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Research on Plant Genomics and Breeding 2023

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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 August 2024 | Viewed by 11241

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Dr. Zhiyong Li

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Guest Editor

State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, China
Interests: plant genomics and genetics; molecular breeding; plant physiology; carbon partitioning; seed development
Special Issues, Collections and Topics in MDPI journals

Dr. Jian Zhang

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State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
Interests: plant genetics; molecular biology; biochemistry; transcriptome; proteome approaches; synthetic biology
Special Issues, Collections and Topics in MDPI journals

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Dear Colleagues,

Over the past two decades, plant breeding has greatly accelerated by the knowledge of plant genomics, genetics and the development of modern biotechnologies, as well as the remarkable efforts of community-based projects. It is imperative to explore the genetic basis and molecular mechanisms underlying various plant developmental and growth processes, as it underpins crop yield, quality, nutrient utilization and stress adaptions. Here, we propose a Special Issue, “Research on Plant Genomics and Breeding” in Plants is to bring together the latest fundamental advances in plant genomics and molecular basis associated with agronomic traits, as well as the potential utilization of biotechnologies in crop genetic improvement. We therefore welcome all types of submissions, including original research and review articles covering:

Genetic and functional characterization of genes regulating important plant development processes or agronomic traits;
Gene regulatory networks and epigenetic landscapes in plant
Comparative study of discovery, characterization, and application of germplasm resources with elite traits;
Genetic improvement in crops using gene editing and other modern biotechnologies;

Dr. Zhiyong Li
Dr. Jian Zhang
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 developmental and growth
gene cloning and function
regulatory mechanisms
molecular genetics
epigenetic
genetic engineering
genome editing
germplasm enhancement
molecular breeding and marker-assisted selection

Published Papers (10 papers)

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Research

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13 pages, 3731 KiB

Open AccessCommunication

Fine Mapping of qAL5.2 Controlling Anther Length in Oryza sativa

by Xinyong Liu, Zixuan Yu, Xiaohong Tong, Longxue Chang, Jie Huang, Yifeng Wang, Jiezheng Ying, Xingwang Li, Shen Ni and Jian Zhang

Plants 2024, 13(8), 1130; https://doi.org/10.3390/plants13081130 - 18 Apr 2024

Viewed by 440

Abstract

Anther length is the critical floral trait determining hybrid rice seed production and is controlled by many quantitative trait loci (QTL). However, the cloning of genes specifically controlling anther size has yet to be reported. Here, we report the fine mapping of qAL5.2 for anther size using backcross inbred lines (BILs) in the genetic background of Oryza sativa indica Huazhan (HZ). Gene chip analysis on the BC₄F₂ and BC₅F₁ population identified effective loci on Chr1, Chr5, and Chr8 and two genomic regions on Chr5, named qAL5.1 and qAL5.2. qAL5.2 was identified in both populations with LOD values of 17.54 and 10.19, which explained 35.73% and 25.1% of the phenotypic variances, respectively. Ultimately qAL5.2 was localized to a 73 kb region between HK139 and HK140 on chromosome 5. And we constructed two near-isogenic lines (NILs) for RNA-seq analysis, named NIL-qAL5.2^HZ and NIL-qAL5.2^KLY, respectively. The result of the GO enrichment analysis revealed that differential genes were significantly enriched in the carbohydrate metabolic process, extracellular region, and nucleic acid binding transcription, and KEGG enrichment analysis revealed that alpha-linolenic acid metabolism was significantly enriched. Meanwhile, candidate genes of qAL5.2 were analyzed in RNA-seq, and it was found that ORF8 is differentially expressed between NIL-qAL5.2^HZ and NIL-qAL5.2^KLY. The fine mapping of qAL5.2 conferring anther length will promote the breed improvement of the restorer line and understanding of the mechanisms driving crop mating patterns. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding 2023)

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14 pages, 2338 KiB

Open AccessArticle

Dissecting the Genetic Basis of Yield Traits and Validation of a Novel Quantitative Trait Locus for Grain Width and Weight in Rice

by Man Yin, Xiaohong Tong, Jinyu Yang, Yichen Cheng, Panpan Zhou, Guan Li, Yifeng Wang and Jiezheng Ying

