Submit to Special Issue Submit Abstract to Special Issue Review for IJMS Propose a Special Issue

Journal Menu

Journal Browser

Understanding the Genetics of Complex Traits in Plants: Association Analysis and Genomic Selection Methods

Special Issue Editors
Special Issue Information
Keywords
Benefits of Publishing in a Special Issue
Published Papers

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 June 2025 | Viewed by 7130

Share This Special Issue

Special Issue Editor

Dr. Wenxin Liu

E-Mail Website
Guest Editor

Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
Interests: quantitative genetics; statistical genomics; biostatistics; molecular breeding
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Crops provide food and nutrition for humankind both directly and indirectly. It is obligatory to maintain or even improve crop production in order to feed the arising world population under climate change. Thus, in targeting genetic improvement and highly efficient breeding, it is crucial to dissect the genetic architecture, understand the molecular mechanism, and explore the new favorable gene resource of yield, quality, biotic, and abiotic stress resistance in plants. Association analysis and genomic selection methods have already displayed wonderful achievements and high efficiency in such fields. All research relating to association analysis and genomic selection for complex traits in plants are welcome for this Special Issue.

The research goal could be genetic architecture, molecular biology, or genotype–environment interaction. The accepted article types include research, reviews, perspectives, or comments. Submit to this Special Issue and contribute to the development of food and crop production worldwide.

Dr. Wenxin Liu
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

association analysis
genomic selection
plant
complex trait
genetic architecture
molecular biology
molecular breeding
genotype–environment interaction

Benefits of Publishing in a Special Issue

Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

Further information on MDPI's Special Issue policies can be found here.

Published Papers (9 papers)

Download All Papers

Order results

Result details

Show export options Show export options

Select all

Export citation of selected articles as:

Research

18 pages, 5469 KiB

Open AccessArticle

Identification of the SAUR Members in Woodland Strawberry (Fragaria vesca) and Detection of Their Expression Profiles in Response to Auxin Signals

by Ruian Zhou, Jiahui Feng, Zhihong Zhang and Yuexue Liu

Int. J. Mol. Sci. 2025, 26(8), 3638; https://doi.org/10.3390/ijms26083638 - 11 Apr 2025

Viewed by 216

Abstract

The SAUR (Small Auxin-Upregulated RNA) family members are important early auxin responsive genes in plants, playing a key regulatory role in the auxin metabolism, signal transduction, plant organ development, and abiotic stress response. Auxin signaling is also crucial for strawberry fruit development, but its specific regulatory mechanism remains unclear. In this study, bioinformatics methods were used to systematically identify and evaluate the FvSAUR gene family members associated with the auxin signaling in strawberry. The woodland strawberry Yellow Wonder line ‘YW5AF7’ was used as the material to further investigate the expressional characteristics of FvSAUR members in response to the auxin signals. A total of 64 members of the SAUR gene family were identified in the woodland strawberry genome, associated with FvSAUR1-64. Further bioinformatics analysis revealed that the FvSAUR members have undergone significant structural differentiation during evolution, and their encoded proteins exhibit diversity in folding stability, physicochemical properties, and other aspects. The prediction of the cis-elements in the promoter sequences of these genes suggests that the FvSAUR genes may mediate multiple hormonal and environmental signals, participating in a wide range of biological processes. RNA seq data analysis combined with RT-qPCR analysis revealed a dynamic spatiotemporal expression pattern of the FvSAUR genes in the vegetative and reproductive organs of strawberries, particularly the high expression levels of FvSAUR11, 17, 19, 21, and other genes in flowers and young fruits, suggesting their potential regulatory roles in strawberry fruit development. Exogenous auxin treatment experiments further suggested that the expression of FvSAUR11 and FvSAUR19 is sensitive to the changes in auxin levels, indicating their potential involvement in auxin signal transduction during strawberry fruit development. Subcellular localization results showed that both proteins are located in the nucleus. The results of this study systematically analyzed the sequence structure characteristics, evolutionary history, expression patterns, and potential functions of the strawberry FvSAUR family members, providing important insights for further elucidating the roles of FvSAUR genes in strawberry fruit growth and development. Full article

(This article belongs to the Special Issue Understanding the Genetics of Complex Traits in Plants: Association Analysis and Genomic Selection Methods)

► Show Figures

Figure 1

22 pages, 3134 KiB

Open AccessArticle

Cell Wall–Based Machine Learning Models to Predict Plant Growth Using Onion Epidermis

by Celia Khoulali, Juan Manuel Pastor, Javier Galeano, Kris Vissenberg and Eva Miedes

