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Crop Molecular Breeding: Current Status and Future Directions
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Crop Molecular Breeding: Current Status and Future Directions

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 August 2024) | Viewed by 3462

Special Issue Editors

Dr. Qian-Hao Zhu

E-Mail Website
Guest Editor
CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
Interests: cotton biology; genomics; molecular breeding; plant noncoding RNAs; biostress tolerance
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Jie Sun

E-Mail Website
Guest Editor
Key Laboratory of Oasis Eco-Agriculture, College of Agriculture, Shihezi University, Shihezi, China
Interests: cotton genetics; genomics; molecular breeding; genetic improvement
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

With the continuous advances in sequencing technology, the development of analytical tools for discovery, annotation and deciphering of genetic variants existing amongst diverse germplasm of every crop species, and precisely engineering target genes by genome editing, breeding new crop varieties is now entering a new era in which functional genetic variants can be rationally and rapidly combined and created as required to develop the next generation of crop varieties.

As an example, cotton (Gossypium spp.) is a multi-purpose crop, producing not only natural fiber for the global textile industry, but also oil and protein-rich seeds for downstream industries. Since the release of the first cotton reference genome (G. raimondii) in 2012, the genome sequences of 22 diploids and all 7 allotetraploids have been published, and thousands of accessions of both the diploid- and allotetraploid-cultivated cotton species have been re-sequenced. The genome data provide a rich source for investigating cotton evolution and finding genetic variants associated with important agronomic traits of cotton. As a result, not only marker-assisted selection but also genomic prediction has been adopted in cotton breeding, with the aim of increasing breeding efficiency and shortening the breeding cycle. Thus, we are launching a Special Issue on “Corp Molecular Breeding: Current Status and Future Directions” to present the accomplishments achieved in crop molecular genetics and genomics and to explore new opportunities in developing and deploying molecular tools in breeding the next generation of elite crop varieties.

This Special Issue will accept original research manuscripts reporting novel results on the topics mentioned above and covered by the keywords, as well as review and perspective articles on topics related to crop molecular breeding.

Dr. Qian-Hao Zhu
Prof. Dr. Jie Sun
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

  • crop molecular breeding
  • marker-assisted breeding
  • genomics-enabled molecular breeding
  • QTL mapping and annotation
  • genome-wide association study
  • genomic prediction and selection
  • functional genomic variations
  • gene editing

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Published Papers (4 papers)

