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Functional Genomics and Molecular Breeding of Crops—2nd Edition
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Functional Genomics and Molecular Breeding of Crops—2nd Edition

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 December 2025 | Viewed by 4886

Special Issue Editors

Prof. Dr. Miaoyun Xu

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Guest Editor
Biotechnology Research Institute, The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Interests: plant molecular biology; abiotic response; plant development; RNA silencing; plant genomics; nitrogen use efficiency
Special Issues, Collections and Topics in MDPI journals
Dr. Junjie Zou

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Guest Editor
Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Interests: plant molecular physiology; abiotic stress biology; functional genomics; molecular breeding
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Yong-Gu Cho

E-Mail Website
Guest Editor
Department of Crop Science, College of Agriculture, Life and Environment Sciences, Chungbuk National University, Cheongju 28644, Republic of Korea
Interests: marker-assisted breeding (MAS); genome editing; functional genomics; GWAS; functional analysis of genes; plant biotechnology; molecular breeding in rice
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The functional genomics involved in model development link genotype to phenotype. The aim of functional genomics is to understand the expression pattern of genes, gene expression regulation, the interaction of genes and their products, changes in gene expression during the onset of various stress responses, and the functional roles of different genes in cellular processes, and thus to resolve how genes work together to produce a particular phenotype.

The molecular breeding of crops is a technique using DNA markers tightly linked to phenotypic traits to assist in a selection scheme for a particular crop-breeding objective. The molecular breeding of crops is involved in the identification and characterization of suitable genetic markers, and is thus used to improve crops.

The focus of this Special Issue is on functional genomics and the molecular breeding of crops. Examples of topics of interest for this Special Issue include developmental processes, stress responses, functional genomics, comparative genomics, and the molecular breeding of crops. The formats suitable for submission include original research reports, reviews, perspectives/opinions, and methodology articles.

Prof. Dr. Miaoyun Xu
Dr. Junjie Zou
Prof. Dr. Yong-Gu Cho
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. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). 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

  • plant development
  • function of genes
  • transcriptomics
  • transcription factors
  • plant gene regulation
  • stress biology
  • yield improvement
  • quality improvement
  • molecular breeding

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Published Papers (6 papers)

