scholarly journals Composite plants for a composite plant: An efficient protocol for root studies in the sunflower using composite plants approach

2019 ◽  
Author(s):  
Tyler Parks ◽  
Yordan S. Yordanov
Keyword(s):  
Gene Families ◽  
Oilseed Crop ◽  
Transgenic Roots ◽  
Gene Characterization ◽  
Composite Plants ◽  
Functional Studies ◽  
Rate Limiting Step ◽  
Genome Wide ◽  
Related Transcription Factor ◽  
Sunflower Genome

AbstractSunflower (Helianthus annuus L.) is important oilseed crop in the world and the sunflower oil is prized for its’ exceptional quality and flavor. The recent availability of the sunflower genome can allow genome-wide characterization of genes and gene families. With plant transformation usually being the rate limiting step for gene functional studies of sunflower, composite plants can alleviate this bottleneck. Composite plants, produced using Agrobacterium rhizogenes, are plants with transgenic roots and wild type shoots. Composite plants offer benefits over creating fully transgenic plants, namely time and cost. Here we outlined the critical steps and parameters for a protocol for the sunflower composite plants production. We use more than a dozen genotypes and three constitutive promoters to validates the utility and efficiency of this protocol. Moreover, functional gene characterization by overexpression and RNAi silencing of a root related transcription factor HaLBD16 further emphasize the value of the system in the sunflower studies. With the protocol developed here an experiment can be carried out with efficiency and in only two months. This procedure adds to arsenal of approaches for the functional genetics/genomics in sunflower for characterization candidate genes involved in root development and stress adaptation.Key messageComposite plants technique described here is fast and efficient approach for roots functional studies in sunflower.

scholarly journals Phylogeny and Functions of LOB Domain Proteins in Plants

2020 ◽  
Vol 21 (7) ◽  
pp. 2278 ◽  
Author(s):  
Yuwen Zhang ◽  
Ziwen Li ◽  
Biao Ma ◽  
Quancan Hou ◽  
Xiangyuan Wan
Keyword(s):  
Functional Diversity ◽  
Family Members ◽  
Biological Significance ◽  
Gene Families ◽  
Plant Growth And Development ◽  
Functional Characteristics ◽  
Functional Studies ◽  
Genome Wide ◽  
Lateral Organ ◽  
Phylogenetic Framework

Lateral organ boundaries (LOB) domain (LBD) genes, a gene family encoding plant-specific transcription factors, play important roles in plant growth and development. At present, though there have been a number of genome-wide analyses on LBD gene families and functional studies on individual LBD proteins, the diverse functions of LBD family members still confuse researchers and an effective strategy is required to summarize their functional diversity. To further integrate and improve our understanding of the phylogenetic classification, functional characteristics and regulatory mechanisms of LBD proteins, we review and discuss the functional characteristics of LBD proteins according to their classifications under a phylogenetic framework. It is proved that this strategy is effective in the anatomy of diverse functions of LBD family members. Additionally, by phylogenetic analysis, one monocot-specific and one eudicot-specific subclade of LBD proteins were found and their biological significance in monocot and eudicot development were also discussed separately. The review will help us better understand the functional diversity of LBD proteins and facilitate further studies on this plant-specific transcription factor family.

scholarly journals Editing GWAS: experimental approaches to dissect and exploit disease-associated genetic variation

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Shuquan Rao ◽  
Yao Yao ◽  
Daniel E. Bauer
Keyword(s):  
Genome Editing ◽  
Genetic Variants ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Functional Studies ◽  
Functional Genetics ◽  
Genome Wide ◽  
Causal Variants ◽  
Experimental Approaches

