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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 January 2025 | Viewed by 10073

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Special Issue Editors

Dr. Yin Li

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Guest Editor

College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
Interests: crop functional genomics; cereal crop transformation; grain quality; carbohydrate metabolism; cereal nutritional quality; sorghum; maize; wheat
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Mingjie Chen

E-Mail Website
Guest Editor

College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
Interests: crop functional genomics; genetic improvement; food processing quality; seed storage proteins; kernel hardness; wheat; transgenic wheat

Dr. Junli Chang

E-Mail Website
Guest Editor

College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
Interests: crop functional genomics; grain quality; wheat nutritional quality; wheat; transgenic wheat
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Cereal crops include both major staple food crops (etc. rice, maize, wheat and barley) and minor crops, such as sorghum, millet, pearl millet and teff, which are considered as important sources of dietary fibers, micronutrients and bioactive phyto-compounds. However, several factors have been threatening the global production of cereal crops: (1) world population is increasing, demanding more foods; (2) global climate change is leading to a frequent occurrence of extreme climates, requiring higher environmental adaptability to biotic and abiotic stresses; (3) water resources for the agricultural use are gradually decreasing and the land for superior agricultural production are degrading, putting forward higher yield and water and nutrient use efficiency of crops; (4) the trend of eating nutritious staple foods (such as whole-grain staples) demands the breeding of crop varieties with better quality.

At present, to confront the challenges in crop improvement and to breed cereal crops with higher yield, better environmental adaptability and better quality, molecular genetics, genomics and mutli-omics and biotechnology approaches have been integrated in the up- and down-stream lines of molecular breeding of crops. The major biotechnological tools for cereal crop improvements include (but not limited to) map-based cloning, marker-assisted selection, genomic selection, QTL-mapping, GWAS, transgenic and gene editing technologies, as well as nano-agricultural biotechnologies. As such, we develop this Special Issue to provide a forum with which to address these problems and present new strategies and progress in the improvement of cereal crop species.

Please read the “Special Issue Information" and "Keywords" sections.

Dr. Yin Li
Prof. Dr. Mingjie Chen
Dr. Junli Chang
Guest Editors

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Keywords

cereals crops
molecular genetics
molecular breeding
functional genomics
comparative genomics
multi-omics
biotechnology
transgenic crops
gene editing
gene regulation
crop nano-biotechnology
crop improvement

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Published Papers (9 papers)

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Research

26 pages, 1783 KiB

Open AccessArticle

Genotype Performance Estimation in Targeted Production Environments by Using Sparse Genomic Prediction

by Osval A. Montesinos-López, Paolo Vitale, Guillermo Gerard, Leonardo Crespo-Herrera, Carolina Saint Pierre, Abelardo Montesinos-López and José Crossa

Plants 2024, 13(21), 3059; https://doi.org/10.3390/plants13213059 - 31 Oct 2024

Viewed by 516

Abstract

In plant breeding, Multi-Environment Trials (METs) evaluate candidate genotypes across various conditions, which is financially costly due to extensive field testing. Sparse testing addresses this challenge by evaluating some genotypes in selected environments, allowing for a broader range of environments without significantly increasing costs. This approach integrates genomic information to adjust phenotypic data, leading to more accurate genetic effect estimations. Various sparse testing methods have been explored to optimize resource use. This study employed Incomplete Block Design (IBD) to allocate lines to environments, ensuring not all lines were tested in every environment. We compared IBD to Random line allocation, maintaining a consistent number of environments per line across both methods. The primary objective was to estimate grain yield performance of lines using Genomic Estimated Breeding Values (GEBVs) computed through six Genomic Best Linear Unbiased Predictor (GBLUP) methods. In the first five methods, missing values were predicted before cross-environment adjustment; in the sixth, adjustment was performed directly. Using the Bayesian GBLUP model, we analyzed genotype performance under both IBD and random allocation. Results indicate that computing GEBVs for a target population of environments (TPE) using available phenotype and marker data is effective for selection. The IBD method showed superior performance with less variability compared to random allocation. These findings suggest that using IBD designs can enhance selection accuracy and efficiency, and that pre-adjustment prediction of missing lines may not necessarily improve selection outcomes. Full article

