Recent Advances in Plant Genetics and Breeding

Topic Information

Dear Colleagues,

Advancements in plant genetics and breeding are fundamental to enhancing crop productivity, improving nutritional quality, and ensuring sustainable agricultural systems. In the face of global challenges such as climate change, population growth, and environmental degradation, the development of resilient and high-yielding crop varieties through modern genetic and breeding techniques has become increasingly important. These innovations not only contribute to food security but also support the transition toward healthier and more sustainable diets.

This Topic aims to bring together research on the latest developments in plant genetics and breeding, including the application of genomic tools, gene editing technologies, marker-assisted selection, and genomic prediction. We welcome studies that explore the genetic basis of important agronomic traits, the development of stress-tolerant and nutrient-efficient crops, and the integration of breeding programs with sustainable farming practices. Additionally, this Topic encourages contributions that assess the socio-economic, environmental, and health impacts of these advances.

The scope includes, but is not limited to, the following subjects:

• Genomic selection and marker-assisted breeding;
• Gene editing and CRISPR applications in plants;
• Trait discovery and functional genomics;
• High-throughput phenotyping;
• Breeding for biotic and abiotic stress resistance;
• Nutritional quality and biofortification;
• Climate-resilient crop development;
• Integration of genomics with sustainable agriculture.

Dr. Fangping Gong
Dr. Dongmei Yin
Topic Editors

Keywords

Participating Journals

Journal Name	Impact Factor	CiteScore	Launched Year	First Decision (median)	APC
Agriculture agriculture	4.5	7.8	2011	17.4 Days	CHF 2600	Submit
Crops crops	2.1	2.9	2021	20.7 Days	CHF 1200	Submit
Genes genes	3.1	5.9	2010	13.3 Days	CHF 2600	Submit
International Journal of Molecular Sciences ijms	5.6	10.0	2000	17.5 Days	CHF 2900	Submit
International Journal of Plant Biology ijpb	-	4.2	2010	17.5 Days	CHF 1400	Submit
Plants plants	4.7	8.5	2012	14.8 Days	CHF 2700	Submit

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Published Papers (5 papers)

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All Genes IJMS IJPB Plants Agriculture Crops

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Open AccessArticle

Fine Mapping and Candidate Gene Analysis of a Major Locus Controlling Black Seed Coat Color in Mung Bean (Vigna radiata L.)

by Dong Deng, Yuning Huang, Yang Zhao, Ming Feng, Jian Chen, Tao Li, Weide Ge and Renfeng Xue

Plants 2026, 15(17), 2594; https://doi.org/10.3390/plants15172594 - 25 Aug 2026

Abstract

Seed coat color is an important quality trait in mung bean (Vigna radiata) and is closely associated with seed appearance, commercial value, and phytochemical composition. To investigate the genetic basis of black seed coat formation, six F₂ populations were derived [...] Read more.

Seed coat color is an important quality trait in mung bean (Vigna radiata) and is closely associated with seed appearance, commercial value, and phytochemical composition. To investigate the genetic basis of black seed coat formation, six F₂ populations were derived from reciprocal crosses between the black-seeded accession LZL115 and the green-seeded accession LZL156. Among 755 F₂ plants, 559 produced black-coated seeds and 196 produced green-coated seeds, conforming to a 3:1 segregation ratio (χ² = 0.37, p = 0.54). These results indicated that black seed coat color was dominant and consistent with the control by a single dominant locus, designated VrScL115, in the LZL115 × LZL156 genetic background. Bulked segregant analysis sequencing (BSA-seq) initially mapped VrScL115 to an approximately 2.90 Mb region on chromosome 4. Using newly developed KASP markers and recombinant screening in expanded F₂ populations, the locus was further delimited to a 121.79 kb interval between markers LS_K3333 and LS_K3379. Of the 11 annotated genes within this interval, LOC106758748 was the only gene containing high-confidence coding-sequence variants between the parents. This gene encodes a putative R2R3-MYB transcription factor homologous to MYB90. Comparative sequence analysis identified several allelic variants potentially associated with black seed coat color, and protein structure prediction indicated local structural differences between the parental proteins. LOC106758748 showed consistently higher expression in the developing seed coats of LZL115 than in those of LZL156 at 10, 15, and 20 days after pollination, with expression peaking at 15 days. Haplotype analysis of 246 mung bean accessions showed that the LZL115-associated allele combination at LS_K3352, LS_K3365, LS_K3367, and LS_K3370 was present in 21 of 27 black-seeded accessions (77.8%) and absent from all 219 non-black accessions, corresponding to a specificity of 100% and a false-negative rate of 22.2%. These findings support LOC106758748 as the leading candidate gene for VrScL115; however, direct in vivo functional validation is still required to confirm its causal role in black seed coat formation. The four-marker combination may be useful for identifying germplasm carrying the LZL115-associated allele, although further validation in independent germplasm populations is required. Full article

