International Journal of Molecular Sciences

Editorial

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5 pages, 200 KiB

Open AccessEditorial

Emerging Horizons in Plant Genetics and Breeding

by Manosh Kumar Biswas

Int. J. Mol. Sci. 2023, 24(14), 11621; https://doi.org/10.3390/ijms241411621 - 19 Jul 2023

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Abstract

Plant genetics and breeding have made significant progress in recent years, especially with the emergence of genomics [...] Full article

(This article belongs to the Special Issue Plant Genetics and Breeding Research Progress in Genomics to Post-genomics Era)

Research

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21 pages, 5974 KiB

Open AccessArticle

Genome-Wide Identification and Characterization of R2R3-MYB Provide Insight into Anthocyanin Biosynthesis Regulation Mechanism of Ananas comosus var. bracteatus

by Wei Yang, Lijun Feng, Jiaheng Luo, Huiling Zhang, Fuxing Jiang, Yehua He, Xi Li, Juan Du, Mark Owusu Adjei, Aiping Luan and Jun Ma

Int. J. Mol. Sci. 2023, 24(4), 3133; https://doi.org/10.3390/ijms24043133 - 5 Feb 2023

Cited by 5 | Viewed by 1616

Abstract

The R2R3-MYB proteins comprise the largest class of MYB transcription factors, which play an essential role in regulating anthocyanin synthesis in various plant species. Ananas comosus var. bracteatus is an important colorful anthocyanins-rich garden plant. The spatio-temporal accumulation of anthocyanins in chimeric leaves, [...] Read more.

The R2R3-MYB proteins comprise the largest class of MYB transcription factors, which play an essential role in regulating anthocyanin synthesis in various plant species. Ananas comosus var. bracteatus is an important colorful anthocyanins-rich garden plant. The spatio-temporal accumulation of anthocyanins in chimeric leaves, bracts, flowers, and peels makes it an important plant with a long ornamental period and highly improves its commercial value. We conducted a comprehensive bioinformatic analysis of the R2R3-MYB gene family based on genome data from A. comosus var. bracteatus. Phylogenetic analysis, gene structure and motif analysis, gene duplication, collinearity, and promoter analysis were used to analyze the characteristics of this gene family. In this work, a total of 99 R2R3-MYB genes were identified and classified into 33 subfamilies according to phylogenetic analysis, and most of them were localized in the nucleus. We found these genes were mapped to 25 chromosomes. Gene structure and protein motifs were conserved among AbR2R3-MYB genes, especially within the same subfamily. Collinearity analysis revealed four pairs of tandem duplicated genes and 32 segmental duplicates in AbR2R3-MYB genes, indicating that segmental duplication contributed to the amplification of the AbR2R3-MYB gene family. A total of 273 ABRE responsiveness, 66 TCA elements, 97 CGTCA motifs, and TGACG motifs were the main cis elements in the promoter region under response to ABA, SA, and MEJA. These results revealed the potential function of AbR2R3-MYB genes in response to hormone stress. Ten R2R3-MYBs were found to have high homology to MYB proteins reported to be involved in anthocyanin biosynthesis from other plants. RT-qPCR results revealed the 10 AbR2R3-MYB genes showed tissue-specific expression patterns, six of them expressed the highest in the flower, two genes in the bract, and two genes in the leaf. These results suggested that these genes may be the candidates that regulate anthocyanin biosynthesis of A. comosus var. bracteatus in the flower, leaf, and bract, respectively. In addition, the expressions of these 10 AbR2R3-MYB genes were differentially induced by ABA, MEJA, and SA, implying that these genes may play crucial roles in hormone-induced anthocyanin biosynthesis. Our study provided a comprehensive and systematic analysis of AbR2R3-MYB genes and identified the AbR2R3-MYB genes regulating the spatial-temporal anthocyanin biosynthesis in A. comosus var. bracteatus, which would be valuable for further study on the anthocyanin regulation mechanism of A. comosus var. bracteatus. Full article

(This article belongs to the Special Issue Plant Genetics and Breeding Research Progress in Genomics to Post-genomics Era)

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21 pages, 4279 KiB

Open AccessArticle

Identification of NPF Family Genes in Brassica rapa Reveal Their Potential Functions in Pollen Development and Response to Low Nitrate Stress

by Xiaoshuang Yang, Wenyu Han, Jiao Qi, Yueying Li, Xingbo Chen, Yiwen Zhang, Jingyu Wu, Genze Li, Jing Gao and Xiangshu Dong

Int. J. Mol. Sci. 2023, 24(1), 754; https://doi.org/10.3390/ijms24010754 - 1 Jan 2023

Cited by 3 | Viewed by 1908

Abstract

Nitrate Transporter 1/Peptide Transporter Family (NPF) genes encode membrane transporters involved in the transport of diverse substrates. However, little is known about the diversity and functions of NPFs in Brassica rapa. In this study, 85 NPFs were identified in B. [...] Read more.