(This article belongs to the Special Issue Genetics, Genomics, and Biotechnology for Cereal Crop Improvements)

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13 pages, 2662 KiB

Open AccessArticle

Optimization of Plant Oxalate Quantification and Generation of Low-Oxalate Maize (Zea mays L.) through O7 Overexpression

by Kai Zhao, Tao Wang, Bin-Bin Zhao and Jun Yang

Plants 2024, 13(21), 2950; https://doi.org/10.3390/plants13212950 - 22 Oct 2024

Viewed by 521

Abstract

Oxalate, the simplest dicarboxylic acid, is a prevalent antinutrient that chelates with various metals and can lead to the formation of kidney stones in humans. The accurate detection of the oxalate concentration in food and the cultivation of low-oxalate crops are important for enhancing public health. In this study, we established a high-throughput and highly sensitive technique for oxalate detection using ultra-high-performance liquid chromatographic–triple quadrupole tandem mass spectrometry (UPLC-QqQ-MS/MS). Additionally, we overexpressed the gene O7, which encodes oxalyl-CoA synthetase in the maize oxalate degradation pathway, resulting in O7-OE lines. By employing the UPLC-QqQ-MS/MS method to measure oxalate levels in these transgenic lines, we observed that the oxalate content in the kernels of O7-OE lines was reduced by approximately 43%, with a concurrent increase in some micronutrients such as zinc. Importantly, the transgenic maize showed normal seed storage compound accumulation or other agronomic characteristics. In summary, we developed a high-throughput detection method that advances oxalate measurement. Furthermore, by generating new maize germplasm with diminished oxalate, our work offers potential health advantages to consumers. Full article

(This article belongs to the Special Issue Genetics, Genomics, and Biotechnology for Cereal Crop Improvements)

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20 pages, 5789 KiB

Open AccessArticle

Characterization and Transcriptomic Analysis of Sorghum EIN/EIL Family and Identification of Their Roles in Internode Maturation

by Min Tu, Yuqing Hua, Ti Shao, Siyu Zhang, Zihan Xiang, Manting Yu, Guoli Wang, Zhuang Li, Yun He, Lin Yang and Yin Li

Plants 2024, 13(18), 2615; https://doi.org/10.3390/plants13182615 - 19 Sep 2024

Viewed by 662

Abstract

Ethylene-insensitive 3/Ethylene-insensitive3-like proteins (EIN3/EIL) represent a group of transcription factors critical for the ethylene signaling transduction that manipulate downstream ethylene-responsive genes, thereby regulating plant growth, development, and stress responses. However, the identification, evolution, and divergence of the EIL family remain to be studied in Sorghum bicolor. Here, we identified eight SbEILs, which were expanded due to whole-genome-duplication (WGD) events. Characterization of the protein sequences and expression atlas demonstrates that the WGD-duplicated SbEILs could become divergent due to the differential expression patterns, rather than domain and motif architectures. Comparative expression analysis was performed between the RNA-seq data sets of internodes from several sorghum cultivars to understand the potential roles of SbEIL members in internode elongation and maturation. Our results identified SbEIL3 and 7 (the latter as a homolog of OsEIL7/OsEIL1) to be the highly expressed SbEIL genes in sorghum internodes and revealed a potential functional link between SbEIL7 and internode maturation. The co-expression analysis and comparative expression analysis with ethylene-regulated gene sets found that SbEIL7 was co-regulated with a set of ubiquitin-related protein degradation genes, suggesting possible involvement of SbEIL7 in protein degradation and processing during the post-anthesis stages. Altogether, our findings lay a foundation for future functional studies of ethylene signaling-mediated gene regulation and improvement of sorghum internode development. Full article

(This article belongs to the Special Issue Genetics, Genomics, and Biotechnology for Cereal Crop Improvements)

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32 pages, 7169 KiB

Open AccessArticle

Dissection of the Genetic Basis of Genotype by Environment Interactions for Morphological Traits and Protein Content in Winter Wheat Panel Grown in Morocco and Spain

by Adil El Baouchi, Mohammed Ibriz, Susanne Dreisigacker, Marta S. Lopes and Miguel Sanchez-Garcia