(This article belongs to the Topic Recent Advances in Plant Genetics and Breeding)

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13 pages, 4539 KB  

Open AccessArticle

TaKMT-7A Gene Positively Regulates Spike Number in Wheat

by Qun Wu, Junsheng Sun, Shengfu Yang, Mingxia Zhang, Di Yang, Hao Xue, Haimeng Wu, Ying Guo, Sishen Li and Yanrong An

Genes 2026, 17(6), 630; https://doi.org/10.3390/genes17060630 - 30 May 2026

Cited by 1 | Viewed by 518

Abstract

Wheat (Triticum aestivum L.) is a crucial global food crop that plays a central role in agricultural production and food security. The spike number per unit area (SN) is one of the three component factors of grain yield. In this study, we [...] Read more.

Wheat (Triticum aestivum L.) is a crucial global food crop that plays a central role in agricultural production and food security. The spike number per unit area (SN) is one of the three component factors of grain yield. In this study, we combined the UG-Map with 27 environments of a recombinant inbred line (RIL) population, and mapped a quantitative trait locus (QTL) for SN, QSn-7A-9048, in which the meta-QTL interval contains only one candidate gene, TraesCS7A02G-364700 (TaKMT-7A). Using the CRISPR/Cas9 system, we generated two homozygous mutant lines, aa-1 and aa-2 of TaKMT-7A, which resulted in frameshift mutations, leading to the premature termination of the translation process. The SN values for the wild type (WT), aa-1, and aa-2 were 4.48, 3.43, and 3.48, respectively. Compared with the WT, the SN of the two mutant lines significantly decreased, and no significant differences for grain number per spike (GNS) and thousand-grain weight (TGW) were detected. We also obtained two overexpression (OE) lines of TaKMT-7A, OE-1 and OE-2. The SN values for the negative control (NC), OE-1, and OE-2 were 2.31, 3.33, and 3.00, respectively. Compared with NC, the SN values in the OE lines significantly increased. The phenotypes of the knockout (KO) lines and OE lines demonstrate that TaKMT-7A acts as a positive regulator of SN in wheat. We performed RNA-Seq analysis using young tiller buds from the WT and aa-1 mutant lines at the tillering stage, and a total of 2315 differentially expressed genes (DEGs) were identified. We screened 22 wheat genes, of which 18 orthologous genes have previously been cloned and are associated with branching in rice and Arabidopsis. These genes included nitrogen transporter, amino metabolism, auxin transporter, auxin homeostasis, auxin response, auxin biosynthesis, strigolactone biosynthesis, and repress gibberellin responses. These genes may represent potential downstream targets of TaKMT-7A. Full article

(This article belongs to the Topic Recent Advances in Plant Genetics and Breeding)

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15 pages, 1688 KB  

Open AccessArticle

Dissection of the Genetic Basis of Maize Plant Architecture and Candidate Gene Mining Based on the MAGIC Population

by Xiaoming Xu, Kang Zhao, Yukang Zeng, Shaohang Lin, Nadeem Muhammad, Wenhui Gao, Jiaojiao Ren and Penghao Wu

Genes 2026, 17(4), 399; https://doi.org/10.3390/genes17040399 - 31 Mar 2026

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Abstract

Background/Objectives: Plant architecture is a critical determinant of high-density tolerance and yield potential in maize (Zea mays L.), yet the genetic networks orchestrating these complex traits require deeper elucidation. Methods: In this study, we utilized a Multi-parent Advanced Generation Inter-cross (MAGIC) population [...] Read more.

