Plant Breeding, Genetics and Genomics, 2nd Edition

Topic Information

Dear Colleagues,

The scientific community currently has access to more than two thousand sequenced and annotated plant genomes, encompassing both model organisms and crop species. This invaluable repository of genomic information plays a critical role in advancing the fields of plant genetics and breeding. Traditional breeding techniques are increasingly being enhanced through the integration of marker-assisted selection, genomic selection methods, genetic engineering, genome editing, and bioinformatics. The strategic application of molecular markers and genomic tools associated with agronomically significant traits—such as disease resistance and tolerance to abiotic stress—has been refined to facilitate precise genotype selection. Moreover, the utilization of molecular markers in extensive analyses spanning entire genomes has significantly streamlined the development of customized new varieties, resulting in substantial reductions in both time and costs associated with breeding programs. A comprehensive understanding of genome structure, along with the functional characterization of specific gene loci, provides essential foundations for genetic engineering and genome editing projects aimed at enhancing the agronomic performance of next-generation crop varieties, particularly to improve their resilience to climate change and qualitative traits. We encourage you to contribute to this Topic by submitting research articles or reviews that emphasize the tangible advantages and potential future applications of genetics and genomics in the selection and development of novel crop plant varieties. Your contributions are vital for advancing our knowledge and applications in this dynamic field.

Prof. Dr. Gianni Barcaccia
Dr. Alessandro Vannozzi
Dr. Fabio Palumbo
Dr. Silvia Farinati
Dr. Francesco Scariolo
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Participating Journals

Journal Name	Impact Factor	CiteScore	Launched Year	First Decision (median)	APC
Agriculture agriculture	3.6	6.3	2011	18 Days	CHF 2600	Submit
Agronomy agronomy	3.4	6.7	2011	17.2 Days	CHF 2600	Submit
Crops crops	1.9	2.4	2021	23.5 Days	CHF 1200	Submit
Horticulturae horticulturae	3.0	5.1	2015	17.1 Days	CHF 2200	Submit
Plants plants	4.1	7.6	2012	17.7 Days	CHF 2700	Submit

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Published Papers (8 papers)

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All Agriculture Agronomy Crops Horticulturae Plants

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Open AccessArticle

The Regulatory Role of R2R3-MYB Family Genes in Trichome Formation in Solanum aculeatissimum

by Fan Yang, Yanbo Yang, Wanqi Li, Qihang Cai, Man Miao, Zhenghai Sun and Liping Li

Agronomy 2025, 15(11), 2637; https://doi.org/10.3390/agronomy15112637 - 18 Nov 2025

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Abstract

Solanum aculeatissimum is a medicinally and economically significant crop characterized by its aerial organs, which are densely covered with trichomes and spines. Trichomes serve as crucial sites for the synthesis of secondary metabolites in medicinal plants and represent important structural adaptations for resisting [...] Read more.

Solanum aculeatissimum is a medicinally and economically significant crop characterized by its aerial organs, which are densely covered with trichomes and spines. Trichomes serve as crucial sites for the synthesis of secondary metabolites in medicinal plants and represent important structural adaptations for resisting biotic and abiotic stresses. Elucidating the molecular mechanisms underlying trichome formation in S. aculeatissimum holds significant implications for enhancing both its medicinal value and stress resistance. The R2R3-MYB subfamily, the largest within the MYB transcription factor family, plays a pivotal role in regulating trichome development. Here, we present the first genome-wide identification of the R2R3-MYB gene family in S. aculeatissimum, characterizing 99 members. Phylogenetic analysis classified these SaMYBs into 10 groups. Cis-element predictions in their promoter regions revealed an abundance of light-responsive, phytohormone-responsive, and abiotic stress-responsive elements, suggesting roles in environmental adaptation. Furthermore, synteny analysis identified 25 segmentally duplicated gene pairs, and the purifying selection has been the dominant evolutionary force. Through comparative transcriptomic analysis of leaves from wild-type and sparse-trichome plants, we identified 16 differentially expressed SaMYB genes, comprising 3 upregulated and 13 downregulated genes. Subsequent qRT-PCR analysis showed that SaMYB1, SaMYB59, and SaMYB36 were highly expressed during early leaf development. Virus-induced gene silencing (VIGS) targeting these candidates demonstrated that silencing SaMYB59 significantly reduced trichome density, whereas silencing SaMYB1 or SaMYB36 produced no observable phenotypic change, confirming SaMYB59 as a key positive regulator of trichome formation. Our findings provide crucial molecular targets for elucidating the mechanisms of trichome development in S. aculeatissimum and establish a theoretical foundation for genetic improvement of this medicinal plant through regulation of the SaMYB59 gene. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics, 2nd Edition)