AbstractGenome-wide association studies (GWAS) have uncovered thousands of genetic variants that influence risk for human diseases and traits. Yet understanding the mechanisms by which these genetic variants, mainly noncoding, have an impact on associated diseases and traits remains a significant hurdle. In this review, we discuss emerging experimental approaches that are being applied for functional studies of causal variants and translational advances from GWAS findings to disease prevention and treatment. We highlight the use of genome editing technologies in GWAS functional studies to modify genomic sequences, with proof-of-principle examples. We discuss the challenges in interrogating causal variants, points for consideration in experimental design and interpretation of GWAS locus mechanisms, and the potential for novel therapeutic opportunities. With the accumulation of knowledge of functional genetics, therapeutic genome editing based on GWAS discoveries will become increasingly feasible.

scholarly journals Genome-wide search and structural and functional analyses for late embryogenesis-abundant (LEA) gene family in poplar

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zihan Cheng ◽  
Xuemei Zhang ◽  
Wenjing Yao ◽  
Kai Zhao ◽  
Lin Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Higher Plants ◽  
Abiotic Stress Tolerance ◽  
Gene Families ◽  
Regulatory Elements ◽  
Late Embryogenesis Abundant ◽  
Genome Wide ◽  
Lea Gene ◽  
Late Embryogenesis ◽  
Genome Wide Search

Abstract Background The Late Embryogenesis-Abundant (LEA) gene families, which play significant roles in regulation of tolerance to abiotic stresses, widely exist in higher plants. Poplar is a tree species that has important ecological and economic values. But systematic studies on the gene family have not been reported yet in poplar. Results On the basis of genome-wide search, we identified 88 LEA genes from Populus trichocarpa and renamed them as PtrLEA. The PtrLEA genes have fewer introns, and their promoters contain more cis-regulatory elements related to abiotic stress tolerance. Our results from comparative genomics indicated that the PtrLEA genes are conserved and homologous to related genes in other species, such as Eucalyptus robusta, Solanum lycopersicum and Arabidopsis. Using RNA-Seq data collected from poplar under two conditions (with and without salt treatment), we detected 24, 22 and 19 differentially expressed genes (DEGs) in roots, stems and leaves, respectively. Then we performed spatiotemporal expression analysis of the four up-regulated DEGs shared by the tissues, constructed gene co-expression-based networks, and investigated gene function annotations. Conclusion Lines of evidence indicated that the PtrLEA genes play significant roles in poplar growth and development, as well as in responses to salt stress.

scholarly journals Genome wide association analyses to understand genetic basis of flowering and plant height under three levels of nitrogen application in Brassica juncea (L.) Czern & Coss

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Javed Akhatar ◽  
Anna Goyal ◽  
Navneet Kaur ◽  
Chhaya Atri ◽  
Meenakshi Mittal ◽  
...  
Keyword(s):  
Plant Height ◽  
Indian Subcontinent ◽  
Association Studies ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Strong Interactions ◽  
N Availability ◽  
Oilseed Crop ◽  
Genome Wide Association Studies ◽  
Genome Wide

AbstractTimely transition to flowering, maturity and plant height are important for agronomic adaptation and productivity of Indian mustard (B. juncea), which is a major edible oilseed crop of low input ecologies in Indian subcontinent. Breeding manipulation for these traits is difficult because of the involvement of multiple interacting genetic and environmental factors. Here, we report a genetic analysis of these traits using a population comprising 92 diverse genotypes of mustard. These genotypes were evaluated under deficient (N75), normal (N100) or excess (N125) conditions of nitrogen (N) application. Lower N availability induced early flowering and maturity in most genotypes, while high N conditions delayed both. A genotyping-by-sequencing approach helped to identify 406,888 SNP markers and undertake genome wide association studies (GWAS). 282 significant marker-trait associations (MTA's) were identified. We detected strong interactions between GWAS loci and nitrogen levels. Though some trait associated SNPs were detected repeatedly across fertility gradients, majority were identified under deficient or normal levels of N applications. Annotation of the genomic region (s) within ± 50 kb of the peak SNPs facilitated prediction of 30 candidate genes belonging to light perception, circadian, floral meristem identity, flowering regulation, gibberellic acid pathways and plant development. These included over one copy each of AGL24, AP1, FVE, FRI, GID1A and GNC. FLC and CO were predicted on chromosomes A02 and B08 respectively. CDF1, CO, FLC, AGL24, GNC and FAF2 appeared to influence the variation for plant height. Our findings may help in improving phenotypic plasticity of mustard across fertility gradients through marker-assisted breeding strategies.

scholarly journals Genome-Wide Identification and Characterization of Hsf and Hsp Gene Families and Gene Expression Analysis under Heat Stress in Eggplant (Solanum melongema L.)