Nitrate Transporter 1/Peptide Transporter Family (NPF) genes encode membrane transporters involved in the transport of diverse substrates. However, little is known about the diversity and functions of NPFs in Brassica rapa. In this study, 85 NPFs were identified in B. rapa (BrNPFs) which comprised eight subfamilies. Gene structure and conserved motif analysis suggested that BrNFPs were conserved throughout the genus. Stress and hormone-responsive cis-acting elements and transcription factor binding sites were identified in BrNPF promoters. Syntenic analysis suggested that tandem duplication contributed to the expansion of BrNPFs in B. rapa. Transcriptomic profiling analysis indicated that BrNPF2.6, BrNPF2.15, BrNPF7.6, and BrNPF8.9 were expressed in fertile floral buds, suggesting important roles in pollen development. Thirty-nine BrNPFs were responsive to low nitrate availability in shoots or roots. BrNPF2.10, BrNPF2.19, BrNPF2.3, BrNPF5.12, BrNPF5.16, BrNPF5.8, and BrNPF6.3 were only up-regulated in roots under low nitrate conditions, indicating that they play positive roles in nitrate absorption. Furthermore, many genes were identified in contrasting genotypes that responded to vernalization and clubroot disease. Our results increase understanding of BrNPFs as candidate genes for genetic improvement studies of B. rapa to promote low nitrate availability tolerance and for generating sterile male lines based on gene editing methods. Full article

(This article belongs to the Special Issue Plant Genetics and Breeding Research Progress in Genomics to Post-genomics Era)

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20 pages, 8775 KiB

Open AccessArticle

CRISPR/Cas9 Mutant Rice Ospmei12 Involved in Growth, Cell Wall Development, and Response to Phytohormone and Heavy Metal Stress

by Zhaoyang Li, Muhammad Junaid Rao, Jiaying Li, Yanting Wang, Peng Chen, Hua Yu, Chongjian Ma and Lingqiang Wang

Int. J. Mol. Sci. 2022, 23(24), 16082; https://doi.org/10.3390/ijms232416082 - 16 Dec 2022

Cited by 5 | Viewed by 1824

Abstract

Pectin is one of the constituents of the cell wall, distributed in the primary cell wall and middle lamella, affecting the rheological properties and the cell wall stickiness. Pectin methylesterase (PME) and pectin methylesterase inhibitor (PMEI) are the most important factors for modifying [...] Read more.

Pectin is one of the constituents of the cell wall, distributed in the primary cell wall and middle lamella, affecting the rheological properties and the cell wall stickiness. Pectin methylesterase (PME) and pectin methylesterase inhibitor (PMEI) are the most important factors for modifying methyl esterification. In this study, 45 PMEI genes from rice (Oryza sativa L.) were screened by bioinformatics tools, and their structure, motifs, cis-acting elements in the promoter region, chromosomal distribution, gene duplication, and phylogenetic relationship were analyzed. Furthermore, CRISPR/Cas9 was used to edit the OsPMEI12 (LOC_Os03G01020) and two mutant pmei12 lines were obtained to explore the functions of OsPMEI in plant growth and development, and under cadmium (Cd) stress. Compared to wild type (WT) Nipponbare, the second inverted internodes of the mutant plants shortened significantly, resulting in the reduction in plant height at mature stage. The seed setting rate, and fresh and dry weights of the mutants were also decreased in mutant plants. In addition, the pectin methylation of pmei12 lines is decreased as expected, and the pectin content of the cell wall increased at both seedling and maturity stages; however, the cellulose and hemicellulose increased only at seedling stage. Interestingly, the growth of the pmei12 lines was better than the WT in both normal conditions and under two phytohormone (GA₃ and NAA) treatments at seedling stage. Under Cd stress, the fresh and dry weights were increased in pmei12 lines. These results indicated that OsPMEI12 was involved in the regulation of methyl esterification during growth, affected cell wall composition and agronomic traits, and might play an important role in responses to phytohormones and stress. Full article

(This article belongs to the Special Issue Plant Genetics and Breeding Research Progress in Genomics to Post-genomics Era)

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13 pages, 2966 KiB

Open AccessArticle

Combined Metabolomic and Quantitative RT-PCR Analyses Revealed the Synthetic Differences of 2-Acetyl-1-pyrroline in Aromatic and Non-Aromatic Vegetable Soybeans

by Man Zhao, Linlin Qian, Zhuoyu Chi, Xiaoli Jia, Fengjie Qi, Fengjie Yuan, Zhiqiang Liu and Yuguo Zheng

Int. J. Mol. Sci. 2022, 23(23), 14529; https://doi.org/10.3390/ijms232314529 - 22 Nov 2022

Cited by 2 | Viewed by 1099

Abstract

Aroma is an important economic trait of vegetable soybeans, which greatly influences their market value. The 2-acetyl-1-pyrroline (2AP) is considered as an important substance affecting the aroma of plants. Although the 2AP synthesis pathway has been resolved, the differences of the 2AP synthesis [...] Read more.

