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Molecular Genetics and Breeding of Oilseed Crops

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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: closed (31 March 2024) | Viewed by 13156

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Dr. Cunmin Qu

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College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
Interests: rapeseed; seedcoat; metabolic; GWAS; QTL mapping; plant biotechnology (RNAi, Gene editing, transgenic); genome and genomics
Special Issues, Collections and Topics in MDPI journals

Dr. Qi Peng

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Guest Editor

Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
Interests: Brassica napus L.; Sclerotinia sclerotiorum; BrYV/TuYV Virus; pathogen-host Interactions; plant biotechnology (RNAi, gene editing, transgenic)
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Huajian Zhang

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College of Plant Protection, Anhui Agricultural University, Hefei, China
Interests: rapeseed diseases; disease resiatance; molecular breeding; stomatal immunity; non-host resistance
Special Issues, Collections and Topics in MDPI journals

Dr. Yongtai Yin

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Guest Editor

Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
Interests: Brassica napus; oil content; fatty acid; oil crops
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The yield potential, production, and quality of oilseed crops (e.g., rapeseed, groundnut, castor, soybean, and sunflower) are the potential objectives for breeders worldwide. However, oilseed crop production still faces numerous challenges, including the impacts of biologic and abiological factors in addition to the demand for improved yield and nutritional quality.

For the present, molecular genetics and breeding mainly include many biotechnologies, such as QTL, GWAS, MAS, map-based cloning, and gene or genome editing, which have been widely studied and achieved significant progress in plant science. As such, we develop this Special Issue, which will provide a forum with which to address these problems and present new progress in oilseed crop research.

Dr. Cunmin Qu
Dr. Qi Peng
Prof. Dr. Huajian Zhang
Dr. Yongtai Yin
Guest Editors

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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.

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Keywords

oilseed crops
breeding
molecular genomics
plant germplasm
gene mapping

Related Special Issue

Molecular Genetics and Breeding of Oilseed Crops—2nd Edition in Plants

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Research

22 pages, 2957 KiB

Open AccessArticle

The Physiological Response Mechanism of Peanut Leaves under Al Stress

by Jianning Shi, Jianyu Li, Yuhu Pan, Min Zhao, Rui Zhang, Yingbin Xue and Ying Liu

Plants 2024, 13(12), 1606; https://doi.org/10.3390/plants13121606 - 10 Jun 2024

Viewed by 585

Abstract

Aluminum (Al) toxicity in acidic soils can significantly reduce peanut yield. The physiological response of peanut leaves to Al poisoning stress still has not been fully explored. This research examined the influences of Al toxicity on peanut leaves by observing the leaf phenotype, scanning the leaf area and perimeter, and by measuring photosynthetic pigment content, physiological response indices, leaf hormone levels, and mineral element accumulation. Fluorescence quantitative RT–PCR (qPCR) was utilized to determine the relative transcript level of specific genes. The results indicated that Al toxicity hindered peanut leaf development, reducing their biomass, surface area, and perimeter, although the decrease in photosynthetic pigment content was minimal. Al toxicity notably affected the activity of antioxidative enzymes, proline content, and MDA (malondialdehyde) levels in the leaves. Additionally, Al poisoning resulted in the increased accumulation of iron (Fe), potassium (K), and Al in peanut leaves but reduced the levels of calcium (Ca), manganese (Mn), copper (Cu), zinc (Zn), and magnesium (Mg). There were significant changes in the content of hormones and the expression level of genes connected with hormones in peanut leaves. High Al concentrations may activate cellular defense mechanisms, enhancing antioxidative activity to mitigate excess reactive oxygen species (ROS) and affecting hormone-related gene expression, which may impede leaf biomass and development. This research aimed to elucidate the physiological response mechanisms of peanut leaves to Al poisoning stress, providing insights for breeding new varieties resistant to Al poisoning. Full article

(This article belongs to the Special Issue Molecular Genetics and Breeding of Oilseed Crops)

