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Molecular Breeding and Genetic Regulation of Crops
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Molecular Breeding and Genetic Regulation of Crops

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 April 2024 | Viewed by 3314

Special Issue Editor

Dr. Chiara Biselli

E-Mail Website
Guest Editor
Council for Agricultural Research and Economics—Research Centre for Viticulture and Enology, Viale Santa Margherita 80, 52100 Arezzo, Italy
Interests: plant–pathogen interaction; plant response to environmental stresses; GWAS; linkage mapping; plant genomics; plant transcriptomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Molecular breeding and genetic regulation of crops are pivotal in modern agriculture, offering innovative solutions to enhancing crop productivity, nutritional quality, and resilience. Molecular breeding can be used to harness biotechnology and genomics to expedite the development of improved crop varieties through the identification of specific genetic markers associated with desirable traits. Marker-assisted selection and genome-editing techniques enable precision breeding, reducing the time and resources required in comparison to traditional methods. Genetic regulation, on the other hand, can be used to explore the intricate mechanisms controlling gene expression in response to environmental and developmental cues. Understanding epigenetic modifications further increases our ability to fine-tune crops for specific needs. The synergy between molecular breeding and genetic regulation provides a powerful approach to addressing food security challenges through creating crop varieties adapted to a changing climate.

This Special Issue will cover molecular breeding and genetic regulation research, with the aim of presenting the significance of these fields in shaping the future of sustainable and resilient agriculture.

Dr. Chiara Biselli
Guest Editor

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

  • molecular breeding
  • genetic regulation
  • genomics
  • genome-editing techniques
  • epigenetic modifications

Published Papers (5 papers)