Aroma is an important economic trait of vegetable soybeans, which greatly influences their market value. The 2-acetyl-1-pyrroline (2AP) is considered as an important substance affecting the aroma of plants. Although the 2AP synthesis pathway has been resolved, the differences of the 2AP synthesis in the aromatic and non-aromatic vegetable soybeans are unknown. In this study, a broad targeted metabolome analysis including measurement of metabolites levels and gene expression levels was performed to reveal pathways of aroma formation in the two developmental stages of vegetable soybean grains [35 (S5) and 40 (S6) days after anthesis] of the ‘Zhexian No. 8’ (ZX8, non-aromatic) and ZK1754 (aromatic). The results showed that the differentially accumulated metabolites (DAMs) of the two varieties can be classified into nine main categories including flavonoids, lipids, amino acids and derivatives, saccharides and alcohols, organic acids, nucleotides and derivatives, phenolic acids, alkaloids and vitamin, which mainly contributed to their phenotypic differences. Furthermore, in combination with the 2AP synthesis pathway, the differences of amino acids and derivatives were mainly involved in the 2AP synthesis. Furthermore, 2AP precursors’ analysis revealed that the accumulation of 2AP mainly occurred from 1-pyrroline-5-carboxylate (P5C), not 4-aminobutyraldehyde (GABald). The quantitative RT-PCR showed that the associated synthetic genes were 1-pyrroline-5-carboxylate dehydrogenase (P5CDH), ∆¹-pyrroline-5-carboxylate synthetase (P5CS), proline dehydrogenase (PRODH) and pyrroline-5-carboxylate reductase (P5CR), which further verified the synthetic pathway of 2AP. Furthermore, the betaine aldehyde dehydrogenase 2 (GmBADH2) mutant was not only vital for the occurrence of 2AP, but also for the synthesis of 4-aminobutyric acid (GABA) in vegetable soybean. Therefore, the differences of 2AP accumulation in aromatic and non-aromatic vegetable soybeans have been revealed, and it also provides an important theoretical basis for aromatic vegetable soybean breeding. Full article

(This article belongs to the Special Issue Plant Genetics and Breeding Research Progress in Genomics to Post-genomics Era)

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18 pages, 1867 KiB

Open AccessArticle

Comparative Seeds Storage Transcriptome Analysis of Astronium fraxinifolium Schott, a Threatened Tree Species from Brazil

by Leonel Gonçalves Pereira Neto, Bruno Cesar Rossini, Celso Luis Marino, Peter E. Toorop and Edvaldo Aparecido Amaral Silva

Int. J. Mol. Sci. 2022, 23(22), 13852; https://doi.org/10.3390/ijms232213852 - 10 Nov 2022

Cited by 1 | Viewed by 1682

Abstract

Astronium fraxinifolium Schott (Anacardiaceae), also known as a ‘gonçalo-alves’, is a tree of the American tropics, with distribution in Mexico, part of Central America, Argentina, Bolivia, Brazil and Paraguay. In Brazil it is an endangered species that occurs in the Cerrado, Caatinga and [...] Read more.

Astronium fraxinifolium Schott (Anacardiaceae), also known as a ‘gonçalo-alves’, is a tree of the American tropics, with distribution in Mexico, part of Central America, Argentina, Bolivia, Brazil and Paraguay. In Brazil it is an endangered species that occurs in the Cerrado, Caatinga and in the Amazon biomes. In support of ex situ conservation, this work aimed to study two accessions with different longevity (p50) of A. fraxinifolium collected from two different geographic regions, and to evaluate the transcriptome during aging of the seeds in order to identify genes related to seed longevity. Artificial ageing was performed at a constant temperature of 45 °C and 60% relative humidity. RNA was extracted from 100 embryonic axes exposed to control and aging conditions for 21 days. The transcriptome analysis revealed differentially expressed genes such as Late Embryogenesis Abundant (LEA) genes, genes involved in the photosystem, glycine rich protein (GRP) genes, and several transcription factors associated with embryo development and ubiquitin-conjugating enzymes. Thus, these results contribute to understanding which genes play a role in seed ageing, and may serve as a basis for future functional characterization of the seed aging process in A. fraxinifolium. Full article