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14 pages, 4284 KiB

Open AccessArticle

Associations of the Seed Fatty Acid Composition of Sesame (Sesamum indicum L.) Germplasm with Agronomic Traits and FAD2 Variations

by Eun-Gyeong Kim, Sookyeong Lee, Tae-Jin Yang, Jae-Eun Lee, Eunae Yoo, Gi-An Lee and Jungsook Sung

Plants 2024, 13(12), 1590; https://doi.org/10.3390/plants13121590 - 7 Jun 2024

Viewed by 312

Abstract

Sesame is an important oilseed crop grown for human consumption in many countries, with a high commercial value due to its high oleic/linoleic acid ratio (O/L ratio). However, its properties may vary among different accessions. In the current study, 282 sesame accessions were evaluated to determine the effects of agronomic traits and genotypes on the O/L ratio. The O/L ratio was positively correlated with the oleic acid (C18:1), stearic acid (C18:0), and myristic acid (C14:0) concentrations, as well as the capsule zone length (CZL), capsule width (CW), and capsule length (CL), and negatively correlated with the linoleic acid (C18:2) and linolenic acid (C18:3) concentrations, the days to maturity (DTM), days to flowering (DTF), and the height of the first capsule-bearing node (HFC) (p < 0.05). In addition, the O/L ratio was affected by the FAD2 haplotype, as the Hap2 and Hap3 sesame accessions had lower O/L ratios. Therefore, we suggest that the increase and decrease in the contents of C18:1 and C18:2 are associated with the FAD2 haplotype. A total of 25 agronomic traits and fatty acid compositions were compared via statistical analysis, and accessions with a high O/L ratio were selected. The results of this study can be used as a basis for further research on the development of new sesame varieties through enhancing nutritional functionality. Full article

(This article belongs to the Special Issue Molecular Genetics and Breeding of Oilseed Crops)

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20 pages, 16788 KiB

Open AccessArticle

Genome-Wide Identification of Peanut B-Boxs and Functional Characterization of AhBBX6 in Salt and Drought Stresses

by Haohong Tang, Cuiling Yuan, Haonan Shi, Feng Liu, Shihua Shan, Zhijun Wang, Quanxi Sun and Jie Sun

Plants 2024, 13(7), 955; https://doi.org/10.3390/plants13070955 - 26 Mar 2024

Viewed by 845

Abstract

The B-box (BBX) gene family includes zinc finger protein transcription factors that regulate a multitude of physiological and developmental processes in plants. While BBX gene families have been previously determined in various plants, the members and roles of peanut BBXs are largely unknown. In this research, on the basis of the genome-wide identification of BBXs in three peanut species (Arachis hypogaea, A. duranensis, and A. ipaensis), we investigated the expression profile of the BBXs in various tissues and in response to salt and drought stresses and selected AhBBX6 for functional characterization. We identified a total of 77 BBXs in peanuts, which could be grouped into five subfamilies, with the genes from the same branch of the same subgroup having comparable exon–intron structures. In addition, a significant number of cis-regulatory elements involved in the regulation of responses to light and hormones and abiotic stresses were found in the promoter region of peanut BBXs. Based on the analysis of transcriptome data and qRT-PCR, we identified AhBBX6, AhBBX11, AhBBX13, and AhBBX38 as potential genes associated with tolerance to salt and drought. Silencing AhBBX6 using virus-induced gene silencing compromised the tolerance of peanut plants to salt and drought stresses. The results of this study provide knowledge on peanut BBXs and establish a foundation for future research into their functional roles in peanut development and stress response. Full article

(This article belongs to the Special Issue Molecular Genetics and Breeding of Oilseed Crops)