Plants 2024, 13(11), 1477; https://doi.org/10.3390/plants13111477 - 27 May 2024

Viewed by 1016

Abstract

To fulfill the growing demand for wheat consumption, it is important to focus on enhancement breeding strategies targeting key parameters such as yield, thousand kernel weight (TKW), quality characteristics including morphological traits, and protein content. These elements are key to the ongoing and future objectives of wheat breeding programs. Prioritizing these factors will effectively help meet the rising demand for wheat, especially given the challenges posed by unpredictable weather patterns. This study evaluated the morphological traits and protein content of 249 winter wheat varieties and advanced lines grown in eleven different environments in Morocco and Spain incorporating three varied sowing dates. The results showed considerable variability in morphological traits and protein content. Significant correlations were observed among various grain traits, with most grain morphological parameters exhibiting negative correlations with protein content. Differences across environments (p ≤ 0.01) in all traits, genotypes, and genotype by environment interaction were significant. A factorial regression analysis revealed significant impacts of environmental conditions on all grain morphological parameters, protein content, and TKW during the three growth stages. The study identified several high-performing and stable genotypes across diverse environments, providing valuable insights for wheat breeding programs such as genotypes 129, 234, 241, and 243. Genome-Wide Association Studies pinpointed 603 significant markers across 11 environments, spread across chromosomes. Among these, 400 markers were linked with at least two traits or observed in at least two different environments. Moreover, twelve marker-trait associations were detected that surpassed the Bonferroni correction threshold. These findings highlight the importance of targeted breeding efforts to enhance wheat quality and adaptability to different environmental conditions. Full article

(This article belongs to the Special Issue Genetics, Genomics, and Biotechnology for Cereal Crop Improvements)

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17 pages, 4422 KiB

Open AccessArticle

QTL Mapping of Yield-Related Traits in Tetraploid Wheat Based on Wheat55K SNP Array

by Yatao Jia, Yifan Zhang, Yingkai Sun, Chao Ma, Yixiong Bai, Hanbing Zhang, Junbin Hou, Yong Wang, Wanquan Ji, Haibo Bai, Shuiyuan Hao and Zhonghua Wang

Plants 2024, 13(10), 1285; https://doi.org/10.3390/plants13101285 - 7 May 2024

Viewed by 946

Abstract

To enhance the understanding of yield-related traits in tetraploid wheat, it is crucial to investigate and identify genes that govern superior yield characteristics. This study utilized the wheat55K single nucleotide polymorphism array to genotype a recombinant inbred line (RIL) population consisting of 120 lines developed through the crossbreeding of two tetraploid wheat varieties, Qin Hei-1 (QH-1) and Durum Wheat (DW). An investigation and analysis were conducted on 11 yield-related traits, including peduncle length (PL), neck length (NL), spike length (SL), flowering date (FD), heading date (HD), thousand-kernel weight (TKW), kernel area ratio (KAR), kernel circumference (KC), kernel length (KL), kernel width (KW), and kernel length–width ratio (KL-WR), over a period of three years in two locations, Yang Ling, Shaanxi, and Lin He, Inner Mongolia. The analysis identified nine stable loci among eight agronomic traits, named QSL.QD-1A.1, QNL.QD-4B.2, QPL.QD-4B.1, QFD.QD-2B, QHD.QD-2B.1, QHD.QD-4B, QKC.QD-4B.2, QKL-WR.QD-4B.6, and QKL.QD-4B.2. Among them, the additive effects of three QTLs, QSL.QD-1A.1, QNL.QD-4B.2, and QFD.QD-2B, were positive, indicating that the enhancing alleles at these loci were derived from the parent line QH-1. These three QTLs showed significant positive effects on the phenotypes of the population materials. Furthermore, potential functional genes were identified within the mapping intervals of QSL.QD-1A.1 and QNL.QD-4B.2, which regulate the development of spike length and neck length, respectively. These results provide potential QTLs and candidate genes, which broaden the genetic basis of agronomic traits related to yield, such as SL, NL, PL, and FD, and benefits for wheat breeding and improvement. Full article

(This article belongs to the Special Issue Genetics, Genomics, and Biotechnology for Cereal Crop Improvements)

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25 pages, 11184 KiB

Open AccessArticle

Bioinformatic Identification and Expression Analyses of the MAPK–MAP4K Gene Family Reveal a Putative Functional MAP4K10-MAP3K7/8-MAP2K1/11-MAPK3/6 Cascade in Wheat (Triticum aestivum L.)