(This article belongs to the Special Issue Plant Genetics and Breeding Research Progress in Genomics to Post-genomics Era)

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13 pages, 3283 KiB

Open AccessArticle

Genome-Wide Association Mapping Identifies New Candidate Genes for Cold Stress and Chilling Acclimation at Seedling Stage in Rice (Oryza sativa L.)

by Jianguo Li, Ahmed Adel Khatab, Lihua Hu, Liyan Zhao, Jiangyi Yang, Lingqiang Wang and Guosheng Xie

Int. J. Mol. Sci. 2022, 23(21), 13208; https://doi.org/10.3390/ijms232113208 - 30 Oct 2022

Cited by 4 | Viewed by 1687

Abstract

Rice (Oryza sativa L.) is a chilling-sensitive staple food crop, and thus, low temperature significantly affects rice growth and yield. Many studies have focused on the cold shock of rice although chilling acclimation is more likely to happen in the field. In [...] Read more.

Rice (Oryza sativa L.) is a chilling-sensitive staple food crop, and thus, low temperature significantly affects rice growth and yield. Many studies have focused on the cold shock of rice although chilling acclimation is more likely to happen in the field. In this paper, a genome-wide association study (GWAS) was used to identify the genes that participated in cold stress and chilling accumulation. A total of 235 significantly associated single-nucleotide polymorphisms (SNPs) were identified. Among them, we detected 120 and 88 SNPs for the relative shoot fresh weight under cold stress and chilling acclimation, respectively. Furthermore, 11 and 12 quantitative trait loci (QTLs) were identified for cold stress and chilling acclimation, respectively, by integrating the co-localized SNPs. Interestingly, we identified 10 and 15 candidate genes in 11 and 12 QTLs involved in cold stress and chilling acclimation, respectively, and two new candidate genes (LOC_Os01g62410, LOC_Os12g24490) were obviously up-regulated under chilling acclimation. Furthermore, OsMYB3R-2 (LOC_Os01g62410) that encodes a R1R2R3 MYB gene was associated with cold tolerance, while a new C3HC4-type zinc finger protein-encoding gene LOC_Os12g24490 was found to function as a putative E3 ubiquitin-protein ligase in rice. Moreover, haplotype, distribution, and Wright’s fixation index (FST) of both genes showed that haplotype 3 of LOC_Os12g24490 is more stable in chilling acclimation, and the SNP (A > T) showed a difference in latitudinal distribution. FST analysis of SNPs in OsMYB3R-2 (LOC_Os01g62410) and LOC_Os12g24490 indicated that several SNPs were under selection in rice indica and japonica subspecies. This study provided new candidate genes in genetic improvement of chilling acclimation response in rice. Full article

(This article belongs to the Special Issue Plant Genetics and Breeding Research Progress in Genomics to Post-genomics Era)

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17 pages, 3966 KiB

Open AccessArticle

BaZFP1, a C2H2 Subfamily Gene in Desiccation-Tolerant Moss Bryum argenteum, Positively Regulates Growth and Development in Arabidopsis and Mosses

by Ping Zhou, Xiujin Liu, Xiaoshuang Li and Daoyuan Zhang

Int. J. Mol. Sci. 2022, 23(21), 12894; https://doi.org/10.3390/ijms232112894 - 25 Oct 2022

Cited by 2 | Viewed by 1402

Abstract

C2H2 zinc finger protein (C2H2-ZFP) plays an important role in regulating plant growth, development, and response to abiotic stress. To date, there have been no analyses of the C2H2-ZFP family in desiccation-tolerant moss. In this study, we identified 57 BaZFP transcripts across the [...] Read more.

C2H2 zinc finger protein (C2H2-ZFP) plays an important role in regulating plant growth, development, and response to abiotic stress. To date, there have been no analyses of the C2H2-ZFP family in desiccation-tolerant moss. In this study, we identified 57 BaZFP transcripts across the Bryum argenteum (B. argenteum) transcriptome. The BaZFP proteins were phylogenetically divided into four groups (I–IV). Additionally, we studied the BaZFP1 gene, which is a nuclear C2H2-ZFP and acts as a positive regulator of growth and development in both moss and Arabidopsis thaliana. The complete coding sequence of the BaZFP1 gene was isolated from B. argenteum cDNA, which showed a high expression level in a dehydration–rehydration treatment process. The overexpression of the BaZFP1 gene in the Physcomitrium patens and B. argenteum promoted differentiation and growth of gametophytes. Heterologous expression in Arabidopsis regulated the whole growth and development cycle. In addition, we quantitatively analyzed the genes related to growth and development in transgenic moss and Arabidopsis, including HLS1, HY5, ANT, LFY, FT, EIN3, MUS, APB4, SEC6, and STM1, and found that their expression levels changed significantly. This study may pave the way for substantial insights into the role of C2H2-ZFPs in plants as well as suggest appropriate candidate genes for crop breeding. Full article