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Research

18 pages, 5501 KiB  
Article
Identification of Quantitative Trait Loci Controlling Root Morphological Traits in an Interspecific Soybean Population Using 2D Imagery Data
by Mohammad Shafiqul Islam, Amit Ghimire, Liny Lay, Waleed Khan, Jeong-Dong Lee, Qijian Song, Hyun Jo and Yoonha Kim
Int. J. Mol. Sci. 2024, 25(9), 4687; https://doi.org/10.3390/ijms25094687 - 25 Apr 2024
Viewed by 154
Abstract
Roots are the hidden and most important part of plants. They serve as stabilizers and channels for uptaking water and nutrients and play a crucial role in the growth and development of plants. Here, two-dimensional image data were used to identify quantitative trait [...] Read more.
Roots are the hidden and most important part of plants. They serve as stabilizers and channels for uptaking water and nutrients and play a crucial role in the growth and development of plants. Here, two-dimensional image data were used to identify quantitative trait loci (QTL) controlling root traits in an interspecific mapping population derived from a cross between wild soybean ‘PI366121’ and cultivar ‘Williams 82’. A total of 2830 single-nucleotide polymorphisms were used for genotyping, constructing genetic linkage maps, and analyzing QTLs. Forty-two QTLs were identified on twelve chromosomes, twelve of which were identified as major QTLs, with a phenotypic variation range of 36.12% to 39.11% and a logarithm of odds value range of 12.01 to 17.35. Two significant QTL regions for the average diameter, root volume, and link average diameter root traits were detected on chromosomes 3 and 13, and both wild and cultivated soybeans contributed positive alleles. Six candidate genes, Glyma.03G027500 (transketolase/glycoaldehyde transferase), Glyma.03G014500 (dehydrogenases), Glyma.13G341500 (leucine-rich repeat receptor-like protein kinase), Glyma.13G341400 (AGC kinase family protein), Glyma.13G331900 (60S ribosomal protein), and Glyma.13G333100 (aquaporin transporter) showed higher expression in root tissues based on publicly available transcriptome data. These results will help breeders improve soybean genetic components and enhance soybean root morphological traits using desirable alleles from wild soybeans. Full article
(This article belongs to the Special Issue Molecular Breeding and Genetic Regulation of Crops)
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14 pages, 5554 KiB  
Article
Genome-Wide Association Study to Identify Marker–Trait Associations for Seed Color in Colored Wheat (Triticum aestivum L.)
by Min Jeong Hong, Chan Seop Ko and Dae Yeon Kim
Int. J. Mol. Sci. 2024, 25(7), 3600; https://doi.org/10.3390/ijms25073600 - 22 Mar 2024
Viewed by 501
Abstract
This study conducted phenotypic evaluations on a wheat F3 population derived from 155 F2 plants. Traits related to seed color, including chlorophyll a, chlorophyll b, carotenoid, anthocyanin, L*, a*, and b*, were assessed, revealing highly significant correlations among [...] Read more.
This study conducted phenotypic evaluations on a wheat F3 population derived from 155 F2 plants. Traits related to seed color, including chlorophyll a, chlorophyll b, carotenoid, anthocyanin, L*, a*, and b*, were assessed, revealing highly significant correlations among various traits. Genotyping using 81,587 SNP markers resulted in 3969 high-quality markers, revealing a genome-wide distribution with varying densities across chromosomes. A genome-wide association study using fixed and random model circulating probability unification (FarmCPU) and Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK) identified 11 significant marker–trait associations (MTAs) associated with L*, a*, and b*, and chromosomal distribution patterns revealed predominant locations on chromosomes 2A, 2B, and 4B. A comprehensive annotation uncovered 69 genes within the genomic vicinity of each MTA, providing potential functional insights. Gene expression analysis during seed development identified greater than 2-fold increases or decreases in expression in colored wheat for 16 of 69 genes. Among these, eight genes, including transcription factors and genes related to flavonoid and ubiquitination pathways, exhibited distinct expression patterns during seed development, providing further approaches for exploring seed coloration. This comprehensive exploration expands our understanding of the genetic basis of seed color and paves the way for informed discussions on the molecular intricacies contributing to this phenotypic trait. Full article
(This article belongs to the Special Issue Molecular Breeding and Genetic Regulation of Crops)
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22 pages, 4200 KiB  
Article
High- or Low-Yielding F2 Progeny of Wheat Is Result of Specific TaCKX Gene Coexpression Patterns in Association with Grain Yield in Paternal Parent
by Karolina Szala, Marta Dmochowska-Boguta, Joanna Bocian, Wacław Orczyk and Anna Nadolska-Orczyk
Int. J. Mol. Sci. 2024, 25(6), 3553; https://doi.org/10.3390/ijms25063553 - 21 Mar 2024
Viewed by 507
Abstract
Members of the TaCKX gene family (GFM) encode oxidase/dehydrogenase cytokinin degrading enzymes (CKX), which play an important role in the homeostasis of phytohormones, affecting wheat development and productivity. Therefore, the objective of this investigation was to test how the expression patterns of the [...] Read more.