Horticulturae ◽  
2021 ◽  
Vol 7 (6) ◽  
pp. 149
Author(s):  
Chao Gong ◽  
Qiangqiang Pang ◽  
Zhiliang Li ◽  
Zhenxing Li ◽  
Riyuan Chen ◽  
...  
Keyword(s):  
Heat Stress ◽  
Gene Families ◽  
High Temperature Stress ◽  
Pcr Analysis ◽  
Rna Seq ◽  
Genome Wide ◽  
Motif Composition ◽  
Hsp Genes ◽  
Identification And Characterization

Under high temperature stress, a large number of proteins in plant cells will be denatured and inactivated. Meanwhile Hsfs and Hsps will be quickly induced to remove denatured proteins, so as to avoid programmed cell death, thus enhancing the thermotolerance of plants. Here, a comprehensive identification and analysis of the Hsf and Hsp gene families in eggplant under heat stress was performed. A total of 24 Hsf-like genes and 117 Hsp-like genes were identified from the eggplant genome using the interolog from Arabidopsis. The gene structure and motif composition of Hsf and Hsp genes were relatively conserved in each subfamily in eggplant. RNA-seq data and qRT-PCR analysis showed that the expressions of most eggplant Hsf and Hsp genes were increased upon exposure to heat stress, especially in thermotolerant line. The comprehensive analysis indicated that different sets of SmHsps genes were involved downstream of particular SmHsfs genes. These results provided a basis for revealing the roles of SmHsps and SmHsp for thermotolerance in eggplant, which may potentially be useful for understanding the thermotolerance mechanism involving SmHsps and SmHsp in eggplant.

scholarly journals Genome-Wide Analysis of the Trihelix Gene Family and Their Response to Cold Stress in Dendrobium officinale

2021 ◽  
Vol 13 (5) ◽  
pp. 2826
Author(s):  
Yan Tong ◽  
Hui Huang ◽  
YuHua Wang
Keyword(s):  
Stress Responses ◽  
Cold Treatment ◽  
Dendrobium Officinale ◽  
Functional Domain ◽  
Cis Elements ◽  
Genome Wide Analysis ◽  
Functional Studies ◽  
Genome Wide ◽  
Growth Development ◽  
Chinese Medicinal Plant

Trihelix transcription factors play important roles in plant growth, development and various stress responses. In this study, we identified 32 trihelix family genes (DoGT) in the important Chinese medicinal plant Dendrobium officinale. These trihelix genes could be classified into five different subgroups. The gene structure and conserved functional domain of these trihelix genes were similar in the same subfamily but diverged between different subfamilies. Various stresses responsive cis-elements presented in the promoters of DoGT genes, suggesting that the trihelix genes might respond to the environmental stresses. Expressional changes of DoGT genes in three tissues and under cold treatment suggested that trihelix genes were involved in diverse functions during D. officinale development and cold tolerance. This study provides novel insights into the phylogenetic relationships and functions of the D. officinaletrihelix genes, which will aid future functional studies investigating the divergent roles of trihelix genes belonging to other species.

scholarly journals Genome-wide identification and expression profiling of thes MAPK, MAPKK, and MAPKKK gene families in Ophiocordyceps sinensis

Gene ◽  
2022 ◽  
Vol 807 ◽  
pp. 145930
Author(s):  
Pan Yue ◽  
Han Zhang ◽  
Xinxin Tong ◽  
Ting Peng ◽  
Pan Tang ◽  
...  
Keyword(s):  
Expression Profiling ◽  
Gene Families ◽  
Ophiocordyceps Sinensis ◽  
Genome Wide
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