(This article belongs to the Special Issue Plant Genetics and Breeding Research Progress in Genomics to Post-genomics Era)

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17 pages, 3521 KiB

Open AccessArticle

Identification of KFB Family in Moso Bamboo Reveals the Potential Function of PeKFB9 Involved in Stress Response and Lignin Polymerization

by Kebin Yang, Ziyang Li, Chenglei Zhu, Yan Liu, Huayu Sun, Xueping Li and Zhimin Gao

Int. J. Mol. Sci. 2022, 23(20), 12568; https://doi.org/10.3390/ijms232012568 - 19 Oct 2022

Cited by 2 | Viewed by 1504

Abstract

The Kelch repeat F-box (KFB) protein is an important E3 ubiquitin ligase that has been demonstrated to perform an important post-translational regulatory role in plants by mediating multiple biological processes. Despite their importance, KFBs have not yet been identified and characterized in bamboo. [...] Read more.

The Kelch repeat F-box (KFB) protein is an important E3 ubiquitin ligase that has been demonstrated to perform an important post-translational regulatory role in plants by mediating multiple biological processes. Despite their importance, KFBs have not yet been identified and characterized in bamboo. In this study, 19 PeKFBs were identified with F-box and Kelch domains; genes encoding these PeKFBs were unevenly distributed across 12 chromosomes of moso bamboo. Phylogenetic analysis indicated that the PeKFBs were divided into eight subclades based on similar gene structures and highly conserved motifs. A tissue-specific gene expression analysis showed that the PeKFBs were differentially expressed in various tissues of moso bamboo. All the promoters of the PeKFBs contained stress-related cis-elements, which was supported by the differentially expression of PeKFBs of moso bamboo under drought and cold stresses. Sixteen proteins were screened from the moso bamboo shoots’ cDNA library using PeKFB9 as a bait through a yeast two-hybrid (Y2H) assay. Moreover, PeKFB9 physically interacted with PeSKP1-like-1 and PePRX72-1, which mediated the activity of peroxidase in proteolytic turnover. Taken together, these findings improved our understanding of PeKFBs, especially in response to stresses, and laid a foundation for revealing the molecular mechanism of PeKFB9 in regulating lignin polymerization by degrading peroxidase. Full article

(This article belongs to the Special Issue Plant Genetics and Breeding Research Progress in Genomics to Post-genomics Era)

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19 pages, 6209 KiB

Open AccessArticle

A Comprehensive Gene Co-Expression Network Analysis Reveals a Role of GhWRKY46 in Responding to Drought and Salt Stresses

by Pengyun Chen, Fei Wei, Hongliang Jian, Tingli Hu, Baoquan Wang, Xiaoyan Lv, Hantao Wang, Xiaokang Fu, Shuxun Yu, Hengling Wei and Liang Ma

Int. J. Mol. Sci. 2022, 23(20), 12181; https://doi.org/10.3390/ijms232012181 - 12 Oct 2022

Cited by 3 | Viewed by 1746

Abstract

Abiotic stress, such as drought and salinity stress, seriously inhibit the growth and development of plants. Therefore, it is vital to understand the drought and salinity resistance mechanisms to enable cotton to provide more production under drought and salt conditions. In this study, [...] Read more.

Abiotic stress, such as drought and salinity stress, seriously inhibit the growth and development of plants. Therefore, it is vital to understand the drought and salinity resistance mechanisms to enable cotton to provide more production under drought and salt conditions. In this study, we identified 8806 and 9108 differentially expressed genes (DEGs) through a comprehensive analysis of transcriptomic data related to the PEG-induced osmotic and salt stress in cotton. By performing weighted gene co-expression network analysis (WGCNA), we identified four co-expression modules in PEG treatment and five co-expression modules in salinity stress, which included 346 and 324 predicted transcription factors (TFs) in these modules, respectively. Correspondingly, whole genome duplication (WGD) events mainly contribute to the expansion of those TFs. Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO) analyses revealed those different modules were associated with stress resistance, including regulating macromolecule metabolic process, peptidase activity, transporter activity, lipid metabolic process, and responses to stimulus. Quantitative RT-PCR analysis was used to confirm the expression levels of 15 hub TFs in PEG6000 and salinity treatments. We found that the hub gene GhWRKY46 could alter salt and PEG-induced drought resistance in cotton through the virus-induced gene silencing (VIGS) method. Our results provide a preliminary framework for further investigation of the cotton response to salt and drought stress, which is significant to breeding salt- and drought-tolerant cotton varieties. Full article

