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Genetics- and Genomics-Based Crop Improvement and Breeding: 3rd Edition

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: 30 December 2024 | Viewed by 2374

Special Issue Editor

Special Issue Information

Dear Colleagues,

In recent decades, although plant breeding has greatly and steadily improved the performance of crops, including wheat and its related species, maize, oat, rye, rice, barley, millet, and sorghum, the global growing food demand due to the increasing population and decrease in the amount of available land requires these cereal crops to be both more productive and resistant to harsher environmental conditions as a result of climate change.

The development of next-generation sequencing (NGS) has greatly improved the course of science research. Researchers are facing an unprecedented opportunity to identify genes controlling complex phenotypes and understand how the genes fulfill functions through the interaction between genes and environmental factors. This provides a new approach for breeding programs in cereals that can significantly reduce the cost and time needed by traditional breeding or domestication approaches. However, we should note that most breeding programs still mainly depend on conventional breeding selection to be performed in repeated and time-consuming field work.

Therefore, it is rather essential to make full use of the advancements in the NGS of cereal crops and high-throughput phenotyping and genotyping platforms to genetically identify, evaluate, excavate, and characterize more germplasm resources and loci/genes to work towards crop improvement.

In this Special Issue, we aim to promote an improvement in cereal crops; thus, we invite the submission of original research, review, methods, mini-review, perspective, and opinion articles on topics related, but not limited, to the following areas:

  • Identification, evaluation, and characterization of various germplasm;
  • Identification and breeding utilization of favorable alleles which have not been fully explored;
  • Genetic mapping, fine mapping, and genome-wide association analysis of loci/genes for important traits;
  • Development and breeding utilization of molecular markers tightly linked to important traits;
  • Structural and functional genomics in crops, proteomics and metabolic profiling, and field evaluation of crops containing particular traits.

Prof. Dr. Jian Ma
Guest Editor

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Keywords

  • crop
  • germplasm
  • genetics
  • genomics
  • breeding

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Published Papers (4 papers)

