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Open AccessEditor’s ChoiceArticle

Oligo-FISH Can Identify Chromosomes and Distinguish Hippophaë rhamnoides L. Taxa

by Xiaomei Luo, Juncheng Liu and Zhoujian He

Genes 2022, 13(2), 195; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13020195 - 22 Jan 2022

Cited by 9 | Viewed by 2692

Oligo-fluorescence in situ hybridization (FISH) facilitates precise chromosome identification and comparative cytogenetic analysis. Detection of autosomal chromosomes of Hippophaë rhamnoides has not been achieved using oligonucleotide sequences. Here, the chromosomes of five H. rhamnoides taxa in the mitotic metaphase and mitotic metaphase to [...] Read more.

Oligo-fluorescence in situ hybridization (FISH) facilitates precise chromosome identification and comparative cytogenetic analysis. Detection of autosomal chromosomes of Hippophaë rhamnoides has not been achieved using oligonucleotide sequences. Here, the chromosomes of five H. rhamnoides taxa in the mitotic metaphase and mitotic metaphase to anaphase were detected using the oligo-FISH probes (AG₃T₃)₃, 5S rDNA, and (TTG)₆. In total, 24 small chromosomes were clearly observed in the mitotic metaphase (0.89–3.03 μm), whereas 24–48 small chromosomes were observed in the mitotic metaphase to anaphase (0.94–3.10 μm). The signal number and intensity of (AG₃T₃)₃, 5S rDNA, and (TTG)₆ in the mitotic metaphase to anaphase chromosomes were nearly consistent with those in the mitotic metaphase chromosomes when the two split chromosomes were integrated as one unit. Of note, 14 chromosomes (there is a high chance that sex chromosomes are included) were exclusively identified by (AG₃T₃)₃, 5S rDNA, and (TTG)₆. The other 10 also showed a terminal signal with (AG₃T₃)₃. Moreover, these oligo-probes were able to distinguish one wild H. rhamnoides taxon from four H. rhamnoides taxa. These chromosome identification and taxa differentiation data will help in elucidating visual and elaborate physical mapping and guide breeders’ utilization of wild resources of H. rhamnoides. Full article

(This article belongs to the Special Issue Tree Genetics and Improvement)

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15 pages, 2512 KiB

Open AccessArticle

Genetic Diversity and Population Structure Analysis of the USDA Olive Germplasm Using Genotyping-By-Sequencing (GBS)

by A. S. M. Faridul Islam, Dean Sanders, Amit Kumar Mishra and Vijay Joshi

Genes 2021, 12(12), 2007; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12122007 - 17 Dec 2021

Cited by 12 | Viewed by 3686

Abstract

Olives are one of the most important fruit and woody oil trees cultivated in many parts of the world. Olive oil is a critical component of the Mediterranean diet due to its importance in heart health. Olives are believed to have been brought [...] Read more.

Olives are one of the most important fruit and woody oil trees cultivated in many parts of the world. Olive oil is a critical component of the Mediterranean diet due to its importance in heart health. Olives are believed to have been brought to the United States from the Mediterranean countries in the 18th century. Despite the increase in demand and production areas, only a few selected olive varieties are grown in most traditional or new growing regions in the US. By understanding the genetic background, new sources of genetic diversity can be incorporated into the olive breeding programs to develop regionally adapted varieties for the US market. This study aimed to explore the genetic diversity and population structure of 90 olive accessions from the USDA repository along with six popular varieties using genotyping-by-sequencing (GBS)-generated SNP markers. After quality filtering, 54,075 SNP markers were retained for the genetic diversity analysis. The average gene diversity (GD) and polymorphic information content (PIC) values of the SNPs were 0.244 and 0.206, respectively, indicating a moderate genetic diversity for the US olive germplasm evaluated in this study. The structure analysis showed that the USDA collection was distributed across seven subpopulations; 63% of the accessions were grouped into an identifiable subpopulation. The phylogenetic and principal coordinate analysis (PCoA) showed that the subpopulations did not align with the geographical origins or climatic zones. An analysis of the molecular variance revealed that the major genetic variation sources were within populations. These findings provide critical information for future olive breeding programs to select genetically distant parents and facilitate future gene identification using genome-wide association studies (GWAS) or a marker-assisted selection (MAS) to develop varieties suited to production in the US. Full article

