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Special Issue "Advances and Innovations in Maize Genetics and Breeding Research"

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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: 15 March 2024 | Viewed by 6974

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Dr. Wenxin Liu

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Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100083, China
Interests: statistical genetics and genomics; molecular mechanism of maize resistance to abiotic stress; maize breeding
Special Issues, Collections and Topics in MDPI journals

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Dear Colleagues,

Maize is the largest crop in the world. Significant heterosis, wide adaptability, efficient photosynthesis, and characteristics apt to planting are its charm. Extensive genetic germplasm and a large number of new artificial mutagenic materials as abundant gene resources could be provided for maize breeding. A large number of new technologies and novel methods have been applied to maize genetic research and breeding.

Various studies on maize genetics and breeding are welcome to this Special Issue, including but not limited to classic quantitative genetics, genomics, proteomics, and new technologies such as big data, artificial intelligence, gene editing, and synthetic biology. The research goals of the manuscripts could be general biological, physiological, and genetic phenomena or breeding resistance to biotic and abiotic stress. Manuscripts can be original research or reviews. We believe your contribution will have a significant influence on future maize genetic research and breeding.

Dr. Wenxin Liu
Guest Editor

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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

maize
genetics
genomics
proteomics
big data
artificial intelligence
gene editing
synthetic biology

Published Papers (6 papers)

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Open AccessArticle

Integrated Multi-Omics Reveals Significant Roles of Non-Additively Expressed Small RNAs in Heterosis for Maize Plant Height

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Int. J. Mol. Sci. 2023, 24(11), 9150; https://doi.org/10.3390/ijms24119150 - 23 May 2023

Viewed by 766

Abstract

Heterosis is a complex biological phenomenon regulated by genetic variations and epigenetic changes. However, the roles of small RNAs (sRNAs), an important epigenetic regulatory element, on plant heterosis are still poorly understood. Here, an integrative analysis was performed with sequencing data from multi-omics layers of maize hybrids and their two homologous parental lines to explore the potential underlying mechanisms of sRNAs in plant height (PH) heterosis. sRNAome analysis revealed that 59 (18.61%) microRNAs (miRNAs) and 64,534 (54.00%) 24-nt small interfering RNAs (siRNAs) clusters were non-additively expressed in hybrids. Transcriptome profiles showed that these non-additively expressed miRNAs regulated PH heterosis through activating genes involved in vegetative growth-related pathways while suppressing those related to reproductive and stress response pathways. DNA methylome profiles showed that non-additive methylation events were more likely to be induced by non-additively expressed siRNA clusters. Genes associated with low-parental expression (LPE) siRNAs and trans-chromosomal demethylation (TCdM) events were enriched in developmental processes as well as nutrients and energy metabolism, whereas genes associated with high-parental expression (HPE) siRNAs and trans-chromosomal methylation (TCM) events were gathered in stress response and organelle organization pathways. Our results provide insights into the expression and regulation patterns of sRNAs in hybrids and help to elucidate their potential targeting pathways contributing to PH heterosis. Full article

(This article belongs to the Special Issue Advances and Innovations in Maize Genetics and Breeding Research)

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Open AccessArticle

ZmDRR206 Regulates Nutrient Accumulation in Endosperm through Its Role in Cell Wall Biogenesis during Maize Kernel Development

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Int. J. Mol. Sci. 2023, 24(10), 8735; https://doi.org/10.3390/ijms24108735 - 13 May 2023

