studies
  • genome-wide association study
  • gene expression analysis
  • genomics-assisted breeding
  • genome selection
  • tree biotechnology
  • gene functions

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Published Papers (6 papers)

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Research

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14 pages, 9029 KiB  
Article
A Pectate Lyase Gene Plays a Critical Role in Xylem Vascular Development in Arabidopsis
by Yun Bai, Dongdong Tian, Peng Chen, Dan Wu, Kebing Du, Bo Zheng and Xueping Shi
Int. J. Mol. Sci. 2023, 24(13), 10883; https://doi.org/10.3390/ijms241310883 - 29 Jun 2023
Cited by 5 | Viewed by 2018
Abstract
As a major component of the plant primary cell wall, structure changes in pectin may affect the formation of the secondary cell wall and lead to serious consequences on plant growth and development. Pectin-modifying enzymes including pectate lyase-like proteins (PLLs) participate in the [...] Read more.
As a major component of the plant primary cell wall, structure changes in pectin may affect the formation of the secondary cell wall and lead to serious consequences on plant growth and development. Pectin-modifying enzymes including pectate lyase-like proteins (PLLs) participate in the remodeling of pectin during organogenesis, especially during fruit ripening. In this study, we used Arabidopsis as a model system to identify critical PLL genes that are of particular importance for vascular development. Four PLL genes, named AtPLL15, AtPLL16, AtPLL19, and AtPLL26, were identified for xylem-specific expression. A knock-out T-DNA mutant of AtPLL16 displayed an increased amount of pectin, soluble sugar, and acid-soluble lignin (ASL). Interestingly, the atpll16 mutant exhibited an irregular xylem phenotype, accompanied by disordered xylem ray cells and an absence of interfascicular phloem fibers. The xylem fiber cell walls in the atpll16 mutant were thicker than those of the wild type. On the contrary, AtPLL16 overexpression resulted in expansion of the phloem and a dramatic change in the xylem-to-phloem ratios. Altogether, our data suggest that AtPLL16 as a pectate lyase plays an important role during vascular development in Arabidopsis. Full article
(This article belongs to the Special Issue Genomics-Based Tree Breeding to Improve Resilience in the Face of Global Climate Change)
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15 pages, 8494 KiB  
Article
PeGSTU58, a Glutathione S-Transferase from Populus euphratica, Enhances Salt and Drought Stress Tolerance in Transgenic Arabidopsis
by Huijing Meng, Jinna Zhao, Yanfei Yang, Kehao Diao, Guangshun Zheng, Tao Li, Xinren Dai and Jianbo Li
Int. J. Mol. Sci. 2023, 24(11), 9354; https://doi.org/10.3390/ijms24119354 - 27 May 2023
Cited by 13 | Viewed by 1969
Abstract
Glutathione S-transferases (GSTs) play a crucial role in responding to abiotic stress and are an important target for research on plant stress tolerance mechanisms. Populus euphratica is a promising candidate species for investigating the abiotic tolerance mechanisms in woody plants. In our previous [...] Read more.
Glutathione S-transferases (GSTs) play a crucial role in responding to abiotic stress and are an important target for research on plant stress tolerance mechanisms. Populus euphratica is a promising candidate species for investigating the abiotic tolerance mechanisms in woody plants. In our previous study, PeGSTU58 was identified as being associated with seed salinity tolerance. In the present study, PeGSTU58 was cloned from P. euphratica and functionally characterized. PeGSTU58 encodes a Tau class GST and is located in both the cytoplasm and nucleus. Transgenic Arabidopsis overexpressing PeGSTU58 displayed enhanced tolerance to salt and drought stress. Under salt and drought stress, the transgenic plants exhibited significantly higher activities of antioxidant enzymes, including SOD, POD, CAT, and GST, compared to the wild-type (WT) plants. Additionally, the expression levels of several stress-responsive genes, including DREB2A, COR47, RD22, CYP8D11, and SOD1 were upregulated in PeGSTU58 overexpression lines compared to those in WT Arabidopsis under salt and drought stress conditions. Furthermore, yeast one-hybrid assays and luciferase analysis showed that PebHLH35 can directly bind to the promoter region of PeGSTU58 and activate its expression. These results indicated that PeGSTU58 was involved in salt and drought stress tolerances by maintaining ROS homeostasis, and its expression was positively regulated by PebHLH35. Full article
(This article belongs to the Special Issue Genomics-Based Tree Breeding to Improve Resilience in the Face of Global Climate Change)
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17 pages, 4881 KiB  
Article
Genome-Wide Analysis of the Expansin Gene Family in Populus and Characterization of Expression Changes in Response to Phytohormone (Abscisic Acid) and Abiotic (Low-Temperature) Stresses
by Zhihui Yin, Fangwei Zhou, Yingnan Chen, Huaitong Wu and Tongming Yin
Int. J. Mol. Sci. 2023, 24(9), 7759; https://doi.org/10.3390/ijms24097759 - 24 Apr 2023
Cited by 11 | Viewed by 2896
Abstract
Expansins are a group of cell wall enzyme proteins that help to loosen cell walls by breaking hydrogen bonds between cellulose microfibrils and hemicellulose. Expansins are essential plant proteins that are involved in several key processes, including seed germination, the growth of pollen [...] Read more.