(This article belongs to the Special Issue Tree Genetics and Improvement)

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12 pages, 1953 KiB

Open AccessArticle

Cloning, Expression, and Tobacco Overexpression Analyses of a PISTILLATA/GLOBOSA-like (OfGLO1) Gene from Osmanthus fragrans

by Zhanghui Zeng, Si Chen, Mingrui Xu, Min Wang, Zhehao Chen, Lilin Wang and Jiliang Pang

Genes 2021, 12(11), 1748; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12111748 - 30 Oct 2021

Viewed by 1776

Abstract

GLOBOSA (GLO), a B-class MADS-box gene, is involved in floral organ determination but has rarely been studied in Osmanthus fragrans, which is a very popular ornamental tree species in China. Here, the full-length cDNA of a homologous GLO1 gene (named [...] Read more.

GLOBOSA (GLO), a B-class MADS-box gene, is involved in floral organ determination but has rarely been studied in Osmanthus fragrans, which is a very popular ornamental tree species in China. Here, the full-length cDNA of a homologous GLO1 gene (named OfGLO1) was cloned from a flower bud of O. fragrans using the RACE technique. The OfGLO1 has a 645 bp open reading frame, encoding 214 amino acids. Similar to other PI/GLO proteins, OfGLO1 has two conserved domains, MADS MEF2-like and K-box, and a 16-amino-acid PI motif in the C terminal region. Our phylogeny analysis classified OfGLO1 as a PI-type member of the B-class MADS-box gene family. The qRT-PCR assay showed that the expression of OfGLO1 in O. fragrans was continuously upregulated from the tight bud stage to the full flowering stage but barely expressed in the pistils, sepals, and non-floral organs, such as root, leaf, and stem. The genetic effect of OfGLO1 was assayed by ectopic expression in tobacco plants. Compared with the wild-type, OfGLO1 transformants showed reduced plant size, earlier flowering, shorter stamens, and lower seed setting rates. Furthermore, some stamens were changed into petal-like structures. These findings indicate that OfGLO1 plays an important role in the regulation of flower development. This study improved our understanding of class B gene function in woody plants. Full article

(This article belongs to the Special Issue Tree Genetics and Improvement)

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15 pages, 1122 KiB

Open AccessArticle

Genetic Dissection of Growth and Eco-Physiological Traits Associated with Altitudinal Adaptation in Sakhalin Fir (Abies sachalinensis) Based on QTL Mapping

by Susumu Goto, Hideki Mori, Kentaro Uchiyama, Wataru Ishizuka, Haruhiko Taneda, Masaru Kono, Hiromi Kajiya-Kanegae and Hiroyoshi Iwata

Genes 2021, 12(8), 1110; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12081110 - 22 Jul 2021

Cited by 2 | Viewed by 3696

Abstract

(1) Background: The genetic basis of local adaptation in conifers remains poorly understood because of limited research evidence and the lack of suitable genetic materials. Sakhalin fir (Abies sachalinensis) is an ideal organism for elucidating the genetic basis of local adaptation [...] Read more.

(1) Background: The genetic basis of local adaptation in conifers remains poorly understood because of limited research evidence and the lack of suitable genetic materials. Sakhalin fir (Abies sachalinensis) is an ideal organism for elucidating the genetic basis of local adaptation because its altitudinal adaptation has been demonstrated, and suitable materials for its linkage mapping are available. (2) Method: We constructed P336 and P236 linkage maps based on 486 and 516 single nucleotide polymorphisms, respectively, that were derived from double digest restriction site-associated DNA sequences. We measured the growth and eco-physiological traits associated with morphology, phenology, and photosynthesis, which are considered important drivers of altitudinal adaptation. (3) Results: The quantitative trait loci (QTLs) for growth traits, phenology, needle morphology, and photosynthetic traits were subsequently detected. Similar to previous studies on conifers, most traits were controlled by multiple QTLs with small or moderate effects. Notably, we detected that one QTL for the crown area might be a type-A response regulator, a nuclear protein responsible for the cytokinin-induced shoot elongation. (4) Conclusion: The QTLs detected in this study include potentially important genomic regions linked to altitudinal adaptation in Sakhalin fir. Full article

