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Special Issue "Plant Genetics and Molecular Breeding"

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: 20 February 2019

Special Issue Editor

Guest Editor
Dr. Pedro Martínez-Gómez

CEBAS- CSIC, Centro de Edafología y Biología Aplicada del Segura, Department of Plant Breeding, Murcia, Spain
Website 1 | Website 2 | Website 3 | E-Mail
Phone: +34968396200
Interests: plant breeding approaches; marker assisted selection; evaluation of agronomical traits; integrating genetic, genomic, transcriptomic and proteomic approaches

Special Issue Information

Dear Colleagues,

The development of new plant varieties is a long and tedious process involving the generation of large seedling populations for the selection of the best individuals. While the ability of breeders to generate large populations is almost unlimited, the management, phenotyping (genetic studies) and selection of these seedlings are the main factors limiting the generation of new cultivars. Genomic (DNA) studies for the development of marker-assisted selection (MAS) strategies are particularly useful when the evaluation of the character is expensive, time-consuming or with long juvenile periods. More recently, proteomic (proteins and enzymes) and transcriptomic (RNA) studies have been used for the clarification of the mentioned genomic studies.

Papers submitted to this Special Issue must report high novelty results and/or plausible and testable new models for the integrative analysis of the different approaches applied to plant breeding including genetic (phenotyping and transmission of agronomic characters), genomic (DNA regions responsible for the different agronomic characters), proteomic (proteins and enzymes involved in the expression of the characters) and transcriptomic (gene expression analysis of the characters) approaches for the development of new MAS strategies. In addition, the application of massive sequencing methodologies ("deep-sequencing") of the genome (DNA-Seq) and transcriptome (RNA-Seq), based on lowering the costs of DNA sequencing, could be an additional interesting approach in this Special Issue.

Dr. Pedro Martínez-Gómez
Guest Editor

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • breeding
  • genetic
  • genomic
  • transcriptomic
  • proteomic
  • throughput analysis
  • assisted selection

Published Papers (28 papers)

