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

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 18011

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Prof. Dr. Xueli An

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Guest Editor

Research Center of Biology and Agriculture, Shunde Graduate School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
Interests: plant transformation; genome editing; male sterility; pollen and anther development; molecular breeding

Prof. Dr. Yan Long

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Guest Editor

Research Center of Biology and Agriculture, Shunde Graduate School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
Interests: genetic mapping; gene cloning; QTL; GWAS; genomic selection; marker-assisted selection

Special Issue Information

Dear Colleagues,

Biotechnology is a fast-developing field of genetics, molecular biology, biochemistry and cellular biology, focusing on gene engineering, cell engineering, enzyme engineering and fermentation engineering. Recent development of biotechnologies and advances in crop breeding have facilitated the cultivation of many varieties with high yield, multiple resistance and good quality.

The purpose of this Special Issue is to report the recent progress achieved in biotechnologies and crop breeding. This includes, but is not limited to, plant transformation, genome editing, genetic modification, genome sequencing, gene synthesis, bioinformatics, genetic mapping, SNP discovery, quantitative trait loci analysis, genome-wide association study, genomic selection or prediction, molecular-assisted selection and plant molecular farming.

Manuscripts can be in the form of original research articles or reviews. We believe your contribution will have a significant influence on future biotechnology utilization in crop breeding.

Prof. Dr. Xueli An
Prof. Dr. Yan Long
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

bioinformatics
genetic engineering
genome editing
genome sequencing
genomic selection or prediction
genome-wide association study
map-based cloning
molecular-assisted selection plant molecular farming
plant genetic transformation
quantitative trait loci analysis

Published Papers (10 papers)

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Research

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20 pages, 8752 KiB

Open AccessArticle

Transfer of Stress Resilient QTLs and Panicle Traits into the Rice Variety, Reeta through Classical and Marker-Assisted Breeding Approaches

by Saumya Ranjan Barik, Arpita Moharana, Elssa Pandit, Abhisarika Behera, Ankita Mishra, Shakti Prakash Mohanty, Shibani Mohapatra, Priyadarsini Sanghamitra, Jitendriya Meher, Dipti Ranjan Pani, Vijai Pal Bhadana, Shiv Datt, Chita Ranjan Sahoo, Reshmi Raj K. R. and Sharat Kumar Pradhan

Int. J. Mol. Sci. 2023, 24(13), 10708; https://doi.org/10.3390/ijms241310708 - 27 Jun 2023

Cited by 2 | Viewed by 1472

Abstract

Reeta is a popular late-maturing high-yielding rice variety recommended for cultivation in the eastern Indian states. The cultivar is highly sensitive to submergence stress. Phosphorus deficiency is an additional constraint for realizing high yield. The quantitative trait loci (QTLs), Sub1, for submergence and Pup1 for low phosphorus stress tolerance along with narrow-grained trait, GW5 were introgressed into the variety from the donor parent, Swarna-Sub1 through marker-assisted breeding. In addition, phenotypic selections for higher panicle weight, grain number, and spikelet fertility were performed in each segregating generation. Foreground selection detected the 3 target QTLs in 9, 8 and 7 progenies in the BC₁F₁, BC₂F₁, and BC₃F₁ generation, respectively. Recurrent parent’s genome recovery was analyzed using 168 SSR polymorphic markers. The foreground analysis in 452 BC₃F₂ progenies showed five pyramided lines in homozygous condition for the target QTLs. No donor fragment drag was noticed in the Sub1 and GW5 QTLs carrier while a segmentwas observed in the Pup1 carrier chromosome. The developed lines were higher yielding, had submergence, and had low phosphorus stress-tolerance alongwith similar to the recipient parent in the studied morpho-quality traits. A promising pyramided line is released in the name of Reeta-Panidhan (CR Dhan 413) for the flood-prone areas of Odisha state. Full article

(This article belongs to the Special Issue Biotechnology and Crop Breeding)

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14 pages, 4511 KiB

Open AccessArticle

Comparative Transcriptome Analysis Reveals the Effect of the DHN Melanin Biosynthesis Pathway on the Appressorium Turgor Pressure of the Poplar Anthracnose-Causing Fungus Colletotrichum gloeosporioides

by Xinyu Qin, Chengming Tian and Fanli Meng

Int. J. Mol. Sci. 2023, 24(8), 7411; https://doi.org/10.3390/ijms24087411 - 18 Apr 2023