(This article belongs to the Special Issue Plant Genetics and Breeding Research Progress in Genomics to Post-genomics Era)

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15 pages, 2577 KiB

Open AccessArticle

De Novo Assembly of a Sarcocarp Transcriptome Set Identifies AaMYB1 as a Regulator of Anthocyanin Biosynthesis in Actinidia arguta var. purpurea

by Bei Niu, Qiaohong Li, Lijuan Fan, Xiaodong Shi, Yuan Liu, Qiguo Zhuang and Xiaobo Qin

Int. J. Mol. Sci. 2022, 23(20), 12120; https://doi.org/10.3390/ijms232012120 - 11 Oct 2022

Viewed by 1624

Abstract

The kiwifruit (Actinidia arguta var. purpurea) produces oval shaped fruits containing a slightly green or mauve outer exocarp and a purple-flesh endocarp with rows of tiny black seeds. The flesh color of the fruit results from a range of anthocyanin compounds, and [...] Read more.

The kiwifruit (Actinidia arguta var. purpurea) produces oval shaped fruits containing a slightly green or mauve outer exocarp and a purple-flesh endocarp with rows of tiny black seeds. The flesh color of the fruit results from a range of anthocyanin compounds, and is an important trait for kiwifruit consumers. To elucidate the molecular mechanisms involved in anthocyanin biosynthesis of the sarcocarp during A. arguta fruit development, de novo assembly and transcriptomic profile analyses were performed. Based on significant Gene Ontology (GO) biological terms, differentially expressed genes were identified in flavonoid biosynthetic and metabolic processes, pigment biosynthesis, carbohydrate metabolic processes, and amino acid metabolic processes. The genes closely related to anthocyanin biosynthesis, such as phenylalanine ammonia-lyase (PAL), chalcone synthase (CHS), and anthocyanidin synthase (ANS), displayed significant up-regulation during fruit development according to the transcriptomic data, which was further confirmed by qRT-PCR. Meanwhile, a series of transcription factor genes were identified among the DEGs. Through a correlation analysis. AaMYB1 was found to be significantly correlated with key genes of anthocyanin biosynthesis, especially with CHS. Through a transient expression assay, AaMYB1 induced anthocyanin accumulation in tobacco leaves. These data provide an important basis for exploring the related mechanisms of sarcocarp anthocyanin biosynthesis in A. arguta. This study will provide a strong foundation for functional studies on A. arguta and will facilitate improved breeding of A. arguta fruit. Full article

(This article belongs to the Special Issue Plant Genetics and Breeding Research Progress in Genomics to Post-genomics Era)

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16 pages, 4031 KiB

Open AccessArticle

Identification of the 14-3-3 Gene Family in Bamboo and Characterization of Pe14-3-3b Reveals Its Potential Role in Promoting Growth

by Dong Guo, Chenglei Zhu, Kebin Yang, Yan Liu, Xiaoyan Xiao, Ziyang Li and Zhimin Gao

Int. J. Mol. Sci. 2022, 23(19), 11221; https://doi.org/10.3390/ijms231911221 - 23 Sep 2022

Cited by 4 | Viewed by 1546

Abstract

The 14-3-3 protein family plays an important role in regulating plant growth and development. The genes of the 14-3-3 family have been reported in multiple species. However, little is known about the 14-3-3 gene family in bamboo. In this study, a total of [...] Read more.

The 14-3-3 protein family plays an important role in regulating plant growth and development. The genes of the 14-3-3 family have been reported in multiple species. However, little is known about the 14-3-3 gene family in bamboo. In this study, a total of 58 genes belonging to the 14-3-3 family were identified in three representative bamboo species, i.e., Olyra latifolia, Phyllostachys edulis, and Bonia amplexicaulis, whose encoding proteins were grouped into ε and non-ε groups by phylogeny analysis with 14-3-3 proteins from Arabidopsis thaliana and Oryza sativa. The 14-3-3s had diverse gene structures and motif characteristics among the three bamboo species. Collinearity analysis suggested that the genes of the 14-3-3 family in bamboo had undergone a strong purification selection during evolution. Tissue-specific expression analysis showed the expression of Pe14-3-3s varied in different tissues of P. edulis, suggesting that they had functional diversity during growth and development. Co-expression analysis showed that four Pe14-3-3s co-expressed positively with eight ribosomal genes. Yeast two-hybrid (Y2H) assays showed that Pe14-3-3b/d could interact with Pe_ribosome-1/5/6, and qPCR results demonstrated that Pe14-3-3b/d and Pe_ribosome-1/5/6 had similar expression trends with the increase in shoot height, which further confirmed that they would work together to participate in the shoot growth and development of bamboo. Additionally, the transgenic Arabidopsis plants overexpressing Pe14-3-3b had longer roots, a larger stem diameter, an earlier bolting time and a faster growth rate than wild-type Arabidopsis, indicating that Pe14-3-3b acted as a growth promoter. Our results provide comprehensive information on 14-3-3 genes in bamboo and highlight Pe14-3-3b as a potential target for bamboo improvement. Full article

