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Crop Functional Genomics and Biological Breeding
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Crop Functional Genomics and Biological Breeding

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: 31 December 2024 | Viewed by 4851

Special Issue Editors

Dr. Yifeng Wang

E-Mail Website
Guest Editor
State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
Interests: functional genomics; crop; biological breeding; phytohormone; molecular mechanism
Special Issues, Collections and Topics in MDPI journals
Dr. Jie Huang

E-Mail Website
Guest Editor
State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
Interests: plant genetics; molecular biology; biochemistry; seed science; functional genomics; synthetic biology
Special Issues, Collections and Topics in MDPI journals
Dr. Jian Zhang

E-Mail Website
Guest Editor
State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
Interests: rice (Oryza sativa L.); reproductive development; germination; fertility; synthetic biology; protein interactome
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Jiezheng Ying

E-Mail Website
Guest Editor
State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
Interests: rice (Oryza sativa L.); quantitative trait locus; seed development; grain weight
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Currently, crop breeders focus on improving crop yield, resistance and quality through biological breeding. The study of the functional genomics of crops is a crucial approach in biological breeding. Understanding the functional genomics of crops provides insights into the genetic mechanisms governing crucial traits such as yield, resistance to diseases and pests, tolerance to environmental stresses and quality. This knowledge is instrumental in developing improved crop varieties with enhanced productivity and resilience, contributing to global efforts to ensure an adequate and stable food supply. The goal of this Special Issue of Plants, titled “Crop Functional Genomics and Biological Breeding”, is to provide an overview of the latest research and discoveries in the functional genomics of crops, including the mapping and cloning of novel genes related to crops yield, resistance, germination and quality. The included research can encompass the functional analysis of these genes and investigate their applications in biological breeding. We welcome all types of submissions, including original research, reviews and methodologies in this field, including (but not limited to) research covering the following topics:

  • Cloning and functional studies of new crop genes;
  • Bioinformatics analysis of functional genes in crops;
  • The application of rice functional genomics in crop breeding.

Dr. Yifeng Wang
Dr. Jie Huang
Dr. Jian Zhang
Prof. Dr. Jiezheng Ying
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. Plants 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 2700 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

  • crops
  • functional genomics
  • biological breeding
  • yield
  • resistance
  • seed germination
  • quality
  • genetic improvement

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Published Papers (5 papers)