Viewed by 890

Abstract

Dirigent proteins (DIRs) contribute to plant fitness by dynamically reorganizing the cell wall and/or by generating defense compounds during plant growth, development, and interactions with environmental stresses. ZmDRR206 is a maize DIR, it plays a role in maintaining cell wall integrity during seedling growth and defense response in maize, but its role in regulating maize kernel development is unclear. Association analysis of candidate genes indicated that the natural variations of ZmDRR206 were significantly associated with maize hundred-kernel weight (HKW). ZmDRR206 plays a dominant role in storage nutrient accumulation in endosperm during maize kernel development, ZmDRR206 overexpression resulted in small and shrunken maize kernel with significantly reduced starch content and significantly decreased HKW. Cytological characterization of the developing maize kernels revealed that ZmDRR206 overexpression induced dysfunctional basal endosperm transfer layer (BETL) cells, which were shorter with less wall ingrowth, and defense response was constitutively activated in developing maize kernel at 15 and 18 DAP by ZmDRR206 overexpression. The BETL-development-related genes and auxin signal-related genes were down-regulated, while cell wall biogenesis-related genes were up-regulated in developing BETL of the ZmDRR206-overexpressing kernel. Moreover, the developing ZmDRR206-overexpressing kernel had significantly reduced contents of the cell wall components such as cellulose and acid soluble lignin. These results suggest that ZmDRR206 may play a regulatory role in coordinating cell development, storage nutrient metabolism, and stress responses during maize kernel development through its role in cell wall biogenesis and defense response, and provides new insights into understanding the mechanisms of kernel development in maize. Full article

(This article belongs to the Special Issue Advances and Innovations in Maize Genetics and Breeding Research)

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Open AccessArticle

Multi-Trait Genomic Prediction Improves Accuracy of Selection among Doubled Haploid Lines in Maize

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Int. J. Mol. Sci. 2022, 23(23), 14558; https://doi.org/10.3390/ijms232314558 - 22 Nov 2022

Cited by 1 | Viewed by 910

Abstract

Recent advances in maize doubled haploid (DH) technology have enabled the development of large numbers of DH lines quickly and efficiently. However, testing all possible hybrid crosses among DH lines is a challenge. Phenotyping haploid progenitors created during the DH process could accelerate the selection of DH lines. Based on phenotypic and genotypic data of a DH population and its corresponding haploids, we compared phenotypes and estimated genetic correlations between the two populations, compared genomic prediction accuracy of multi-trait models against conventional univariate models within the DH population, and evaluated whether incorporating phenotypic data from haploid lines into a multi-trait model could better predict performance of DH lines. We found significant phenotypic differences between DH and haploid lines for nearly all traits; however, their genetic correlations between populations were moderate to strong. Furthermore, a multi-trait model taking into account genetic correlations between traits in the single-environment trial or genetic covariances in multi-environment trials can significantly increase genomic prediction accuracy. However, integrating information of haploid lines did not further improve our prediction. Our findings highlight the superiority of multi-trait models in predicting performance of DH lines in maize breeding, but do not support the routine phenotyping and selection on haploid progenitors of DH lines. Full article

(This article belongs to the Special Issue Advances and Innovations in Maize Genetics and Breeding Research)

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Open AccessArticle

Genetic Analysis and Fine Mapping of ZmGHT1 Conferring Glufosinate Herbicide Tolerance in Maize (Zea mays L.)

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Int. J. Mol. Sci. 2022, 23(19), 11481; https://doi.org/10.3390/ijms231911481 - 29 Sep 2022

Viewed by 972

Abstract

Weed interference in the crop field is one of the major biotic stresses causing dramatic crop yield losses, and the development of herbicide-resistant crops is critical for weed control in the application of herbicide technologies. To identify herbicide-resistant germplasms, we screened 854 maize inbreed lines and 25,620 seedlings by spraying them with 1 g/L glufosinate. One plant (L336R), possibly derived from a natural variation of line L336, was identified to have the potential for glufosinate tolerance. Genetic analysis validated that the glufosinate tolerance of L336R is conferred by a single locus, which was tentatively designated as ZmGHT1. By constructing a bi-parental population derived from L336R, and a glufosinate sensitive line L312, ZmGHT1 was mapped between molecular markers M9 and M10. Interestingly, genomic comparation between the two sequenced reference genomes showed that large scale structural variations (SVs) occurred within the mapped region, resulting in 2.16 Mb in the inbreed line B73, and 11.5 kb in CML277, respectively. During the fine mapping process, we did not detect any additional recombinant, even by using more than 9500 F₂ and F₃ plants, suspecting that SVs should also have occurred between L336R and L312 in this region, which inhibited recombination. By evaluating the expression of the genes within the mapped interval and using functional annotation, we predict that the gene Zm00001eb361930, encoding an aminotransferase, is the most likely causative gene. After glufosinate treatment, lower levels of ammonia content and a higher activity of glutamine synthetase (GS) in L336R were detected compared with those of L336 and L312, suggesting that the target gene may participate in ammonia elimination involving GS activity. Collectively, our study can provide a material resource for maize herbicide resistant breeding, with the potential to reveal a new mechanism for herbicide resistance. Full article