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18 pages, 569 KB  

Open AccessArticle

Genomic Confirmation of Resistance Genes for Blast, Bacterial Leaf Blight, Rice Tungro Spherical Virus, and Brown Planthopper in Tropically Adapted Temperate Japonica Rice Varieties

by Myrish Alvarez Pacleb, Seongkyeong Lee, Sherry Lou Hechanova, Thelma Padolina, Lenie Pautin, Jesson Del-Amen, Dong-Soo Park, Il-Ryong Choi, Sung-Ryul Kim, Dongjin Shin and Jung-Pil Suh

Agronomy 2025, 15(11), 2585; https://doi.org/10.3390/agronomy15112585 - 10 Nov 2025

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Abstract

The Rural Development Administration (RDA) of the Republic of Korea, in collaboration with International Rice Research Institute (IRRI), developed six temperate japonica rice varieties—MS11, Japonica 1, 2, 6, 7, and Cordillera 4—which were officially approved for release in tropical environments. These varieties offer [...] Read more.

The Rural Development Administration (RDA) of the Republic of Korea, in collaboration with International Rice Research Institute (IRRI), developed six temperate japonica rice varieties—MS11, Japonica 1, 2, 6, 7, and Cordillera 4—which were officially approved for release in tropical environments. These varieties offer improved eating quality, enhanced lodging resistance, and increased market value. Although initial evaluations indicated that the varieties were resistant to moderately resistant to major biotic stresses, recent field trials revealed a gradual increase in susceptibility over time. To address this, we conducted comprehensive evaluations of these varieties against rice blast under both greenhouse and field conditions and assessed their responses to bacterial leaf blight (BLB), rice tungro spherical virus (RTSV), and brown planthopper (BPH) under controlled environments. Additionally, whole-genome sequencing was employed to confirm the presence of known resistance alleles. Our findings revealed variable resistance profiles across the six varieties. Japonica 1 exhibited the most stable resistance to blast, supported by the presence of the Pi5 allele. Japonica 7 showed strong resistance to key BLB isolates and moderate resistance to a broader range of Xoo races, supported by the resistant Xa25/OsSWEET13 haplotype. In addition, Japonica 7, along with Japonica 6, carried the tsv1 gene for RTSV resistance. However, none of the six varieties possessed other major resistance genes for BPH. These results highlight the urgent need to introgress durable resistance genes into tropical japonica rice to enhance resilience and broaden the spectrum of biotic stress resistance—critical traits for sustainable rice production in tropical environments. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics, 2nd Edition)

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19 pages, 4047 KB  

Open AccessArticle

Compound Sodium Nitrophenolate (CSN) Improves Photo-Synthesis and Forage Quality in Hemarthria compressa

by Zhongpeng Liu, Peng Han, Ruijie Zhao, Yuanyuan Wu, Wenxuan Wei, Fahui He and Chenfei Dong

Agronomy 2025, 15(11), 2526; https://doi.org/10.3390/agronomy15112526 - 30 Oct 2025

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Abstract

Hemarthria compressa is a valuable C₄ forage grass, prized for its high biomass (dry weight, DW) and palatability, that plays a significant role in forage production and ecological restoration. Improving its nutritional quality and productivity remains a key objective. Although compound sodium [...] Read more.