Expansins are a group of cell wall enzyme proteins that help to loosen cell walls by breaking hydrogen bonds between cellulose microfibrils and hemicellulose. Expansins are essential plant proteins that are involved in several key processes, including seed germination, the growth of pollen tubes and root hairs, fruit ripening and abscission processes. Currently, there is a lack of knowledge concerning the role of expansins in woody plants. In this study, we analyzed expansin genes using Populus genome as the study target. Thirty-six members of the expansin gene family were identified in Populus that were divided into four subfamilies (EXPA, EXPB, EXLA and EXLB). We analyzed the molecular structure, chromosome localization, evolutionary relationships and tissue specificity of these genes and investigated expression changes in responses to phytohormone and abiotic stresses of the expansin genes of Populus tremula L. (PtEXs). Molecular structure analysis revealed that each PtEX protein had several conserved motifs and all of the PtEXs genes had multiple exons. Chromosome structure analysis showed that the expansin gene family is distributed on 14 chromosomes. The PtEXs gene family expansion patterns showed segmental duplication. Transcriptome data of Populus revealed that 36 PtEXs genes were differently expressed in different tissues. Cis-element analysis showed that the PtEXs were closely associated with plant development and responses to phytohormone and abiotic stress. Quantitative real-time PCR showed that abscisic acid (ABA) and low-temperature treatment affected the expression of some PtEXs genes, suggesting that these genes are involved in responses to phytohormone and abiotic stress. This study provides a further understanding of the expansin gene family in Populus and forms a basis for future functional research studies. Full article
(This article belongs to the Special Issue Genomics-Based Tree Breeding to Improve Resilience in the Face of Global Climate Change)
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17 pages, 5602 KiB  
Article
Comprehensive Analysis of the INDETERMINATE DOMAIN (IDD) Gene Family and Their Response to Abiotic Stress in Zea mays
by Xue Feng, Qian Yu, Jianbin Zeng, Xiaoyan He, Wujun Ma, Lei Ge and Wenxing Liu
Int. J. Mol. Sci. 2023, 24(7), 6185; https://doi.org/10.3390/ijms24076185 - 24 Mar 2023
Cited by 5 | Viewed by 2583
Abstract
Transcription factors (TFs) are important regulators of numerous gene expressions due to their ability to recognize and combine cis-elements in the promoters of target genes. The INDETERMINATE DOMAIN (IDD) gene family belongs to a subfamily of C2H2 zinc finger proteins and has been [...] Read more.
Transcription factors (TFs) are important regulators of numerous gene expressions due to their ability to recognize and combine cis-elements in the promoters of target genes. The INDETERMINATE DOMAIN (IDD) gene family belongs to a subfamily of C2H2 zinc finger proteins and has been identified only in terrestrial plants. Nevertheless, little study has been reported concerning the genome-wide analysis of the IDD gene family in maize. In total, 22 ZmIDD genes were identified, which can be distributed on 8 chromosomes in maize. On the basis of evolutionary relationships and conserved motif analysis, ZmIDDs were categorized into three clades (1, 2, and 3), each owning 4, 6, and 12 genes, respectively. We analyzed the characteristics of gene structure and found that 3 of the 22 ZmIDD genes do not contain an intron. Cis-element analysis of the ZmIDD promoter showed that most ZmIDD genes possessed at least one ABRE or MBS cis-element, and some ZmIDD genes owned the AuxRR-core, TCA-element, TC-rich repeats, and LTR cis-element. The Ka:Ks ratio of eight segmentally duplicated gene pairs demonstrated that the ZmIDD gene families had undergone a purifying selection. Then, the transcription levels of ZmIDDs were analyzed, and they showed great differences in diverse tissues as well as abiotic stresses. Furthermore, regulatory networks were constructed through the prediction of ZmIDD-targeted genes and miRNAs, which can inhibit the transcription of ZmIDDs. In total, 6 ZmIDDs and 22 miRNAs were discovered, which can target 180 genes and depress the expression of 9 ZmIDDs, respectively. Taken together, the results give us valuable information for studying the function of ZmIDDs involved in plant development and climate resilience in maize. Full article
(This article belongs to the Special Issue Genomics-Based Tree Breeding to Improve Resilience in the Face of Global Climate Change)
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16 pages, 2855 KiB  
Article
Genome-Wide Identification of the CER Gene Family and Significant Features in Climate Adaptation of Castanea mollissima
by Shuqing Zhao, Xinghua Nie, Xueqing Liu, Biyao Wang, Song Liu, Ling Qin and Yu Xing
Int. J. Mol. Sci. 2022, 23(24), 16202; https://doi.org/10.3390/ijms232416202 - 19 Dec 2022
Cited by 4 | Viewed by 2097
Abstract
The plant cuticle is the outermost layer of the aerial organs and an important barrier against biotic and abiotic stresses. The climate varies greatly between the north and south of China, with large differences in temperature and humidity, but Chinese chestnut is found [...] Read more.
