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Advances in Plant Genetic Breeding and Molecular Biology

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

Deadline for manuscript submissions: closed (30 April 2023) | Viewed by 13094

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Special Issue Editors

Prof. Dr. Chang-Hyu Bae

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Guest Editor

Department of Agricultural Life Science Science, Sunchon National University, Suncheon 57922, Korea
Interests: bellflower radix; bioactive compounds; functional genomics; genetic diversity; genetic transformation; horticultural crop; mutation; rape; plant resources

Dr. Bo-Keun Ha

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Guest Editor

Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Korea
Interests: soybean; cowpea; QTL mapping; GWAS; MAS
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Si-Yong Kang

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Guest Editor

Department of Horticulture, Kongju National University, 54 Daehak-ro, Yeasan, Chungnam 32439, Korea
Interests: plant mutation breeding and genetics; biotechnology; crop genetic resources

Special Issue Information

Dear Colleagues,

According to advances in plant molecular biology, studies on plant breeding using molecular biological technology have been activated in the field of major crops, as well as horticultural crops. Meanwhile, the application of advanced technologies was restrictively used in the fields of special crops and industry crops compared with major crops. The importance of special crops and industry crops is relatively low compared with major crops in the world. However, the development of industry crops provides high economic benefits. The aim of this Special Issue is to find and collect advanced or new plant breeding technologies around molecular biology in the field of special and industry crops. In addition, this Special Issue intends to report recent advances in plant genetic breeding including new molecular breeding technologies, and newly developed genetic resources combined with biotechnologies and advanced omics research, such as genomics, proteomics, transcriptomics, phenomics, metabolomics, etc.

This Special Issue welcomes the submission of review and research papers or short communications on topics related to plant genetic breeding, molecular biology and their related fusion technologies.

Prof. Dr. Chang-Hyu Bae
Dr. Bo-Keun Ha
Prof. Dr. Si-Yong Kang
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

genetic diversity
genotyping‐by‐sequencing
GWAS
molecular breeding
molecular biology
molecular markers
mutation breeding
special crops
industry crops

Published Papers (6 papers)

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Research

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21 pages, 5024 KiB

Open AccessArticle

Genome-Wide Association Study (GWAS) of the Agronomic Traits and Phenolic Content in Sorghum (Sorghum bicolor L.) Genotypes

by Ye-Jin Lee, Baul Yang, Woon Ji Kim, Juyoung Kim, Soon-Jae Kwon, Jae Hoon Kim, Joon-Woo Ahn, Sang Hoon Kim, Eui-Shik Rha, Bo-Keun Ha, Chang-Hyu Bae and Jaihyunk Ryu

Agronomy 2023, 13(6), 1449; https://doi.org/10.3390/agronomy13061449 - 24 May 2023

Cited by 1 | Viewed by 1886

Abstract

Sorghum (Sorghum bicolor L.) is a promising biomass crop with high yields of cellulose, hemicellulose, and lignin. Sorghum biomass has emerged as an eco-friendly industrial material useful for producing biofuels and bioplastics. This study conducted genotyping-by-sequencing (GBS)-based genome-wide association studies (GWAS) to establish the genetic basis of traits associated with biomass. Specifically, the researchers evaluated agronomic traits and phenolic compounds using 96 sorghum genotypes. Six phenolic compounds, luteolinidin diglucoside, luteolin glucoside, apigeninidin glucoside, luteolinidin, apigeninidin, and 5-O-Me luteolinidin, were found to be the major phenolic compounds in all genotypes. Out of our six detected phenolic compounds (luteolinidin diglucoside, luteolin glucoside, apigeninidin glucoside, luteolinidin, apigeninidin, and 5-O-Me luteolinidin), luteolinidin was the major phenolic compound in all genotypes. Next, a GWAS analysis was performed to confirm significant associations between 192,040 filtered single-nucleotide polymorphisms (SNPs) and biomass-related traits. The study identified 40 SNPs on 10 chromosomes that were significantly associated with heading date (4 SNPs), plant height (3 SNPs), dry yield (2 SNPs), and phenolic compounds (31 SNPs). The GWAS analysis showed that SbRio.10G099600 (FUT1) was associated with heading date, SbRio.09G149200 with plant height, SbRio.06G211400 (MAFB) with dry yield, SbRio.04G259800 (PDHA1) with total phenolic content and luteolinidin diglucoside, and SbRio.02G343600 (LeETR4) with total phenolic content and luteolinidin, suggesting that these genes could play key roles in sorghum. These findings demonstrate the potential value of sorghum as a biomass resource and the potential for selecting sorghum genotypes with reduced phenolic contents for use in the bioindustry. Full article

(This article belongs to the Special Issue Advances in Plant Genetic Breeding and Molecular Biology)