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22 pages, 23951 KiB

Open AccessArticle

Development of an NLR-ID Toolkit and Identification of Novel Disease-Resistance Genes in Soybean

by Wei Shao, Gongfu Shi, Han Chu, Wenjia Du, Zikai Zhou and Hada Wuriyanghan

Plants 2024, 13(5), 668; https://doi.org/10.3390/plants13050668 - 28 Feb 2024

Viewed by 1041

Abstract

The recognition of pathogen effectors through the nucleotide-binding leucine-rich repeat receptor (NLR) family is an important component of plant immunity. In addition to typical domains such as TIR, CC, NBS, and LRR, NLR proteins also contain some atypical integrated domains (IDs), the roles of which are rarely investigated. Here, we carefully screened the soybean (Glycine max) genome and identified the IDs that appeared in the soybean TNL-like proteins. Our results show that multiple IDs (36) are widely present in soybean TNL-like proteins. A total of 27 Gm-TNL-ID genes (soybean TNL-like gene encoding ID) were cloned and their antiviral activity towards the soybean mosaic virus (SMV)/tobacco mosaic virus (TMV) was verified. Two resistance (R) genes, SRA2 (SMV resistance gene contains AAA_22 domain) and SRZ4 (SMV resistance gene contains zf-RVT domain), were identified to possess broad-spectrum resistance characteristics towards six viruses including SMV, TMV, plum pox virus (PPV), cabbage leaf curl virus (CaLCuV), barley stripe mosaic virus (BSMV), and tobacco rattle virus (TRV). The effects of Gm-TNL-ID^X (the domain of the Gm-TNL-ID gene after the TN domain) on the antiviral activity of a R protein SRC7^TN (we previously reported the TN domain of the soybean broad-spectrum resistance gene SRC7) were validated, and most of Gm-TNL-ID^X inhibits antiviral activity mediated by SRC7^TN, possibly through intramolecular interactions. Yeast-two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays showed that seven Gm-TNL-ID^X interacted with SMV-component proteins. Truncation analysis on a broad-spectrum antiviral protein SRZ4 indicated that SRZ4^TIR is sufficient to mediate antiviral activity against SMV. Soybean cDNA library screening on SRZ4 identified 48 interacting proteins. In summary, our results indicate that the integration of IDs in soybean is widespread and frequent. The NLR-ID toolkit we provide is expected to be valuable for elucidating the functions of atypical NLR proteins in the plant immune system and lay the foundation for the development of engineering NLR for plant-disease control in the future. Full article

(This article belongs to the Special Issue Molecular Genetics and Breeding of Oilseed Crops)

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21 pages, 4775 KiB

Open AccessArticle

Physiological Mechanism through Which Al Toxicity Inhibits Peanut Root Growth

by Jianning Shi, Min Zhao, Feng Zhang, Didi Feng, Shaoxia Yang, Yingbin Xue and Ying Liu

Plants 2024, 13(2), 325; https://doi.org/10.3390/plants13020325 - 22 Jan 2024

Cited by 3 | Viewed by 1135

Abstract

Al (Aluminum) poisoning is a significant limitation to crop yield in acid soil. However, the physiological process involved in the peanut root response to Al poisoning has not been clarified yet and requires further research. In order to investigate the influence of Al toxicity stress on peanut roots, this study employed various methods, including root phenotype analysis, scanning of the root, measuring the physical response indices of the root, measurement of the hormone level in the root, and quantitative PCR (qPCR). This research aimed to explore the physiological mechanism underlying the reaction of peanut roots to Al toxicity. The findings revealed that Al poisoning inhibits the development of peanut roots, resulting in reduced biomass, length, surface area, and volume. Al also significantly affects antioxidant oxidase activity and proline and malondialdehyde contents in peanut roots. Furthermore, Al toxicity led to increased accumulations of Al and Fe in peanut roots, while the contents of zinc (Zn), cuprum (Cu), manganese (Mn), kalium (K), magnesium (Mg), and calcium (Ca) decreased. The hormone content and related gene expression in peanut roots also exhibited significant changes. High concentrations of Al trigger cellular defense mechanisms, resulting in differentially expressed antioxidase genes and enhanced activity of antioxidases to eliminate excessive ROS (reactive oxygen species). Additionally, the differential expression of hormone-related genes in a high-Al environment affects plant hormones, ultimately leading to various negative effects, for example, decreased biomass of roots and hindered root development. The purpose of this study was to explore the physiological response mechanism of peanut roots subjected to aluminum toxicity stress, and the findings of this research will provide a basis for cultivating Al-resistant peanut varieties. Full article

