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Genetics- and Genomics-Based Crop Improvement and Breeding : 2nd Edition

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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: closed (28 June 2024) | Viewed by 8310

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Prof. Dr. Jian Ma

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State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
Interests: wheat molecular genetics and genomics
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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 to, 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

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.

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Keywords

crop
germplasm
genetics
genomics
breeding

Published Papers (9 papers)

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22 pages, 12584 KiB

Open AccessArticle

Long Noncoding RNAs in Response to Hyperosmolarity Stress, but Not Salt Stress, Were Mainly Enriched in the Rice Roots

by Yanrong Pang, Kaifeng Zheng, Qinyue Min, Yinxing Wang, Xiuhua Xue, Wanjie Li, Heping Zhao, Feng Qiao and Shengcheng Han

Int. J. Mol. Sci. 2024, 25(11), 6226; https://doi.org/10.3390/ijms25116226 - 5 Jun 2024

Viewed by 467

Abstract

Due to their immobility and possession of underground parts, plants have evolved various mechanisms to endure and adapt to abiotic stresses such as extreme temperatures, drought, and salinity. However, the contribution of long noncoding RNAs (lncRNAs) to different abiotic stresses and distinct rice seedling parts remains largely uncharacterized beyond the protein-coding gene (PCG) layer. Using transcriptomics and bioinformatics methods, we systematically identified lncRNAs and characterized their expression patterns in the roots and shoots of wild type (WT) and ososca1.1 (reduced hyperosmolality-induced [Ca²⁺]_i increase in rice) seedlings under hyperosmolarity and salt stresses. Here, 2937 candidate lncRNAs were identified in rice seedlings, with intergenic lncRNAs representing the largest category. Although the detectable sequence conservation of lncRNAs was low, we observed that lncRNAs had more orthologs within the Oryza. By comparing WT and ososca1.1, the transcription level of OsOSCA1.1-related lncRNAs in roots was greatly enhanced in the face of hyperosmolality stress. Regarding regulation mode, the co-expression network revealed connections between trans-regulated lncRNAs and their target PCGs related to OsOSCA1.1 and its mediation of hyperosmolality stress sensing. Interestingly, compared to PCGs, the expression of lncRNAs in roots was more sensitive to hyperosmolarity stress than to salt stress. Furthermore, OsOSCA1.1-related hyperosmolarity stress-responsive lncRNAs were enriched in roots, and their potential cis-regulated genes were associated with transcriptional regulation and signaling transduction. Not to be ignored, we identified a motif-conserved and hyperosmolarity stress-activated lncRNA gene (OSlncRNA), speculating on its origin and evolutionary history in Oryza. In summary, we provide a global perspective and a lncRNA resource to understand hyperosmolality stress sensing in rice roots, which helps to decode the complex molecular networks involved in plant sensing and adaptation to stressful environments. Full article

(This article belongs to the Special Issue Genetics- and Genomics-Based Crop Improvement and Breeding : 2nd Edition)

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23 pages, 21627 KiB

Open AccessArticle

The Mechanism of Exogenous Salicylic Acid and 6-Benzylaminopurine Regulating the Elongation of Maize Mesocotyl

by Xue Qi, Zelong Zhuang, Xiangzhuo Ji, Jianwen Bian and Yunling Peng

Int. J. Mol. Sci. 2024, 25(11), 6150; https://doi.org/10.3390/ijms25116150 - 3 Jun 2024