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Research

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Open AccessArticle Importance of the Interaction between Heading Date Genes Hd1 and Ghd7 for Controlling Yield Traits in Rice
Int. J. Mol. Sci. 2019, 20(3), 516; https://doi.org/10.3390/ijms20030516
Received: 3 January 2019 / Revised: 20 January 2019 / Accepted: 23 January 2019 / Published: 26 January 2019
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Abstract
Appropriate flowering time is crucial for successful grain production, which relies on not only the action of individual heading date genes, but also the gene-by-gene interactions. In this study, influences of interaction between Hd1 and Ghd7 on flowering time and yield traits were [...] Read more.
Appropriate flowering time is crucial for successful grain production, which relies on not only the action of individual heading date genes, but also the gene-by-gene interactions. In this study, influences of interaction between Hd1 and Ghd7 on flowering time and yield traits were analyzed using near isogenic lines derived from a cross between indica rice cultivars ZS97 and MY46. In the non-functional ghd7ZS97 background, the functional Hd1ZS97 allele promoted flowering under both the natural short-day (NSD) conditions and natural long-day (NLD) conditions. In the functional Ghd7MY46 background, Hd1ZS97 remained to promote flowering under NSD conditions, but repressed flowering under NLD conditions. For Ghd7, the functional Ghd7MY46 allele repressed flowering under both conditions, which was enhanced in the functional Hd1ZS97 background under NLD conditions. With delayed flowering, spikelet number and grain weight increased under both conditions, but spikelet fertility and panicle number fluctuated. Rice lines carrying non-functional hd1MY46 and functional Ghd7MY46 alleles had the highest grain yield under both conditions. These results indicate that longer growth duration for a larger use of available temperature and light does not always result in higher grain production. An optimum heading date gene combination needs to be carefully selected for maximizing grain yield in rice. Full article
(This article belongs to the Special Issue Plant Genetics and Molecular Breeding)
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Open AccessArticle Expression of Maize MADS Transcription Factor ZmES22 Negatively Modulates Starch Accumulation in Rice Endosperm
Int. J. Mol. Sci. 2019, 20(3), 483; https://doi.org/10.3390/ijms20030483
Received: 31 December 2018 / Revised: 15 January 2019 / Accepted: 17 January 2019 / Published: 23 January 2019
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Abstract
As major component in cereals grains, starch has been one of the most important carbohydrate consumed by a majority of world’s population. However, the molecular mechanism for regulation of biosynthesis of starch remains elusive. In the present study, ZmES22, encoding a MADS-type [...] Read more.
As major component in cereals grains, starch has been one of the most important carbohydrate consumed by a majority of world’s population. However, the molecular mechanism for regulation of biosynthesis of starch remains elusive. In the present study, ZmES22, encoding a MADS-type transcription factor, was modestly characterized from maize inbred line B73. ZmES22 exhibited high expression level in endosperm at 10 days after pollination (DAP) and peaked in endosperm at 20 DAP, indicating that ZmES22 was preferentially expressed in maize endosperm during active starch synthesis. Transient expression of ZmES22 in tobacco leaf revealed that ZmES22 protein located in nucleus. No transactivation activity could be detected for ZmES22 protein via yeast one-hybrid assay. Transformation of overexpressing plasmid 35S::ZmES22 into rice remarkedly reduced 1000-grain weight as well as the total starch content, while the soluble sugar was significantly higher in transgenic rice lines. Moreover, overexpressing ZmES22 reduced fractions of long branched starch. Scanning electron microscopy images of transverse sections of rice grains revealed that altered expression of ZmES22 also changed the morphology of starch granule from densely packed, polyhedral starch granules into loosely packed, spherical granules with larger spaces. Furthermore, RNA-seq results indicated that overexpressing ZmES22 could significantly influence mRNA expression levels of numerous key regulatory genes in starch synthesis pathway. Y1H assay illustrated that ZmES22 protein could bind to the promoter region of OsGIF1 and downregulate its mRNA expression during rice grain filling stages. These findings suggest that ZmES22 was a novel regulator during starch synthesis process in rice endosperm. Full article
(This article belongs to the Special Issue Plant Genetics and Molecular Breeding)
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Open AccessArticle GmBRC1 is a Candidate Gene for Branching in Soybean (Glycine max (L.) Merrill)
Int. J. Mol. Sci. 2019, 20(1), 135; https://doi.org/10.3390/ijms20010135
Received: 15 November 2018 / Revised: 24 December 2018 / Accepted: 25 December 2018 / Published: 1 January 2019
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Abstract
Branch number is one of the main factors affecting the yield of soybean (Glycine max (L.)). In this study, we conducted a genome-wide association study combined with linkage analysis for the identification of a candidate gene controlling soybean branching. Five quantitative trait [...] Read more.
Branch number is one of the main factors affecting the yield of soybean (Glycine max (L.)). In this study, we conducted a genome-wide association study combined with linkage analysis for the identification of a candidate gene controlling soybean branching. Five quantitative trait nucleotides (QTNs) were associated with branch numbers in a soybean core collection. Among these QTNs, a linkage disequilibrium (LD) block qtnBR6-1 spanning 20 genes was found to overlap a previously identified major quantitative trait locus qBR6-1. To validate and narrow down qtnBR6-1, we developed a set of near-isogenic lines (NILs) harboring high-branching (HB) and low-branching (LB) alleles of qBR6-1, with 99.96% isogenicity and different branch numbers. A cluster of single nucleotide polymorphisms (SNPs) segregating between NIL-HB and NIL-LB was located within the qtnBR6-1 LD block. Among the five genes showing differential expression between NIL-HB and NIL-LB, BRANCHED1 (BRC1; Glyma.06G210600) was down-regulated in the shoot apex of NIL-HB, and one missense mutation and two SNPs upstream of BRC1 were associated with branch numbers in 59 additional soybean accessions. BRC1 encodes TEOSINTE-BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTORS 1 and 2 transcription factor and functions as a regulatory repressor of branching. On the basis of these results, we propose BRC1 as a candidate gene for branching in soybean. Full article
(This article belongs to the Special Issue Plant Genetics and Molecular Breeding)
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Open AccessArticle Expression Characteristics and Functional Analysis of the ScWRKY3 Gene from Sugarcane
Int. J. Mol. Sci. 2018, 19(12), 4059; https://doi.org/10.3390/ijms19124059
Received: 26 October 2018 / Revised: 10 December 2018 / Accepted: 11 December 2018 / Published: 14 December 2018
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Abstract
The plant-specific WRKY transcriptional regulatory factors have been proven to play vital roles in plant growth, development, and responses to biotic and abiotic stresses. However, there are few studies on the WRKY gene family in sugarcane (Saccharum spp.). In the present study, [...] Read more.
The plant-specific WRKY transcriptional regulatory factors have been proven to play vital roles in plant growth, development, and responses to biotic and abiotic stresses. However, there are few studies on the WRKY gene family in sugarcane (Saccharum spp.). In the present study, the characterization of a new subgroup, IIc WRKY protein ScWRKY3, from a Saccharum hybrid cultivar is reported. The ScWRKY3 protein was localized in the nucleus of Nicotiana benthamiana leaves and showed no transcriptional activation activity and no toxic effects on the yeast strain Y2HGold. An interaction between ScWRKY3 and a reported sugarcane protein ScWRKY4, was confirmed in the nucleus. The ScWRKY3 gene had the highest expression level in sugarcane stem pith. The transcript of ScWRKY3 was stable in the smut-resistant Saccharum hybrid cultivar Yacheng05-179, while it was down-regulated in the smut-susceptible Saccharum hybrid cultivar ROC22 during inoculation with the smut pathogen (Sporisorium scitamineum) at 0–72 h. ScWRKY3 was remarkably up-regulated by sodium chloride (NaCl), polyethylene glycol (PEG), and plant hormone abscisic acid (ABA), but it was down-regulated by salicylic acid (SA) and methyl jasmonate (MeJA). Moreover, transient overexpression of the ScWRKY3 gene in N. benthamiana indicated a negative regulation during challenges with the fungal pathogen Fusarium solani var. coeruleum or the bacterial pathogen Ralstonia solanacearum in N. benthamiana. The findings of the present study should accelerate future research on the identification and functional characterization of the WRKY family in sugarcane. Full article
(This article belongs to the Special Issue Plant Genetics and Molecular Breeding)
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Open AccessArticle RrGT2, A Key Gene Associated with Anthocyanin Biosynthesis in Rosa rugosa, Was Identified Via Virus-Induced Gene Silencing and Overexpression
Int. J. Mol. Sci. 2018, 19(12), 4057; https://doi.org/10.3390/ijms19124057
Received: 21 November 2018 / Revised: 6 December 2018 / Accepted: 12 December 2018 / Published: 14 December 2018