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15 pages, 3198 KiB

Open AccessArticle

Genome-Wide Association Study for Agronomic Traits in Wild Soybean (Glycine soja)

by Woon Ji Kim, Byeong Hee Kang, Chang Yeok Moon, Sehee Kang, Seoyoung Shin, Sreeparna Chowdhury, Soon-Chun Jeong, Man-Soo Choi, Soo-Kwon Park, Jung-Kyung Moon and Bo-Keun Ha

Agronomy 2023, 13(3), 739; https://doi.org/10.3390/agronomy13030739 - 01 Mar 2023

Cited by 1 | Viewed by 2113

Abstract

The agronomic traits of soybean are important because they are directly or indirectly related to its yield. Cultivated soybean (Glycine max (L.) Merr) has lost genetic diversity during domestication and selective breeding. However, wild soybean (G. soja) represents a useful breeding material because it has a diverse gene pool. In this study, a total of 96,432 single-nucleotide polymorphisms (SNPs) across 203 wild soybean accessions from the 180K Axiom^® Soya SNP array were employed in the association analysis. Wild soybean accessions were divided into four clusters based on their genetic distance using ADMIXTURE, principal component analysis, and neighbor-joining clusters. The linkage disequilibrium decayed rapidly in wild soybean. A genome-wide association study was conducted for days to flowering (DtF), days to maturity (DtM), the number of pods (NoP), and the 100-seed weight (100SW), which are major agronomic traits for wild soybean accessions. A total of 22 significant SNPs were found to be associated with DtF, DtM, and the 100SW. Based on the detected SNP markers, Glyma.12g210400, a gene related to DtF, Glyma.17g115300, a gene related to DtM, and Glyma.14g140200, a gene related to the 100SW, were selected as candidate genes. The SNP markers related to agronomic traits identified in this study are expected to help improve the quality of soybean cultivars through selective breeding. Full article

(This article belongs to the Special Issue Advances in Plant Genetic Breeding and Molecular Biology)

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13 pages, 3725 KiB

Open AccessArticle

Comparative Transcriptome Analysis Identified Potential Genes and Transcription Factors for Flower Coloration in Kenaf (Hibiscus cannabinus L.)

by Jae Il Lyu, Jaihyunk Ryu, Dong-Gun Kim, Jung Min Kim, Joon-Woo Ahn, Soon-Jae Kwon, Sang Hoon Kim and Si-Yong Kang

Agronomy 2023, 13(3), 715; https://doi.org/10.3390/agronomy13030715 - 27 Feb 2023

Cited by 1 | Viewed by 1263

Abstract

The biochemical compounds in kenaf leaves and flowers mainly consist of flavonoids, including flavonoid glycosides and floral anthocyanins. In the present study, we performed comparative transcriptome analysis using RNA-sequencing and identified putative genes involved in flower coloration in different flower developmental stages of three kenaf mutants including Baekma (white flower), Jangdae (ivory flower), and Bora (purple flower). A total of 36.1 Gb reads were generated for two kenaf accessions and 38,601 representative transcripts with an average length of 1350 bp were yielded, of which 33,057 (85.64%) were annotated against two databases. Expression profiling of the transcripts identified 1044 and 472 differentially expressed genes (DEGs) among three mutants in the young bud and full bloom stages, respectively. KEGG enrichment analysis of these DEGs revealed that the representative pathway was “biosynthesis of secondary metabolites”, including phenylpropanoid biosynthesis and flavonoid biosynthesis. Consequently, we investigated genes related to the phenylpropanoid pathway, which included 45 DEGs from a total of 1358. Our results provide useful information for understanding gene functions of flower coloration in kenaf, which will be useful in further studies. Full article

(This article belongs to the Special Issue Advances in Plant Genetic Breeding and Molecular Biology)

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16 pages, 2619 KiB

Open AccessEditor’s ChoiceArticle

Field Performance of Disease-Free Plants of Ginger Produced by Tissue Culture and Agronomic, Cytological, and Molecular Characterization of the Morphological Variants

by Xiaoqin Zhao, Shuangying Yu, Yida Wang, Dongzhu Jiang, Yiming Zhang, Liu Hu, Yongxing Zhu, Qie Jia, Junliang Yin, Yiqing Liu and Xiaodong Cai