(This article belongs to the Special Issue Tree Genetics and Improvement)

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21 pages, 4119 KiB

Open AccessArticle

Phenotypic Variability and Genetic Diversity in a Pinus koraiensis Clonal Trial in Northeastern China

by David Kombi Kaviriri, Qinhui Zhang, Xinxin Zhang, Luping Jiang, Jinpeng Zhang, Jingyuan Wang, Damase P. Khasa, Xiangling You and Xiyang Zhao

Genes 2020, 11(6), 673; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11060673 - 19 Jun 2020

Cited by 12 | Viewed by 2735

Abstract

Combining phenotypic and genetic characteristics in a genetic variation study is of paramount importance to effectively orient the selection of producers’ elite trees in a seed orchard. In total, 28 phenotypic characteristics and 16 microsatellite loci were used to analyze the clonal genetic [...] Read more.

Combining phenotypic and genetic characteristics in a genetic variation study is of paramount importance to effectively orient the selection of producers’ elite trees in a seed orchard. In total, 28 phenotypic characteristics and 16 microsatellite loci were used to analyze the clonal genetic variation, to characterize the genetic diversity, and to refine the genetic classifications of 110 Pinus koraiensis clones grown in the Naozhi orchard in northeastern China. All clones were significantly different in most traits. Most of the phenotypic characteristics showed great genetic variation among clones, while the genotypic differentiation was weak between the selection sites of clones. The SSR markers showed a relatively high level of genetic diversity (Na = 4.67 ± 0.43, Ne = 2.916 ± 0.18, I = 1.15 ± 0.07, Ho = 0.69 ± 0.04, He = 0.62 ± 0.02, and mean polymorphic information content (PIC) of 0.574), with higher heterozygosity as an indication of a lower probability of inbreeding events in the orchard. Despite weak correlation coefficients between dissimilarity matrices (r(A/B), range equal to 0.022, p-value < 0.001), the genetic and phenotypic classifications congruently subdivided all the clones into three major groups. The patterns of phenotypic trait variations and genetic diversity are valuable to effectively select materials in breeding programs of P. koraiensis. Full article

(This article belongs to the Special Issue Tree Genetics and Improvement)

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16 pages, 2018 KiB

Open AccessArticle

Transcriptome Analysis of Genes Involved in Cold Hardiness of Peach Tree (Prunus persica) Shoots during Cold Acclimation and Deacclimation

by Duk Jun Yu, Sung Hoon Jun, Junhyung Park, Jung Hyun Kwon and Hee Jae Lee

Genes 2020, 11(6), 611; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11060611 - 01 Jun 2020

Cited by 9 | Viewed by 2514

Abstract

We analyzed the transcriptomes in the shoots of five-year-old ‘Soomee’ peach trees (Prunus persica) during cold acclimation (CA), from early CA (end of October) to late CA (middle of January), and deacclimation (DA), from late CA to late DA (middle of [...] Read more.

We analyzed the transcriptomes in the shoots of five-year-old ‘Soomee’ peach trees (Prunus persica) during cold acclimation (CA), from early CA (end of October) to late CA (middle of January), and deacclimation (DA), from late CA to late DA (middle of March), to identify the genes involved in cold hardiness. Cold hardiness of the shoots increased from early to late CA, but decreased from late CA to late DA, as indicated by decreased and increased the median lethal temperature (LT₅₀), respectively. Transcriptome analysis identified 17,208 assembled transcripts during all three stages. In total, 1891 and 3008 transcripts were differentially expressed with a |fold change| > 2 (p < 0.05) between early and late CA, and between late CA and late DA, respectively. Among them, 1522 and 2830, respectively, were functionally annotated with gene ontology (GO) terms having a greater proportion of differentially expressed genes (DEGs) associated with molecular function than biological process or cellular component categories. The biochemical pathways best represented both periods from early to late CA and from late CA to late DA were ‘metabolic pathway’ and ‘biosynthesis of secondary metabolites’. We validated these transcriptomic results by performing reverse transcription quantitative polymerase chain reaction on the selected DEGs showing significant fold changes. The relative expressions of the selected DEGs were closely related to the LT₅₀ values of the peach tree shoots: ‘Soomee’ shoots exhibited higher relative expressions of the selected DEGs than shoots of the less cold-hardy ‘Odoroki’ peach trees. Irrespective of the cultivar, the relative expressions of the DEGs that were up- and then down-regulated during CA, from early to late CA, and DA, from late CA to late DA, were more closely correlated with cold hardiness than those of the DEGs that were down- and then up-regulated. Therefore, our results suggest that the significantly up- and then down-regulated DEGs are associated with cold hardiness in peach tree shoots. These DEGs, including early light-induced protein 1, chloroplastic, 14-kDa proline-rich protein DC2.15, glutamate dehydrogenase 2, and triacylglycerol lipase 2, could be candidate genes to determine cold hardiness. Full article