Int. J. Mol. Sci. 2025, 26(7), 2946; https://doi.org/10.3390/ijms26072946 - 24 Mar 2025

Viewed by 362

Abstract

The plant cell wall (CW) is a physical barrier that plays a dual role in plant physiology, providing structural support for growth and development. Understanding the dynamics of CW growth is crucial for optimizing crop yields. In this study, we employed onion (Allium cepa L.) epidermis as a model system, leveraging its layered organization to investigate growth stages. Microscopic analysis revealed proportional variations in cell size in different epidermal layers, offering insights into growth dynamics and CW structural adaptations. Fourier transform infrared spectroscopy (FTIR) identified 11 distinct spectral intervals associated with CW components, highlighting structural modifications that influence wall elasticity and rigidity. Biochemical assays across developmental layers demonstrated variations in cellulose, soluble sugars, and antioxidant content, reflecting biochemical shifts during growth. The differential expression of ten cell wall enzyme (CWE) genes, analyzed via RT-qPCR, revealed significant correlations between gene expression patterns and CW composition changes across developmental layers. Notably, the gene expression levels of the pectin methylesterase and fucosidase enzymes were associated with the contents in cellulose, soluble sugar, and antioxidants. To complement these findings, machine learning models, including Support Vector Machines (SVM), k-Nearest Neighbors (kNN), and Neural Networks, were employed to integrate FTIR data, biochemical parameters, and CWE gene expression profiles. Our models achieved high accuracy in predicting growth stages. This underscores the intricate interplay among CW composition, CW enzymatic activity, and growth dynamics, providing a predictive framework with applications in enhancing crop productivity and sustainability. Full article

(This article belongs to the Special Issue Understanding the Genetics of Complex Traits in Plants: Association Analysis and Genomic Selection Methods)

► Show Figures

Figure 1

20 pages, 2945 KiB

Open AccessArticle

Genomic Prediction for Germplasm Improvement Through Inter-Heterotic-Group Line Crossing in Maize

by Dehe Cheng, Jinlong Li, Shuwei Guo, Yuandong Wang, Shizhong Xu, Shaojiang Chen and Wenxin Liu

Int. J. Mol. Sci. 2025, 26(6), 2662; https://doi.org/10.3390/ijms26062662 - 15 Mar 2025

Viewed by 386

Abstract

Germplasm improvement is essential for maize breeding. Currently, intra-heterotic-group crossing is the major method for germplasm improvement, while inter-heterotic-group crossing is also used in breeding but not in a systematic way. In this study, five inbred lines from four heterotic groups were used to develop a connected segregating population through inter-heterotic-group line crossing (CSPIC), which comprised 5 subpopulations with 535 doubled haploid (DH) lines and 15 related test-cross populations including 1568 hybrids. Significant genetic variation was observed in most subpopulations, with several DH populations exhibiting superior phenotypes regarding traits such as plant height (PH), ear height (EH), days to anthesis (DTA), and days to silking (DTS). Notably, 10.8% of hybrids in the population POP5/C229 surpassed the high-yielding hybrid ND678 (CK). To reduce field planting costs and quickly screen for the best inter-heterotic-group DH lines and test-cross hybrids, we assessed the accuracy of genomic selection (GS) for within- and between-population predictions in the DH populations and the test-cross populations. Within the DH or the hybrid population, the prediction accuracy varied across populations and traits, with an average hybrid yield prediction accuracy of 0.41, reaching 0.54 in POP5/Z58. In the cross DH population predictions, the prediction accuracy of the half-sib population exceeded that of the non-sib cross population prediction, with the highest accuracy observed when the non-shared parents were from the same heterotic group, and the average phenotypic prediction accuracies of POP3 predicting POP2 and POP2 predicting POP3 were 0.54 and 0.45, respectively. In the cross hybrid population predictions, the accuracy was highest when both the training and the test sets came from the same DH populations, with an average accuracy of 0.43. The proportion of shared polymorphisms with respect to SNPs between the training and the test sets (PSP) exhibited a significant and strong correlation with the prediction accuracy of cross population prediction. This study demonstrates the feasibility of creating new heterotic groups through inter-heterotic-group crossing in germplasm improvement, and some cross population prediction patterns exhibited excellent prediction accuracy. Full article

(This article belongs to the Special Issue Understanding the Genetics of Complex Traits in Plants: Association Analysis and Genomic Selection Methods)