Hemarthria compressa is a valuable C₄ forage grass, prized for its high biomass (dry weight, DW) and palatability, that plays a significant role in forage production and ecological restoration. Improving its nutritional quality and productivity remains a key objective. Although compound sodium nitrophenolate (CSN) is known to promote growth and stress tolerance in crops, its impact on forage grasses is unclear. Therefore, this study investigated the effects of foliar-applied CSN on the photosynthesis, growth, and nutritional quality of H. compressa and explored the underlying molecular mechanisms. The results demonstrated that CSN significantly improved the photosynthetic efficiency (Fv/Fm), increased the chlorophyll and carotenoid content, enhanced carbon fixation, and promoted biomass (DW) accumulation. Additionally, the crude protein content rose while the acid detergent fiber content decreased. Transcriptome analysis revealed the enrichment of differentially expressed genes involved in photosynthesis antenna proteins, carbon fixation, and starch/sucrose metabolism. Consequently, CSN reduced the lignin content while improving both biomass and forage quality. These findings provide molecular insights and practical strategies for forage cultivation and breeding. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics, 2nd Edition)

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12 pages, 3520 KB  

Open AccessArticle

A Diploid–Tetraploid Cytochimera of Dashu Tea Selected from a Natural Bud Mutant

by Chi Zhang, Sulei She, Haiyan Wang, Jiaheng Li, Xiao Long, Guolu Liang, Qigao Guo, Songkai Li, Ge Li, Lanyan Qian, Di Wu and Jiangbo Dang

Horticulturae 2025, 11(10), 1259; https://doi.org/10.3390/horticulturae11101259 - 18 Oct 2025

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Abstract

Polyploids play significant roles in tea production due to their strong tolerance to adverse environmental conditions and their high levels of certain chemical components. Tetraploid can be used to produce more polyploid tea plants, but there have been only a handful of tetraploids [...] Read more.

Polyploids play significant roles in tea production due to their strong tolerance to adverse environmental conditions and their high levels of certain chemical components. Tetraploid can be used to produce more polyploid tea plants, but there have been only a handful of tetraploids found in tea plants. In spite of the extremely low probabilities, bud mutant selection is an effective way to obtain polyploid tree crops. In the present study, a Dashu tea, cytochimera, derived from a bud mutation was identified by using flow cytometry and chromosome observation. The morphology and photosynthetic characteristics of leaves were investigated briefly. Some chemical components were determined. Finally, the pollen viability and ploidy of progeny were detected. The results show that tetraploid cells account for 71.48 ± 3.88%–72.19 ± 2.80% of the leaf tissue in this cytochimera. Compared with the original diploid, the cytochimera exhibited broader, longer, and thicker leaves. Its net photosynthetic rate (high to 41.77 ± 0.38 μmol CO₂·m⁻²·s⁻¹) was higher than that of the original diploid (peak value 28.00 ± 2.29 μmol CO₂·m⁻²·s⁻¹) for most of the day when measured in September. Notably, the total content of 19 free amino acids in the tender spring shoots of cytochimera was 22.96 ± 0.58 mg/g, approximately twice of that of the diploid materials analyzed. The contents of 10 free amino acids, including theanine, were significantly higher than those in diploids, with some free amino acid contents reaching up to seven times those observed in diploids. In addition, the cytochimera produced larger pollen grains than the original diploid, although the in vitro germination rate was lower (14.63 ± 1.11%). Three open-pollinated progenies of cytochimera were identified as triploids. To sum up, cytochimera has larger and thicker leaves, a higher photosynthetic rate, and higher content of total free amino acids and some free amino acids, especially theanine, than the original diploid. Moreover, cytochimera has a certain level of fertility and can produce triploids. These findings suggest the potential for selecting polyploid tea plants from bud mutants and for developing new tea germplasms with enhanced amino acid contents. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics, 2nd Edition)

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23 pages, 2625 KB  

Open AccessArticle

Mitochondrial Genome Assembly and Comparative Analysis of Three Closely Related Oaks

by Zhi-Tong Xiao, Ying Song, Lu-Ting Liu, Bo Chen, Yue Xu, Li-Jun Huang, He Li, Xiao-Long Jiang, Xiong-Sheng Liu and Min Deng

Horticulturae 2025, 11(10), 1231; https://doi.org/10.3390/horticulturae11101231 - 12 Oct 2025

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Abstract

The genus Quercus is an ecological keystone and economically vital component of Northern Hemisphere forests. While genomic studies have advanced our understanding of its nuclear and chloroplast genomes, the mitochondrial genomes of oaks remain less explored due to their complex evolutionary dynamics, which [...] Read more.