by Yongliang Li, You Li, Xiaoxiao Zou, Shuai Jiang, Miyuan Cao, Fenglin Chen, Yan Yin, Wenjun Xiao, Shucan Liu and Xinhong Guo

Plants 2024, 13(7), 941; https://doi.org/10.3390/plants13070941 - 24 Mar 2024

Viewed by 1560

Abstract

The mitogen-activated protein kinase (MAPK) cascades act as crucial signaling modules that regulate plant growth and development, response to biotic/abiotic stresses, and plant immunity. MAP3Ks can be activated through MAP4K phosphorylation in non-plant systems, but this has not been reported in plants to date. Here, we identified a total of 234 putative TaMAPK family members in wheat (Triticum aestivum L.). They included 48 MAPKs, 17 MAP2Ks, 144 MAP3Ks, and 25 MAP4Ks. We conducted systematic analyses of the evolution, domain conservation, interaction networks, and expression profiles of these TaMAPK–TaMAP4K (representing TaMAPK, TaMAP2K, TaMAP3K, and TaMAP4K) kinase family members. The 234 TaMAPK–TaMAP4Ks are distributed on 21 chromosomes and one unknown linkage group (Un). Notably, 25 of these TaMAP4K family members possessed the conserved motifs of MAP4K genes, including glycine-rich motif, invariant lysine (K) motif, HRD motif, DFG motif, and signature motif. TaMAPK3 and 6, and TaMAP4K10/24 were shown to be strongly expressed not only throughout the growth and development stages but also in response to drought or heat stress. The bioinformatics analyses and qRT-PCR results suggested that wheat may activate the MAP4K10–MEKK7–MAP2K11–MAPK6 pathway to increase drought resistance in wheat, and the MAP4K10–MAP3K8–MAP2K1/11-MAPK3 pathway may be involved in plant growth. In general, our work identified members of the MAPK–MAP4K cascade in wheat and profiled their potential roles during their response to abiotic stresses and plant growth based on their expression pattern. The characterized cascades might be good candidates for future crop improvement and molecular breeding. Full article

(This article belongs to the Special Issue Genetics, Genomics, and Biotechnology for Cereal Crop Improvements)

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26 pages, 13180 KiB

Open AccessArticle

Genome-Wide Comparative Analysis of Five Amaranthaceae Species Reveals a Large Amount of Repeat Content

by Akshay Singh, Avantika Maurya, Subramani Rajkumar, Amit Kumar Singh, Rakesh Bhardwaj, Surinder Kumar Kaushik, Sandeep Kumar, Kuldeep Singh, Gyanendra Pratap Singh and Rakesh Singh

Plants 2024, 13(6), 824; https://doi.org/10.3390/plants13060824 - 13 Mar 2024

Viewed by 1478

Abstract

Amaranthus is a genus of C4 dicotyledonous herbaceous plant species that are widely distributed in Asia, Africa, Australia, and Europe and are used as grain, vegetables, forages, and ornamental plants. Amaranth species have gained significant attention nowadays as potential sources of nutritious food and industrial products. In this study, we performed a comparative genome analysis of five amaranth species, namely, Amaranthus hypochondriacus, Amaranthus tuberculatus, Amaranthus hybridus, Amaranthus palmeri, and Amaranthus cruentus. The estimated repeat content ranged from 54.49% to 63.26% and was not correlated with the genome sizes. Out of the predicted repeat classes, the majority of repetitive sequences were Long Terminal Repeat (LTR) elements, which account for about 13.91% to 24.89% of all amaranth genomes. Phylogenetic analysis based on 406 single-copy orthologous genes revealed that A. hypochondriacus is most closely linked to A. hybridus and distantly related to A. cruentus. However, dioecious amaranth species, such as A. tuberculatus and A. palmeri, which belong to the subgenera Amaranthus Acnida, have formed their distinct clade. The comparative analysis of genomic data of amaranth species will be useful to identify and characterize agronomically important genes and their mechanisms of action. This will facilitate genomics-based, evolutionary studies, and breeding strategies to design faster, more precise, and predictable crop improvement programs. Full article