Members of the TaCKX gene family (GFM) encode oxidase/dehydrogenase cytokinin degrading enzymes (CKX), which play an important role in the homeostasis of phytohormones, affecting wheat development and productivity. Therefore, the objective of this investigation was to test how the expression patterns of the yield-related TaCKX genes and TaNAC2-5A (NAC2) measured in 7 days after pollination (DAP) spikes and the seedling roots of parents are inherited to apply this knowledge in the breeding process. The expression patterns of these genes were compared between parents and their F2 progeny in crosses of one mother with different paterns of awnless cultivars and reciprocal crosses of awned and awnless lines. We showed that most of the genes tested in the 7 DAP spikes and seedling roots of the F2 progeny showed paternal expression patterns in crosses of awnless cultivars as well as reciprocal crosses of awned and awnless lines. Consequently, the values of grain yield in the F2 progeny were similar to the pater; however, the values of seedling root mass were similar to the mother or both parents. The correlation analysis of TaCKX GFMs and NAC2 in spikes and spikes per seedling roots reveals that the genes correlate with each other specifically with the pater and the F2 progeny or the mother and the F2 progeny, which shape phenotypic traits. The numbers of spikes and semi-empty spikes are mainly correlated with the specific coexpression of the TaCKX and NAC2 genes expressed in spikes or spikes per roots of the pater and F2 progeny. Variable regression analysis of grain yield and root mass with TaCKX GFMs and NAC2 expressed in the tested tissues of five crosses revealed a significant dependency of these parameters on the mother and F2 and/or the pater and F2 progeny. We showed that the inheritance of yield-related traits depends on the specific cooperative expression of some TaCKX GFMs, in some crosses coupled with NAC2, and is strongly dependent on the genotypes used for the crosses. Indications for parental selection in the breeding of high-yielding lines are discussed. Full article
(This article belongs to the Special Issue Molecular Breeding and Genetic Regulation of Crops)
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15 pages, 3929 KiB  
Article
Identification and Validation of Key Genes Related to Preferred Flavour Profiles in Australian Commercial Papaya (Carica papaya L.)
by Ziwei Zhou, Chutchamas Kanchana-udomkan, Rebecca Ford and Ido Bar
Int. J. Mol. Sci. 2024, 25(5), 3046; https://doi.org/10.3390/ijms25053046 - 06 Mar 2024
Viewed by 524
Abstract
Commercial papaya varieties grown in Australia vary greatly in taste and aroma. Previous profiling has identified undesirable ‘off tastes’ in existing varieties, discouraging a portion of the population from consuming papayas. Our focus on enhancing preferred flavours led to an exploration of the [...] Read more.
Commercial papaya varieties grown in Australia vary greatly in taste and aroma. Previous profiling has identified undesirable ‘off tastes’ in existing varieties, discouraging a portion of the population from consuming papayas. Our focus on enhancing preferred flavours led to an exploration of the genetic mechanisms and biosynthesis pathways that underlie these desired taste profiles. To identify genes associated with consumer-preferred flavours, we conducted whole RNA sequencing and de novo genome assembly on papaya varieties RB1 (known for its sweet flavour and floral aroma) and 1B (less favoured due to its bitter taste and musty aroma) at both ripe and unripe stages. In total, 180,368 transcripts were generated, and 118 transcripts related to flavours were differentially expressed between the two varieties at the ripe stage. Five genes (cpBGH3B, cpPFP, cpSUS, cpGES and cpLIS) were validated through qPCR and significantly differentially expressed. These genes are suggested to play key roles in sucrose metabolism and aromatic compound production pathways, holding promise for future selective breeding strategies. Further exploration will involve assessing their potential across broader germplasm and various growth environments. Full article
(This article belongs to the Special Issue Molecular Breeding and Genetic Regulation of Crops)
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19 pages, 4971 KiB  
Article
A Comprehensive Identification and Expression Analysis of the WUSCHEL Homeobox-Containing Protein Family Reveals Their Special Role in Development and Abiotic Stress Response in Zea mays L.
by Xuanxuan Chen, Yunyan Hou, Yongyan Cao, Bo Wei and Lei Gu
Int. J. Mol. Sci. 2024, 25(1), 441; https://doi.org/10.3390/ijms25010441 - 28 Dec 2023
Cited by 1 | Viewed by 768
Abstract
Maize is an important food and cash crop worldwide. The WUSCHEL (WUS)-related homeobox (WOX) transcription factor (TF) family plays a significant role in the development process and the response to abiotic stress of plants. However, few studies have been reported on the function [...] Read more.
Maize is an important food and cash crop worldwide. The WUSCHEL (WUS)-related homeobox (WOX) transcription factor (TF) family plays a significant role in the development process and the response to abiotic stress of plants. However, few studies have been reported on the function of WOX genes in maize. This work, utilizing the latest maize B73 reference genome, results in the identification of 22 putative ZmWOX gene family members. Except for chromosome 5, the 22 ZmWOX genes were homogeneously distributed on the other nine chromosomes and showed three tandem duplication and 10 segmental duplication events. Based on phylogenetic characteristics, ZmWOXs are divided into three clades (e.g., WUS, intermediate, and ancient groups), and the majority of ZmWOXs in same group display similar gene and protein structures. Cross-species collinearity results indicated that some WOX genes might be evolutionarily conservative. The promoter region of ZmWOX family members is enriched in light, plant growth/hormone, and abiotic stress-responsive elements. Tissue-specific expression evaluation showed that ZmWOX genes might play a significant role in the occurrence of maize reproductive organs. Transcriptome data and RT-qPCR analysis further showed that six ZmWOX genes (e.g., ZmWOX1, 4, 6, 13, 16, and 18) were positively or negatively modulated by temperature, salt, and waterlogging stresses. Moreover, two ZmWOXs, ZmWOX1 and ZmWOX18, both were upregulated by abiotic stress. ZmWOX18 was localized in the nucleus and had transactivation activities, while ZmWOX1 was localized in both the cytoplasm and nucleus, without transactivation activity. Overall, this work offers new perspectives on the evolutionary relationships of ZmWOX genes and might provide a resource for further detecting the biological functions of ZmWOXs. Full article
(This article belongs to the Special Issue Molecular Breeding and Genetic Regulation of Crops)
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