The genus Quercus is an ecological keystone and economically vital component of Northern Hemisphere forests. While genomic studies have advanced our understanding of its nuclear and chloroplast genomes, the mitochondrial genomes of oaks remain less explored due to their complex evolutionary dynamics, which include extreme size variation, frequent rearrangements, and recurrent horizontal gene transfer. This study presents the assembly, annotation, and comparative analysis of mitogenomes from three closely related Asian oaks—Q. engleriana, Q. kongshanensis, and Q. tungmaiensis—using PacBio HiFi sequencing. The assemblies revealed distinct structural organizations: the Q. engleriana and Q. kongshanensis mitogenomes each comprised one circular contig and one linear contig, whereas the Q. tungmaiensis mitogenome comprised one circular contig and two linear contigs. Comparative analyses revealed variations in codon usage bias, simple sequence repeats, and predicted RNA editing sites. Notably, RNA editing in rps12 was uniquely observed in Q. kongshanensis. Mitochondrial targeting of plastid transcripts constituted 1.39%, 1.79%, and 2.24% of the mitogenomes, respectively. Phylogenetic reconstruction based on mitochondrial PCGs robustly resolved Q. kongshanensis and Q. tungmaiensis as sister species, with all three forming a distinct clade separate from other Quercus species. This study provides comprehensive mitogenomic resources essential for elucidating Quercus evolutionary biology and supporting germplasm development. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics, 2nd Edition)

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19 pages, 6720 KB  

Open AccessArticle

Beyond IbMYB1: Identification and Characterization of Two Additional Anthocyanin MYB Activators, IbMYB2 and IbMYB3, in Sweetpotato

by Jian Wang, Zhuo Chen, Yang Lu, Xiaobei Zhang, Yizhao Chen, Xiangrui Li, Yi Liu, Yonghua Liu, Sunjeet Kumar, Zhixin Zhu and Guopeng Zhu

Plants 2025, 14(18), 2896; https://doi.org/10.3390/plants14182896 - 18 Sep 2025

Cited by 1 | Viewed by 620

Abstract

Sweetpotato displays diverse purple pigmentation due to anthocyanin accumulation. While current research on the underlying MYB activators has focused on IbMYB1 in purple-fleshed tubers, the color diversity suggests the involvement of other MYB activators. We previously identified IbMYB2 and IbMYB3 in leaf coloration. [...] Read more.

Sweetpotato displays diverse purple pigmentation due to anthocyanin accumulation. While current research on the underlying MYB activators has focused on IbMYB1 in purple-fleshed tubers, the color diversity suggests the involvement of other MYB activators. We previously identified IbMYB2 and IbMYB3 in leaf coloration. Here, we explored the chromosomal localization, phylogeny, and evolutionary scenario of IbMYB1/2/3 using four Ipomoea genomes. IbMYB1/2/3 are located adjacently as an anthocyanin MYB gene cluster, likely resulting from tandem duplications. All three IbMYBs induced anthocyanins in tobacco and activated the promoters of the key anthocyanin pathway genes IbCHS-D and IbDFR-B. Expression analysis across sweetpotato varieties indicated that IbMYB1 dominates purple tuber flesh, whereas IbMYB2/3 contribute to leaf and tuber skin coloration. Overexpression of IbMYB1/2/3 in sweetpotato all induced purple fibrous roots. Transcriptomics of IbMYB2-OX fibrous roots revealed upregulation of the entire anthocyanin pathway genes. Among the most highly upregulated transcription factors were IbMYB27 and IbHLH2. An inhibitory effect induced by IbMYB27 likely accounts for the faint pigmentation in IbMYB2-OX storage roots. The role of IbMYB2/3 in fine-tuning sweetpotato’s purple pigmentation was highlighted. This study supplements previous work on IbMYB1, providing valuable insights into the intricate anthocyanin regulatory network and supporting sweetpotato breeding efforts for improved nutritional and aesthetic qualities. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics, 2nd Edition)

