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Agronomy
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Advances in Crop Molecular Breeding and Genetics—2nd Edition
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Advances in Crop Molecular Breeding and Genetics—2nd Edition

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Crop Breeding and Genetics".

Deadline for manuscript submissions: 31 October 2025 | Viewed by 1613

Special Issue Editors

Dr. Zhiyong Li

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Guest Editor
State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
Interests: plant genomics and genetics; molecular breeding; rice yield; carbon partitioning; seed development
Special Issues, Collections and Topics in MDPI journals
Dr. Chaolei Liu

E-Mail Website
Guest Editor
China National Rice Research Institute, Hangzhou, China
Interests: rice; synthetic apomixis; haploid breeding; QTL; genome editing
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Jiezheng Ying

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Guest Editor
State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
Interests: rice (Oryza sativa L.); quantitative trait locus; seed development; grain weight
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Dawei Xue

E-Mail Website
Guest Editor
College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
Interests: molecular physiology of crops; abiotic stress; crop molecular genetics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Due to the booming population, deteriorating environments, and degrading farmland, it is estimated that crop yields must double by 2050 to ensure food security worldwide. To achieve this goal, crop breeders must take full advantage of modern molecular biology technologies to accelerate breeding and genetic improvement. Over recent decades, the tremendous efforts focused on plant genomics and genetics have greatly accelerated the process of crop breeding. However, crop yields have stabilized in recent years. Therefore, it is imperative to improve the understanding of the molecular basis underlying crop yield, grain quality, nutrient utilization, and stress adaptions to produce higher crop yields. This Special Issue of Agronomy will focus on the latest fundamental discoveries in the field of crop genetics in regulating important plant development processes or agronomic traits, germplasm resources with elite traits, and adaptive practices to climate change for high crop yield, as well as the potential utilization of biotechnologies in crop genetics improvement. This Special Issue welcomes all original research papers and reviews; we believe your contributions will significantly influence future crop breeding.

Dr. Zhiyong Li
Dr. Chaolei Liu
Prof. Dr. Jiezheng Ying
Prof. Dr. Dawei Xue
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. Agronomy is an international peer-reviewed open access monthly 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 2600 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

  • molecular genetics and breeding
  • gene cloning and function
  • genetic diversity
  • agricultural genomics
  • crop adaptability
  • crop improvement
  • genetic engineering
  • germplasm resources

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Related Special Issue

Published Papers (3 papers)