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Abstract
In this study, a gene with a full-length cDNA of 1422 bp encoding 473 amino acids, designated RrGT2, was isolated from R. rugosa ‘Zizhi’ and then functionally characterized. RrGT2 transcripts were detected in various tissues and were proved that their expression patterns [...] Read more.
In this study, a gene with a full-length cDNA of 1422 bp encoding 473 amino acids, designated RrGT2, was isolated from R. rugosa ‘Zizhi’ and then functionally characterized. RrGT2 transcripts were detected in various tissues and were proved that their expression patterns corresponded with anthocyanins accumulation. Functional verification of RrGT2 in R. rugosa was performed via VIGS. When RrGT2 was silenced, the Rosa plants displayed a pale petal color phenotype. The detection results showed that the expression of RrGT2 was significantly downregulated, which was consistent with the decrease of all anthocyanins; while the expression of six key upstream structural genes was normal. Additionally, the in vivo function of RrGT2 was investigated via its overexpression in tobacco. In transgenic tobacco plants expressing RrGT2, anthocyanin accumulation was induced in the flowers, indicating that RrGT2 could encode a functional GT protein for anthocyanin biosynthesis and could function in other species. The application of VIGS in transgenic tobacco resulted in the treated tobacco plants presenting flowers whose phenotypes were lighter in color than those of normal plants. These results also validated and affirmed previous conclusions. Therefore, we speculated that glycosylation of RrGT2 plays a crucial role in anthocyanin biosynthesis in R. rugosa. Full article
(This article belongs to the Special Issue Plant Genetics and Molecular Breeding)
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Open AccessArticle Transcriptome and Hormone Comparison of Three Cytoplasmic Male Sterile Systems in Brassica napus
Int. J. Mol. Sci. 2018, 19(12), 4022; https://doi.org/10.3390/ijms19124022
Received: 1 November 2018 / Revised: 7 December 2018 / Accepted: 11 December 2018 / Published: 12 December 2018
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Abstract
The interaction between plant mitochondria and the nucleus markedly influences stress responses and morphological features, including growth and development. An important example of this interaction is cytoplasmic male sterility (CMS), which results in plants producing non-functional pollen. In current research work, we compared [...] Read more.
The interaction between plant mitochondria and the nucleus markedly influences stress responses and morphological features, including growth and development. An important example of this interaction is cytoplasmic male sterility (CMS), which results in plants producing non-functional pollen. In current research work, we compared the phenotypic differences in floral buds of different Brassica napus CMS (Polima, Ogura, Nsa) lines with their corresponding maintainer lines. By comparing anther developmental stages between CMS and maintainer lines, we identified that in the Nsa CMS line abnormality occurred at the tetrad stage of pollen development. Phytohormone assays demonstrated that IAA content decreased in sterile lines as compared to maintainer lines, while the total hormone content was increased two-fold in the S2 stage compared with the S1 stage. ABA content was higher in the S1 stage and exhibited a two-fold decreasing trend in S2 stage. Sterile lines however, had increased ABA content at both stages compared with the corresponding maintainer lines. Through transcriptome sequencing, we compared differentially expressed unigenes in sterile and maintainer lines at both (S1 and S2) developmental stages. We also explored the co-expressed genes of the three sterile lines in the two stages and classified these genes by gene function. By analyzing transcriptome data and validating by RT-PCR, it was shown that some transcription factors (TFs) and hormone-related genes were weakly or not expressed in the sterile lines. This research work provides preliminary identification of the pollen abortion stage in Nsa CMS line. Our focus on genes specifically expressed in sterile lines may be useful to understand the regulation of CMS. Full article
(This article belongs to the Special Issue Plant Genetics and Molecular Breeding)
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Open AccessArticle OsGPAT3 Plays a Critical Role in Anther Wall Programmed Cell Death and Pollen Development in Rice
Int. J. Mol. Sci. 2018, 19(12), 4017; https://doi.org/10.3390/ijms19124017
Received: 13 November 2018 / Revised: 30 November 2018 / Accepted: 4 December 2018 / Published: 12 December 2018
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Abstract
In flowering plants, ideal male reproductive development requires the systematic coordination of various processes, in which timely differentiation and degradation of the anther wall, especially the tapetum, is essential for both pollen formation and anther dehiscence. Here, we show that OsGPAT3, a [...] Read more.
In flowering plants, ideal male reproductive development requires the systematic coordination of various processes, in which timely differentiation and degradation of the anther wall, especially the tapetum, is essential for both pollen formation and anther dehiscence. Here, we show that OsGPAT3, a conserved glycerol-3-phosphate acyltransferase gene, plays a critical role in regulating anther wall degradation and pollen exine formation. The gpat3-2 mutant had defective synthesis of Ubisch bodies, delayed programmed cell death (PCD) of the inner three anther layers, and abnormal degradation of micropores/pollen grains, resulting in failure of pollen maturation and complete male sterility. Complementation and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) experiments demonstrated that OsGPAT3 is responsible for the male sterility phenotype. Furthermore, the expression level of tapetal PCD-related and nutrient metabolism-related genes changed significantly in the gpat3-2 anthers. Based on these genetic and cytological analyses, OsGPAT3 is proposed to coordinate the differentiation and degradation of the anther wall and pollen grains in addition to regulating lipid biosynthesis. This study provides insights for understanding the function of GPATs in regulating rice male reproductive development, and also lays a theoretical basis for hybrid rice breeding. Full article
(This article belongs to the Special Issue Plant Genetics and Molecular Breeding)
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Open AccessArticle A Conserved Glycine Is Identified to be Essential for Desaturase Activity of IpFAD2s by Analyzing Natural Variants from Idesia polycarpa
Int. J. Mol. Sci. 2018, 19(12), 3932; https://doi.org/10.3390/ijms19123932
Received: 25 August 2018 / Revised: 2 December 2018 / Accepted: 5 December 2018 / Published: 7 December 2018
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Abstract
High amounts of polyunsaturated fatty acids (PUFAs) in vegetable oil are not desirable for biodiesel or food oil due to their lower oxidative stability. The oil from Idesia polycarpa fruit contains 65–80% (mol%) linoleic acid (C18:2). Therefore, development of Idesia polycarpa cultivars with [...] Read more.
High amounts of polyunsaturated fatty acids (PUFAs) in vegetable oil are not desirable for biodiesel or food oil due to their lower oxidative stability. The oil from Idesia polycarpa fruit contains 65–80% (mol%) linoleic acid (C18:2). Therefore, development of Idesia polycarpa cultivars with low PUFAs is highly desirable for Idesia polycarpa oil quality. Fatty acid desaturase 2 (FAD2) is the key enzyme converting oleic acid (C18:1) to C18:2. We isolated four FAD2 homologs from the fruit of Idesia polycarpa. Yeast transformed with IpFAD2-1, IpFAD2-2 and IpFAD2-3 can generate appreciable amounts of hexadecadienoic acid (C16:2) and C18:2, which are not present in wild-type yeast cells, revealing that the proteins encoded by these genes have Δ12 desaturase activity. Only trace amounts of C18:2 and little C16:2 were detected in yeast cells transformed with IpFAD2-4, suggesting IpFAD2-4 displays low activity. We also analyzed the activity of several FAD2 natural variants of Idesia polycarpa in yeast and found that a highly conserved Gly376 substitution caused the markedly reduced products catalyzed by IpFAD2-3. This glycine is also essential for the activity of IpFAD2-1 and IpFAD2-2, but its replacement in other plant FAD2 proteins displays different effects on the desaturase activity, suggesting its distinct roles across plant FAD2s proteins. Full article
(This article belongs to the Special Issue Plant Genetics and Molecular Breeding)
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Open AccessArticle Molecular Characterization and Overexpression of SmJMT Increases the Production of Phenolic Acids in Salvia miltiorrhiza
Int. J. Mol. Sci. 2018, 19(12), 3788; https://doi.org/10.3390/ijms19123788
Received: 13 October 2018 / Revised: 20 November 2018 / Accepted: 25 November 2018 / Published: 28 November 2018
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Abstract
Jasmonic acid (JA) carboxyl methyltransferase (JMT), a key enzyme in jasmonate-regulated plant responses, may be involved in plant defense and development by methylating JA to MeJA, thus influencing the concentrations of MeJA in plant. In this study, we isolated the JMT gene from [...] Read more.