Viewed by 293

Abstract

The elongation of the mesocotyl plays an important role in the emergence of maize deep-sowing seeds. This study was designed to explore the function of exogenous salicylic acid (SA) and 6-benzylaminopurine (6-BA) in the growth of the maize mesocotyl and to examine its regulatory network. The results showed that the addition of 0.25 mmol/L exogenous SA promoted the elongation of maize mesocotyls under both 3 cm and 15 cm deep-sowing conditions. Conversely, the addition of 10 mg/L exogenous 6-BA inhibited the elongation of maize mesocotyls. Interestingly, the combined treatment of exogenous SA–6-BA also inhibited the elongation of maize mesocotyls. The longitudinal elongation of mesocotyl cells was the main reason affecting the elongation of maize mesocotyls. Transcriptome analysis showed that exogenous SA and 6-BA may interact in the hormone signaling regulatory network of mesocotyl elongation. The differential expression of genes related to auxin (IAA), jasmonic acid (JA), brassinosteroid (BR), cytokinin (CTK) and SA signaling pathways may be related to the regulation of exogenous SA and 6-BA on the growth of mesocotyls. In addition, five candidate genes that may regulate the length of mesocotyls were screened by Weighted Gene Co-Expression Network Analysis (WGCNA). These genes may be involved in the growth of maize mesocotyls through auxin-activated signaling pathways, transmembrane transport, methylation and redox processes. The results enhance our understanding of the plant hormone regulation of mesocotyl growth, which will help to further explore and identify the key genes affecting mesocotyl growth in plant hormone signaling regulatory networks. Full article

(This article belongs to the Special Issue Genetics- and Genomics-Based Crop Improvement and Breeding : 2nd Edition)

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17 pages, 8172 KiB

Open AccessArticle

Genome-Wide Identification of WRKY Gene Family and Functional Characterization of CcWRKY25 in Capsicum chinense

by Liping Zhang, Dan Wu, Wei Zhang, Huangying Shu, Peixia Sun, Chuang Huang, Qin Deng, Zhiwei Wang and Shanhan Cheng

Int. J. Mol. Sci. 2023, 24(14), 11389; https://doi.org/10.3390/ijms241411389 - 13 Jul 2023

Cited by 5 | Viewed by 1565

Abstract

Pepper is renowned worldwide for its distinctive spicy flavor. While the gene expression characteristics of the capsaicinoid biosynthesis pathway have been extensively studied, there are already a few reports regarding transcriptional regulation in capsaicin biosynthesis. In this study, 73 WRKYs were identified in the genome of Capsicum chinense, and their physicochemical traits, DNA, and protein sequence characteristics were found to be complex. Combining RNA-seq and qRT-PCR data, the WRKY transcription factor CA06g13580, which was associated with the accumulation tendency of capsaicinoid, was screened and named CcWRKY25. CcWRKY25 was highly expressed in the placenta of spicy peppers. The heterologous expression of CcWRKY25 in Arabidopsis promoted the expression of genes PAL, 4CL1, 4CL2, 4CL3, CCR, and CCoAOMT and led to the accumulation of lignin and flavonoids. Furthermore, the expression of the capsaicinoid biosynthesis pathway genes (CBGs) pAMT, AT3, and KAS was significantly reduced in CcWRKY25-silenced pepper plants, resulting in a decrease in the amount of capsaicin. However, there was no noticeable difference in lignin accumulation. The findings suggested that CcWRKY25 could be involved in regulating capsaicinoid synthesis by promoting the expression of genes upstream of the phenylpropanoid pathway and inhibiting CBGs’ expression. Moreover, the results highlighted the role of CcWRKY25 in controlling the pungency of pepper and suggested that the competitive relationship between lignin and capsaicin could also regulate the spiciness of the pepper. Full article

(This article belongs to the Special Issue Genetics- and Genomics-Based Crop Improvement and Breeding : 2nd Edition)

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18 pages, 10795 KiB

Open AccessArticle

NopAA and NopD Signaling Association-Related Gene GmNAC27 Promotes Nodulation in Soybean (Glycine max)

by Yue Wang, Xiaoke Jia, Yansong Li, Shengnan Ma, Chao Ma, Dawei Xin, Jinhui Wang, Qingshan Chen and Chunyan Liu

Int. J. Mol. Sci. 2023, 24(24), 17498; https://doi.org/10.3390/ijms242417498 - 15 Dec 2023