Cited by 1 | Viewed by 953

Abstract

Anthracnose of poplar caused by Colletotrichum gloeosporioides is a leaf disease that seriously affects poplar growth. The pathogen invades the host in the form of adherent cells, which generate turgor pressure through the metabolism of intracellular substances prior to penetrating the epidermis of poplar leaves. In this study, the expansion-related pressure of the mature appressorium of the wild-type C. gloeosporioides was approximately 13.02 ± 1.54 MPa at 12 h, whereas it was 7.34 ± 1.23 MPa and 9.34 ± 2.22 MPa in the melanin synthesis-related gene knockout mutants ΔCgCmr1 and ΔCgPks1, respectively. The CgCmr1 and CgPks1 genes were highly expressed at 12 h in the wild-type control, implying that the DHN melanin biosynthesis pathway may play an important role in the mature appressorium stage. The transcriptome sequencing analysis indicated that the upregulated melanin biosynthesis genes in C. gloeosporioides, such as CgScd1, CgAyg1, CgThr1, CgThr2, and CgLac1, are involved in specific KEGG pathways (i.e., fatty acid biosynthesis, fatty acid metabolism, and biotin metabolism). Therefore, we speculate that the melanin synthesis-related genes and fatty acid metabolism pathway genes contribute to the regulation of the turgor pressure in the mature C. gloeosporioides appressorium, ultimately leading to the formation of infection pegs that enter plant tissues. These observations may reflect the co-evolution of C. gloeosporioides and its host. Full article

(This article belongs to the Special Issue Biotechnology and Crop Breeding)

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16 pages, 3414 KiB

Open AccessArticle

Concomitant Activation of OsNAS2 and OsNAS3 Contributes to the Enhanced Accumulation of Iron and Zinc in Rice

by Sichul Lee, Md Mizanor Rahman, Hiromi Nakanishi, Naoko K. Nishizawa, Gynheung An, Hong Gil Nam and Jong-Seong Jeon

Int. J. Mol. Sci. 2023, 24(7), 6568; https://doi.org/10.3390/ijms24076568 - 31 Mar 2023

Cited by 5 | Viewed by 1410

Abstract

Nicotianamine (NA) is produced by NA synthase (NAS), which contains three genes in rice and is responsible for chelating metals such as iron (Fe) and zinc (Zn), as well as preserving metal homeostasis. In this study, we generated a transgenic plant (23D) that shows simultaneous activation of OsNAS2 and OsNAS3 by crossing two previously identified activation-tagged mutants, OsNAS2-D1 (2D) and OsNAS3-D1 (3D). Concomitant activation of both genes resulted in the highest Fe and Zn concentrations in shoots and roots of the 23D plants grown under normal conditions and Fe and Zn limited growth conditions. Expression of genes for the biosynthesis of mugineic acid family phytosiderophores (MAs) and Fe and Zn uptake were enhanced in 23D roots. Additionally, 23D plants displayed superior growth to other plants at higher pH levels. Importantly, 23D seeds had NA and 2′-deoxymugineic acid (DMA) concentrations that were 50.6- and 10.0-fold higher than those of the WT. As a result, the mature grain Fe and Zn concentrations of the 23D plant were 4.0 and 3.5 times greater, respectively, than those of the WT. Furthermore, 23D plants exhibited the greatest resistance to excess metals. Our research suggests that simultaneous activation of OsNAS2 and OsNAS3 can enhance Fe and Zn accumulation in rice grains while also increasing plant tolerance to growing situations with metal deficiency and excess metal availability. Full article

(This article belongs to the Special Issue Biotechnology and Crop Breeding)

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11 pages, 2660 KiB

Open AccessArticle

A LuALS Mutation with High Sulfonylurea Herbicide Resistance in Linum usitatissimum L.

by Caiyue Liu, Tianbao Zhang, Xinsen Yang, Liu Wang, Yan Long, Agula Hasi and Xinwu Pei

Int. J. Mol. Sci. 2023, 24(3), 2820; https://doi.org/10.3390/ijms24032820 - 01 Feb 2023