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22 pages, 6569 KiB  
Article
Bioinformatics Identification and Expression Analysis of Acetyl-CoA Carboxylase Reveal Its Role in Isoflavone Accumulation during Soybean Seed Development
by Xu Wu, Zhenhong Yang, Yina Zhu, Yuhang Zhan, Yongguang Li, Weili Teng, Yingpeng Han and Xue Zhao
Int. J. Mol. Sci. 2024, 25(18), 10221; https://doi.org/10.3390/ijms251810221 - 23 Sep 2024
Viewed by 539
Abstract
Isoflavones belong to the class of flavonoid compounds, which are important secondary metabolites that play a crucial role in plant development and defense. Acetyl-CoA carboxylase (ACCase) is a biotin-dependent enzyme that catalyzes the conversion of Acetyl-CoA into Malonyl-CoA in plants. It is a [...] Read more.
Isoflavones belong to the class of flavonoid compounds, which are important secondary metabolites that play a crucial role in plant development and defense. Acetyl-CoA carboxylase (ACCase) is a biotin-dependent enzyme that catalyzes the conversion of Acetyl-CoA into Malonyl-CoA in plants. It is a key enzyme in fatty acid synthesis and also catalyzes the production of various secondary metabolites. However, information on the ACC gene family in the soybean (Glycine max L. Merr.) genome and the specific members involved in isoflavone biosynthesis is still lacking. In this study, we identified 20 ACC family genes (GmACCs) from the soybean genome and further characterized their evolutionary relationships and expression patterns. Phylogenetic analysis showed that the GmACCs could be divided into five groups, and the gene structures within the same groups were highly conserved, indicating that they had similar functions. The GmACCs were randomly distributed across 12 chromosomes, and collinearity analysis suggested that many GmACCs originated from tandem and segmental duplications, with these genes being under purifying selection. In addition, gene expression pattern analysis indicated that there was functional divergence among GmACCs in different tissues. The GmACCs reached their peak expression levels during the early or middle stages of seed development. Based on the transcriptome and isoflavone content data, a weighted gene co-expression network was constructed, and three candidate genes (Glyma.06G105900, Glyma.13G363500, and Glyma.13G057400) that may positively regulate isoflavone content were identified. These results provide valuable information for the further functional characterization and application of GmACCs in isoflavone biosynthesis in soybean. Full article
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18 pages, 4075 KiB  
Article
QTL Mapping and Candidate Gene Analysis for Starch-Related Traits in Tartary Buckwheat (Fagopyrum tataricum (L.) Gaertn)
by Juan Huang, Fei Liu, Rongrong Ren, Jiao Deng, Liwei Zhu, Hongyou Li, Fang Cai, Ziye Meng, Qingfu Chen and Taoxiong Shi
Int. J. Mol. Sci. 2024, 25(17), 9243; https://doi.org/10.3390/ijms25179243 - 26 Aug 2024
Viewed by 445
Abstract
Starch is the main component that determines the yield and quality of Tartary buckwheat. As a quantitative trait, using quantitative trait locus (QTL) mapping to excavate genes associated with starch-related traits is crucial for understanding the genetic mechanisms involved in starch synthesis and [...] Read more.
Starch is the main component that determines the yield and quality of Tartary buckwheat. As a quantitative trait, using quantitative trait locus (QTL) mapping to excavate genes associated with starch-related traits is crucial for understanding the genetic mechanisms involved in starch synthesis and molecular breeding of Tartary buckwheat varieties with high-quality starch. Employing a recombinant inbred line population as research material, this study used QTL mapping to investigate the amylose, amylopectin, and total starch contents across four distinct environments. The results identified a total of 20 QTLs spanning six chromosomes, which explained 4.07% to 14.41% of the phenotypic variation. One major QTL cluster containing three stable QTLs governing both amylose and amylopectin content, qClu-4-1, was identified and located in the physical interval of 39.85–43.34 Mbp on chromosome Ft4. Within this cluster, we predicted 239 candidate genes and analyzed their SNP/InDel mutations, expression patterns, and enriched KEGG pathways. Ultimately, five key candidate genes, namely FtPinG0004897100.01, FtPinG0002636200.01, FtPinG0009329200.01, FtPinG0007371600.01, and FtPinG0005109900.01, were highlighted, which are potentially involved in starch synthesis and regulation, paving the way for further investigative studies. This study, for the first time, utilized QTL mapping to detect major QTLs controlling amylose, amylopectin, and total starch contents in Tartary buckwheat. The QTLs and candidate genes would provide valuable insights into the genetic mechanisms underlying starch synthesis and improving starch-related traits of Tartary buckwheat. Full article
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16 pages, 5538 KiB  
Article
The Complex FtBBX22 and FtHY5 Positively Regulates Light-Induced Anthocyanin Accumulation by Activating FtMYB42 in Tartary Buckwheat Sprouts
by Jiao Deng, Lan Zhang, Lijuan Wang, Jiali Zhao, Chaojie Yang, Hongyou Li, Juan Huang, Taoxiong Shi, Liwei Zhu, Rebecca Njeri Damaris and Qingfu Chen
Int. J. Mol. Sci. 2024, 25(15), 8376; https://doi.org/10.3390/ijms25158376 - 31 Jul 2024
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Abstract
Anthocyanin is one important nutrition composition in Tartary buckwheat (Fagopyrum tataricum) sprouts, a component missing in its seeds. Although anthocyanin biosynthesis requires light, the mechanism of light-induced anthocyanin accumulation in Tartary buckwheat is unclear. Here, comparative transcriptome analysis of Tartary buckwheat [...] Read more.
Anthocyanin is one important nutrition composition in Tartary buckwheat (Fagopyrum tataricum) sprouts, a component missing in its seeds. Although anthocyanin biosynthesis requires light, the mechanism of light-induced anthocyanin accumulation in Tartary buckwheat is unclear. Here, comparative transcriptome analysis of Tartary buckwheat sprouts under light and dark treatments and biochemical approaches were performed to identify the roles of one B-box protein BBX22 and ELONGATED HYPOCOTYL 5 (HY5). The overexpression assay showed that FtHY5 and FtBBX22 could both promote anthocyanin synthesis in red-flower tobacco. Additionally, FtBBX22 associated with FtHY5 to form a complex that activates the transcription of MYB transcription factor genes FtMYB42 and FtDFR, leading to anthocyanin accumulation. These findings revealed the regulation mechanism of light-induced anthocyanin synthesis and provide excellent gene resources for breeding high-quality Tartary buckwheat. Full article
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13 pages, 2827 KiB  
Perspective
Metabolomics-Assisted Breeding in Oil Palm: Potential and Current Perspectives
by Rizki Anjal P. Nugroho, Ismail Zaag, Emmanuelle Lamade, Rudy Lukman, Jean-Pierre Caliman and Guillaume Tcherkez
Int. J. Mol. Sci. 2024, 25(18), 9833; https://doi.org/10.3390/ijms25189833 - 11 Sep 2024
Viewed by 520
Abstract
Oil palm is presently the most important oil-producing crop worldwide in terms of oil production and consumption. However, oil palm cultivation faces important challenges such as adverse climatic conditions, expensive fertilization requirements, and fungal pathogens, including Ganoderma. Intense efforts in oil palm [...] Read more.
Oil palm is presently the most important oil-producing crop worldwide in terms of oil production and consumption. However, oil palm cultivation faces important challenges such as adverse climatic conditions, expensive fertilization requirements, and fungal pathogens, including Ganoderma. Intense efforts in oil palm breeding are devoted to improving both oil production yield and resistance to environmental cues. Metabolomics can be of interest because it provides many quantitative traits and metabolic signatures that can be selected for to optimize oil palm performance. Here, we briefly review how metabolomics can help oil palm breeding, and to do so, we give examples of recent metabolomics analyses and provide a roadmap to use metabolomics-assisted breeding. Full article
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