Plants 2024, 13(6), 770; https://doi.org/10.3390/plants13060770 - 8 Mar 2024

Viewed by 562

Abstract

Grain yield in rice is a complex trait and it is controlled by a number of quantitative trait loci (QTL). To dissect the genetic basis of rice yield, QTL analysis for nine yield traits was performed using an F₂ population containing 190 plants, which was developed from a cross between Youyidao (YYD) and Sanfenhe (SFH), and each plant in the population evaluated with respect to nine yield traits. In this study, the correlations among the nine yield traits were analyzed. The grain yield per plant positively correlated with six yield traits, except for grain length and grain width, and showed the highest correlation coefficient of 0.98 with the number of filled grains per plant. A genetic map containing 133 DNA markers was constructed and it spanned 1831.7 cM throughout 12 chromosomes. A total of 36 QTLs for the yield traits were detected on nine chromosomes, except for the remaining chromosomes 5, 8, and 9. The phenotypic variation was explained by a single QTL that ranged from 6.19% to 36.01%. Furthermore, a major QTL for grain width and weight, qGW2-1, was confirmed to be newly identified and was narrowed down to a relatively smaller interval of about ~2.94-Mb. Collectively, we detected a total of 36 QTLs for yield traits and a major QTL, qGW2-1, was confirmed to control grain weight and width, which laid the foundation for further map-based cloning and molecular design breeding in rice. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding 2023)

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18 pages, 4912 KiB

Open AccessArticle

Simultaneous Application of Several Exogenous dsRNAs for the Regulation of Anthocyanin Biosynthesis in Arabidopsis thaliana

by Konstantin V. Kiselev, Andrey R. Suprun, Olga A. Aleynova, Zlata V. Ogneva and Alexandra S. Dubrovina

Plants 2024, 13(4), 541; https://doi.org/10.3390/plants13040541 - 16 Feb 2024

Viewed by 612

Abstract

Plant surface treatment with double-stranded RNAs (dsRNAs) has gained recognition as a promising method for inducing gene silencing and combating plant pathogens. However, the regulation of endogenous plant genes by external dsRNAs has not been sufficiently investigated. Also, the effect of the simultaneous application of multiple gene-specific dsRNAs has not been analyzed. The aim of this study was to exogenously target five genes in Arabidopsis thaliana, namely, three transcription factor genes (AtCPC, AtMybL2, AtANAC032), a calmodulin-binding protein gene (AtCBP60g), and an anthocyanidin reductase gene (AtBAN), which are known as negative regulators of anthocyanin accumulation. Exogenous dsRNAs encoding these genes were applied to the leaf surface of A. thaliana either individually or in mixtures. The mRNA levels of the five targets were analyzed using qRT-PCR, and anthocyanin content was evaluated through HPLC-MS. The results demonstrated significant downregulation of all five target genes by the exogenous dsRNAs, resulting in enhanced expression of chalcone synthase (AtCHS) gene and increased anthocyanin content. The simultaneous foliar application of the five dsRNAs proved to be more efficient in activating anthocyanin accumulation compared to the application of individual dsRNAs. These findings hold considerable importance in plant biotechnology and gene function studies. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding 2023)

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14 pages, 2430 KiB

Open AccessArticle

Genome-Wide Association Study for Agronomic Traits in Gamma-Ray-Derived Mutant Kenaf (Hibiscus cannabinus L.)

by Woon Ji Kim, Baul Yang, Ye-jin Lee, Jae Hoon Kim, Sang Hoon Kim, Joon-Woo Ahn, Si-Yong Kang, Seong-Hoon Kim and Jaihyunk Ryu