► Show Figures

Figure 1

17 pages, 7242 KiB

Open AccessArticle

Identification of Submergence Tolerance Loci in Dongxiang Wild Rice (DXWR) by Genetic Linkage and Transcriptome Analyses

by Jilin Wang, Cheng Huang, Lijuan Tang, Hongping Chen, Ping Chen, Dazhou Chen and Dianwen Wang

Int. J. Mol. Sci. 2025, 26(5), 1829; https://doi.org/10.3390/ijms26051829 - 20 Feb 2025

Viewed by 441

Abstract

The submergence tolerance of rice is a key factor in promoting rice direct seeding technology and resisting flood disasters. Dongxiang wild rice (DXWR) has strong submergence tolerance, but its genetic basis is still unclear. Here, we report quantitative trait loci (QTLs) analysis for hypoxic germination rate (HGR), hypoxic seedling rate (HSR), budlet submergence survival rate (BSSR) and seedling submergence survival rate (SSSR) using a linkage map in the backcross recombinant inbred lines (BRILs) that were derived from a cross of DXWR, and an indica cultivar, GZX49. A total of 20 QTLs related to submergence tolerance of rice were detected, explaining phenotypic variations ranging from 2% to 8.5%. Furthermore, transcriptome sequencing was performed on the seeds and seedlings of DXWR before and after submergence. During the seed hypoxic germination and seedling submergence stages, 6306 and 3226 differentially expressed genes (DEGs) were detected respectively. Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) analyses were conducted on these differentially expressed genes. Using genetic linkage analysis and transcriptome data, combined with qRT-PCR, sequence comparison, and bioinformatics, LOC_Os05g32820 was putatively identified as a candidate gene for qHGR5.2 co-located with HGR and SSSR. These results will provide insights into the mechanism of rice submergence tolerance and provide a basis for improving rice submergence tolerance. Full article

(This article belongs to the Special Issue Understanding the Genetics of Complex Traits in Plants: Association Analysis and Genomic Selection Methods)

► Show Figures

Figure 1

26 pages, 8066 KiB

Open AccessArticle

Identification of MAPK Genes in Phaseolus vulgaris and Analysis of Their Expression Patterns in Response to Anthracnose

by Huiling Liu, Da Wang, Zhenyu Wang, Tong Zhao, Jingying Zhang, Yan Wang, Hongyu Qiao and Yuzhu Han

Int. J. Mol. Sci. 2024, 25(23), 13101; https://doi.org/10.3390/ijms252313101 - 5 Dec 2024

Viewed by 818

Abstract

The oil bean is a high-quality, economically valuable variety of kidney bean (Phaseolus vulgaris L.) that is widely cultivated in Northeast China. However, the prevalence of anthracnose, caused by a combination of factors, including continuous cropping over many years, has led to significant declines in both yield and quality. The mitogen-activated protein kinase (MAPK) cascade is a highly conserved plant cell signaling pathway that plays a pivotal role in plant growth and development, as well as responses to biotic stress. However, its role in the response of P. vulgaris to anthracnose infection has not previously been reported. We identified and characterized thirteen MAPK genes (PvMAPK01–PvMAPK13) in the P. vulgaris genome. These genes were found on eight of the eleven chromosomes of P. vulgaris, and phylogenetic analyses classified them into four previously established subgroups (A–D). Analysis of the cis-acting elements in their promoter regions revealed the presence of multiple elements associated with light, hormone regulation, stress responses, and growth and development. An analysis of intraspecific collinearity revealed that whole-genome and/or segmental duplication, rather than tandem duplication, has been the primary driver of PvMAPK family expansion in P. vulgaris. Transcriptome data revealed that the PvMAPKs differed in their tissue-specific expression patterns, with PvMAPK05 showing particularly high expression in stems and stem tips and PvMAPK07 and PvMAPK11 showing relatively low expression across all tissues. In general, expression of the PvMAPKs was higher in stems, stem tips, and pods than in other tissues and organs, suggesting that they may be particularly important for regulating stem and pod development. Analysis of the expression of PvMAPKs in field-grown plants infected or uninfected with anthracnose revealed that the relative expression levels of PvMAPK05, PvMAPK07, PvMAPK09, and PvMAPK11 exhibited particularly significant changes in response to anthracnose infection across different varieties, suggesting their potential involvement in the anthracnose response of Phaseolus vulgaris. This study reports the fundamental characteristics of the thirteen MAPK genes in P. vulgaris, documents their expression patterns in diverse tissues, and offers preliminary insights into their responses to anthracnose infection, establishing a foundation for subsequent functional validation. Full article

(This article belongs to the Special Issue Understanding the Genetics of Complex Traits in Plants: Association Analysis and Genomic Selection Methods)