Viewed by 1645

Abstract

The cultivation of herbicide-resistant crops is an effective tool for weed management in agriculture. Weed control in flax (Linum usitatissimum L.) remains challenging due to the lack of available herbicide-resistant cultivars. In this study, a mutant resistant to acetolactate synthase (ALS)-inhibiting herbicides was obtained by ethyl methanesulphonate (EMS) mutagenesis using an elite cultivar, Longya10. Whole-plant dose–response assays revealed that, compared to Longya10, the mutant was 11.57-fold more resistant to tribenuron-methyl (TBM) and slightly resistant to imazethapyr (resistance index (mutant/Longya10) < 3). In vitro acetolactate synthase assays showed that the relative resistance of the mutant was 12.63 times more than that of Longya10. A biochemical analysis indicated that there was a Pro197Ser (relative to the Arabidopsis thaliana ALS sequence) substitution within the LuALS1, conferring high resistance to sulfonylurea herbicides in the mutant. Additionally, two cleaved amplified polymorphic sequence (CAPS) markers, BsaI-LuALS1 and EcoO109I-LuALS1, were developed based on the mutation site for marker assistant selection in breeding. Moreover, the mutant did not cause losses in natural field conditions. We find a mutant with ALS-inhibiting herbicide resistance chemically induced by EMS mutagenesis, providing a valuable germplasm for breeding herbicide-resistant flax varieties. Full article

(This article belongs to the Special Issue Biotechnology and Crop Breeding)

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20 pages, 5533 KiB

Open AccessArticle

Genome-Wide Identification and Expression Analysis of UBiA Family Genes Associated with Abiotic Stress in Sunflowers (Helianthus annuus L.)

by Mingzhe Sun, Maohong Cai, Qinzong Zeng, Yuliang Han, Siqi Zhang, Yingwei Wang, Qinyu Xie, Youheng Chen, Youling Zeng and Tao Chen

Int. J. Mol. Sci. 2023, 24(3), 1883; https://doi.org/10.3390/ijms24031883 - 18 Jan 2023

Cited by 1 | Viewed by 1316

Abstract

The UBiA genes encode a large class of isopentenyltransferases, which are involved in the synthesis of secondary metabolites such as chlorophyll and vitamin E. They performed important functions in the whole plant’s growth and development. Current studies on UBiA genes were not comprehensive enough, especially for sunflower UBiA genes. In this study, 10 HaUBiAs were identified by domain analysis these HaUBiAs had five major conserved domains and were unevenly distributed on six chromosomes. By constructing phylogenetic trees, 119 UBiA genes were found in 12 species with different evolutionary levels and divided into five major groups, which contained seven conserved motifs and eight UBiA subsuper family domains. Tissue expression analysis showed that HaUBiAs were highly expressed in the roots, leaves, and seeds. By using promoter analysis, the cis-elements of UBiA genes were mainly in hormone signaling and stress responses. The qRT-PCR results showed that HaUBiA1 and HaUBiA5 responded strongly to abiotic stresses. Under ABA and MeJA treatments, HaUBiA1 significantly upregulated, while HaUBiA5 significantly decreased. Under cold stress, the expression of UBiA1 was significantly upregulated in the roots and stems, while UBiA5 expression was increased only in the leaves. Under anaerobic induction, UBiA1 and UBiA5 were both upregulated in the roots, stems and leaves. In summary, this study systematically classified the UBiA family and identified two abiotic stress candidate genes in the sunflower. It expands the understanding of the UBiA family and provides a theoretical basis for future abiotic stress studies in sunflowers. Full article

(This article belongs to the Special Issue Biotechnology and Crop Breeding)

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22 pages, 8924 KiB

Open AccessArticle

A Systematic Investigation of Lipid Transfer Proteins Involved in Male Fertility and Other Biological Processes in Maize

by Chaowei Fang, Suowei Wu, Ziwen Li, Shuangshuang Pan, Yuru Wu, Xueli An, Yan Long, Xun Wei and Xiangyuan Wan

Int. J. Mol. Sci. 2023, 24(2), 1660; https://doi.org/10.3390/ijms24021660 - 14 Jan 2023