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Research

16 pages, 4910 KiB  
Article
Transcriptome Analysis and Identification of Genes Associated with Cotton Seed Size
by Bing Jia, Pan Feng, Jikun Song, Caoyi Zhou, Yajie Wang, Bingbing Zhang, Man Wu, Jinfa Zhang, Quanjia Chen and Jiwen Yu
Int. J. Mol. Sci. 2024, 25(18), 9812; https://doi.org/10.3390/ijms25189812 - 11 Sep 2024
Viewed by 251
Abstract
Cotton seeds, as the main by-product of cotton, are not only an important raw material for edible oil and feed but also a source of biofuel. The quality of cotton seeds directly affects cotton planting and is closely related to the yield and [...] Read more.
Cotton seeds, as the main by-product of cotton, are not only an important raw material for edible oil and feed but also a source of biofuel. The quality of cotton seeds directly affects cotton planting and is closely related to the yield and fiber quality. However, the molecular mechanism governing cotton seed size remains largely unexplored. This study investigates the regulatory mechanisms of cotton seed size by focusing on two cotton genotypes, N10 and N12, which exhibit notable phenotypic variations across multiple environments. Developing seeds were sampled at various stages (5, 20, 30, and 35 DPA) and subjected to RNA-seq. Temporal pattern clustering and WGCNA on differentially expressed genes identified 413 candidate genes, including these related to sugar metabolism that were significantly enriched in transcriptional regulation. A genetic transformation experiment indicated that the overexpression of the GhUXS5 gene encoding UDP-glucuronate decarboxylase 5 significantly increased seed size, suggesting an important role of GhUXS5 in regulating cotton seed size. This discovery provides crucial insights into the molecular mechanisms controlling cotton seed size, helping to unravel the complex regulatory network and offering new strategies and targets for cotton breeding to enhance the economic value of cotton seeds and overall cotton yield. Full article
(This article belongs to the Special Issue Crop Molecular Breeding: Current Status and Future Directions)
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21 pages, 2564 KiB  
Article
Effect of Chromosomal Localization of NGS-Based Markers on Their Applicability for Analyzing Genetic Variation and Population Structure of Hexaploid Triticale
by Justyna Leśniowska-Nowak, Piotr T. Bednarek, Karolina Czapla, Michał Nowak and Agnieszka Niedziela
Int. J. Mol. Sci. 2024, 25(17), 9568; https://doi.org/10.3390/ijms25179568 - 3 Sep 2024
Viewed by 370
Abstract
This study aimed to determine whether using DNA-based markers assigned to individual chromosomes would detect the genetic structures of 446 winter triticale forms originating from two breeding companies more effectively than using the entire pool of markers. After filtering for quality control parameters, [...] Read more.
This study aimed to determine whether using DNA-based markers assigned to individual chromosomes would detect the genetic structures of 446 winter triticale forms originating from two breeding companies more effectively than using the entire pool of markers. After filtering for quality control parameters, 6380 codominant single nucleotide polymorphisms (SNPs) markers and 17,490 dominant diversity array technology (silicoDArT) markers were considered for analysis. The mean polymorphic information content (PIC) values varied depending on the chromosomes and ranged from 0.30 (2R) to 0.43 (7A) for the SNPs and from 0.28 (2A) to 0.35 (6R) for the silicoDArTs. The highest correlation of genetic distance (GD) matrices based on SNP markers was observed among the 5B–5R (0.642), 5B–7B (0.626), and 5A–5R (0.605) chromosomes. When silicoDArTs were used for the analysis, the strongest correlations were found between 5B–5R (0.732) and 2B–5B (0.718). A Bayesian analysis showed that SNPs (total marker pool) allowed for the identification of a more complex structure (K = 4, ΔK = 2460.2) than the analysis based on silicoDArTs (K = 2, ΔK = 128). Triticale lines formed into groups, ranging from two (most of the chromosomes) to four (7A) groups depending on the analyzed chromosome when SNP markers were used for analysis. Linkage disequilibrium (LD) varied among individual chromosomes, ranging from 0.031 for 1A to 0.228 for 7R. Full article
(This article belongs to the Special Issue Crop Molecular Breeding: Current Status and Future Directions)
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20 pages, 11662 KiB  
Article
Chitinase Gene FoChi20 in Fusarium oxysporum Reduces Its Pathogenicity and Improves Disease Resistance in Cotton
by Hui Lou, Jincheng Zhu, Zengqiang Zhao, Zegang Han and Wei Zhang
Int. J. Mol. Sci. 2024, 25(15), 8517; https://doi.org/10.3390/ijms25158517 - 4 Aug 2024
Viewed by 1017
Abstract
Chitinase genes, as a class of cell wall hydrolases, are essential for the development and pathogenesis of Fusarium oxysporum f.sp. vasinfectum (F. ox) in cotton, but related research focused on chitinase genes are limited. This study explored two island cotton root [...] Read more.
Chitinase genes, as a class of cell wall hydrolases, are essential for the development and pathogenesis of Fusarium oxysporum f.sp. vasinfectum (F. ox) in cotton, but related research focused on chitinase genes are limited. This study explored two island cotton root secretions from the highly resistant cultivar Xinhai 41 and sensitive cultivar Xinhai 14 to investigate their interaction with F. ox by a weighted correlation network analysis (WGCNA). As a result, two modules that related to the fungal pathogenicity emerged. Additionally, a total of twenty-five chitinase genes were identified. Finally, host-induced gene silencing (HIGS) of FoChi20 was conducted, and the cotton plants showed noticeably milder disease with a significantly lower disease index than the control. This study illuminated that chitinase genes play crucial roles in the pathogenicity of cotton wilt fungi, and the FoChi20 gene could participate in the pathogenesis of F. ox and host–pathogen interactions, which establishes a theoretical framework for disease control in Sea Island cotton. Full article
(This article belongs to the Special Issue Crop Molecular Breeding: Current Status and Future Directions)
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25 pages, 6195 KiB  
Article
VdPT1 Encoding a Neutral Trehalase of Verticillium dahliae Is Required for Growth and Virulence of the Pathogen
by Lihua Chen, Xiaohu Ma, Tiange Sun, Qian-Hao Zhu, Hongjie Feng, Yongtai Li, Feng Liu, Xinyu Zhang, Jie Sun and Yanjun Li
Int. J. Mol. Sci. 2024, 25(1), 294; https://doi.org/10.3390/ijms25010294 - 25 Dec 2023
Cited by 2 | Viewed by 1137
Abstract
Verticillum dahliae is a soil-borne phytopathogenic fungus causing destructive Verticillium wilt disease. We previously found a trehalase-encoding gene (VdPT1) in V. dahliae being significantly up-regulated after sensing root exudates from a susceptible cotton variety. In this study, we characterized the function [...] Read more.
Verticillum dahliae is a soil-borne phytopathogenic fungus causing destructive Verticillium wilt disease. We previously found a trehalase-encoding gene (VdPT1) in V. dahliae being significantly up-regulated after sensing root exudates from a susceptible cotton variety. In this study, we characterized the function of VdPT1 in the growth and virulence of V. dahliae using its deletion-mutant strains. The VdPT1 deletion mutants (ΔVdPT1) displayed slow colony expansion and mycelial growth, reduced conidial production and germination rate, and decreased mycelial penetration ability and virulence on cotton, but exhibited enhanced stress resistance, suggesting that VdPT1 is involved in the growth, pathogenesis, and stress resistance of V. dahliae. Host-induced silencing of VdPT1 in cotton reduced fungal biomass and enhanced cotton resistance against V. dahliae. Comparative transcriptome analysis between wild-type and mutant identified 1480 up-regulated and 1650 down-regulated genes in the ΔVdPT1 strain. Several down-regulated genes encode plant cell wall-degrading enzymes required for full virulence of V. dahliae to cotton, and down-regulated genes related to carbon metabolism, DNA replication, and amino acid biosynthesis seemed to be responsible for the decreased growth of the ΔVdPT1 strain. In contrast, up-regulation of several genes related to glycerophospholipid metabolism in the ΔVdPT1 strain enhanced the stress resistance of the mutated strain. Full article
(This article belongs to the Special Issue Crop Molecular Breeding: Current Status and Future Directions)
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