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Research

21 pages, 7526 KiB  
Article
Integrated Metabolome and Transcriptome Analysis Reveals the Mechanism of Anthocyanin Biosynthesis in Pisum sativum L. with Different Pod Colors
by Weijun Ye, Zejiang Wu, Dongfeng Tian and Bin Zhou
Agronomy 2025, 15(7), 1609; https://doi.org/10.3390/agronomy15071609 - 30 Jun 2025
Viewed by 68
Abstract
Pea (Pisum sativum L.) is a significant source of dietary protein, starch, fiber, and minerals, offering health benefits and serving as both a green vegetable and dry grain. The pigment contents in pea pods with different colors and related genes are still [...] Read more.
Pea (Pisum sativum L.) is a significant source of dietary protein, starch, fiber, and minerals, offering health benefits and serving as both a green vegetable and dry grain. The pigment contents in pea pods with different colors and related genes are still unclear. We conducted an integrated transcriptome and metabolome analysis on three cultivars, including QiZhen (QZ) with green immature pods, FengMi (FM) with yellow immature pods, and ZiYu (ZY) with purple immature pods, to identify the key genes and metabolites involved in anthocyanin accumulation. ZY showed the highest total anthocyanin content compared with FM and QZ. Subsequent quantification revealed that four metabolites, including Delphinidin-3-O-galactoside, Delphinidin-3-O-(6″-O-xylosyl)glucoside, Cyanidin-3-O-galactoside, and Pelargonidin-3-O-(xylosyl)glucoside, were the most highly accumulated in the ZY cultivar, suggesting their role in the purple pigmentation of ZY pea pods. There were 49 differentially accumulated anthocyanidins in ZY vs. FM, 43 differentially accumulated anthocyanidins in ZY vs. QZ, and 21 differentially accumulated anthocyanidins in FM vs. QZ. These findings highlight the importance of the type and concentration of anthocyanin compounds, especially those based on delphinidin, cyanidin, and pelargonidin, in the development of purple pea pods. The transcriptomic analysis revealed that certain anthocyanin biosynthetic genes were expressed at higher levels in ZY than in FM and QZ. In ZY, the higher expression levels of five key genes (PAL, 4CL, CHS, F3H, and UFGT) resulted in elevated anthocyanin content compared to FM and QZ. Furthermore, the BSA-seq analysis identified a candidate region associated with purple color in pea pods, which is located on chromosome 6 and contains 21 DEGs. Sequence variation in KIW84_061698, which encodes a bHLH transcription factor, was identified as the key candidate gene controlling anthocyanin content. This study clarifies the molecular mechanisms behind pea pod coloration and identifies potential genetic engineering targets for breeding anthocyanin-rich sugar snap peas. Full article
(This article belongs to the Special Issue Advances in Crop Molecular Breeding and Genetics—2nd Edition)
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17 pages, 3922 KiB  
Article
Improvement of Morkhor 60-3 Upland Rice Variety for Blast and Bacterial Blight Resistance Using Marker–Assisted Backcross Selection
by Sawinee Panmaha, Chaiwat Netpakdee, Tanawat Wongsa, Sompong Chankaew, Tidarat Monkham and Jirawat Sanitchon
Agronomy 2025, 15(7), 1600; https://doi.org/10.3390/agronomy15071600 - 30 Jun 2025
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Abstract
Morkhor 60-3 is an upland rice variety primarily cultivated in northeastern Thailand. This glutinous rice is valued for its adaptability and rich aroma but remains susceptible to significant diseases, particularly blast and bacterial blight. Using resistant varieties represents the most cost-effective approach to [...] Read more.
Morkhor 60-3 is an upland rice variety primarily cultivated in northeastern Thailand. This glutinous rice is valued for its adaptability and rich aroma but remains susceptible to significant diseases, particularly blast and bacterial blight. Using resistant varieties represents the most cost-effective approach to address this limitation. This study incorporated the QTLs/genetic markers qBl1, qBl2, and xa5 from Morkhor 60-1 through marker-assisted backcrossing. From the BC1F3 population, ten lines were selected based on their parentage and evaluated for blast resistance using a spray inoculation method with 12 isolates of Pyricularia oryzae, and for bacterial blight (BB) resistance using a leaf-clipping method with nine isolates of Xanthomonas oryzae pv. oryzae. Broad-spectrum resistance (BSR) was also assessed in the lines for both diseases. Subsequently, BC1F4 lines were evaluated for field performance, including agronomic traits and aroma. Results identified three superior lines, BC1F4 22-7-140-4, BC1F4 22-7-322-5, and BC1F4 22-7-311-9, that demonstrated resistance to both BB and blast pathogens with average BSR values of 0.61 and 1.00, 0.66 and 1.00, and 0.55 and 0.87, respectively. These lines also exhibited enhanced performance in flowering date, plant height, panicle number per plant, grain number per plant, and grain weight. These findings demonstrate the effectiveness of marker-assisted selection (MAS) for gene pyramiding in rice improvement. Full article
(This article belongs to the Special Issue Advances in Crop Molecular Breeding and Genetics—2nd Edition)
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13 pages, 1178 KiB  
Article
Molecular Characterization of an EMS-Induced Ab-γg-Rich Saponin Mutant in Soybean (Glycine max (L.) Merr.)
by Junbeom Park, Haereon Son, Hyun Jo, Chigen Tsukamoto, Jinwon Lee, Jeong-Dong Lee, Hak Soo Seo and Jong Tae Song
Agronomy 2025, 15(3), 648; https://doi.org/10.3390/agronomy15030648 - 5 Mar 2025
Viewed by 1081
Abstract
Soybean is particularly known for accumulating saponins in its seeds. This study aimed to identify a causal gene to control an increase in Ab-γg saponin in PE1607 from an EMS-treated population of the soybean cultivar Pungsannamul. Segregation analysis in F2 seeds verified [...] Read more.
Soybean is particularly known for accumulating saponins in its seeds. This study aimed to identify a causal gene to control an increase in Ab-γg saponin in PE1607 from an EMS-treated population of the soybean cultivar Pungsannamul. Segregation analysis in F2 seeds verified that a single recessive allele controlled the increased Ab-γg saponin in PE1607. Bulk segregant analysis and mutant individuals identified the candidate region, containing the previously reported Sg-3 (Glyma.10G104700) gene, encoding a glucosyltransferase responsible for conjugating glucose as the third sugar at the C-3 position of the aglycone. NGS identified SNPs in the upstream of the Sg-3 gene, designated as the sg-3b allele. Expression analysis revealed that PE1607 exhibited a threefold decrease in Sg-3 expression in the hypocotyls compared to the Pungsannamul. Moreover, Sg-3 expressions significantly differed between the hypocotyls and cotyledons in developing seeds, with relatively low expression observed in the cotyledons. The results conclude that sg-3b allele may contribute to the reduced Sg-3 expression, resulting in an increase in Ab-γg saponin in PE1607. In addition, in the cotyledons, DDMP-βg and DDMP-βa saponins are present, containing rhamnose instead of glucose as the third sugar at the C-3 position of aglycone. This suggests that Sg-3, known as glucosyltransferase, does not significantly contribute to saponin biosynthesis in cotyledons. Full article
(This article belongs to the Special Issue Advances in Crop Molecular Breeding and Genetics—2nd Edition)
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