Viewed by 1012

Abstract

Rhizobia secrete effectors that are essential for the effective establishment of their symbiotic interactions with leguminous host plants. However, the signaling pathways governing rhizobial type III effectors have yet to be sufficiently characterized. In the present study, the type III effectors, NopAA and NopD, which perhaps have signaling pathway crosstalk in the regulation of plant defense responses, have been studied together for the first time during nodulation. Initial qRT-PCR experiments were used to explore the impact of NopAA and NopD on marker genes associated with symbiosis and defense responses. The effects of these effectors on nodulation were then assessed by generating bacteria in which both NopAA and NopD were mutated. RNA-sequencing analyses of soybean roots were further utilized to assess signaling crosstalk between NopAA and NopD. NopAA mutant and NopD mutant were both found to repress GmPR1, GmPR2, and GmPR5 expression in these roots. The two mutants also significantly reduced nodules dry weight and the number of nodules and infection threads, although these changes were not significantly different from those observed following inoculation with double-mutant (HH103ΩNopAA&NopD). NopAA and NopD co-mutant inoculation was primarily found to impact the plant–pathogen interaction pathway. Common differentially expressed genes (DEGs) associated with both NopAA and NopD were enriched in the plant–pathogen interaction, plant hormone signal transduction, and MAPK signaling pathways, and no further changes in these common DEGs were noted in response to inoculation with HH103ΩNopAA&NopD. Glyma.13G279900 (GmNAC27) was ultimately identified as being significantly upregulated in the context of HH103ΩNopAA&NopD inoculation, serving as a positive regulator of nodulation. These results provide new insight into the synergistic impact that specific effectors can have on the establishment of symbiosis and the responses of host plant proteins. Full article

(This article belongs to the Special Issue Genetics- and Genomics-Based Crop Improvement and Breeding : 2nd Edition)

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21 pages, 3274 KiB

Open AccessReview

Promotion of Ca²⁺ Accumulation in Roots by Exogenous Brassinosteroids as a Key Mechanism for Their Enhancement of Plant Salt Tolerance: A Meta-Analysis and Systematic Review

by Xian Wang, Jiali Chai, Wenyu Liu, Xiaolin Zhu, Haixun Liu and Xiaohong Wei

Int. J. Mol. Sci. 2023, 24(22), 16123; https://doi.org/10.3390/ijms242216123 - 9 Nov 2023

Viewed by 1233

Abstract

Brassinosteroids (BRs), the sixth major phytohormone, can regulate plant salt tolerance. Many studies have been conducted to investigate the effects of BRs on plant salt tolerance, generating a large amount of research data. However, a meta-analysis on regulating plant salt tolerance by BRs has not been reported. Therefore, this study conducted a meta-analysis of 132 studies to elucidate the most critical physiological mechanisms by which BRs regulate salt tolerance in plants from a higher dimension and analyze the best ways to apply BRs. The results showed that exogenous BRs significantly increased germination, plant height, root length, and biomass (total dry weight was the largest) of plants under salt stress. There was no significant difference between seed soaking and foliar spraying. However, the medium method (germination stage) and stem application (seedling stage) may be more effective in improving plant salt tolerance. BRs only inhibit germination in Solanaceae. BRs (2 μM), seed soaking for 12 h, and simultaneous treatment with salt stress had the highest germination rate. At the seedling stage, the activity of Brassinolide (C₂₈H₄₈O₆) was higher than that of Homobrassinolide (C₂₉H₅₀O₆), and post-treatment, BRs (0.02 μM) was the best solution. BRs are unsuitable for use in the germination stage when Sodium chloride is below 100 mM, and the effect is also weakest in the seedling stage. Exogenous BRs promoted photosynthesis, and antioxidant enzyme activity increased the accumulation of osmoregulatory and antioxidant substances and reduced the content of harmful substances and Na⁺, thus reducing cell damage and improving plant salt tolerance. BRs induced the most soluble protein, chlorophyll a, stomatal conductance, net photosynthetic rate, Glutathione peroxidase, and root-Ca²⁺, with BRs causing Ca²⁺ signals in roots probably constituting the most important reason for improving salt tolerance. BRs first promoted the accumulation of Ca²⁺ in roots, which increased the content of the above vital substances and enzyme activities through the Ca²⁺ signaling pathway, improving plant salt tolerance. Full article