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Research

18 pages, 4341 KiB  
Article
Unveiling Novel Genetic Loci and Superior Alleles for Nickel Accumulation in Wheat via Genome-Wide Association Study
by Xia Shi, Shenghui Geng, Jinna Hou, Taotao Shi, Maomao Qin, Wenxu Li, Ziju Dai, Zhengfu Zhou, Minghui Zhang and Zhensheng Lei
Plants 2025, 14(8), 1262; https://doi.org/10.3390/plants14081262 - 21 Apr 2025
Abstract
Nickel (Ni) pollution poses significant threats to human health and crop development through the food chain. This study aimed to identify the novel genomic regions and superior alleles associated with Ni accumulation in wheat (Triticum aestivum L.) grains using genome-wide association analysis [...] Read more.
Nickel (Ni) pollution poses significant threats to human health and crop development through the food chain. This study aimed to identify the novel genomic regions and superior alleles associated with Ni accumulation in wheat (Triticum aestivum L.) grains using genome-wide association analysis (GWAS) with a diversity panel of 207 bread wheat varieties. In total, five unique genetic loci associated with Ni accumulation were identified and they explained, on average, 8.20–11.29% of the phenotypic variation. Among them, three unique genetic loci were mutually verified by different statistical models in at least two environments, indicating their stability across different environments. Moreover, the highest effect quantitative trait nucleotide (QTN) AX-111126872 with a quantitative trait locus (QTL) hotspot on chromosome 6B identified in this study was not reported previously. Three putative candidate genes linked to Ni accumulation were revealed from the stable genetic loci. Among them, one gene associated with the stable genetic locus on chromosome 6B (AX-111126872) encodes the glycine-rich proteins (GRPs) as a critical factor influencing Ni accumulation in wheat grains. This study increases our understanding of the genetic architecture of Ni accumulation in wheat grains, which is potentially helpful for breeding wheat varieties without Ni toxicity. Full article
(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Crops—2nd Edition)
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22 pages, 4396 KiB  
Article
Evaluating Genome Assemblies for Optimized Completeness and Accuracy of Reference Gene Sequences in Wheat, Rye, and Triticale
by Mingke Yan, Guodong Yang, Dongming Yang, Xin Zhang, Quanzhen Wang, Jinghui Gao and Chugang Mei
Plants 2025, 14(7), 1140; https://doi.org/10.3390/plants14071140 - 6 Apr 2025
Viewed by 314
Abstract
Recent years have witnessed a surge in the publication of dozens of genome assemblies for Triticeae crops, which have significantly advanced gene-related research in wheat, rye, and triticale. However, this progress has also introduced challenges in selecting universally efficient and applicable reference genomes [...] Read more.
Recent years have witnessed a surge in the publication of dozens of genome assemblies for Triticeae crops, which have significantly advanced gene-related research in wheat, rye, and triticale. However, this progress has also introduced challenges in selecting universally efficient and applicable reference genomes for genotypes with distant or ambiguous phylogenetic relationships. In this study, we assessed the completeness and accuracy of genome assemblies for wheat, rye, and triticale using comparative benchmarking universal single-copy orthologue (BUSCO) analysis and transcript mapping approaches. BUSCO analysis revealed that the proportion of complete genes positively correlated with RNA-seq read mappability, while the frequency of internal stop codons served as a significant negative indicator of assembly accuracy and RNA-seq data mappability in wheat. By integrated analysis of alignment rate, covered length, and total depth from RNA-seq data, we identified the assemblies of SY Mattis, Lo7, and SY Mattis plus Lo7 as the most robust references for gene-related studies in wheat, rye, and triticale, respectively. Furthermore, we recommend that the D genome sequence be incorporated in reference assemblies in bioinformatic analyses for triticale, as introgression, translocation, and substitution of the D genome into triticale genome frequently occurs during triticale breeding. The frequency of internal stop codons could help in evaluating correctness of assemblies published in the future, and other findings are expected to support gene-related research in wheat, rye, triticale, and other closely related species. Full article
(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Crops—2nd Edition)
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15 pages, 4201 KiB  
Article
ZmSPL12 Enhances Root Penetration and Elongation in Maize Under Compacted Soil Conditions by Responding to Ethylene Signaling
by Hua Xu, Zhigang Zheng, Lei Ma, Qingyun Zhang, Lian Jin, Ke Zhang, Junjie Zou, Hada Wuriyanghan and Miaoyun Xu
Plants 2024, 13(24), 3525; https://doi.org/10.3390/plants13243525 - 17 Dec 2024
Viewed by 651
Abstract
Soil compaction poses a significant challenge in modern agriculture, as it constrains root development and hinders crop growth. The increasing evidence indicated that various phytohormones collaborate in distinct root zones to regulate root growth in compacted soils. However, the study of root development [...] Read more.
Soil compaction poses a significant challenge in modern agriculture, as it constrains root development and hinders crop growth. The increasing evidence indicated that various phytohormones collaborate in distinct root zones to regulate root growth in compacted soils. However, the study of root development in maize under such conditions has been relatively limited. Here, we identified that the ZmSPL12 gene, belonging to the SPL transcription factor family, plays a crucial and positive role in regulating root development in the compacted soil. Specifically, the overexpression of ZmSPL12 resulted in significantly less inhibition of root growth than the wild-type plants when subjected to soil compaction. Histological analysis revealed that the capacity for root growth in compacted soil is closely associated with the development of the root cap. Further exploration demonstrated that ZmSPL12 modulates root growth through regulating ethylene signaling. Our findings underscored that ZmSPL12 expression level is induced by soil compaction and then enhances root penetration by regulating root cap and development, thereby enabling roots to thrive better in the compacted soil environment. Full article
(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Crops—2nd Edition)
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15 pages, 1884 KiB  
Article
Development and Validation of Kompetitive Allele-Specific Polymerase Chain Reaction Markers for Seed Protein Content in Soybean
by Shuangzhe Li, Chenyijun Guo, Xuezhen Feng, Jing Wang, Wenjing Pan, Chang Xu, Siming Wei, Xue Han, Mingliang Yang, Qingshan Chen, Jinxing Wang, Limin Hu and Zhaoming Qi