Jasmonic acid (JA) carboxyl methyltransferase (JMT), a key enzyme in jasmonate-regulated plant responses, may be involved in plant defense and development by methylating JA to MeJA, thus influencing the concentrations of MeJA in plant. In this study, we isolated the JMT gene from Salvia miltiorrhiza, an important medicinal plant widely used to treat cardiovascular disease. We present a genetic manipulation strategy to enhance the production of phenolic acids by overexpresion SmJMT in S. miltiorrhiza. Global transcriptomic analysis using RNA sequencing showed that the expression levels of genes involved in the biosynthesis pathway of phenolic acids and MeJA were upregulated in the overexpression lines. In addition, the levels of endogenous MeJA, and the accumulation of rosmarinic acid (RA) and salvianolic acid (Sal B), as well as the concentrations of total phenolics and total flavonoids in transgenic lines, were significantly elevated compared with the untransformed control. Our results demonstrate that overexpression of SmJMT promotes the production of phenolic acids through simultaneously activating genes encoding key enzymes involved in the biosynthesis pathway of phenolic acids and enhancing the endogenous MeJA levels in S. miltiorrhiza. Full article
(This article belongs to the Special Issue Plant Genetics and Molecular Breeding)
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Open AccessArticle Identification, Classification, and Functional Analysis of AP2/ERF Family Genes in the Desert Moss Bryum argenteum
Int. J. Mol. Sci. 2018, 19(11), 3637; https://doi.org/10.3390/ijms19113637
Received: 8 October 2018 / Revised: 11 November 2018 / Accepted: 13 November 2018 / Published: 19 November 2018
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Abstract
Bryum argenteum is a desert moss which shows tolerance to the desert environment and is emerging as a good plant material for identification of stress-related genes. AP2/ERF transcription factor family plays important roles in plant responses to biotic and abiotic stresses. AP2/ERF genes [...] Read more.
Bryum argenteum is a desert moss which shows tolerance to the desert environment and is emerging as a good plant material for identification of stress-related genes. AP2/ERF transcription factor family plays important roles in plant responses to biotic and abiotic stresses. AP2/ERF genes have been identified and extensively studied in many plants, while they are rarely studied in moss. In the present study, we identified 83 AP2/ERF genes based on the comprehensive dehydrationrehydration transcriptomic atlas of B. argenteum. BaAP2/ERF genes can be classified into five families, including 11 AP2s, 43 DREBs, 26 ERFs, 1 RAV, and 2 Soloists. RNA-seq data showed that 83 BaAP2/ERFs exhibited elevated transcript abundances during dehydration–rehydration process. We used RT-qPCR to validate the expression profiles of 12 representative BaAP2/ERFs and confirmed the expression trends using RNA-seq data. Eight out of 12 BaAP2/ERFs demonstrated transactivation activities. Seven BaAP2/ERFs enhanced salt and osmotic stress tolerances of yeast. This is the first study to provide detailed information on the identification, classification, and functional analysis of the AP2/ERFs in B. argenteum. This study will lay the foundation for the further functional analysis of these genes in plants, as well as provide greater insights into the molecular mechanisms of abiotic stress tolerance of B. argenteum. Full article
(This article belongs to the Special Issue Plant Genetics and Molecular Breeding)
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Open AccessArticle DNA Methylation Analysis of Dormancy Release in Almond (Prunus dulcis) Flower Buds Using Epi-Genotyping by Sequencing
Int. J. Mol. Sci. 2018, 19(11), 3542; https://doi.org/10.3390/ijms19113542
Received: 24 September 2018 / Revised: 5 November 2018 / Accepted: 7 November 2018 / Published: 10 November 2018
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Abstract
DNA methylation and histone post-translational modifications have been described as epigenetic regulation mechanisms involved in developmental transitions in plants, including seasonal changes in fruit trees. In species like almond (Prunus dulcis (Mill.) D.A: Webb), prolonged exposure to cold temperatures is required for [...] Read more.
DNA methylation and histone post-translational modifications have been described as epigenetic regulation mechanisms involved in developmental transitions in plants, including seasonal changes in fruit trees. In species like almond (Prunus dulcis (Mill.) D.A: Webb), prolonged exposure to cold temperatures is required for dormancy release and flowering. Aiming to identify genomic regions with differential methylation states in response to chill accumulation, we carried out Illumina reduced-representation genome sequencing on bisulfite-treated DNA from floral buds. To do this, we analyzed almond genotypes with different chilling requirements and flowering times both before and after dormancy release for two consecutive years. The study was performed using epi-Genotyping by Sequencing (epi-GBS). A total of 7317 fragments were sequenced and the samples compared. Out of these fragments, 677 were identified as differentially methylated between the almond genotypes. Mapping these fragments using the Prunus persica (L.) Batsch v.2 genome as reference provided information about coding regions linked to early and late flowering methylation markers. Additionally, the methylation state of ten gene-coding sequences was found to be linked to the dormancy release process. Full article
(This article belongs to the Special Issue Plant Genetics and Molecular Breeding)
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Open AccessArticle Floral Scent Emission from Nectaries in the Adaxial Side of the Innermost and Middle Petals in Chimonanthus praecox
Int. J. Mol. Sci. 2018, 19(10), 3278; https://doi.org/10.3390/ijms19103278
Received: 10 September 2018 / Revised: 15 October 2018 / Accepted: 18 October 2018 / Published: 22 October 2018
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Abstract
Wintersweet (Chimonanthus praecox) is a well-known traditional fragrant plant and a winter-flowering deciduous shrub that originated in China. The five different developmental stages of wintersweet, namely, flower-bud period (FB), displayed petal stage (DP), open flower stage (OF), later blooming period (LB), [...] Read more.
Wintersweet (Chimonanthus praecox) is a well-known traditional fragrant plant and a winter-flowering deciduous shrub that originated in China. The five different developmental stages of wintersweet, namely, flower-bud period (FB), displayed petal stage (DP), open flower stage (OF), later blooming period (LB), and wilting period (WP) were studied using a scanning electron microscope (SEM) to determine the distribution characteristics of aroma-emitting nectaries. Results showed that the floral scent was probably emitted from nectaries distributed on the adaxial side of the innermost and middle petals, but almost none on the abaxial side. The nectaries in different developmental periods on the petals differ in numbers, sizes, and characteristics. Although the distribution of nectaries on different rounds of petals showed a diverse pattern at the same developmental periods, that of the nectaries on the same round of petals showed some of regularity. The nectary is concentrated on the adaxial side of the petals, especially in the region near the axis of the lower part of the petals. Based on transcriptional sequence and phylogenetic analysis, we report one nectary development related gene CpCRC (CRABS CLAW), and the other four YABBY family genes, CpFIL (FILAMENTOUS FLOWER), CpYABBY2, CpYABBY5-1, and CpYABBY5-2 in C. praecox (accession no. MH718960-MH718964). Quantitative RT-PCR (qRT-PCR) results showed that the expression characteristics of these YABBY family genes were similar to those of 11 floral scent genes, namely, CpSAMT, CpDMAPP, CpIPP, CpGPPS1, CpGPPS2, CpGPP, CpLIS, CpMYR1, CpFPPS, CpTER3, and CpTER5. The expression levels of these genes were generally higher in the lower part of the petals than in the upper halves in different rounds of petals, the highest being in the innermost petals, but the lowest in the outer petals. Relative expression level of CpFIL, CpCRC, CpYABBY5-1, and CpLIS in the innermost and middle petals in OF stages is significant higher than that of in outer petals, respectively. SEM and qRT-PCR results in C. praecox showed that floral scent emission is related to the distribution of nectaries. Full article
(This article belongs to the Special Issue Plant Genetics and Molecular Breeding)
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Open AccessArticle Effects of OsCDPK1 on the Structure and Physicochemical Properties of Starch in Developing Rice Seeds
Int. J. Mol. Sci. 2018, 19(10), 3247; https://doi.org/10.3390/ijms19103247
Received: 2 September 2018 / Revised: 7 October 2018 / Accepted: 16 October 2018 / Published: 19 October 2018
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Abstract
Overexpression of a constitutively active truncated form of OsCDPK1 (OEtr) in rice produced smaller seeds, but a double-stranded RNA gene-silenced form of OsCDPK1 (Ri) yielded larger seeds, suggesting that OsCDPK1 plays a functional role in rice seed development. In [...] Read more.
Overexpression of a constitutively active truncated form of OsCDPK1 (OEtr) in rice produced smaller seeds, but a double-stranded RNA gene-silenced form of OsCDPK1 (Ri) yielded larger seeds, suggesting that OsCDPK1 plays a functional role in rice seed development. In the study presented here, we propose a model in which OsCDPK1 plays key roles in negatively controlling the grain size, amylose content, and endosperm appearance, and also affects the physicochemical properties of the starch. The dehulled transgenic OEtr grains were smaller than the dehulled wild-type grains, and the OEtr endosperm was opaque and had a low amylose content and numerous small loosely packed polyhedral starch granules. However, the OEtr grain sizes and endosperm appearances were not affected by temperature, which ranged from low (22 °C) to high (31 °C) during the grain-filling phase. In contrast, the transgenic Ri grains were larger, had higher amylose content, and had more transparent endosperms filled with tightly packed polyhedral starch granules. This demonstrates that OsCDPK1 plays a novel functional role in starch biosynthesis during seed development and affects the transparent appearance of the endosperm. These results improve our understanding of the molecular mechanisms through which the grain-filling process occurs in rice. Full article