► Show Figures

Figure 1

17 pages, 7080 KiB

Open AccessArticle

Genome-Wide Identification and Expression Analysis of FD Gene Family in Bamboos

by Lihan Hou, Huiting Zhang, Yakun Fan, Yaling Zhang, Wengen Zhang, Guangyao Yang, Chunce Guo and Meixia Wang

Int. J. Mol. Sci. 2024, 25(23), 13062; https://doi.org/10.3390/ijms252313062 - 5 Dec 2024

Viewed by 866

Abstract

The regulation of flowering time is a highly coordinative process that involves the interplay of multiple genes. The FLOWERING LOCUS D (FD) gene is one of those important players. In this study, we identified and characterized FD genes in bamboo, a plant with the unique monocarpy flowering phenomenon. An angiosperm-wide FD gene family analysis demonstrated that unlike the most recent common ancestor (MRCA) of angiosperms, which had only one FD gene, five FD copies were present in the MRCA of Poaceae, and the same gene copy number was retained in the MRCA of the Bambusoideae subfamily. Further analysis of the Poaceae FD gene family revealed five distinctive clades resulted from four duplication events, with two of these events being specific to the Bambusoideae subfamily. High levels of conservation were observed in the gene structure and amino acid composition of structural domain among the FD genes across bamboos and their close relatives, indicating functional conservation. Furthermore, gene expression profiling indicated that FD gene expression in bamboo closely resemble the expression patterns of their homologs in rice. Additionally, overexpression of two bamboo genes (Phy.ed_05093.t1 and Phy.ed_14669.t1) in Arabidopsis resulted in an early flowering phenotype, demonstrating their involvement in the regulation of the flowering process in plants. Our findings provide a comprehensive resource for understanding the evolution, structure, expression, and function of FD genes in Poaceae and Bambusoideae. Full article

(This article belongs to the Special Issue Understanding the Genetics of Complex Traits in Plants: Association Analysis and Genomic Selection Methods)

► Show Figures

Figure 1

19 pages, 3594 KiB

Open AccessArticle

A Multi-Omics View of Maize’s (Zea mays L.) Response to Low Temperatures During the Seedling Stage

by Tao Yu, Jianguo Zhang, Xuena Ma, Shiliang Cao, Wenyue Li and Gengbin Yang

Int. J. Mol. Sci. 2024, 25(22), 12273; https://doi.org/10.3390/ijms252212273 - 15 Nov 2024

Cited by 1 | Viewed by 930

Abstract

Maize (Zea mays L.) is highly sensitive to temperature during its growth and development stage. A 1 °C drop in temperature can delay maturity by 10 days, resulting in a yield reduction of over 10%. Low-temperature tolerance in maize is a complex quantitative trait, and different germplasms exhibit significant differences in their responses to low-temperature stress. To explore the differences in gene expression and metabolites between B144 (tolerant) and Q319 (susceptible) during germination under low-temperature stress and to identify key genes and metabolites that respond to this stress, high-throughput transcriptome sequencing was performed on the leaves of B144 and Q319 subjected to low-temperature stress for 24 h and their respective controls using Illumina HiSeq^TM 4000 high-throughput sequencing technology. Additionally, high-throughput metabolite sequencing was conducted on the samples using widely targeted metabolome sequencing technology. The results indicated that low-temperature stress triggered the accumulation of stress-related metabolites such as amino acids and their derivatives, lipids, phenolic acids, organic acids, flavonoids, lignin, coumarins, and alkaloids, suggesting their significant roles in the response to low temperature. This stress also promoted gene expression and metabolite accumulation involved in the flavonoid biosynthesis pathway. Notably, there were marked differences in gene expression and metabolites related to the glyoxylate and dicarboxylate metabolism pathways between B144 and Q319. This study, through multi-omics integrated analysis, provides valuable insights into the identification of metabolites, elucidation of metabolic pathways, and the biochemical and genetic basis of plant responses to stress, particularly under low-temperature conditions. Full article

(This article belongs to the Special Issue Understanding the Genetics of Complex Traits in Plants: Association Analysis and Genomic Selection Methods)

► Show Figures

Figure 1

19 pages, 9522 KiB

Open AccessArticle

Ubiquitin-Specific Protease 15 Plays an Important Role in Controlling the Tolerance to Salt, Drought and Abscisic Acid in Arabidopsis thaliana

by Xiaoxiao Zou, Huangping Yin, Daolong Xie, Jiajin Xu, Yongliang Li, Wenjun Xiao, Shucan Liu and Xinhong Guo