(This article belongs to the Special Issue Molecular Genetics and Breeding of Oilseed Crops)

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19 pages, 4895 KiB

Open AccessArticle

Integrative Analysis of Oleosin Genes Provides Insights into Lineage-Specific Family Evolution in Brassicales

by Zhi Zou, Li Zhang and Yongguo Zhao

Plants 2024, 13(2), 280; https://doi.org/10.3390/plants13020280 - 18 Jan 2024

Viewed by 1045

Abstract

Oleosins (OLEs) are a class of small but abundant structural proteins that play essential roles in the formation and stabilization of lipid droplets (LDs) in seeds of oil crops. Despite the proposal of five oleosin clades (i.e., U, SL, SH, T, and M) in angiosperms, their evolution in eudicots has not been well-established. In this study, we employed Brassicales, an economically important order of flowering plants possessing the lineage-specific T clade, as an example to address this issue. Three to 10 members were identified from 10 species representing eight plant families, which include Caricaceae, Moringaceae, Akaniaceae, Capparaceae, and Cleomaceae. Evolutionary and reciprocal best hit-based homologous analyses assigned 98 oleosin genes into six clades (i.e., U, SL, SH, M, N, and T) and nine orthogroups (i.e., U1, U2, SL, SH1, SH2, SH3, M, N, and T). The newly identified N clade represents an ancient group that has already appeared in the basal angiosperm Amborella trichopoda, which are constitutively expressed in the tree fruit crop Carica papaya, including pulp and seeds of the fruit. Moreover, similar to Clade N, the previously defined M clade is actually not Lauraceae-specific but an ancient and widely distributed group that diverged before the radiation of angiosperm. Compared with A. trichopoda, lineage-specific expansion of the family in Brassicales was largely contributed by recent whole-genome duplications (WGDs) as well as the ancient γ event shared by all core eudicots. In contrast to the flower-preferential expression of Clade T, transcript profiling revealed an apparent seed/embryo/endosperm-predominant expression pattern of most oleosin genes in Arabidopsis thaliana and C. papaya. Moreover, the structure and expression divergence of paralogous pairs was frequently observed, and a good example is the lineage-specific gain of an intron. These findings provide insights into lineage-specific family evolution in Brassicales, which facilitates further functional studies in nonmodel plants such as C. papaya. Full article

(This article belongs to the Special Issue Molecular Genetics and Breeding of Oilseed Crops)

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20 pages, 8556 KiB

Open AccessArticle

Identification of the High-Affinity Potassium Transporter Gene Family (HKT) in Brassica U-Triangle Species and Its Potential Roles in Abiotic Stress in Brassica napus L.

by Xiaoran Yang, Ran Hu, Fujun Sun, Shulin Shen, Mengzhen Zhang, Yiwei Liu, Yi Zhang, Hai Du, Kun Lu, Cunmin Qu and Nengwen Yin