Cited by 5 | Viewed by 2025

Abstract

Plant lipid transfer proteins (LTPs) play essential roles in various biological processes, including anther and pollen development, vegetative organ development, seed development and germination, and stress response, but the research progress varies greatly among Arabidopsis, rice and maize. Here, we presented a preliminary introduction and characterization of the whole 65 LTP genes in maize, and performed a phylogenetic tree and gene ontology analysis of the LTP family members in maize. We compared the research progresses of the reported LTP genes involved in male fertility and other biological processes in Arabidopsis and rice, and thus provided some implications for their maize orthologs, which will provide useful clues for the investigation of LTP transporters in maize. We predicted the functions of LTP genes based on bioinformatic analyses of their spatiotemporal expression patterns by using RNA-seq and qRT-PCR assays. Finally, we discussed the advances and challenges in substrate identification of plant LTPs, and presented the future research directions of LTPs in plants. This study provides a basic framework for functional research and the potential application of LTPs in multiple plants, especially for male sterility research and application in maize. Full article

(This article belongs to the Special Issue Biotechnology and Crop Breeding)

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30 pages, 5326 KiB

Open AccessArticle

A Systemic Investigation of Genetic Architecture and Gene Resources Controlling Kernel Size-Related Traits in Maize

by Cheng Wang, Huangai Li, Yan Long, Zhenying Dong, Jianhui Wang, Chang Liu, Xun Wei and Xiangyuan Wan

Int. J. Mol. Sci. 2023, 24(2), 1025; https://doi.org/10.3390/ijms24021025 - 05 Jan 2023

Cited by 5 | Viewed by 1923

Abstract

Grain yield is the most critical and complex quantitative trait in maize. Kernel length (KL), kernel width (KW), kernel thickness (KT) and hundred-kernel weight (HKW) associated with kernel size are essential components of yield-related traits in maize. With the extensive use of quantitative trait locus (QTL) mapping and genome-wide association study (GWAS) analyses, thousands of QTLs and quantitative trait nucleotides (QTNs) have been discovered for controlling these traits. However, only some of them have been cloned and successfully utilized in breeding programs. In this study, we exhaustively collected reported genes, QTLs and QTNs associated with the four traits, performed cluster identification of QTLs and QTNs, then combined QTL and QTN clusters to detect consensus hotspot regions. In total, 31 hotspots were identified for kernel size-related traits. Their candidate genes were predicted to be related to well-known pathways regulating the kernel developmental process. The identified hotspots can be further explored for fine mapping and candidate gene validation. Finally, we provided a strategy for high yield and quality maize. This study will not only facilitate causal genes cloning, but also guide the breeding practice for maize. Full article

(This article belongs to the Special Issue Biotechnology and Crop Breeding)

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17 pages, 6677 KiB

Open AccessArticle

MbICE1 Confers Drought and Cold Tolerance through Up-Regulating Antioxidant Capacity and Stress-Resistant Genes in Arabidopsis thaliana

by Yadong Duan, Jiaxin Han, Baitao Guo, Wenbo Zhao, Shuang Zhou, Chunwei Zhou, Lei Zhang, Xingguo Li and Deguo Han

Int. J. Mol. Sci. 2022, 23(24), 16072; https://doi.org/10.3390/ijms232416072 - 16 Dec 2022

Cited by 8 | Viewed by 1309

Abstract

Malus baccata (L.) Borkh is an apple rootstock with good drought and cold resistance. The ICE gene is a key factor in the molecular mechanisms of plant drought and cold resistance. In the present research, the function of drought- and cold-induced MbICE1 of Malus baccata was investigated in Arabidopsis. According to GFP fluorescence images, MbICE1 was determined to be a nuclear protein. The MbICE1 was transferred to Arabidopsis, showing enhanced tolerance to drought and cold stresses. Under drought and cold treatments, the transgenic Arabidopsis had higher chlorophyll content and free proline content than WT plants, but the Malondialdehyde (MDA) content and electrolyte leakage (EL) were lower than those of WT plants. In addition, drought and cold led to a large accumulation of ROS (H₂O₂ and O²⁻) content in Arabidopsis, while overexpression of MbICE1 enhanced the antioxidant enzyme activity in Arabidopsis and improved the plant’s resistance to stresses. Moreover, the accumulation of MbICE1 promoted the expression of AtCBF1, AtCBF2, AtCBF3, AtCOR15a, AtCOR47 and AtKIN1 genes in Arabidopsis. These data indicate that MbICE1 is a key regulator of drought and cold and can be used as a backup gene for breeding Malus rootstocks. Full article