(This article belongs to the Special Issue Plant Genetics and Molecular Breeding)
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Open AccessArticle iTRAQ-Based Proteomic Analysis of Ogura-CMS Cabbage and Its Maintainer Line
Int. J. Mol. Sci. 2018, 19(10), 3180; https://doi.org/10.3390/ijms19103180
Received: 21 September 2018 / Revised: 8 October 2018 / Accepted: 8 October 2018 / Published: 15 October 2018
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Abstract
Ogura cytoplasmic male sterility (CMS) contributes considerably to hybrid seed production in Brassica crops. To detect the key protein species and pathways involved in Ogura-CMS, we analysed the proteome of the cabbage Ogura-CMS line CMS01-20 and its corresponding maintainer line F01-20 using the [...] Read more.
Ogura cytoplasmic male sterility (CMS) contributes considerably to hybrid seed production in Brassica crops. To detect the key protein species and pathways involved in Ogura-CMS, we analysed the proteome of the cabbage Ogura-CMS line CMS01-20 and its corresponding maintainer line F01-20 using the isobaric tags for the relative and absolute quantitation (iTRAQ) approach. In total, 162 differential abundance protein species (DAPs) were identified between the two lines, of which 92 were down-accumulated and 70 were up-accumulated in CMS01-20. For energy metabolism in the mitochondrion, eight DAPs involved in oxidative phosphorylation were down-accumulated in CMS01-20, whereas in the tricarboxylic acid (TCA) cycle, five DAPs were up-accumulated, which may compensate for the decreased respiration capacity and may be associated with the elevated O2 consumption rate in Ogura-CMS plants. Other key protein species and pathways involved in pollen wall assembly and programmed cell death (PCD) were also identified as being male-sterility related. Transcriptome profiling revealed 3247 differentially expressed genes between the CMS line and the fertile line. In a conjoint analysis of the proteome and transcriptome data, 30 and 9 protein species/genes showed the same and opposite accumulation patterns, respectively. Nine noteworthy genes involved in sporopollenin synthesis, callose wall degeneration, and oxidative phosphorylation were presumably associated with the processes leading to male sterility, and their expression levels were validated by qRT-PCR analysis. This study will improve our understanding of the protein species involved in pollen development and the molecular mechanisms underlying Ogura-CMS. Full article
(This article belongs to the Special Issue Plant Genetics and Molecular Breeding)
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Open AccessArticle Genome-Wide Association Study Reveals Novel Genomic Regions for Grain Yield and Yield-Related Traits in Drought-Stressed Synthetic Hexaploid Wheat
Int. J. Mol. Sci. 2018, 19(10), 3011; https://doi.org/10.3390/ijms19103011
Received: 20 August 2018 / Revised: 27 September 2018 / Accepted: 29 September 2018 / Published: 2 October 2018
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Abstract
Synthetic hexaploid wheat (SHW; 2n = 6x = 42, AABBDD, Triticum aestivum L.) is produced from an interspecific cross between durum wheat (2n = 4x = 28, AABB, T. turgidum L.) and goat grass (2n = 2x [...] Read more.
Synthetic hexaploid wheat (SHW; 2n = 6x = 42, AABBDD, Triticum aestivum L.) is produced from an interspecific cross between durum wheat (2n = 4x = 28, AABB, T. turgidum L.) and goat grass (2n = 2x = 14, DD, Aegilops tauschii Coss.) and is reported to have significant novel alleles-controlling biotic and abiotic stresses resistance. A genome-wide association study (GWAS) was conducted to unravel these loci [marker–trait associations (MTAs)] using 35,648 genotyping-by-sequencing-derived single nucleotide polymorphisms in 123 SHWs. We identified 90 novel MTAs (45, 11, and 34 on the A, B, and D genomes, respectively) and haplotype blocks associated with grain yield and yield-related traits including root traits under drought stress. The phenotypic variance explained by the MTAs ranged from 1.1% to 32.3%. Most of the MTAs (120 out of 194) identified were found in genes, and of these 45 MTAs were in genes annotated as having a potential role in drought stress. This result provides further evidence for the reliability of MTAs identified. The large number of MTAs (53) identified especially on the D-genome demonstrate the potential of SHWs for elucidating the genetic architecture of complex traits and provide an opportunity for further improvement of wheat under rapidly changing climatic conditions. Full article
(This article belongs to the Special Issue Plant Genetics and Molecular Breeding)
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Open AccessArticle Differentially Expressed Genes Associated with the Cabbage Yellow-Green-Leaf Mutant in the ygl-1 Mapping Interval with Recombination Suppression
Int. J. Mol. Sci. 2018, 19(10), 2936; https://doi.org/10.3390/ijms19102936
Received: 12 August 2018 / Revised: 7 September 2018 / Accepted: 20 September 2018 / Published: 27 September 2018
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Abstract
Although the genetics and preliminary mapping of the cabbage yellow-green-leaf mutant YL-1 has been extensively studied, transcriptome profiling associated with the yellow-green-leaf mutant of YL-1 has not been discovered. Positional mapping with two populations showed that the yellow-green-leaf gene ygl-1 is located in [...] Read more.
Although the genetics and preliminary mapping of the cabbage yellow-green-leaf mutant YL-1 has been extensively studied, transcriptome profiling associated with the yellow-green-leaf mutant of YL-1 has not been discovered. Positional mapping with two populations showed that the yellow-green-leaf gene ygl-1 is located in a recombination-suppressed genomic region. Then, a bulk segregant RNA-seq (BSR) was applied to identify differentially expressed genes (DEGs) using an F3 population (YL-1 × 11-192) and a BC2 population (YL-1 × 01-20). Among the 37,286 unique genes, 5730 and 4118 DEGs were detected between the yellow-leaf and normal-leaf pools from the F3 and BC2 populations. BSR analysis with four pools greatly reduced the number of common DEGs from 4924 to 1112. In the ygl-1 gene mapping region with suppressed recombination, 43 common DEGs were identified. Five of the DEGs were related to chloroplasts, including the down-regulated Bo1g087310, Bo1g094360, and Bo1g098630 and the up-regulated Bo1g059170 and Bo1g098440. The Bo1g098440 and Bo1g098630 genes were excluded by qRT-PCR. Hence, we inferred that these three DEGs (Bo1g094360, Bo1g087310, and Bo1g059170) in the mapping interval may be tightly associated with the development of the yellow-green-leaf mutant phenotype. Full article
(This article belongs to the Special Issue Plant Genetics and Molecular Breeding)
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Open AccessArticle Genome-Wide Association Studies of 39 Seed Yield-Related Traits in Sesame (Sesamum indicum L.)
Int. J. Mol. Sci. 2018, 19(9), 2794; https://doi.org/10.3390/ijms19092794
Received: 23 August 2018 / Revised: 7 September 2018 / Accepted: 13 September 2018 / Published: 17 September 2018
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Abstract
Sesame is poised to become a major oilseed crop owing to its high oil quality and adaptation to various ecological areas. However, the seed yield of sesame is very low and the underlying genetic basis is still elusive. Here, we performed genome-wide association [...] Read more.
Sesame is poised to become a major oilseed crop owing to its high oil quality and adaptation to various ecological areas. However, the seed yield of sesame is very low and the underlying genetic basis is still elusive. Here, we performed genome-wide association studies of 39 seed yield-related traits categorized into five major trait groups, in three different environments, using 705 diverse lines. Extensive variation was observed for the traits with capsule size, capsule number and seed size-related traits, found to be highly correlated with seed yield indexes. In total, 646 loci were significantly associated with the 39 traits (p < 10−7) and resolved to 547 quantitative trait loci QTLs. We identified six multi-environment QTLs and 76 pleiotropic QTLs associated with two to five different traits. By analyzing the candidate genes for the assayed traits, we retrieved 48 potential genes containing significant functional loci. Several homologs of these candidate genes in Arabidopsis are described to be involved in seed or biomass formation. However, we also identified novel candidate genes, such as SiLPT3 and SiACS8, which may control capsule length and capsule number traits. Altogether, we provided the highly-anticipated basis for research on genetics and functional genomics towards seed yield improvement in sesame. Full article
(This article belongs to the Special Issue Plant Genetics and Molecular Breeding)
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Open AccessArticle Normal and Abortive Buds Transcriptomic Profiling of Broccoli ogu Cytoplasmic Male Sterile Line and Its Maintainer
Int. J. Mol. Sci. 2018, 19(9), 2501; https://doi.org/10.3390/ijms19092501
Received: 30 June 2018 / Revised: 12 August 2018 / Accepted: 14 August 2018 / Published: 24 August 2018