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Research

31 pages, 60968 KiB  
Article
Unveiling Salt Tolerance Mechanisms and Hub Genes in Alfalfa (Medicago sativa L.) Through Transcriptomic and WGCNA Analysis
by Fengdan Wang, Hanfu Wu, Mei Yang, Wen Xu, Wenjie Zhao, Rui Qiu, Ning Kang and Guowen Cui
Plants 2024, 13(22), 3141; https://doi.org/10.3390/plants13223141 - 8 Nov 2024
Viewed by 513
Abstract
Alfalfa (Medicago sativa L.), an important forage crop with high nutritional value and good palatability, plays a vital role in the development of animal husbandry in China. In Northeast China, there are vast areas of saline–alkali land that remain undeveloped. Given that [...] Read more.
Alfalfa (Medicago sativa L.), an important forage crop with high nutritional value and good palatability, plays a vital role in the development of animal husbandry in China. In Northeast China, there are vast areas of saline–alkali land that remain undeveloped. Given that alfalfa is a highly adaptable forage crop, exploring its salt tolerance at the molecular transcriptional level and identifying salt-tolerant genes has great significance for breeding salt-resistant alfalfa varieties. This also provides valuable genetic resources for better utilization of saline–alkali land. In this study, we conducted two rounds of screening on 41 alfalfa varieties and identified WL168 as a salt-sensitive variety and Longmu801 as a salt-tolerant variety. After 7 days of 300 mM salt stress, both varieties showed a decreasing trend in plant height, fresh weight, and dry weight over time, but Longmu801 demonstrated better water retention ability compared to WL168. Chlorophyll content also declined, but chlorophyll a and total chlorophyll levels in Longmu801 were higher than in WL168. Hydrogen peroxide and malondialdehyde levels increased overall, but Longmu801 had significantly lower levels than WL168 under prolonged stress. Both varieties showed increasing trends in soluble sugars, proline, and antioxidant enzymes (SOD, POD, CAT), with Longmu801 significantly outperforming WL168. This suggests that the two varieties share similar growth and physiological response mechanisms, with their differences primarily arising from variations in indicator levels. In the above, comparisons between varieties were conducted based on the relative values of the indicators in relation to their controls. Transcriptomic analysis revealed that under salt stress, Longmu801 had 16,485 differentially expressed genes (DEGs) relative to its control, while WL168 had 18,726 DEGs compared to its control. Among these, 2164 DEGs shared the same expression trend, with GO functions enriched in response to oxidative stress, nucleus, plasma membrane, and others. The KEGG pathways were enriched in phenylpropanoid biosynthesis, protein processing in the endoplasmic reticulum, starch and sucrose metabolism, and others. This suggests that alfalfa’s transcriptional response mechanism to salt stress involves these pathways. Additionally, the variety-specific DEGs were also enriched in the same KEGG pathways and GO functions, indicating that the differences between the two varieties stem from their unique stress-responsive DEGs, while their overall mechanisms for coping with stress remain similar. To further identify salt stress-related genes, this study conducted WGCNA analysis using 32,683 genes and physiological indicators. Six modules closely related to physiological traits were identified, and the top five genes ranked by degree in each module were selected as hub genes. Further analysis of these hub genes identified five genes directly related to salt stress: Msa085011, Msa0605650, Msa0397400, Msa1258740, and Msa0958830. Mantel test analysis revealed that these genes showed strong correlations with physiological indicators. This study will provide important insights for breeding salt-tolerant alfalfa varieties. Full article
(This article belongs to the Special Issue Crop Functional Genomics and Biological Breeding)
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14 pages, 5392 KiB  
Article
Phenotypic Analysis and Gene Cloning of Rice Floury Endosperm Mutant wcr (White-Core Rice)
by Yihao Yang, Xiaoyi Yang, Lingjun Wu, Zixing Sun, Yi Zhang, Ziyan Shen, Juan Zhou, Min Guo and Changjie Yan
Plants 2024, 13(18), 2653; https://doi.org/10.3390/plants13182653 - 22 Sep 2024
Viewed by 641
Abstract
The composition and distribution of storage substances in rice endosperm directly affect grain quality. A floury endosperm mutant, wcr (white-core rice), was identified, exhibiting a loose arrangement of starch granules with a floury opaque appearance in the inner layer of mature grains, resulting [...] Read more.
The composition and distribution of storage substances in rice endosperm directly affect grain quality. A floury endosperm mutant, wcr (white-core rice), was identified, exhibiting a loose arrangement of starch granules with a floury opaque appearance in the inner layer of mature grains, resulting in reduced grain weight. The total starch and amylose content remained unchanged, but the levels of the four component proteins in the mutant brown rice significantly decreased. Additionally, the milled rice (inner endosperm) showed a significant decrease in total starch and amylose content, accompanied by a nearly threefold increase in albumin content. The swelling capacity of mutant starch was reduced, and its chain length distribution was altered. The target gene was mapped on chromosome 5 within a 65 kb region. A frameshift mutation occurred due to an insertion of an extra C base in the second exon of the cyOsPPDKB gene, which encodes pyruvate phosphate dikinase. Expression analysis revealed that wcr not only affected genes involved in starch metabolism but also downregulated expression levels of genes associated with storage protein synthesis. Overall, wcr plays a crucial role as a regulator factor influencing protein synthesis and starch metabolism in rice grains. Full article
(This article belongs to the Special Issue Crop Functional Genomics and Biological Breeding)
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19 pages, 5052 KiB  
Article
Genome-Wide Analysis of the Nramp Gene Family in Kenaf (Hibiscus cannabinus): Identification, Expression Analysis, and Response to Cadmium Stress
by Qin Liu, Shaocui Li, Guanghui Du and Xia An
Plants 2024, 13(17), 2514; https://doi.org/10.3390/plants13172514 - 7 Sep 2024