(This article belongs to the Special Issue Advances and Innovations in Maize Genetics and Breeding Research)

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Open AccessArticle

Combined QTL Mapping across Multiple Environments and Co-Expression Network Analysis Identified Key Genes for Embryogenic Callus Induction from Immature Maize Embryos

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Int. J. Mol. Sci. 2022, 23(15), 8786; https://doi.org/10.3390/ijms23158786 - 07 Aug 2022

Cited by 2 | Viewed by 1329

Abstract

The ability of immature embryos to induce embryogenic callus (EC) is crucial for genetic transformation in maize, which is highly genotype-dependent. To dissect the genetic basis of maize EC induction, we conducted QTL mapping for four EC induction-related traits, the rate of embryogenic callus induction (REC), rate of shoot formation (RSF), length of shoot (LS), and diameter of callus (DC) under three environments by using an IBM Syn10 DH population derived from a cross of B73 and Mo17. These EC induction traits showed high broad-sense heritability (>80%), and significantly negative correlations were observed between REC and each of the other traits across multiple environments. A total of 41 QTLs for EC induction were identified, among which 13, 12, 10, and 6 QTLs were responsible for DC, RSF, LS, and REC, respectively. Among them, three major QTLs accounted for >10% of the phenotypic variation, including qLS1-1 (11.54%), qLS1-3 (10.68%), and qREC4-1 (11.45%). Based on the expression data of the 215 candidate genes located in these QTL intervals, we performed a weighted gene co-expression network analysis (WGCNA). A combined use of KEGG pathway enrichment and eigengene-based connectivity (KME) values identified the EC induction-associated module and four hub genes (Zm00001d028477, Zm00001d047896, Zm00001d034388, and Zm00001d022542). Gene-based association analyses validated that the variations in Zm00001d028477 and Zm00001d034388, which were involved in tryptophan biosynthesis and metabolism, respectively, significantly affected EC induction ability among different inbred lines. Our study brings novel insights into the genetic and molecular mechanisms of EC induction and helps to promote marker-assisted selection of high-REC varieties in maize. Full article

(This article belongs to the Special Issue Advances and Innovations in Maize Genetics and Breeding Research)

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ATP-Binding Cassette G Transporters and Their Multiple Roles Especially for Male Fertility in Arabidopsis, Rice and Maize

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Int. J. Mol. Sci. 2022, 23(16), 9304; https://doi.org/10.3390/ijms23169304 - 18 Aug 2022

Cited by 3 | Viewed by 1386

Abstract

ATP-binding cassette subfamily G (ABCG) transporters are extensive in plants and play essential roles in various processes influencing plant fitness, but the research progress varies greatly among Arabidopsis, rice and maize. In this review, we present a consolidated nomenclature and characterization of the whole 51 ABCG transporters in maize, perform a phylogenetic analysis and classification of the ABCG subfamily members in maize, and summarize the latest research advances in ABCG transporters for these three plant species. ABCG transporters are involved in diverse processes in Arabidopsis and rice, such as anther and pollen development, vegetative and female organ development, abiotic and biotic stress response, and phytohormone transport, which provide useful clues for the functional investigation of ABCG transporters in maize. Finally, we discuss the current challenges and future perspectives for the identification and mechanism analysis of substrates for plant ABCG transporters. This review provides a basic framework for functional research and the potential application of ABCG transporters in multiple plants, including maize. Full article

(This article belongs to the Special Issue Advances and Innovations in Maize Genetics and Breeding Research)

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