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Abstract
Bud abortion is the main factor affecting hybrid seeds’ yield during broccoli cross breeding when using ogura cytoplasmic male sterile (ogu CMS) lines. However, the genes associated with bud abortion are poorly understood. We applied RNA sequencing to analyze the transcriptomes of [...] Read more.
Bud abortion is the main factor affecting hybrid seeds’ yield during broccoli cross breeding when using ogura cytoplasmic male sterile (ogu CMS) lines. However, the genes associated with bud abortion are poorly understood. We applied RNA sequencing to analyze the transcriptomes of normal and abortive buds of broccoli maintainer and ogu CMS lines. Functional analysis showed that among the 54,753 annotated unigenes obtained, 74 and 21 differentially expressed genes in common were upregulated and downregulated in ogu CMS abortive buds compared with ogu CMS normal buds, maintainer normal, and abortive buds, respectively. Nineteen of the common differentially expressed genes were enriched by GO terms associated with glycosyl hydrolases, reactive oxygen species scavenging, inhibitor, and protein degradation. Ethylene-responsive transcription factor 115 and transcriptional factor basic helix-loop-helix 137 were significantly upregulated; transcription factors DUO1 and PosF21/RF2a/BZIP34 were downregulated in ogu CMS abortive buds compared with the other groups. Genes related to polygalacturonase metabolism, glycosyl hydrolases, oxidation reduction process, phenylalanine metabolism, and phenylpropanoid biosynthesis were significantly changed in ogu CMS abortive buds. Our results increase our understanding of bud abortion, provide a valuable resource for further functional characterization of ogu CMS during bud abortion, and will aid in future cross breeding of Brassica crops. Full article
(This article belongs to the Special Issue Plant Genetics and Molecular Breeding)
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Open AccessArticle Genome-Wide Characterization and Analysis of Metallothionein Family Genes That Function in Metal Stress Tolerance in Brassica napus L.
Int. J. Mol. Sci. 2018, 19(8), 2181; https://doi.org/10.3390/ijms19082181
Received: 25 June 2018 / Revised: 21 July 2018 / Accepted: 24 July 2018 / Published: 26 July 2018
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Abstract
Brassica plants exhibit both high biomass productivity and high rates of heavy metal absorption. Metallothionein (MT) proteins are low molecular weight, cysteine-rich, metal-binding proteins that play crucial roles in protecting plants from heavy metal toxicity. However, to date, MT proteins have not been [...] Read more.
Brassica plants exhibit both high biomass productivity and high rates of heavy metal absorption. Metallothionein (MT) proteins are low molecular weight, cysteine-rich, metal-binding proteins that play crucial roles in protecting plants from heavy metal toxicity. However, to date, MT proteins have not been systematically characterized in Brassica. In this study, we identified 60 MTs from Arabidopsis thaliana and five Brassica species. All the MT family genes from Brassica are closely related to Arabidopsis MTs, encoding putative proteins that share similar functions within the same clades. Genome mapping analysis revealed high levels of synteny throughout the genome due to whole genome duplication and segmental duplication events. We analyzed the expression levels of 16 Brassica napus MTs (BnaMTs) by RNA-sequencing and real-time RT-PCR (RT-qPCR) analysis in plants under As3+ stress. These genes exhibited different expression patterns in various tissues. Our results suggest that BnaMT3C plays a key role in the response to As3+ stress in B. napus. This study provides insight into the phylogeny, origin, and evolution of MT family members in Brassica, laying the foundation for further studies of the roles of MT proteins in these important crops. Full article
(This article belongs to the Special Issue Plant Genetics and Molecular Breeding)
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Open AccessArticle Molecular Mapping of QTLs for Heat Tolerance in Chickpea
Int. J. Mol. Sci. 2018, 19(8), 2166; https://doi.org/10.3390/ijms19082166
Received: 19 June 2018 / Revised: 12 July 2018 / Accepted: 19 July 2018 / Published: 25 July 2018
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Abstract
Chickpea (Cicer arietinum L.), a cool-season legume, is increasingly affected by heat-stress at reproductive stage due to changes in global climatic conditions and cropping systems. Identifying quantitative trait loci (QTLs) for heat tolerance may facilitate breeding for heat tolerant varieties. The present [...] Read more.
Chickpea (Cicer arietinum L.), a cool-season legume, is increasingly affected by heat-stress at reproductive stage due to changes in global climatic conditions and cropping systems. Identifying quantitative trait loci (QTLs) for heat tolerance may facilitate breeding for heat tolerant varieties. The present study was aimed at identifying QTLs associated with heat tolerance in chickpea using 292 F8-9 recombinant inbred lines (RILs) developed from the cross ICC 4567 (heat sensitive) × ICC 15614 (heat tolerant). Phenotyping of RILs was undertaken for two heat-stress (late sown) and one non-stress (normal sown) environments. A genetic map spanning 529.11 cM and comprising 271 genotyping by sequencing (GBS) based single nucleotide polymorphism (SNP) markers was constructed. Composite interval mapping (CIM) analysis revealed two consistent genomic regions harbouring four QTLs each on CaLG05 and CaLG06. Four major QTLs for number of filled pods per plot (FPod), total number of seeds per plot (TS), grain yield per plot (GY) and % pod setting (%PodSet), located in the CaLG05 genomic region, were found to have cumulative phenotypic variation of above 50%. Nineteen pairs of epistatic QTLs showed significant epistatic effect, and non-significant QTL × environment interaction effect, except for harvest index (HI) and biomass (BM). A total of 25 putative candidate genes for heat-stress were identified in the two major genomic regions. This is the first report on QTLs for heat-stress response in chickpea. The markers linked to the above mentioned four major QTLs can facilitate marker-assisted breeding for heat tolerance in chickpea. Full article
(This article belongs to the Special Issue Plant Genetics and Molecular Breeding)
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Open AccessArticle WB1, a Regulator of Endosperm Development in Rice, Is Identified by a Modified MutMap Method
Int. J. Mol. Sci. 2018, 19(8), 2159; https://doi.org/10.3390/ijms19082159
Received: 3 July 2018 / Revised: 15 July 2018 / Accepted: 19 July 2018 / Published: 24 July 2018
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Abstract
Abnormally developed endosperm strongly affects rice (Oryza sativa) appearance quality and grain weight. Endosperm formation is a complex process, and although many enzymes and related regulators have been identified, many other related factors remain largely unknown. Here, we report the isolation [...] Read more.
Abnormally developed endosperm strongly affects rice (Oryza sativa) appearance quality and grain weight. Endosperm formation is a complex process, and although many enzymes and related regulators have been identified, many other related factors remain largely unknown. Here, we report the isolation and characterization of a recessive mutation of White Belly 1 (WB1), which regulates rice endosperm development, using a modified MutMap method in the rice mutant wb1. The wb1 mutant develops a white-belly endosperm and abnormal starch granules in the inner portion of white grains. Representative of the white-belly phenotype, grains of wb1 showed a higher grain chalkiness rate and degree and a lower 1000-grain weight (decreased by ~34%), in comparison with that of Wild Type (WT). The contents of amylose and amylopectin in wb1 significantly decreased, and its physical properties were also altered. We adopted the modified MutMap method to identify 2.52 Mb candidate regions with a high specificity, where we detected 275 SNPs in chromosome 4. Finally, we identified 19 SNPs at 12 candidate genes. Transcript levels analysis of all candidate genes showed that WB1 (Os04t0413500), encoding a cell-wall invertase, was the most probable cause of white-belly endosperm phenotype. Switching off WB1 with the CRISPR/cas9 system in Japonica cv. Nipponbare demonstrates that WB1 regulates endosperm development and that different mutations of WB1 disrupt its biological function. All of these results taken together suggest that the wb1 mutant is controlled by the mutation of WB1, and that the modified MutMap method is feasible to identify mutant genes, and could promote genetic improvement in rice. Full article
(This article belongs to the Special Issue Plant Genetics and Molecular Breeding)
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Open AccessArticle Constitutive Expression of Aechmea fasciata SPL14 (AfSPL14) Accelerates Flowering and Changes the Plant Architecture in Arabidopsis
Int. J. Mol. Sci. 2018, 19(7), 2085; https://doi.org/10.3390/ijms19072085
Received: 21 June 2018 / Revised: 10 July 2018 / Accepted: 14 July 2018 / Published: 18 July 2018
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Abstract
Variations in flowering time and plant architecture have a crucial impact on crop biomass and yield, as well as the aesthetic value of ornamental plants. Aechmea fasciata, a member of the Bromeliaceae family, is a bromeliad variety that is commonly cultivated worldwide. [...] Read more.