The plant cuticle is the outermost layer of the aerial organs and an important barrier against biotic and abiotic stresses. The climate varies greatly between the north and south of China, with large differences in temperature and humidity, but Chinese chestnut is found in both regions. This study investigated the relationship between the wax layer of chestnut leaves and environmental adaptation. Firstly, semi-thin sections were used to verify that there is a significant difference in the thickness of the epicuticular wax layer between wild chestnut leaves in northwest and southeast China. Secondly, a whole-genome selective sweep was used to resequence wild chestnut samples from two typical regional populations, and significant genetic divergence was identified between the two populations in the CmCER1-1, CmCER1-5 and CmCER3 genes. Thirty-four CER genes were identified in the whole chestnut genome, and a series of predictive analyses were performed on the identified CmCER genes. The expression patterns of CmCER genes were classified into three trends—upregulation, upregulation followed by downregulation and continuous downregulation—when chestnut seedlings were treated with drought stress. Analysis of cultivars from two resource beds in Beijing and Liyang showed that the wax layer of the northern variety was thicker than that of the southern variety. For the Y-2 (Castanea mollissima genome sequencing material) cultivar, there were significant differences in the expression of CmCER1-1, CmCER1-5 and CmCER3 between the southern variety and the northern one-year-grafted variety. Therefore, this study suggests that the CER family genes play a role in environmental adaptations in chestnut, laying the foundation for further exploration of CmCER genes. It also demonstrates the importance of studying the adaptation of Chinese chestnut wax biosynthesis to the southern and northern environments. Full article
(This article belongs to the Special Issue Genomics-Based Tree Breeding to Improve Resilience in the Face of Global Climate Change)
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Review

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15 pages, 1570 KiB  
Review
Molecular Mechanisms of Seasonal Gene Expression in Trees
by Xian Chu, Minyan Wang, Zhengqi Fan, Jiyuan Li and Hengfu Yin
Int. J. Mol. Sci. 2024, 25(3), 1666; https://doi.org/10.3390/ijms25031666 - 30 Jan 2024
Cited by 1 | Viewed by 2041
Abstract
In trees, the annual cycling of active and dormant states in buds is closely regulated by environmental factors, which are of primary significance to their productivity and survival. It has been found that the parallel or convergent evolution of molecular pathways that respond [...] Read more.
In trees, the annual cycling of active and dormant states in buds is closely regulated by environmental factors, which are of primary significance to their productivity and survival. It has been found that the parallel or convergent evolution of molecular pathways that respond to day length or temperature can lead to the establishment of conserved periodic gene expression patterns. In recent years, it has been shown in many woody plants that change in annual rhythmic patterns of gene expression may underpin the adaptive evolution in forest trees. In this review, we summarize the progress on the molecular mechanisms of seasonal regulation on the processes of shoot growth, bud dormancy, and bud break in response to day length and temperature factors. We focus on seasonal expression patterns of genes involved in dormancy and their associated epigenetic modifications; the seasonal changes in the extent of modifications, such as DNA methylation, histone acetylation, and histone methylation, at dormancy-associated loci have been revealed for their actions on gene regulation. In addition, we provide an outlook on the direction of research on the annual cycle of tree growth under climate change. Full article
(This article belongs to the Special Issue Genomics-Based Tree Breeding to Improve Resilience in the Face of Global Climate Change)
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