Background/Objectives: Plant architecture is a critical determinant of high-density tolerance and yield potential in maize (Zea mays L.), yet the genetic networks orchestrating these complex traits require deeper elucidation. Methods: In this study, we utilized a Multi-parent Advanced Generation Inter-cross (MAGIC) population comprising 935 recombinant inbred lines (RILs) derived from 16 diverse elite founders. A comprehensive phenotypic characterization of six pivotal architectural traits—plant height (PH), ear height (EH), ear leaf length (LL), ear leaf width (LW), tassel main axis length (TL), and tassel branch number (TBN)—was conducted across three distinct agro-ecological environments. Results: Phenotypic analysis revealed substantial natural variation and high broad-sense heritability (H² ranging from 60% to 86%), with TBN exhibiting the most pronounced variability. Correlation architecture demonstrated a strong coupling between vertical growth traits (PH and EH, r = 0.73), while lateral leaf expansion (LW) and tassel complexity (TBN) showed significant genetic independence. Using a mixed linear model (MLM) for genome-wide association studies (GWAS), we identified 21 significant SNP–trait associations, including distinct chromosomal clusters on chromosome 8 for EH and chromosome 7 for TBN. By integrating genomic intervals with tissue-specific expression profiling, 23 core candidate genes were prioritized. Notably, Zm00001d042528 (FAS1), involved in chromatin assembly, was implicated in modulating meristematic cell division for plant stature. Other key regulators included Zm00001d020537 (O5) and Zm00001d025360 (F-box protein), which were associated with reproductive organ development and leaf elongation, respectively. Conclusions: These results indicate that maize plant architecture is regulated by a modular genetic framework, with specific loci independently regulating canopy structure and source–sink components. It should be noted that the findings of this study are based solely on statistical models identifying significant associations between genetic loci and phenotypes; the biological regulatory functions of the candidate genes have not yet been experimentally validated. Nevertheless, this study provides new insights into the molecular mechanisms underlying maize morphogenesis and lays a solid theoretical foundation for molecular design breeding aimed at developing high-yielding varieties tolerant of high planting densities. Full article

(This article belongs to the Topic Recent Advances in Plant Genetics and Breeding)

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14 pages, 1973 KB  

Open AccessArticle

Genetic Diversity Analysis of 96 Gossypium hirsutum-Gossypium barbadense Introgression Lines and Early Maturing Northern China Cotton Lines Using a 40K Liquid-Phase Chip

by Pengpeng Chen, Yanlong Yang, Jiaxu Fang, Hang Yu, Yongmei Dong, Zengqiang Zhao, Yousheng Tian, Zongming Xie and Youzhong Li

Genes 2026, 17(4), 388; https://doi.org/10.3390/genes17040388 - 29 Mar 2026

Cited by 1 | Viewed by 687

Abstract

Background: Genetic diversity and genetic differentiation between Gossypium hirsutum-Gossypium barbadense introgression lines (ILs) and early-maturing upland cotton lines are critical for resolving the core breeding contradiction in Xinjiang cotton region: narrow genetic basis of early-maturing cultivars and late maturity of ILs [...] Read more.