Plants 2024, 13(24), 3485; https://doi.org/10.3390/plants13243485 - 13 Dec 2024
Viewed by 959
Abstract
Seed protein content is a critical trait in soybean breeding, as it provides a primary source of high-quality protein for both human consumption and animal feed. This study aimed to enhance molecular marker-assisted selection for high-protein soybean varieties by developing Kompetitive Allele-Specific Polymerase [...] Read more.
Seed protein content is a critical trait in soybean breeding, as it provides a primary source of high-quality protein for both human consumption and animal feed. This study aimed to enhance molecular marker-assisted selection for high-protein soybean varieties by developing Kompetitive Allele-Specific Polymerase Chain Reaction (KASP) markers targeted at loci associated with seed protein content. Nineteen markers with high genotyping efficacy were identified through screening. Utilizing SN76 (a high-protein line) as the male parent and SN49 and DS1 (both low-protein lines) as female parents, 484 F6 generation individuals from these hybrid combinations were selected to validate the predictive accuracy of the 19 KASP markers. Notably, KASP-Pro-1, KASP-Pro-2, and KASP-Pro-3 effectively distinguished genotypes associated with high and low protein content, with prediction accuracies of 68.4%, 75.0%, and 83.3%, respectively. These results underscore the reliability and practical utility of the selected molecular markers, which are located within the genes Glyma.03G219900, Glyma.14G119000, and Glyma.17G074400, respectively. Haplotype analysis and gene pyramiding indicate that these three genes may influence seed protein content. Consequently, these KASP markers can be effectively integrated into genetic and genomic research on soybean seed protein content as well as into marker-assisted breeding. Full article
(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Crops—2nd Edition)
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20 pages, 6059 KiB  
Article
Combined Genome-Wide Association Study and Linkage Analysis for Mining Candidate Genes for the Kernel Row Number in Maize (Zea mays L.)
by Jiao Kong, Fuyan Jiang, Ranjan K. Shaw, Yaqi Bi, Xingfu Yin, Yanhui Pan, Xiaodong Gong, Haiyang Zong, Babar Ijaz and Xingming Fan
Plants 2024, 13(23), 3308; https://doi.org/10.3390/plants13233308 - 26 Nov 2024
Viewed by 1039
Abstract
Kernel row number (KRN) is one of the key traits that significantly affect maize yield and productivity. Therefore, investigating the candidate genes and their functions in regulating KRN provides a theoretical basis and practical direction for genetic improvement in maize breeding, which is [...] Read more.
Kernel row number (KRN) is one of the key traits that significantly affect maize yield and productivity. Therefore, investigating the candidate genes and their functions in regulating KRN provides a theoretical basis and practical direction for genetic improvement in maize breeding, which is vital for increasing maize yield and understanding domestication. In this study, three recombinant inbred line (RIL) populations were developed using the parental lines AN20, YML1218, CM395, and Ye107, resulting in a multiparent population comprising a total of 490 F9 RILs. Phenotypic evaluation of the RILs for KRN was performed in three distinct environments. The heritability estimates of the RILs ranged from 81.40% to 84.16%. Genotyping-by-sequencing (GBS) of RILs identified 569,529 high-quality single nucleotide polymorphisms (SNPs). Combined genome-wide association study (GWAS) and linkage analyses revealed 120 SNPs and 22 quantitative trait loci (QTLs) which were significantly associated with KRN in maize. Furthermore, two novel candidate genes, Zm00001d042733 and Zm00001d042735, regulating KRN in maize were identified, which were located in close proximity to the significant SNP3-178,487,003 and overlapping the interval of QTL qKRN3-1. Zm00001d042733 encodes ubiquitin carboxyl-terminal hydrolase and Zm00001d042735 encodes the Arabidopsis Tóxicos en Levadura family of proteins. This study identified novel candidate loci and established a theoretical foundation for further functional validation of candidate genes. These findings deepen our comprehension of the genetic mechanisms that underpin KRN and offer potential applications of KRN-related strategies in developing maize varieties with higher yield. Full article
(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Crops—2nd Edition)
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17 pages, 1160 KiB  
Article
Association Mapping of Seed Coat Color Characteristics for Near-Isogenic Lines of Colored Waxy Maize Using Simple Sequence Repeat Markers
by Tae Hyeon Heo, Hyeon Park, Nam-Wook Kim, Jungeun Cho, Changyeun Mo, Si-Hwan Ryu, Jae-Keun Choi, Ki Jin Park, Kyu Jin Sa and Ju Kyong Lee
Plants 2024, 13(15), 2126; https://doi.org/10.3390/plants13152126 - 1 Aug 2024
Viewed by 1266
Abstract
Waxy maize is mainly cultivated in South Korea for the production of food and snacks, and colored maize with increased anthocyanin content is used in the production of functional foods and medicinal products. Association mapping analysis (AMA) is supported as the preferred method [...] Read more.
Waxy maize is mainly cultivated in South Korea for the production of food and snacks, and colored maize with increased anthocyanin content is used in the production of functional foods and medicinal products. Association mapping analysis (AMA) is supported as the preferred method for identifying genetic markers associated with complex traits. Our study aimed to identify molecular markers associated with two anthocyanin content and six seed coat color traits in near-isogenic lines (NILs) of colored waxy maize assessed through AMA. We performed AMA for 285 SSR loci and two anthocyanin content and six seed coat color traits in 10 NILs of colored waxy maize. In the analysis of population structure and cluster formation, the two parental lines (HW3, HW9) of “Mibaek 2ho” variety waxy maize and the 10 NILs were clearly divided into two groups, with each group containing one of the two parental inbred lines. In the AMA, 62 SSR markers were associated with two seed anthocyanin content and six seed coat color traits in the 10 NILs. All the anthocyanin content and seed coat color traits were associated with SSR markers, ranging from 2 to 12 SSR markers per characteristic. The 12 SSR markers were together associated with both of the two anthocyanin content (kuromanin and peonidin) traits. Our current results demonstrate the effectiveness of SSR analysis for the examination of genetic diversity, relationships, and population structure and AMA in 10 NILs of colored waxy maize and the two parental lines of the “Mibaek 2ho” variety waxy maize. Full article
(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Crops—2nd Edition)
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