(This article belongs to the Special Issue Genetics- and Genomics-Based Crop Improvement and Breeding : 2nd Edition)

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20 pages, 12753 KiB

Open AccessArticle

Genome-Wide Analysis of the Auxin/Indoleacetic Acid (Aux/IAA) Gene Family in Autopolyploid Sugarcane (Saccharum spontaneum)

by Xiaojin Huang, Munsif Ali Shad, Yazhou Shu, Sikun Nong, Xianlong Li, Songguo Wu, Juan Yang, Muhammad Junaid Rao, Muhammad Zeshan Aslam, Xiaoti Huang, Dige Huang and Lingqiang Wang

Int. J. Mol. Sci. 2024, 25(13), 7473; https://doi.org/10.3390/ijms25137473 - 8 Jul 2024

Viewed by 358

Abstract

The auxin/indoleacetic acid (Aux/IAA) family plays a central role in regulating gene expression during auxin signal transduction. Nonetheless, there is limited knowledge regarding this gene family in sugarcane. In this study, 92 members of the IAA family were identified in Saccharum spontaneum, distributed on 32 chromosomes, and classified into three clusters based on phylogeny and motif compositions. Segmental duplication and recombination events contributed largely to the expansion of this superfamily. Additionally, cis-acting elements in the promoters of SsIAAs involved in plant hormone regulation and stress responsiveness were predicted. Transcriptomics data revealed that most SsIAA expressions were significantly higher in stems and basal parts of leaves, and at nighttime, suggesting that these genes might be involved in sugar transport. QRT-PCR assays confirmed that cold and salt stress significantly induced four and five SsIAAs, respectively. GFP-subcellular localization showed that SsIAA23 and SsIAA12a were localized in the nucleus, consistent with the results of bioinformatics analysis. In conclusion, to a certain extent, the functional redundancy of family members caused by the expansion of the sugarcane IAA gene family is related to stress resistance and regeneration of sugarcane as a perennial crop. This study reveals the gene evolution and function of the SsIAA gene family in sugarcane, laying the foundation for further research on its mode of action. Full article

(This article belongs to the Special Issue Genetics- and Genomics-Based Crop Improvement and Breeding : 2nd Edition)

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13 pages, 3319 KiB

Open AccessArticle

Integrated VIS/NIR Spectrum and Genome-Wide Association Study for Genetic Dissection of Cellulose Crystallinity in Wheat Stems

by Jianguo Li, Peimin Zhao, Liyan Zhao, Qiang Chen, Shikun Nong, Qiang Li and Lingqiang Wang

Int. J. Mol. Sci. 2024, 25(5), 3028; https://doi.org/10.3390/ijms25053028 - 6 Mar 2024

Viewed by 793

Abstract

Cellulose crystallinity is a crucial factor influencing stem strength and, consequently, wheat lodging. However, the genetic dissection of cellulose crystallinity is less reported due to the difficulty of its measurement. In this study, VIS/NIR spectra and cellulose crystallinity were measured for a wheat accession panel with diverse genetic backgrounds. We developed a reliable VIS/NIR model for cellulose crystallinity with a high determination coefficient (R²) (0.95) and residual prediction deviation (RPD) (4.04), enabling the rapid screening of wheat samples. A GWAS of the cellulose crystallinity in 326 wheat accessions revealed 14 significant SNPs and 13 QTLs. Two candidate genes, TraesCS4B03G0029800 and TraesCS5B03G1085500, were identified. In summary, this study establishes an efficient method for the measurement of cellulose crystallinity in wheat stems and provides a genetic basis for enhancing lodging resistance in wheat. Full article