Int. J. Mol. Sci. 2024, 25(21), 11569; https://doi.org/10.3390/ijms252111569 - 28 Oct 2024

Viewed by 1157

Abstract

Ubiquitin-specific proteases (UBPs), the largest subfamily of deubiquitinating enzymes (DUBs), are critical for plant growth and development as well as abiotic-stress responses. In this study, we discovered that the expression of the ubiquitin-specific protease 15 (UBP15) gene was induced by salt, mannitol and abscisic acid (ABA) treatments. Further research revealed that UBP15 is involved in modulation of salt, drought tolerance and ABA signaling during seed germination, early seedling development, post-germination root growth or adult-plant stage. Enrichment analysis showed that many genes related to abiotic stresses and metabolic pathways were altered in the ubp15-1 mutant. Through the joint analysis of the quantitative real-time polymerase chain reaction (qRT-PCR) and differentially-expressed gene relationship network, we found that UBP15 may mainly regulate salt-stress tolerance by modulating the dwarf and delayed flowering 1 (DDF1) pathway through a cascade reaction. In the regulation of drought-stress responses, ring domain ligase1 (RGLG1) may be a direct substrate of UBP15. Moreover, we cannot exclude the possibility that UBP15 acts in a feed-forward loop mechanism in the regulation of drought-stress responses via ethylene response factor 53 (ERF53) and its ubiquitin (Ub) ligase RGLG1. In ABA signal transduction, UBP15 may play a role in at least three aspects of the ABA signaling pathway: ABA synthesis, stomatal closure regulated by ABA signaling, and transcription factors in the ABA pathway. Taken together, our results suggest that UBP15 is involved in salt, osmotic, and drought-stress tolerance and the ABA signaling pathway by directly regulating the stability of key substrates or indirectly affecting the expression of genes related to abiotic stresses in Arabidopsis thaliana. Our research provides new germplasm resources for stress-resistant crops cultivation. These results demonstrate that UBP15 is a key regulator of salt, drought and ABA tolerance in Arabidopsis. Full article

(This article belongs to the Special Issue Understanding the Genetics of Complex Traits in Plants: Association Analysis and Genomic Selection Methods)

► Show Figures

Figure 1

26 pages, 10735 KiB

Open AccessArticle

Comparative Transcriptomic Analysis Reveals Domestication and Improvement Patterns of Broomcorn Millet (Panicum miliaceum L.)

by Xinyu Zhao, Minxuan Liu, Chunxiang Li, Jingyi Zhang, Tianshu Li, Fengjie Sun, Ping Lu and Yue Xu

Int. J. Mol. Sci. 2024, 25(20), 11012; https://doi.org/10.3390/ijms252011012 - 13 Oct 2024

Viewed by 1058

Abstract

Broomcorn millet (Panicum miliaceum L.) is one of the earliest crops, domesticated nearly 8000 years ago in northern China. It gradually spread across the entire Eurasian continent, as well as to America and Africa, with recent improvement in various reproductive and vegetative traits. To identify the genes that were selected during the domestication and improvement processes, we performed a comparative transcriptome analysis based on wild types, landraces, and improved cultivars of broomcorn millet at both seeding and filling stages. The variations in gene expression patterns between wild types and landraces and between landraces and improved cultivars were further evaluated to explore the molecular mechanisms underlying the domestication and improvement of broomcorn millet. A total of 2155 and 3033 candidate genes involved in domestication and a total of 84 and 180 candidate genes related to improvement were identified at seedling and filling stages of broomcorn millet, respectively. The annotation results suggested that the genes related to metabolites, stress resistance, and plant hormones were widely selected during both domestication and improvement processes, while some genes were exclusively selected in either domestication or improvement stages, with higher selection pressure detected in the domestication process. Furthermore, some domestication- and improvement-related genes involved in stress resistance either lost their functions or reduced their expression levels due to the trade-offs between stress resistance and productivity. This study provided novel genetic materials for further molecular breeding of broomcorn millet varieties with improved agronomic traits. Full article

(This article belongs to the Special Issue Understanding the Genetics of Complex Traits in Plants: Association Analysis and Genomic Selection Methods)

► Show Figures

Journal Menu

Journal Browser

Understanding the Genetics of Complex Traits in Plants: Association Analysis and Genomic Selection Methods

Share This Special Issue

Special Issue Editor

Special Issue Information

Keywords

Benefits of Publishing in a Special Issue

Published Papers (9 papers)

Research

Further Information

Guidelines

MDPI Initiatives

Follow MDPI