(This article belongs to the Special Issue Biotechnology and Crop Breeding)

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18 pages, 6185 KiB

Open AccessArticle

Genome-Wide Analysis and Functional Characterization of Pyruvate Kinase (PK) Gene Family Modulating Rice Yield and Quality

by Nannan Dong, Luna Chen, Shakeel Ahmad, Yicong Cai, Yingqing Duan, Xinwei Li, Yongqiang Liu, Guiai Jiao, Lihong Xie, Shikai Hu, Zhonghua Sheng, Gaoneng Shao, Ling Wang, Shaoqing Tang, Xiangjin Wei and Peisong Hu

Int. J. Mol. Sci. 2022, 23(23), 15357; https://doi.org/10.3390/ijms232315357 - 05 Dec 2022

Cited by 3 | Viewed by 1648

Abstract

Pyruvate kinase (PK) is one of the three rate-limiting enzymes of glycolysis, and it plays a pivotal role in energy metabolism. In this study, we have identified 10 PK genes from the rice genome. Initially, these genes were divided into two categories: cytoplasmic pyruvate kinase (PKc) and plastid pyruvate kinase (PKp). Then, an expression analysis revealed that OsPK1, OsPK3, OsPK4, OsPK6, and OsPK9 were highly expressed in grains. Moreover, PKs can form heteropolymers. In addition, it was found that ABA significantly regulates the expression of PK genes (OsPK1, OsPK4, OsPK9, and OsPK10) in rice. Intriguingly, all the genes were found to be substantially involved in the regulation of rice grain quality and yield. For example, the disruption of OsPK3, OsPK5, OsPK7, OsPK8, and OsPK10 and OsPK4, OsPK5, OsPK6, and OsPK10 decreased the 1000-grain weight and the seed setting rate, respectively. Further, the disruption of OsPK4, OsPK6, OsPK8, and OsPK10 through the CRISPR/Cas9 system showed an increase in the content of total starch and a decrease in protein content compared to the WT. Similarly, manipulations of the OsPK4, OsPK8, and OsPK10 genes increased the amylose content. Meanwhile, the grains of all CRISPR mutants and RNAi lines, except ospk6, showed a significant increase in the chalkiness rate compared to the wild type. Overall, this study characterizes the functions of all the genes of the PK gene family and shows their untapped potential to improve rice yield and quality traits. Full article

(This article belongs to the Special Issue Biotechnology and Crop Breeding)

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Review

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21 pages, 1846 KiB

Open AccessReview

Technological Development and Application of Plant Genetic Transformation

by Wenbin Su, Mingyue Xu, Yasmina Radani and Liming Yang

Int. J. Mol. Sci. 2023, 24(13), 10646; https://doi.org/10.3390/ijms241310646 - 26 Jun 2023

Cited by 7 | Viewed by 3627

Abstract

Genetic transformation is an important strategy for enhancing plant biomass or resistance in response to adverse environments and population growth by imparting desirable genetic characteristics. Research on plant genetic transformation technology can promote the functional analysis of plant genes, the utilization of excellent traits, and precise breeding. Various technologies of genetic transformation have been continuously discovered and developed for convenient manipulation and high efficiency, mainly involving the delivery of exogenous genes and regeneration of transformed plants. Here, currently developed genetic transformation technologies were expounded and compared. Agrobacterium-mediated gene delivery methods are commonly used as direct genetic transformation, as well as external force-mediated ways such as particle bombardment, electroporation, silicon carbide whiskers, and pollen tubes as indirect ones. The regeneration of transformed plants usually involves the de novo organogenesis or somatic embryogenesis pathway of the explants. Ectopic expression of morphogenetic transcription factors (Bbm, Wus2, and GRF-GIF) can significantly improve plant regeneration efficiency and enable the transformation of some hard-to-transform plant genotypes. Meanwhile, some limitations in these gene transfer methods were compared including genotype dependence, low transformation efficiency, and plant tissue damage, and recently developed flexible approaches for plant genotype transformation are discussed regarding how gene delivery and regeneration strategies can be optimized to overcome species and genotype dependence. This review summarizes the principles of various techniques for plant genetic transformation and discusses their application scope and limiting factors, which can provide a reference for plant transgenic breeding. Full article

(This article belongs to the Special Issue Biotechnology and Crop Breeding)

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