(This article belongs to the Special Issue Genetics- and Genomics-Based Crop Improvement and Breeding : 2nd Edition)

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18 pages, 4520 KiB

Open AccessArticle

Genome-Wide Identification and Comprehensive Analysis of the FtsH Gene Family in Soybean (Glycine max)

by Qi Shan, Baihui Zhou, Yuanxin Wang, Feiyu Hao, Lin Zhu, Yuhan Liu, Nan Wang, Fawei Wang, Xiaowei Li, Yuanyuan Dong, Keheng Xu, Yonggang Zhou, Haiyan Li, Weican Liu and Hongtao Gao

Int. J. Mol. Sci. 2023, 24(23), 16996; https://doi.org/10.3390/ijms242316996 - 30 Nov 2023

Cited by 2 | Viewed by 1059

Abstract

The filamentation temperature-sensitive H (FtsH) gene family is critical in regulating plant chloroplast development and photosynthesis. It plays a vital role in plant growth, development, and stress response. Although FtsH genes have been identified in a wide range of plants, there is no detailed study of the FtsH gene family in soybean (Glycine max). Here, we identified 34 GmFtsH genes, which could be categorized into eight groups, and GmFtsH genes in the same group had similar structures and conserved protein motifs. We also performed intraspecific and interspecific collinearity analysis and found that the GmFtsH family has large-scale gene duplication and is more closely related to Arabidopsis thaliana. Cis-acting elements analysis in the promoter region of the GmFtsH genes revealed that most genes contain developmental and stress response elements. Expression patterns based on transcriptome data and real-time reverse transcription quantitative PCR (qRT-PCR) showed that most of the GmFtsH genes were expressed at the highest levels in leaves. Then, GO enrichment analysis indicated that GmFtsH genes might function as a protein hydrolase. In addition, the GmFtsH13 protein was confirmed to be localized in chloroplasts by a transient expression experiment in tobacco. Taken together, the results of this study lay the foundation for the functional determination of GmFtsH genes and help researchers further understand the regulatory network in soybean leaf development. Full article

(This article belongs to the Special Issue Genetics- and Genomics-Based Crop Improvement and Breeding : 2nd Edition)

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15 pages, 13370 KiB

Open AccessArticle

Ancient Duplication and Lineage-Specific Transposition Determine Evolutionary Trajectory of ERF Subfamily across Angiosperms

by Xun-Ge Zhu, Ge-Ran Hutang and Li-Zhi Gao

Int. J. Mol. Sci. 2024, 25(7), 3941; https://doi.org/10.3390/ijms25073941 - 1 Apr 2024

Viewed by 862

Abstract

AP2/ERF transcription factor family plays an important role in plant development and stress responses. Previous studies have shed light on the evolutionary trajectory of the AP2 and DREB subfamilies. However, knowledge about the evolutionary history of the ERF subfamily in angiosperms still remains limited. In this study, we performed a comprehensive analysis of the ERF subfamily from 107 representative angiosperm species by combining phylogenomic and synteny network approaches. We observed that the expansion of the ERF subfamily was driven not only by whole-genome duplication (WGD) but also by tandem duplication (TD) and transposition duplication events. We also found multiple transposition events in Poaceae, Brassicaceae, Poales, Brassicales, and Commelinids. These events may have had notable impacts on copy number variation and subsequent functional divergence of the ERF subfamily. Moreover, we observed a number of ancient tandem duplications occurred in the ERF subfamily across angiosperms, e.g., in Subgroup IX, IXb originated from ancient tandem duplication events within IXa. These findings together provide novel insights into the evolution of this important transcription factor family. Full article

(This article belongs to the Special Issue Genetics- and Genomics-Based Crop Improvement and Breeding : 2nd Edition)

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