Plants 2024, 13(2), 249; https://doi.org/10.3390/plants13020249 - 16 Jan 2024

Viewed by 826

Abstract

Kenaf (Hibiscus cannabinus L.), in the Malvaceae family, is an important crop for not only fiber production, but also various other industrial materials. We performed phylogenetic analysis and a genome-wide association study (GWAS) of seven agronomic traits: days to flowering, plant height, fresh weight, dry weight, flower color, stem color, and leaf shape, using 96 kenaf genotypes, including gamma-irradiation-derived mutant lines. Genotypes were determined by genotyping-by-sequencing (GBS) and a total of 49,241 single-nucleotide polymorphisms (SNPs) were used in the analysis. Days to flowering, plant height, fresh weight, and dry weight were positively correlated with each other, and stem color was also correlated with fresh weight and dry weight. The phylogenetic analysis divided the 96 lines into nine related groups within two independent groups, and the GWAS analysis detected a total of 49 SNPs for days to flowering, plant height, fresh weight, dry weight, flower color, stem color, and leaf shape with −log₁₀(P) ≥ 4, of which 22 were located in genic regions. The detected SNPs were located in genes with homology ranging from 45% to 96% to plants of the Malvaceae and Betulaceae, and these genes were found to be involved in plant growth and development via various pathways. Our identification of SNP markers related to agronomic traits is expected to help improve the quality of selective breeding programs for kenaf. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding 2023)

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13 pages, 3358 KiB

Open AccessArticle

Variability of Glucosinolates in Pak Choy (Brassica rapa subsp. chinensis) Germplasm

by Seong-Hoon Kim, Kingsley Ochar, Aejin Hwang, Yoon-Jung Lee and Hae Ju Kang

Plants 2024, 13(1), 9; https://doi.org/10.3390/plants13010009 - 19 Dec 2023

Cited by 2 | Viewed by 753

Abstract

Glucosinolates are sulfur-containing phytochemicals generally abundant in cruciferous vegetables such as pak choy. Glucosinolates participate in a range of biological activities essential for promoting a healthy human body. In this study, we aimed to elucidate glucosinolate variability present in pak choy germplasm that are under conservation at the Rural Development Administration Genebank, Jeonju, Republic of Korea. The Acquity Ultra-Performance Liquid Chromatography (UHPLC) analytical system was used in profiling the glucosinolate content in leaf samples of various accessions. We identified a total of 17 glucosinolates in the germplasm. Based on principal compoment analysis performed, three separate groups of the accessions were obtained. Group 1 contained the cultivar cheongsacholong which recorded high content of glucobrassicin (an indole), glucoerucin (aliphatic), gluconasturtiin (aromatic) and glucoberteroin (aliphatic). Group 2 consisted of six accessions, BRA77/72, Lu ling gaogengbai, 9041, Wuyueman, RP-75 and DH-10, predominatly high in aliphatic compounds including glucoiberin, glucocheirolin, and sinigrin. Group 3 comprised the majority of the accessions which were characterized by high content of glucoraphanin, epiprogoitrin, progoitrin, and glucotropaeolin. These results revealed the presence of variability among the pak choy germplasm based on their glucosinolate content, providing an excellent opprtunity for future breeding for improved glucosinolate content in the crop. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding 2023)

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16 pages, 8502 KiB

Open AccessArticle

Genome Survey and Chromosome-Level Draft Genome Assembly of Glycine max var. Dongfudou 3: Insights into Genome Characteristics and Protein Deficiencies

by Yajuan Duan, Yue Li, Jing Zhang, Yongze Song, Yan Jiang, Xiaohong Tong, Yingdong Bi, Shaodong Wang and Sui Wang