(This article belongs to the Special Issue Plant Genetics and Breeding Research Progress in Genomics to Post-genomics Era)

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23 pages, 4638 KiB

Open AccessArticle

Genome-Wide Association Study in Bread Wheat Identifies Genomic Regions Associated with Grain Yield and Quality under Contrasting Water Availability

by Nikolai Govta, Iris Polda, Hanan Sela, Yafit Cohen, Diane M. Beckles, Abraham B. Korol, Tzion Fahima, Yehoshua Saranga and Tamar Krugman

Int. J. Mol. Sci. 2022, 23(18), 10575; https://doi.org/10.3390/ijms231810575 - 12 Sep 2022

Cited by 9 | Viewed by 2613

Abstract

The objectives of this study were to identify genetic loci in the bread wheat genome that would influence yield stability and quality under water stress, and to identify accessions that can be recommended for cultivation in dry and hot regions. We performed a [...] Read more.

The objectives of this study were to identify genetic loci in the bread wheat genome that would influence yield stability and quality under water stress, and to identify accessions that can be recommended for cultivation in dry and hot regions. We performed a genome-wide association study (GWAS) using a panel of 232 wheat accessions spanning diverse ecogeographic regions. Plants were evaluated in the Israeli Northern Negev, under two environments: water-limited (D; 250 mm) and well-watered (W; 450 mm) conditions; they were genotyped with ~71,500 SNPs derived from exome capture sequencing. Of the 14 phenotypic traits evaluated, 12 had significantly lower values under D compared to W conditions, while the values for two traits were higher under D. High heritability (H² = 0.5–0.9) was observed for grain yield, spike weight, number of grains per spike, peduncle length, and plant height. Days to heading and grain yield could be partitioned based on accession origins. GWAS identified 154 marker-trait associations (MTAs) for yield and quality-related traits, 82 under D and 72 under W, and identified potential candidate genes. We identified 24 accessions showing high and/or stable yields under D conditions that can be recommended for cultivation in regions under the threat of global climate change. Full article

(This article belongs to the Special Issue Plant Genetics and Breeding Research Progress in Genomics to Post-genomics Era)

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17 pages, 4220 KiB

Open AccessArticle

Transcriptome Analysis and Gene Expression Profiling of the Peanut Small Seed Mutant Identified Genes Involved in Seed Size Control

by Fengdan Guo, Xiujin Zhu, Chuanzhi Zhao, Shuzhen Zhao, Jiaowen Pan, Yanxiu Zhao, Xingjun Wang and Lei Hou

Int. J. Mol. Sci. 2022, 23(17), 9726; https://doi.org/10.3390/ijms23179726 - 27 Aug 2022

Cited by 3 | Viewed by 1773

Abstract

Seed size is a key factor affecting crop yield and a major agronomic trait concerned in peanut (Arachis hypogaea L.) breeding. However, little is known about the regulation mechanism of peanut seed size. In the present study, a peanut small seed mutant [...] Read more.

Seed size is a key factor affecting crop yield and a major agronomic trait concerned in peanut (Arachis hypogaea L.) breeding. However, little is known about the regulation mechanism of peanut seed size. In the present study, a peanut small seed mutant1 (ssm1) was identified through irradiating peanut cultivar Luhua11 (LH11) using ⁶⁰Coγ ray. Since the globular embryo stage, the embryo size of ssm1 was significantly smaller than that of LH11. The dry seed weight of ssm1 was only 39.69% of the wild type LH14. The seeds were wrinkled with darker seed coat. The oil content of ssm1 seeds were also decreased significantly. Seeds of ssm1 and LH11 were sampled 10, 20, and 40 days after pegging (DAP) and were used for RNA-seq. The results revealed that genes involved in plant hormones and several transcription factors related to seed development were differentially expressed at all three stages, especially at DAP10 and DAP20. Genes of fatty acid biosynthesis and late embryogenesis abundant protein were significantly decreased to compare with LH11. Interestingly, the gene profiling data suggested that PKp2 and/or LEC1 could be the key candidate genes leading to the small seed phenotype of the mutant. Our results provide valuable clues for further understanding the mechanisms underlying seed size control in peanut. Full article

(This article belongs to the Special Issue Plant Genetics and Breeding Research Progress in Genomics to Post-genomics Era)