(This article belongs to the Special Issue Tree Genetics and Improvement)

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16 pages, 2889 KiB

Open AccessArticle

The WUSCHELa (PtoWUSa) is Involved in Developmental Plasticity of Adventitious Root in Poplar

by Jianbo Li, Huixia Jia, Pei Sun, Jin Zhang, Yongxiu Xia, Jianjun Hu, Lijuan Wang and Mengzhu Lu

Genes 2020, 11(2), 176; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11020176 - 06 Feb 2020

Cited by 14 | Viewed by 3131

Abstract

WUSCHEL-RELATED HOMEOBOX (WOX) transcription factors play critical roles in cell fate determination during plant development. As the founding member of the WOX family, WUSCHEL (WUS) is characterized for its role in maintaining stem cell in meristem. In this study, [...] Read more.

WUSCHEL-RELATED HOMEOBOX (WOX) transcription factors play critical roles in cell fate determination during plant development. As the founding member of the WOX family, WUSCHEL (WUS) is characterized for its role in maintaining stem cell in meristem. In this study, we investigated the function of Populus tomentosa WUSCHELa (PtoWUSa) in adventitious roots (ARs) in poplar. Expression profile analysis showed that PtoWUSa was not only expressed in shoot apical meristem and stem, but also expressed in ARs. Ectopic expression of PtoWUSa in Arabidopsis resulted in shortened primary root, as well as agravitropism and multiple branches. Overexpression of PtoWUSa in poplar increased the number of ARs but decreased their length. Moreover, the AR tip and lateral root tip became larger and swollen. In addition, the expression of auxin transporter genes PIN-FORMED were downregulated in ARs of transgenic plant. Taken together, these results suggest that PtoWUSa could be involved in AR development in poplar through regulating the polar auxin transport in ARs. Full article

(This article belongs to the Special Issue Tree Genetics and Improvement)

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Review

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17 pages, 1700 KiB

Open AccessReview

Beyond Trees: Regulons and Regulatory Motif Characterization

by Xuhua Xia

Genes 2020, 11(9), 995; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11090995 - 25 Aug 2020

Cited by 2 | Viewed by 3679

Abstract

Trees and their seeds regulate their germination, growth, and reproduction in response to environmental stimuli. These stimuli, through signal transduction, trigger transcription factors that alter the expression of various genes leading to the unfolding of the genetic program. A regulon is conceptually defined [...] Read more.

Trees and their seeds regulate their germination, growth, and reproduction in response to environmental stimuli. These stimuli, through signal transduction, trigger transcription factors that alter the expression of various genes leading to the unfolding of the genetic program. A regulon is conceptually defined as a set of target genes regulated by a transcription factor by physically binding to regulatory motifs to accomplish a specific biological function, such as the CO-FT regulon for flowering timing and fall growth cessation in trees. Only with a clear characterization of regulatory motifs, can candidate target genes be experimentally validated, but motif characterization represents the weakest feature of regulon research, especially in tree genetics. I review here relevant experimental and bioinformatics approaches in characterizing transcription factors and their binding sites, outline problems in tree regulon research, and demonstrate how transcription factor databases can be effectively used to aid the characterization of tree regulons. Full article

(This article belongs to the Special Issue Tree Genetics and Improvement)

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