Plants 2023, 12(16), 2994; https://doi.org/10.3390/plants12162994 - 19 Aug 2023

Viewed by 1038

Abstract

Dongfudou 3 is a highly sought-after soybean variety due to its lack of beany flavor. To support molecular breeding efforts, we conducted a genomic survey using next-generation sequencing. We determined the genome size, complexity, and characteristics of Dongfudou 3. Furthermore, we constructed a chromosome-level draft genome and speculated on the molecular basis of protein deficiency in GmLOX1, GmLOX2, and GmLOX3. These findings set the stage for high-quality genome analysis using third-generation sequencing. The estimated genome size is approximately 1.07 Gb, with repetitive sequences accounting for 72.50%. The genome is homozygous and devoid of microbial contamination. The draft genome consists of 916.00 Mb anchored onto 20 chromosomes, with annotations of 46,446 genes and 77,391 transcripts, achieving Benchmarking Single-Copy Orthologue (BUSCO) completeness of 99.5% for genome completeness and 99.1% for annotation. Deletions and substitutions were identified in the three GmLox genes, and they also lack corresponding active proteins. Our proposed approach, involving k-mer analysis after filtering out organellar DNA sequences, is applicable to genome surveys of all plant species, allowing for accurate assessments of size and complexity. Moreover, the process of constructing chromosome-level draft genomes using closely related reference genomes offers cost-effective access to valuable information, maximizing data utilization. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding 2023)

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14 pages, 9142 KiB

Open AccessArticle

MBD3 Regulates Male Germ Cell Division and Sperm Fertility in Arabidopsis thaliana

by Jia Shu, Xiaochang Yin, Yannan Liu, Yingjie Mi, Bin Zhang, Aoyuan Zhang, Hongbo Guo and Juane Dong

Plants 2023, 12(14), 2654; https://doi.org/10.3390/plants12142654 - 15 Jul 2023

Viewed by 1240

Abstract

DNA methylation plays important roles through the methyl-CpG-binding domain (MBD) to realize epigenetic modifications. Thirteen AtMBD proteins have been identified from the Arabidopsis thaliana genome, but the functions of some members are unclear. AtMBD3 was found to be highly expressed in pollen and seeds and it preferably binds methylated CG, CHG, and unmethylated DNA sequences. Then, two mutant alleles at the AtMBD3 locus were obtained in order to further explore its function using CRISPR/Cas9. When compared with 92.17% mature pollen production in the wild type, significantly lower percentages of 84.31% and 78.91% were observed in the mbd3-1 and mbd3-2 mutants, respectively. About 16–21% of pollen from the mbd3 mutants suffered a collapse in reproductive transmission, whereas the other pollen was found to be normal. After pollination, about 16% and 24% of mbd3-1 and mbd3-2 mutant seeds underwent early or late abortion, respectively. Among all the late abortion seeds in mbd3-2 plants, 25% of the abnormal seeds were at the globular stage, 31.25% were at the transition stage, and 43.75% were at the heart stage. A transcriptome analysis of the seeds found 950 upregulated genes and 1128 downregulated genes between wild type and mbd3-2 mutants. Some transcriptional factors involved in embryo development were selected to be expressed, and we found significant differences between wild type and mbd3 mutants, such as WOXs, CUC1, AIB4, and RGL3. Furthermore, we found a gene that is specifically expressed in pollen, named PBL6. PBL6 was found to directly interact with AtMBD3. Our results provide insights into the function of AtMBD3 in plants, especially in sperm fertility. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding 2023)

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14 pages, 2352 KiB

Open AccessArticle

Genotypic Variation of Purple Rice in Response to Shading in Yield, Anthocyanin Content, and Gene Expression

by Nantapat Danpreedanan, Supapohn Yamuangmorn, Sansanee Jamjod, Chanakan Prom-u-thai and Tonapha Pusadee