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13 pages, 3849 KB  

Open AccessArticle

Genetic Basis Identification of a NLR Gene, TaRPM1-2D, That Confers Powdery Mildew Resistance in Wheat Cultivar ‘Brock’

by Xiaoying Liu, Congying Wang, Yikun Wang, Siqi Wu, Huixuan Dong, Yuntao Shang, Chen Dang, Chaojie Xie, Baoli Fan, Yana Tong and Zhenying Wang

Plants 2025, 14(17), 2652; https://doi.org/10.3390/plants14172652 - 26 Aug 2025

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Abstract

Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici, represents one of the most threatening biotic stresses of this crop. The cultivated wheat variety ‘Brock’ exhibits resistance not only to rust but also to powdery mildew, making it a valuable resource [...] Read more.

Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici, represents one of the most threatening biotic stresses of this crop. The cultivated wheat variety ‘Brock’ exhibits resistance not only to rust but also to powdery mildew, making it a valuable resource for exploitation in wheat disease-resistant breeding. This study identified a novel gene in ‘Brock’ distinct from Pm2. In order to identify the disease resistance gene in ‘Brock’, genetic mapping was performed using F₂ and F_2:3 populations derived from the cross ‘Jing411/Brock’. The candidate powdery mildew resistance gene was located within a 6.88 Mb physical interval on chromosome 2D, which harbors a highly expressed gene, TaRPM1-2D. The protein encoded by TaRPM1-2D possesses a typical nucleotide binding, leucine-rich repeat receptor (NLR) domain, and its sequence significantly differs among ‘Jing411’, ‘BJ-1’, and ‘Brock’. Expression of TaRPM1-2D was markedly higher in resistant wheat ‘Brock’ and ‘BJ-1’ compared to the susceptible ‘Jing411’. Both overexpression and gene silencing experiments demonstrated that TaRPM1-2D contributes to enhance resistance against powdery mildew in wheat. These findings reveal the function of TaRPM1-2D in conferring powdery mildew resistance in ‘Brock’ and provide a candidate gene for disease-resistance breeding. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics, 2nd Edition)

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18 pages, 3197 KB  

Open AccessArticle

Exploration of Molecular Mechanism and Key Factors for the Survival of ‘Yueshenda 10’ Cuttings Under ABT1 Treatment

by Zhiling Wang, Hao Dou, Jiajia Sun and Jin’e Quan

Horticulturae 2025, 11(8), 991; https://doi.org/10.3390/horticulturae11080991 - 20 Aug 2025

Viewed by 676

Abstract

Mulberry trees are not only economically significant forest trees with substantial added value but also serve as exceptional candidates for environmental management and ecological enhancement. However, in the widely applied cutting propagation of mulberry, the intensity of adventitious root formation in cuttings has [...] Read more.

Mulberry trees are not only economically significant forest trees with substantial added value but also serve as exceptional candidates for environmental management and ecological enhancement. However, in the widely applied cutting propagation of mulberry, the intensity of adventitious root formation in cuttings has long remained a key challenge in the cutting process. Our research group previously found that 800 mg/L Rooting Powder No. 1 (ABT1) has an obvious promoting effect on the development of adventitious roots in mulberry cuttings, but its molecular mechanism has not yet been studied. In this research, transcriptome sequencing (RNA-seq) technology was employed to sequence the ‘Yueshenda 10’ mulberry during four distinct cutting stages. Through Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analysis, shifts in gene expression and metabolic pathways were scrutinized, pinpointing the pivotal role of plant hormones in this context. Furthermore, using Weighted Gene Co-Expression Network Analysis (WGCNA), the study analyzed gene expression across all samples, identifying two modules, “black” and “blue”. These modules were predominantly expressed in the treatment group during the rooting phase and minimally expressed in the control group. Critical genes such as gene21267 and gene16291 from the black module, alongside gene18291 and gene20028 from the blue module, were identified as key to the rooting success of the ‘Yueshenda 10’ cuttings. This investigation not only supports the nutrient propagation and effective use of mulberry trees but also clarifies the molecular basis of adventitious root formation in these plants, extending the research to other related species. This work fosters the diversification and enhancement of the mulberry industry chain. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics, 2nd Edition)

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