Variations in flowering time and plant architecture have a crucial impact on crop biomass and yield, as well as the aesthetic value of ornamental plants. Aechmea fasciata, a member of the Bromeliaceae family, is a bromeliad variety that is commonly cultivated worldwide. Here, we report the characterization of AfSPL14, a squamosa promoter binding protein-like gene in A. fasciata. AfSPL14 was predominantly expressed in the young vegetative organs of adult plants. The expression of AfSPL14 could be upregulated within 1 h by exogenous ethephon treatment. The constitutive expression of AfSPL14 in Arabidopsis thaliana caused early flowering and variations in plant architecture, including smaller rosette leaves and thicker and increased numbers of main inflorescences. Our findings suggest that AfSPL14 may help facilitate the molecular breeding of A. fasciata, other ornamental and edible bromeliads (e.g., pineapple), and even cereal crops. Full article
(This article belongs to the Special Issue Plant Genetics and Molecular Breeding)
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Open AccessArticle Transcriptome Analyses in Different Cucumber Cultivars Provide Novel Insights into Drought Stress Responses
Int. J. Mol. Sci. 2018, 19(7), 2067; https://doi.org/10.3390/ijms19072067
Received: 21 May 2018 / Revised: 28 June 2018 / Accepted: 10 July 2018 / Published: 16 July 2018
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Abstract
Drought stress is one of the most serious threats to cucumber quality and yield. To gain a good understanding of the molecular mechanism upon water deficiency, we compared and analyzed the RNA sequencing-based transcriptomic responses of two contrasting cucumber genotypes, L-9 (drought-tolerant) and [...] Read more.
Drought stress is one of the most serious threats to cucumber quality and yield. To gain a good understanding of the molecular mechanism upon water deficiency, we compared and analyzed the RNA sequencing-based transcriptomic responses of two contrasting cucumber genotypes, L-9 (drought-tolerant) and A-16 (drought-sensitive). In our present study, combining the analysis of phenotype, twelve samples of cucumber were carried out a transcriptomic profile by RNA-Seq under normal and water-deficiency conditions, respectively. A total of 1008 transcripts were differentially expressed under normal conditions (466 up-regulated and 542 down-regulated) and 2265 transcripts under drought stress (979 up-regulated and 1286 down-regulated). The significant positive correlation between RNA sequencing data and a qRT-PCR analysis supported the results found. Differentially expressed genes (DEGs) involved in metabolic pathway and biosynthesis of secondary metabolism were significantly changed after drought stress. Several genes, which were related to sucrose biosynthesis (Csa3G784370 and Csa3G149890) and abscisic acid (ABA) signal transduction (Csa4M361820 and Csa6M382950), were specifically induced after 4 days of drought stress. DEGs between the two contrasting cultivars identified in our study provide a novel insight into isolating helpful candidate genes for drought tolerance in cucumber. Full article
(This article belongs to the Special Issue Plant Genetics and Molecular Breeding)
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Open AccessArticle Chrysanthemum DgWRKY2 Gene Enhances Tolerance to Salt Stress in Transgenic Chrysanthemum
Int. J. Mol. Sci. 2018, 19(7), 2062; https://doi.org/10.3390/ijms19072062
Received: 22 May 2018 / Revised: 2 July 2018 / Accepted: 10 July 2018 / Published: 16 July 2018
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Abstract
WRKY transcription factors (TFs) play a vital part in coping with different stresses. In this study, DgWRKY2 was isolated from Dendranthema grandiflorum. The gene encodes a 325 amino acid protein, belonging to the group II WRKY family, and contains one typical WRKY [...] Read more.
WRKY transcription factors (TFs) play a vital part in coping with different stresses. In this study, DgWRKY2 was isolated from Dendranthema grandiflorum. The gene encodes a 325 amino acid protein, belonging to the group II WRKY family, and contains one typical WRKY domain (WRKYGQK) and a zinc finger motif (C-X4-5-C-X22-23-H-X1-H). Overexpression of DgWRKY2 in chrysanthemum enhanced tolerance to high-salt stress compared to the wild type (WT). In addition, the activities of antioxidant enzymes (superoxide dismutase (SOD), peroxidase (POD), catalase (CAT)), proline content, soluble sugar content, soluble protein content, and chlorophyll content of transgenic chrysanthemum, as well as the survival rate of the transgenic lines, were on average higher than that of the WT. On the contrary, hydrogen peroxide (H2O2), superoxide anion (O2), and malondialdehyde (MDA) accumulation decreased compared to WT. Expression of the stress-related genes DgCAT, DgAPX, DgZnSOD, DgP5CS, DgDREB1A, and DgDREB2A was increased in the DgWRKY2 transgenic chrysanthemum compared with their expression in the WT. In conclusion, our results indicate that DgWRKY2 confers salt tolerance to transgenic chrysanthemum by enhancing antioxidant and osmotic adjustment. Therefore, this study suggests that DgWRKY2 could be used as a reserve gene for salt-tolerant plant breeding. Full article
(This article belongs to the Special Issue Plant Genetics and Molecular Breeding)
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Open AccessArticle Isolation and Characterization of a Green-Tissue Promoter from Common Wild Rice (Oryza rufipogon Griff.)
Int. J. Mol. Sci. 2018, 19(7), 2009; https://doi.org/10.3390/ijms19072009
Received: 8 June 2018 / Revised: 28 June 2018 / Accepted: 5 July 2018 / Published: 10 July 2018
Cited by 1 | PDF Full-text (5051 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Promoters play a very important role in the initiation and regulation of gene transcription. Green-tissue promoter is of great significance to the development of genetically modified crops. Based on RNA-seq data and RT-PCR expression analysis, this study screened a gene, OrGSE (GREEN SPECIAL [...] Read more.
Promoters play a very important role in the initiation and regulation of gene transcription. Green-tissue promoter is of great significance to the development of genetically modified crops. Based on RNA-seq data and RT-PCR expression analysis, this study screened a gene, OrGSE (GREEN SPECIAL EXPRESS), which is expressed specifically in green tissues. The study also isolated the promoter of the OrGSE gene (OrGSEp), and predicted many cis-acting elements, such as the CAAT-Box and TATA-Box, and light-responding elements, including circadian, G-BOX and GT1 CONSENSUS. Histochemical analysis and quantification of GUS activity in transgenic Arabidopsis thaliana plants expressing GUS under the control of OrGSEp revealed that this promoter is not only green tissue-specific, but also light-inducible. The ability of a series of 5’-deletion fragments of OrGSEp to drive GUS expression in Arabidopsis was also evaluated. We found that the promoter region from −54 to −114 is critical for the promoter function, and the region from −374 to −114 may contain core cis-elements involved in light response. In transgenic rice expressing GUS under the control of OrGSEp, visualization and quantification of GUS activity showed that GUS was preferentially expressed in green tissues and not in endosperm. OrGSEp is a useful regulatory element for breeding pest-resistant crops. Full article
(This article belongs to the Special Issue Plant Genetics and Molecular Breeding)
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Open AccessArticle Particle Bombardment of the cry2A Gene Cassette Induces Stem Borer Resistance in Sugarcane
Int. J. Mol. Sci. 2018, 19(6), 1692; https://doi.org/10.3390/ijms19061692
Received: 3 May 2018 / Revised: 31 May 2018 / Accepted: 4 June 2018 / Published: 6 June 2018
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Abstract
Sugarcane borer is the most common and harmful pest in Chinese sugarcane fields, and can cause damage to the whole plant during the entire growing season. To improve borer resistance in sugarcane, we constructed a plant expression vector pGcry2A0229 with the bar gene [...] Read more.
Sugarcane borer is the most common and harmful pest in Chinese sugarcane fields, and can cause damage to the whole plant during the entire growing season. To improve borer resistance in sugarcane, we constructed a plant expression vector pGcry2A0229 with the bar gene as the marker and the cry2A gene as the target, and introduced it into embryogenic calli of most widely cultivated sugarcane cultivar ROC22 by particle bombardment. After screening with phosphinothricin in vitro and Basta spray, 21 resistance-regenerated plants were obtained, and 10 positive transgenic lines harboring the cry2A gene were further confirmed by conventional PCR detection. Real-time quantitative PCR (RT-qPCR) analysis showed that the copy number of the cry2A gene varied among different transgenic lines but did not exceed four copies. Quantitative ELISA analysis showed that there was no linear relationship with copy number but negatively correlated with the percentage of borer-infested plants. The analysis of industrial and agronomic traits showed that the theoretical sugar yields of transgenic lines TR-4 and TR-10 were slightly lower than that of the control in both plant cane and ratoon cane; nevertheless, TR-4 and TR-10 lines exhibited markedly lower in frequency of borer-infested plants in plant cane and in the ratoon cane compared to the control. Our results indicate that the introduction of the cry2A gene via bombardment produces transgenic lines with obviously increased stem borer resistance and comparable sugar yield, providing a practical value in direct commercial cultivation and crossbreeding for ROC22 has been used as the most popular elite genitor in various breeding programs in China. Full article
(This article belongs to the Special Issue Plant Genetics and Molecular Breeding)
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Review