Agronomy 2023, 13(1), 74; https://doi.org/10.3390/agronomy13010074 - 26 Dec 2022

Cited by 4 | Viewed by 3721

Abstract

Ginger (Zingiber officinale Rosc.) is an important spice crop valued for its flavored and medical properties. It is susceptible to soil-borne diseases, which can cause considerable economic loss to growers. In vitro culture is feasible for the propagation of disease-free ginger plants, but has several disadvantages when producing seed rhizomes that can be commercially used, such as long cultivation cycles (usually 2–3 years) and occurrence of somaclonal variation. In this study, dynamic changes in the morphological characteristics of in vitro-propagated disease-free plants of ‘Wuling’ ginger were evaluated by continuous observation and measurement at 30-day intervals, and morphological variants were screened and characterized by agronomic, cytological, and molecular analysis at harvest. Results showed that the plants grew rapidly within 120 days after planting, and the most active growth period was from 60 to 120 days. Eight plants with clear and stable morphological differences were screened out from approximately 2000 plants grown in the field, and they could be classified into two groups (VT1 and VT2) based on tiller number, plant height, leaf color, and leaf shape. By flow cytometry analysis and chromosome counting, the VT1 was confirmed to be diploid, with the shortest plant height, the largest number of tillers and rhizome knobs, and the smallest tiller diameter and rhizome size among the three types of plants. The VT2 was mixoploid, consisting of diploid and tetraploid cells, with significantly reduced tiller number and rhizome knobs, significantly larger stomatal guard cells/apertures, and significantly lower stomatal density. SSR analysis detected DNA band profile changes in six out of the eight variants, including one plant of the VT1 and all the VT2 plants. The findings of this study might contribute to the commercial production of disease-free seed rhizomes in ginger, and the characterized somaclonal variants could provide useful germplasm resources for future breeding. Full article

(This article belongs to the Special Issue Advances in Plant Genetic Breeding and Molecular Biology)

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32 pages, 5695 KiB

Open AccessArticle

Ideotype Selection of Perennial Flax (Linum spp.) for Herbaceous Plant Habit Traits

by David G. Tork, Neil O. Anderson, Donald L. Wyse and Kevin J. Betts

Agronomy 2022, 12(12), 3127; https://doi.org/10.3390/agronomy12123127 - 09 Dec 2022

Cited by 3 | Viewed by 1305

Abstract

(1) Background: Annual flax (Linum usitatissimum) and many wild relatives possess showy blue flowers and finely textured foliage. To promote the use of blue-flowered flax as ornamentals, an herbaceous perennial flax breeding program was initiated to develop ideotypes and test their effectiveness. The objectives of this study were to (a) compare traits of interest for herbaceous perennials in breeding populations (CF, oilseed) and accessions of annual/perennial species in a common garden; (b) quantify the impact of selection (direct, indirect) for traits of interest; (c) identify top candidate species for continued breeding using the herbaceous perennial flax crop ideotype; (2) Methods: Recorded traits, based on the perennial flax ideotype, included: flower diameter, flowering period, stem length and diameter, plant width and height, summer and winter survival; (3) Results: OS and CF populations had smaller stem diameters, longer flowering periods, larger plant size, more uniform growth, and improved winter survival compared to wild species. Linum austriacum was the top wild species for the CF breeding ideotype but comparable in performance with L. perenne for the herbaceous perennial flax ideotype; (4) Conclusions: The effect of 1–5 yrs. on selection for target/non-target traits in wild species for future R&D is exemplified with selection and release of an herbaceous/garden ornamental perennial flax for the market. Full article

(This article belongs to the Special Issue Advances in Plant Genetic Breeding and Molecular Biology)

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Review

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17 pages, 1270 KiB

Open AccessReview

Molecular Advances in Breeding for Durable Resistance against Pests and Diseases in Wheat: Opportunities and Challenges

by Kun Luo, Dejia He, Jiao Guo, Guangwei Li, Boliao Li and Xiulin Chen

Agronomy 2023, 13(3), 628; https://doi.org/10.3390/agronomy13030628 - 22 Feb 2023

Cited by 4 | Viewed by 1960

Abstract

Wheat production worldwide is severely challenged by different pest and pathogen species, and misguided application of chemicals in farming significantly stimulates crop invaders to develop insecticide resistance. The growing desire for sustainable agriculture has promoted the breeding of wheat cultivars with durable pests and diseases resistance tolerance traits, which have become increasingly imperative for wheat production. Various genetic breeding techniques, including transgenic breeding, molecular marker-assisted breeding, molecular breeding with gene pyramiding, gene silencing, and gene editing, have been successfully deployed into wheat cultivar improvement, and have significantly promoted the process of breeding cultivars with multiple substantial resistance traits. Although the success of practical applications of some of these resistant wheat cultivars in farming has suggested that these approaches are effective strategies for combating fungal diseases and herbivorous insects, there remains significant challenges for wheat molecular breeding programs. Thus, this review illustrates and summarizes the recent advances and drawbacks related to the measures associated with molecular breeding in common wheat cultivar improvement. Full article

(This article belongs to the Special Issue Advances in Plant Genetic Breeding and Molecular Biology)

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