Background: Genetic diversity and genetic differentiation between Gossypium hirsutum-Gossypium barbadense introgression lines (ILs) and early-maturing upland cotton lines are critical for resolving the core breeding contradiction in Xinjiang cotton region: narrow genetic basis of early-maturing cultivars and late maturity of ILs with superior fiber quality. Xinjiang is one of the major cotton-producing regions in China, and breeding high-quality early-maturing upland cotton adapted to local ecological conditions is essential for improving cotton yield and quality. However, the genetic relationship and differentiation between the two types of cotton germplasm remain unclear, which hinders the efficient utilization of germplasm resources in breeding. Therefore, this study aimed to clarify the genetic diversity and differentiation between the two germplasm types and identify key candidate loci related to early maturity and fiber quality, providing support for cotton breeding. Results: Here, we used a 40K Single Nucleotide Polymorphism chip to genotype core cotton germplasm in northern Xinjiang, and analyzed their population structure, genetic diversity and functional SNP loci associated with early maturity and fiber quality. The tested materials were clearly divided into two subgroups (ILs and early-maturing lines). Genetic diversity analysis revealed a significantly narrow genetic basis in the early-maturing subgroup, while the IL subgroup had higher genetic diversity. Specifically, the early-maturing subgroup showed lower nucleotide diversity and polymorphism information content compared with the IL subgroup, indicating that the genetic variation of early-maturing cotton germplasm in northern Xinjiang is relatively limited. A total of 25 non-synonymous SNPs were identified, among which the c.A613G:p.T205A mutation in GH_D09G1484 (mRNA-decapping enzyme 1, DCP1) was a characteristic variation of early-maturing cotton, and a possible non-synonymous mutation in GH_A09G2400 (Heat shock transcription factor A6b, HSFA6B) was associated with fiber development. These two candidate genes were annotated to be involved in plant growth and development, further supporting their potential roles in regulating cotton early maturity and fiber quality. Conclusions: This study clarified the genetic differentiation between the two types of germplasms and identified key candidate loci for early maturity and fiber quality, providing precise molecular markers and theoretical support for breeding high-quality early-maturing upland cotton adapted to Xinjiang’s ecological conditions. The results also highlight the value of Gossypium hirsutum–Gossypium barbadense introgression lines in enriching the genetic basis of early-maturing cotton, which can be further utilized to solve the core breeding contradiction in the Xinjiang cotton region. Full article

(This article belongs to the Topic Recent Advances in Plant Genetics and Breeding)

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11 pages, 1675 KB  

Open AccessArticle

Genome and Transcriptome Sequencing of Oca (Oxalis tuberosa Molina) Reveals Photoperiod-Induced FT Homologs as Candidate Tuberigens

by Maria Gancheva and Aleksandr Tkachenko

Int. J. Plant Biol. 2026, 17(2), 11; https://doi.org/10.3390/ijpb17020011 - 10 Feb 2026

Cited by 1 | Viewed by 1370

Abstract

Oxalis tuberosa (oca) is a tuber crop native to the Andes, valued for its nutrition but understudied genetically. Its strict short-day (SD) tuberization suggests a photoperiodic control mechanism similar to that of potato, where an FT-like protein acts as a mobile “tuberigen” signal. [...] Read more.

Oxalis tuberosa (oca) is a tuber crop native to the Andes, valued for its nutrition but understudied genetically. Its strict short-day (SD) tuberization suggests a photoperiodic control mechanism similar to that of potato, where an FT-like protein acts as a mobile “tuberigen” signal. To identify this key regulator, we generated a de novo genome assembly for oca using long- and short-read sequencing. Integrated transcriptomic analysis of leaves under long-day (LD) and SD conditions, along with stems, roots, and tubers, enabled gene annotation and expression analysis. Our study focused on the Phosphatidylethanolamine-Binding Protein (PEBP) gene family, the source of florigen and tuberigen signals. We identified 23 OtPEBP genes and characterized their expression patterns. Among these, we discovered three FT-like homologs that are specifically and strongly upregulated in leaves under SD conditions. We therefore propose these genes as the prime candidates for the mobile tuberigen signal in oca. This work provides the foundational genomic resource for O. tuberosa and advances our understanding of the conserved photoperiodic network controlling storage organ formation beyond the Solanaceae family. Full article

(This article belongs to the Topic Recent Advances in Plant Genetics and Breeding)

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