Plants 2023, 12(21), 3768; https://doi.org/10.3390/plants12213768 - 4 Nov 2023

Viewed by 1369

Abstract

Members of the high-affinity potassium transporter (HKT) protein family regulate the uptake and homeostasis of sodium and potassium ions, but little research describes their roles in response to abiotic stresses in rapeseed (Brassica napus L.). In this study, we identified and characterized a total of 36 HKT genes from the species comprising the triangle of U model (U-triangle species): B. rapa, B. nigra, B. oleracea, B. juncea, B. napus, and B. carinata. We analyzed the phylogenetic relationships, gene structures, motif compositions, and chromosomal distributions of the HKT family members of rapeseed. Based on their phylogenetic relationships and assemblage of functional domains, we classified the HKT members into four subgroups, HKT1;1 to HKT1;4. Analysis of the nonsynonymous substitutions (Ka), synonymous substitutions (Ks), and the Ka/Ks ratios of HKT gene pairs suggested that these genes have experienced strong purifying selective pressure after duplication, with their evolutionary relationships supporting the U-triangle theory. Furthermore, the expression profiles of BnaHKT genes varies among potassium, phytohormone and heavy-metal treatment. Their repression provides resistance to heavy-metal stress, possibly by limiting uptake. Our results systematically reveal the characteristics of HKT family proteins and their encoding genes in six Brassica species and lay a foundation for further exploration of the role of HKT family genes in heavy-metal tolerance. Full article

(This article belongs to the Special Issue Molecular Genetics and Breeding of Oilseed Crops)

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14 pages, 1975 KiB

Open AccessArticle

Evaluation of Resistance of Oilseed Rape Genotypes to Turnip Yellows Virus

by Emad Ibrahim, Andrea Rychlá, Glenda Alquicer, Lucie Slavíková, Qi Peng, Miroslav Klíma, Viktor Vrbovský, Piotr Trebicki and Jiban Kumar Kundu

Plants 2023, 12(13), 2501; https://doi.org/10.3390/plants12132501 - 30 Jun 2023

Viewed by 1285

Abstract

Turnip yellows virus (TuYV), is one of the most important pathogens of oilseed rape, which has caused enormous yield losses in all growing regions of the world in recent years. Therefore, there is a need for resistant varieties for sustainable crop protection. We have investigated the resistance of known varieties and newly developed advanced-breeding lines of oilseed rape to TuYV in greenhouse and field trials. We have analysed the TuYV titre of individual genotypes inoculated with the virus using viruliferous aphids Myzus persicae. The genotypes ‘DK Temptation’ and ‘Rescator’ had the lowest and highest virus titres, respectively, and were used as resistant and susceptible models for comparative analyses with other genotypes. In the greenhouse, the best results were obtained with the genotypes ‘OP-8143 DH’ (2.94 × 10⁵ copies), OP-BN-72 (3.29 × 10⁵ copies), ‘Navajo’ (3.58 × 10⁵ copies) and ‘SG-C 21215’ (4.09 × 10⁵ copies), which reached virus titres about 2 times higher than the minimum virus concentration measured in ‘DK Temptation’ (1.80 × 10⁵ copies). In the field trials, the genotypes ‘Navajo’ (3.39 × 10⁵ copies), ‘OP-8148 DH’ (4.44 × 10⁵ copies), ‘SG-C 21215’ (6.80 × 10⁵ copies) and OP-8480 (7.19 × 10⁵ copies) had the lowest virus titres and reached about 3 times the virus titre of DK Temptation (2.54 × 10⁵ copies). Both trials showed that at least two commercial varieties (e.g., DK Temptation, Navajo) and three advanced breeding lines (e.g., OP-8143 DH, OP-BN-72, SG-C 21215) had low titres of the virus after TuYV infection. This indicates a high level of resistance to TuYV in ‘Navajo’ or the newly developed breeding lines and the basis of resistance is probably different from R54 (as in ‘DK Temptation’). Furthermore, the greenhouse trials together with RT -qPCR-based virus titre analysis could be a cost-effective and efficient method to assess the level of resistance of a given genotype to TuYV infection compared to the field trials. However, further research is needed to identify the underlying mechanisms causing this difference in susceptibility. Full article

(This article belongs to the Special Issue Molecular Genetics and Breeding of Oilseed Crops)

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17 pages, 4434 KiB

Open AccessArticle

Identification of Trehalose-6-Phosphate Synthase (TPS) Genes Associated with Both Source-/Sink-Related Yield Traits and Drought Response in Rapeseed (Brassica napus L.)