Jump to: Research

Open AccessReview Omics Approaches for Engineering Wheat Production under Abiotic Stresses
Int. J. Mol. Sci. 2018, 19(8), 2390; https://doi.org/10.3390/ijms19082390
Received: 23 June 2018 / Revised: 14 July 2018 / Accepted: 24 July 2018 / Published: 14 August 2018
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Abstract
Abiotic stresses greatly influenced wheat productivity executed by environmental factors such as drought, salt, water submergence and heavy metals. The effective management at the molecular level is mandatory for a thorough understanding of plant response to abiotic stress. Understanding the molecular mechanism of [...] Read more.
Abiotic stresses greatly influenced wheat productivity executed by environmental factors such as drought, salt, water submergence and heavy metals. The effective management at the molecular level is mandatory for a thorough understanding of plant response to abiotic stress. Understanding the molecular mechanism of stress tolerance is complex and requires information at the omic level. In the areas of genomics, transcriptomics and proteomics enormous progress has been made in the omics field. The rising field of ionomics is also being utilized for examining abiotic stress resilience in wheat. Omic approaches produce a huge amount of data and sufficient developments in computational tools have been accomplished for efficient analysis. However, the integration of omic-scale information to address complex genetics and physiological questions is still a challenge. Though, the incorporation of omic-scale data to address complex genetic qualities and physiological inquiries is as yet a challenge. In this review, we have reported advances in omic tools in the perspective of conventional and present day approaches being utilized to dismember abiotic stress tolerance in wheat. Attention was given to methodologies, for example, quantitative trait loci (QTL), genome-wide association studies (GWAS) and genomic selection (GS). Comparative genomics and candidate genes methodologies are additionally talked about considering the identification of potential genomic loci, genes and biochemical pathways engaged with stress resilience in wheat. This review additionally gives an extensive list of accessible online omic assets for wheat and its effective use. We have additionally addressed the significance of genomics in the integrated approach and perceived high-throughput multi-dimensional phenotyping as a significant restricting component for the enhancement of abiotic stress resistance in wheat. Full article
(This article belongs to the Special Issue Plant Genetics and Molecular Breeding)
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Open AccessReview Molecular Genetics and Breeding for Nutrient Use Efficiency in Rice
Int. J. Mol. Sci. 2018, 19(6), 1762; https://doi.org/10.3390/ijms19061762
Received: 25 April 2018 / Revised: 26 May 2018 / Accepted: 1 June 2018 / Published: 14 June 2018
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Abstract
In the coming decades, rice production needs to be carried out sustainably to keep the balance between profitability margins and essential resource input costs. Many fertilizers, such as N, depend primarily on fossil fuels, whereas P comes from rock phosphates. How long these [...] Read more.
In the coming decades, rice production needs to be carried out sustainably to keep the balance between profitability margins and essential resource input costs. Many fertilizers, such as N, depend primarily on fossil fuels, whereas P comes from rock phosphates. How long these reserves will last and sustain agriculture remains to be seen. Therefore, current agricultural food production under such conditions remains an enormous and colossal challenge. Researchers have been trying to identify nutrient use-efficient varieties over the past few decades with limited success. The concept of nutrient use efficiency is being revisited to understand the molecular genetic basis, while much of it is not entirely understood yet. However, significant achievements have recently been observed at the molecular level in nitrogen and phosphorus use efficiency. Breeding teams are trying to incorporate these valuable QTLs and genes into their rice breeding programs. In this review, we seek to identify the achievements and the progress made so far in the fields of genetics, molecular breeding and biotechnology, especially for nutrient use efficiency in rice. Full article
(This article belongs to the Special Issue Plant Genetics and Molecular Breeding)
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: Annotation-based transcriptome SNP discovery in three polyploid blueberry crops using second-generation sequencing without a reference genome sequence
Authors: Wang Yunsheng, Muhammad Qasim Shahid, Faheem Shehzad Baloch, Fozia Ghouri, Nie Fei
Abstract: Blueberry is a kind of new popular fruit with high quality and nutritional value. Currently, the planting area and distribution are expanding rapidly to satisfy the huge demand of people in the world, which bring the utmost need for evolving new varieties to adapt global climate, soil and farming characters. As a perennial fruit crop, molecular marker assisted breeding is an ideal method with the merit of short breeding cycle compared to the conventional breeding methods. Here, we sequenced the leaves transcriptome of 19 rabbit-eye blueberry accessions, 13 southern high-bush blueberry accessions and 22 northern high-bush blueberry accessions by using next generation sequencing technologies. We obtained 80.825G data clean with an average of 1.50G data per accession. We detected 58968, 55973 and 53887 unigenes by using the clean data from rabbit-eye blueberry, southern high-bush blueberry and northern high-bush blueberry, respectively, and identified more than 5000 SSR loci and 50000 SNP from the unigenes annotation of each kind blueberry. We also detected more than 1000 unigenes that are candidate of varied resistance genes. The results would offer large amount of molecular markers for marker assisted breeding to produce blueberry cultivars with different adaptive characteristics, and will also be helpful for the molecular genetics and association analysis of blueberry and the basic molecular information of pest and disease resistance of blueberry.

Title: Identification of quantitative trait loci governing Nutrient Use Efficiency (NuUE) related traits using SNP markers in an early backcross population of rice (Oryza sativa L.)
Authors: Zilhas A. Jewel, Jauhar Ali, Mahender Anumalla, Yulong Pang, and Zhikang Li
Abstract: Development of nutrient use efficient (NuUE) rice cultivars is highly crucial for sustaining the global rice production in Asia and Africa. However, it requires a better understanding of the genetics of NuUE related traits and their relationship to grain yield. In this study, simultaneous efforts were made to develop NuUE rice cultivars and to map quantitative trait loci (QTLs) governing NUE related traits in rice. 230 BC1F5 introgression lines (ILs) developed from a single early backcross population involving Weed Tolerant Rice 1 as recipient parent and Haoannong as donor parent for constructing of high density linkage map through genotyping by a single nucleotide polymorphism (SNP) array. The ILs were cultivated in field conditions with a different combination of fertilizer schedule under six nutrient conditions, i.e., N, -P, -NP, -NPK, 75N and NPK conditions. A total of 261 QTLs mapped for seven promising vital NuUE traits in all 12 chromosomes, of which forty nine QTLs showed high (20.25–34.68%) contribution to phenotypic variation and LOD score ranged from 9.44 to 17.76 respectively. Also, discovered 14 hotspot QTL regions, which had ≥ (more than) five QTLs located on the same region of chromosome 1, 2, 3, 4, 5, 7, 8, 9, and 11. Further analysis of these 14 QTLs, refined to four topmost hotspot QTLs (QTL harbor-I to IV) located on chromosomes 3 (SNP_3_853802), 5 (SNP_5_5588965), 9 (SNP_9_12154616) and 11 (SNP_11_1706087). Majority of the QTLs identified for NuUE allied traits were clustered together in the QTL harbors (q1000Gwt, qPFP, qBY, qFGN, qGY and qPSPF1) under all six nutrient conditions. We identified four novel putative QTLs for agronomic efficiency and 22 QTLs for partial factor productivity (PFP) under –P, and 75N conditions with a LOD score ranged from 2.55-4.52, 3.39-12.15 and together explained their phenotypic variation ranges from 5.92 -10.27% and 7.81-25.28% respectively. The identified potential QTLs were novel and of remarkable value for marker-aided selection and pyramiding of multiple QTLs, which would provide supportive evidence for the enhancement of grain yield and cloning of NuUE tolerance-responsive genes in rice.

Title: GmBRC1 is a Candidate Gene for Branching in Soybean
Author: Suk-Ha Lee
Abstract: The number of branches in soybean is one of the most important factors directly affects the yield. However, only a few QTLs have been reported and the genes controlling the number of branches have not been characterized because it is affected immensely by various environmental factors. In this study, we identified six DNA markers associated with branch numbers in the genomic region of qBR6-1, a major QTL for branching previously reported, from a set of 430 soybean germplasms with three geographical replications through single marker ANOVA and regression analysis. Out of six markers, four were located in the genic regions including BRANCHED 1 (BRC1) and a gene encoding transcription factor TFIIE alpha subunit, and two were in intergenic regions. No significant association with branch numbers was identified by the genome-wide association study. We constructed a set of near isogenic lines (NILs) derived from a F6 residual heterozygous line of Jiyu69 x SS0404-T5-76, which have 99.9% of homozygous genetic background and significant differences in the number of branches. The gene BRC1, reported as a negative regulator of branching in Arabidopsis, was up-regulated in shoot apical meristem of the less-branching NIL while the more-branching NIL showed down-regulated expression of BRC1. No significant difference in the level of gene expression was observed in the other gene. In BRC1 two nucleotide variations were identified between NILs, one in the genic and the other in upstream region. Genetic association of these markers was observed in another set of soybean germplasms comprised by 59 accessions provided by USDA. In conclusion, we suggest the BRC1 gene is a strong candidate gene controlling branch development in soybean.

Title: Date Palm Salinity Tolerance in the Omic Area
Authors: Khaled Hazzouri, Khaled Amiri and Khaled Masmoudi
Abstract: Date palm is a major crop in arid regions of the world contributing to food security. However, its cultivation is facing shortage in water demand. Although date palms are known for their drought and salinity tolerance to a certain extent, the growing salinity of water in the region requires improving the tolerance of date palm to salt in order to ensure the sustainability of this crop. In this review paper, we outline a strategy to address the salinity problem using omics available data. Accomplishing the objective of developing date palm varieties that can tolerate increased saline ground water and soil, we emphasis on breeding and marker assisted selection, as well as discovering and using the microbiome in the arid regions.

Title: A New Theory of Mutation which May Help to Occur the Gene Linkage and Pave a Way to Breed Super Crop in Future
Author: Xuan Tran Dang

Title: DNA Methylation Analysis of Dormancy Breaking in Almond Flower Buds using Cre-epiGBS (cost reduced epi-Genotyping by Sequencing)
Author: Pedro  Martínez-Gómez

 
Int. J. Mol. Sci. EISSN 1422-0067 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
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