Plants 2023, 12(13), 2582; https://doi.org/10.3390/plants12132582 - 7 Jul 2023

Cited by 1 | Viewed by 1469

Abstract

Purple rice (Oryza sativa L.) contains anthocyanin, which acts as an antioxidant and functional food for humans. The levels of anthocyanin growth and production in rice are mainly controlled by the availability of light. However, shade can affect anthocyanin biosynthesis genes. Therefore, the objective of this study was to determine the yield and anthocyanin content among four purple rice varieties, which provide the difference in colors of purple and green leaves. This study also evaluated gene expression affected by shading treatment to understand the relation of grain anthocyanin and expression level. This research was conducted using a split plot design using four levels of shading (levels of shading from anthesis to maturity) with three replications, no shading, 30% shading, 50% shading, and 70% shading, as the main plots and purple rice varieties as subplots, KJ CMU-107, K2, K4, and KDK10, from anthesis to maturity. Shading significantly decreased yield and yield components, but increased grain anthocyanin content. Nonetheless, the response of yield and grain anthocyanin content to shading did not show a significant different between purple and green leaf varieties. In addition, the level of OsDFR gene expression was different depending on the shading level in four rice varieties. The OsDFR gene presented the highest expression at shading levels of 30% for K4 and 50% for KDK10, while the expression of the OsDFR gene was not detected in the purple rice varieties with green leaves (KJ CMU-107 and K2). The response of grain anthocyanin and gene expression of OsDFR to light treatment did not show significantly differences between the purple and green leaf varieties, suggesting that the appearance of anthocyanin in leaves might be not related to anthocyanin synthesis in the grain. Taken together, the results suggest that some purple rice varieties were more suitable for planting under low light intensity based on a lower level of grain yield loss, strong shade tolerance, and high anthocyanin content in leaf and grain pericarp. However, it is necessary to explore the effects of light intensity on genes and intermediates in the anthocyanin synthesis pathway for further study. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding 2023)

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21 pages, 3752 KiB

Open AccessArticle

Transcriptome Analysis Reveals the Genes Related to Water-Melon Fruit Expansion under Low-Light Stress

by Wenrui Gao, Fuchun She, Yanjun Sun, Bing Han, Xiansheng Wang and Gang Xu

Plants 2023, 12(4), 935; https://doi.org/10.3390/plants12040935 - 18 Feb 2023

Cited by 1 | Viewed by 1399

Abstract

Watermelon is one of people’s favorite fruits globally. Fruit size is one of the important characteristics of fruit quality. Low light can seriously affect fruit development, but there have been no reports concerning molecular mechanism analysis in watermelons involved in fruit expansion under low-light stress. To understand this mechanism, the comparative transcriptomic file of watermelon fruit flesh at four different developmental stages under different light levels was studied. The results showed that the fruit size and content of soluble sugar and amino acids at low-light stress significantly decreased compared to the control. In addition, 0–15 DAP was the rapid expansion period of watermelon fruit affected by shading. In total, 8837 differentially expressed genes (DEGs) were identified and 55 DEGs were found to play a role in the four different early fruit development stages. We also found that genes related to oxidation-reduction, secondary metabolites, carbohydrate and amino acid metabolism and transcriptional regulation played a key role in watermelon fruit expansion under low-light stress. This study provides a foundation to investigate the functions of low-light stress-responsive genes and the molecular mechanism of the effects of low-light stress on watermelon fruit expansion. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding 2023)

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Review

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24 pages, 1538 KiB

Open AccessReview

Unlocking the Multifaceted Mechanisms of Bud Outgrowth: Advances in Understanding Shoot Branching

by Yundong Yuan, Said Khourchi, Shujia Li, Yanfang Du and Pierre Delaplace

Plants 2023, 12(20), 3628; https://doi.org/10.3390/plants12203628 - 20 Oct 2023

Cited by 2 | Viewed by 1809

Abstract

Shoot branching is a complex and tightly regulated developmental process that is essential for determining plant architecture and crop yields. The outgrowth of tiller buds is a crucial step in shoot branching, and it is influenced by a variety of internal and external cues. This review provides an extensive overview of the genetic, plant hormonal, and environmental factors that regulate shoot branching in several plant species, including rice, Arabidopsis, tomato, and wheat. We especially highlight the central role of TEOSINTE BRANCHED 1 (TB1), a key gene in orchestrating bud outgrowth. In addition, we discuss how the phytohormones cytokinins, strigolactones, and auxin interact to regulate tillering/branching. We also shed light on the involvement of sugar, an integral component of plant development, which can impact bud outgrowth in both trophic and signaling ways. Finally, we emphasize the substantial influence of environmental factors, such as light, temperature, water availability, biotic stresses, and nutrients, on shoot branching. In summary, this review offers a comprehensive evaluation of the multifaced regulatory mechanisms that underpin shoot branching and highlights the adaptable nature of plants to survive and persist in fluctuating environmental conditions. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding 2023)

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