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16 pages, 5169 KiB

Open AccessArticle

Transcriptional Analysis on Resistant and Susceptible Kiwifruit Genotypes Activating Different Plant-Immunity Processes against Pseudomonas syringae pv. actinidiae

by Xiaobo Qin, Min Zhang, Qiaohong Li, Dalei Chen, Leiming Sun, Xiujuan Qi, Ke Cao and Jinbao Fang

Int. J. Mol. Sci. 2022, 23(14), 7643; https://doi.org/10.3390/ijms23147643 - 11 Jul 2022

Cited by 4 | Viewed by 2047

Abstract

Pseudomonas syringae pv. actinidiae (Psa), a bacterial pathogen, is a severe threat to kiwifruit production. To elucidate the species-specific interaction between Psa and kiwifruit, transcriptomic-profiles analyses were conducted, under Psa-infected treatment and mock-inoculated control, on shoots of resistant Maohua (MH) and susceptible Hongyang [...] Read more.

Pseudomonas syringae pv. actinidiae (Psa), a bacterial pathogen, is a severe threat to kiwifruit production. To elucidate the species-specific interaction between Psa and kiwifruit, transcriptomic-profiles analyses were conducted, under Psa-infected treatment and mock-inoculated control, on shoots of resistant Maohua (MH) and susceptible Hongyang (HY) kiwifruit varieties. The plant hormone-signal transduction and plant–pathogen interaction were significantly enriched in HY compared with MH. However, the starch and sucrose metabolism, antigen processing and presentation, phagosome, and galactose metabolism were significantly enriched in MH compared with HY. Interestingly, the MAP2 in the pathogen/microbe-associated molecular patterns (PAMPs)-triggered immunity (PTI) was significantly up-regulated in MH. The genes RAR1, SUGT1, and HSP90A in the effector-triggered immunity (ETI), and the NPR1 and TGA genes involved in the salicylic acid signaling pathway as regulatory roles of ETI, were significantly up-regulated in HY. Other important genes, such as the CCRs involved in phenylpropanoid biosynthesis, were highly expressed in MH, but some genes in the Ca²⁺ internal flow or involved in the reactive oxygen metabolism were obviously expressed in HY. These results suggested that the PTI and cell walls involved in defense mechanisms were significant in MH against Psa infection, while the ETI was notable in HY against Psa infection. This study will help to understand kiwifruit bacterial canker disease and provide important theoretical support in kiwifruit breeding. Full article

(This article belongs to the Special Issue Plant Genetics and Breeding Research Progress in Genomics to Post-genomics Era)

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11 pages, 1712 KiB

Open AccessArticle

First Report on Genome Editing via Ribonucleoprotein (RNP) in Castanea sativa Mill.

by Vera Pavese, Andrea Moglia, Silvia Abbà, Anna Maria Milani, Daniela Torello Marinoni, Elena Corredoira, Maria Teresa Martínez and Roberto Botta

Int. J. Mol. Sci. 2022, 23(10), 5762; https://doi.org/10.3390/ijms23105762 - 20 May 2022

Cited by 12 | Viewed by 2781

Abstract

Castanea sativa is an important tree nut species worldwide, highly appreciated for its multifunctional role, in particular for timber and nut production. Nowadays, new strategies are needed to achieve plant resilience to diseases, climate change, higher yields, and nutritional quality. Among the new [...] Read more.

Castanea sativa is an important tree nut species worldwide, highly appreciated for its multifunctional role, in particular for timber and nut production. Nowadays, new strategies are needed to achieve plant resilience to diseases, climate change, higher yields, and nutritional quality. Among the new plant breeding techniques (NPBTs), the CRISPR/Cas9 system represents a powerful tool to improve plant breeding in a short time and inexpensive way. In addition, the CRISPR/Cas9 construct can be delivered into the cells in the form of ribonucleoproteins (RNPs), avoiding the integration of exogenous DNA (GMO-free) through protoplast technology that represents an interesting material for gene editing thanks to the highly permeable membrane to DNA. In the present study, we developed the first protoplast isolation protocol starting from European chestnut somatic embryos. The enzyme solution optimized for cell wall digestion contained 1% cellulase Onozuka R-10 and 0.5% macerozyme R-10. After incubation for 4 h at 25 °C in dark conditions, a yield of 4,500,000 protoplasts/mL was obtained (91% viable). The transfection capacity was evaluated using the GFP marker gene, and the percentage of transfected protoplasts was 51%, 72 h after the transfection event. The direct delivery of the purified RNP was then performed targeting the phytoene desaturase gene. Results revealed the expected target modification by the CRISPR/Cas9 RNP and the efficient protoplast editing. Full article

(This article belongs to the Special Issue Plant Genetics and Breeding Research Progress in Genomics to Post-genomics Era)

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