by Bo Yang, Liyuan Zhang, Sirou Xiang, Huan Chen, Cunmin Qu, Kun Lu and Jiana Li

Plants 2023, 12(5), 981; https://doi.org/10.3390/plants12050981 - 21 Feb 2023

Cited by 3 | Viewed by 1768

Abstract

Trehalose-6-phosphate synthase (TPS) is an important enzyme for the synthesis of Trehalose-6-phosphate (T6P). In addition to being a signaling regulator of carbon allocation that improves crop yields, T6P also plays essential roles in desiccation tolerance. However, comprehensive studies, such as evolutionary analysis, expression analysis, and functional classification of the TPS family in rapeseed (Brassica napus L.) are lacking. Here, we identified 35 BnTPSs, 14 BoTPSs, and 17 BrTPSs in cruciferous plants, which were classified into three subfamilies. Phylogenetic and syntenic analysis of TPS genes in four cruciferous species indicated that only gene elimination occurred during their evolution. Combined phylogenetic, protein property, and expression analysis of the 35 BnTPSs suggested that changes in gene structures might have led to changes in their expression profiles and further functional differentiation during their evolution. In addition, we analyzed one set of transcriptome data from Zhongshuang11 (ZS11) and two sets of data from extreme materials associated with source-/sink-related yield traits and the drought response. The expression levels of four BnTPSs (BnTPS6, BnTPS8, BnTPS9, and BnTPS11) increased sharply after drought stress, and three differentially expressed genes (BnTPS1, BnTPS5, and BnTPS9) exhibited variable expression patterns among source and sink tissues between yield-related materials. Our findings provide a reference for fundamental studies of TPSs in rapeseed and a framework for future functional research of the roles of BnTPSs in both yield and drought resistance. Full article

(This article belongs to the Special Issue Molecular Genetics and Breeding of Oilseed Crops)

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19 pages, 4939 KiB

Open AccessArticle

Genome-Wide Association Study of Glucosinolate Metabolites (mGWAS) in Brassica napus L.

by Yunshan Tang, Guorui Zhang, Xinyue Jiang, Shulin Shen, Mingwei Guan, Yuhan Tang, Fujun Sun, Ran Hu, Si Chen, Huiyan Zhao, Jiana Li, Kun Lu, Nengwen Yin and Cunmin Qu

Plants 2023, 12(3), 639; https://doi.org/10.3390/plants12030639 - 1 Feb 2023

Cited by 5 | Viewed by 2354

Abstract

Glucosinolates (GSLs) are secondary plant metabolites that are enriched in rapeseed and related Brassica species, and they play important roles in defense due to their anti-nutritive and toxic properties. Here, we conducted a genome-wide association study of six glucosinolate metabolites (mGWAS) in rapeseed, including three aliphatic glucosinolates (m145 gluconapin, m150 glucobrassicanapin and m151 progoitrin), one aromatic glucosinolate (m157 gluconasturtiin) and two indole glucosinolates (m165 indolylmethyl glucosinolate and m172 4-hydroxyglucobrassicin), respectively. We identified 113 candidate intervals significantly associated with these six glucosinolate metabolites. In the genomic regions linked to the mGWAS peaks, 187 candidate genes involved in glucosinolate biosynthesis (e.g., BnaMAM1, BnaGGP1, BnaSUR1 and BnaMYB51) and novel genes (e.g., BnaMYB44, BnaERF025, BnaE2FC, BnaNAC102 and BnaDREB1D) were predicted based on the mGWAS, combined with analysis of differentially expressed genes. Our results provide insight into the genetic basis of glucosinolate biosynthesis in rapeseed and should facilitate marker-based breeding for improved seed quality in Brassica species. Full article

(This article belongs to the Special Issue Molecular Genetics and Breeding of Oilseed Crops)

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