(This article belongs to the Special Issue Genetics, Genomics, and Biotechnology for Cereal Crop Improvements)

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15 pages, 9423 KiB

Open AccessArticle

A 14-3-3 Protein-Encoding Gene, BdGF14g, Confers Better Drought Tolerance by Regulating ABA Biosynthesis and Signaling

by Yang Zhang, Yuan He, Hongyan Zhao, Yan Zhang, Jing Yang, Xingqi Ou, Jinlong Zhang and Qidi Zhu

Plants 2023, 12(23), 3975; https://doi.org/10.3390/plants12233975 - 26 Nov 2023

Cited by 2 | Viewed by 1301

Abstract

Abscisic acid (ABA), a phytohormone, enacts a cardinal function in coping with abiotic stress. 14-3-3 proteins can interact with ABA-responsive-element-binding transcription factors (ABFs), a chief constituent of ABA signaling, and play critical roles in the dehydration response involving ABA signaling. Meanwhile, whether and how 14-3-3 proteins regulate ABA signaling to respond to aridity stress is yet to be fully investigated. Herein, BdGF14g, a 14-3-3 gene induced by ABA, H₂O₂, and PEG treatments, was identified in Brachypodium distachyon (B. distachyon). Overexpression of BdGF14g improved drought stress tolerance in tobacco plants, with a higher survival rate, longer root length, enhanced cell membrane stability, and increased antioxidase activity compared with non-transgenic controls in coping with dehydration. Both drought and exogenous ABA treatments resulted in smaller stomatal apertures in BdGF14g-transgenic lines. Additionally, when an ABA biosynthesis inhibitor was added, the better growth statuses, less H₂O₂ accumulation, and higher activities of catalase and superoxide dismutase under mannitol stress disappeared. Moreover, BdGF14g interacted with NtABF2, upregulated the endogenous ABA content, and enhanced the transcription of ABA-related genes, including NtNCED1, a crucial ABA biosynthesis gene, under drought conditions. In conclusion, BdGF14g acts as a positive factor in the water deficiency response by affecting ABA biosynthesis and signaling in tobacco plants. Full article

(This article belongs to the Special Issue Genetics, Genomics, and Biotechnology for Cereal Crop Improvements)

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18 pages, 8229 KiB

Open AccessArticle

Pyramiding Breeding of Low-Glutelin-Content Indica Rice with Good Quality and Resistance

by Da-Gang Chen, Jie Guo, Ke Chen, Chan-Juan Ye, Juan Liu, You-Ding Chen, Xin-Qiao Zhou and Chuan-Guang Liu

Plants 2023, 12(21), 3763; https://doi.org/10.3390/plants12213763 - 3 Nov 2023

Cited by 1 | Viewed by 1168

Abstract

Low-glutelin-content rice, a type of functional rice with glutelin levels below 4%, is an essential dietary supplement for chronic kidney disease (CKD) patients. Developing low-glutelin-content rice varieties is crucial to catering to the growing CKD population. In this study, we aimed to create a new low-glutelin indica rice variety with excellent agronomic traits. To achieve this, we employed a combination of molecular-marker-assisted selection and traditional breeding techniques. The cultivars W3660, Wushansimiao (WSSM), and Nantaixiangzhan (NTXZ) were crossbred, incorporating the Lgc-1, Pi-2, Xa23, and fgr alleles into a single line. The result of this breeding effort was “Yishenxiangsimiao”, a new indica rice variety that inherits the desirable characteristics of its parent lines. Yishenxiangsimiao (YSXSM) possesses not only a low glutelin content but also dual resistance to blast and bacterial blight (BB). It exhibits high-quality grains with a fragrant aroma. This new low-glutelin indica cultivar not only ensures a stable food supply for CKD patients but also serves as a healthy dietary option for the general public. We also performed RNA-seq of these rice varieties to investigate their internal gene expression differences. The YSXSM exhibited a higher biotic-resistance gene expression in comparison to NTXZ. In summary, we successfully developed a novel low-glutelin indica rice variety, “Yishenxiangsimiao”, with superior agronomic traits. This rice variety addresses the dietary needs of CKD patients and offers a nutritious choice for all consumers. Full article

(This article belongs to the Special Issue Genetics, Genomics, and Biotechnology for Cereal Crop Improvements)

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