Viewed by 688
Abstract
Kenaf (Hibiscus cannabinu) is a grass bast fiber crop that has the ability to tolerate and accumulate heavy metals, and it has been considered as a potential heavy metal accumulator and remediation plant. Nramp is a natural resistance-related macrophage, which plays [...] Read more.
Kenaf (Hibiscus cannabinu) is a grass bast fiber crop that has the ability to tolerate and accumulate heavy metals, and it has been considered as a potential heavy metal accumulator and remediation plant. Nramp is a natural resistance-related macrophage, which plays an important role in the transport of divalent metal ions, plant growth and development, and abiotic stress. In this study, the Nramp gene family of kenaf was analyzed at the whole genome level. A total of 15 HcNramp genes were identified. They are distributed unevenly on chromosomes. Phylogenetic analysis classified 15 HcNramp proteins into 3 different subfamilies. All proteins share specific motif 4 and motif 6, and the genes belonging to the same subfamily are similar in structure and motif. The promoters are rich in hormone response, meristem expression, and environmental stress response elements. Under different treatments, the expression levels of HcNramp genes vary in different tissues, and most of them are expressed in roots first. These findings can provide a basis for understanding the potential role of the Nramp gene family in kenaf in response to cadmium (Cd) stress, and are of great significance for screening related Cd tolerance genes in kenaf. Full article
(This article belongs to the Special Issue Crop Functional Genomics and Biological Breeding)
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15 pages, 4269 KiB  
Article
Genome-Wide Analysis of the SAUR Gene Family and Its Expression Profiles in Response to Salt Stress in Santalum album
by Qing Zhu, Haoyue Zheng, Xu Hu, Yi Liu, Xinyi Zheng, Libei Li and Minqiang Tang
Plants 2024, 13(10), 1286; https://doi.org/10.3390/plants13101286 - 7 May 2024
Cited by 1 | Viewed by 1194
Abstract
The SAUR (small auxin-up RNA) family constitutes a category of genes that promptly respond to the hormone auxin and play a pivotal role in diverse biological processes encompassing plant growth and the response to abiotic stress. Santalum album L., a semi-parasitic evergreen tree, [...] Read more.
The SAUR (small auxin-up RNA) family constitutes a category of genes that promptly respond to the hormone auxin and play a pivotal role in diverse biological processes encompassing plant growth and the response to abiotic stress. Santalum album L., a semi-parasitic evergreen tree, is renowned for its economically valuable essential oils, positioning it among the most prized tree species. In this study, a meticulous identification and comprehensive analysis of 43 SAUR genes was conducted within S. album. Based on phylogenetic relationships, the SaSAUR genes were systematically categorized into five groups. A collinearity analysis revealed intriguing insights, disclosing 14 segmental duplications and 9 tandem duplications within the SaSAUR genes, emphasizing the pivotal role of duplication in the expansion of this gene family. Noteworthy variations in the expression levels of SaSAUR genes were observed by delving into the SaSAUR transcriptome data from various tissues, including leaves, roots, and heartwood, as well as under salt-stress conditions. Notably, SaSAUR08 and SaSAUR13 were significantly upregulated in heartwood compared with roots and leaves, while SaSAUR18 was markedly more expressed in roots compared with heartwood and leaves. Furthermore, SaSAUR27 and SaSAUR28 were found to respond closely to salt stress, hinting at their potential involvement in the salt-stress response mechanism. This research offers a comprehensive investigation of SAUR genes in S. album and establishes a foundation for future exploration of the SAUR gene family, particularly its relation to growth and salt-stress responses. Full article
(This article belongs to the Special Issue Crop Functional Genomics and Biological Breeding)
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18 pages, 5961 KiB  
Article
Rice Serine Hydroxymethyltransferases: Evolution, Subcellular Localization, Function and Perspectives
by Tian Pan, Hongmiao Jin, Chuanhui Zhou and Mengyuan Yan
Plants 2024, 13(8), 1116; https://doi.org/10.3390/plants13081116 - 16 Apr 2024
Cited by 1 | Viewed by 1132
Abstract
In rice, there is a lack of comprehensive research on the functional aspects of the members of the serine hydroxymethyltransferase (SHMT) gene family. This study provides a comprehensive investigation of the SHMT gene family, covering phylogeny, gene structure, promoter analysis, expression [...] Read more.
In rice, there is a lack of comprehensive research on the functional aspects of the members of the serine hydroxymethyltransferase (SHMT) gene family. This study provides a comprehensive investigation of the SHMT gene family, covering phylogeny, gene structure, promoter analysis, expression analysis, subcellular localization, and protein interaction. Remarkably, we discovered a specific gene loss event occurred in the chloroplast-localized group IIa SHMTs in monocotyledons. However, OsSHMT3, which originally classified within cytoplasmic-localized group Ib, was found to be situated within chloroplasts in rice protoplasts. All five OsSHMTs are capable of forming homodimers, with OsSHMT3 being the only one able to form dimers with other OsSHMTs, except for OsSHMT1. It is proposed that OsSHMT3 functions as a mobile protein, collaborating with other OsSHMT proteins. Furthermore, the results of cis-acting element prediction and expression analysis suggested that members of the OsSHMT family could be involved in diverse stress responses and hormone regulation. Our study aims to provide novel insights for the future exploration of SHMTs. Full article
(This article belongs to the Special Issue Crop Functional Genomics and Biological 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.

1. Genome-Wide Analysis of the SAUR Gene Family and Its Expression Profiles in Response to Salt Stress in Santalum album

2. Rice Serine Hydroxymethyltransferases: Evolution, Subcellular Localization, Function and Perspectives

3. Phenotypic Analysis and Gene Cloning of the Rice Floury Endosperm Mutant wcr

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