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Genetic Dissection of Important Agronomy Characteristics and Gene Function Analysis in Oilseed Crops

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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 17434

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Special Issue Editor

Prof. Dr. Maoteng Li

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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: cruciferae; QTL mapping; gene editing; oil content; seed yield; molecular breeding
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear colleagues,

Oilseed crops include rapeseed, soybean, peanut, and sesame. Increasing the oil production from these is a major task at present. Studying the molecular mechanisms of important characteristics during formation may yield candidate genes that are useful to improve oil production.

Oilseed crops can not only supply vegetables and vegetable oils for human nutrition. With the increased consumption of oil, the demand for oil production has increased. Increasing the oil quality is also an important task for human health at present. Therefore, breeding cultivars with higher oil content and higher yield are both necessary in the future. Genetic dissection and gene function analysis of oil content and seed is very important to our understanding of the molecular mechanisms of these characteristics, and may also supply useful molecular markers for breeding. In the meantime, increasing the disease resistance and creating new germplasm with valuable characteristics are also important for increasing the yield of oilseed crops.

The aim of this Special Issue is to focus on three aspects: (1) Genetic dissection (includign of QTL analysis, GWAS analysis and other kinds of analysis) of important agronomy characteristics (for example, seed oil content, seed quality, seed yield and its related characteristics, disease resistance (Sclerotinia sclerotiorum, clubroot disease), drought and water-logging resistance, and so on). (2) The innovation of new germplasm with higher oil content, higher seed quality, higher disease resistance, and so on (and new methods for plant breeding in oil seed crops). (3) The functional analysis of candidate genes that control the important agronomy characteristics of oilseed crops. Research into other agronomy characteristics not mentioned above are also encouraged.

Dr. MaoTeng Li
Guest Editor

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Keywords

oilseed crops
seed yield
seed quality
disease resistance
QTL mapping
GWAS
gene cloning
gene editing

Published Papers (9 papers)

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Research

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17 pages, 3197 KiB

Open AccessArticle

Genome-Wide Association Studies Revealed the Genetic Loci and Candidate Genes of Pod-Related Traits in Peanut (Arachis hypogaea L.)

by Xiaoli Zhang, Linglong Zhu, Mengyun Ren, Chao Xiang, Xiumei Tang, Youlin Xia, Dulin Song and Fuzhen Li

Agronomy 2023, 13(7), 1863; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy13071863 - 14 Jul 2023

Cited by 2 | Viewed by 1046

Abstract

Cultivated peanut (Arachis hypogaea L.) is one of the most important oilseed crops worldwide. Pod-related traits, including pod length (PL), pod width (PW), ratio of PL to PW (PL/W) and 100-pod weight (100-PW), are crucial factors for pod yield and are key target traits for selection in peanut breeding. However, the studies on the natural variation and genetic mechanism of pod-related traits are not clear in peanut. In this study, we phenotyped 136 peanut accessions for four pod-related traits in two consecutive years and genotyped the population using a re-sequencing technique. Based on 884,737 high-quality single nucleotide polymorphisms (SNPs), genome-wide association studies (GWAS) were conducted for four pod-related traits using a fixed and random model uniform cyclic probability (FarmCPU) model. The results showed that a total of 36 SNPs were identified by GWAS, among which twenty-one, fourteen and one SNPs were significantly associated with PL, PL/W and 100-PW, respectively. The candidate regions where the four peak SNPs (10_76084075, 11_138356586, 16_64420451, and 18_126782541) were located were used for searching genes, and nineteen candidate genes for pod-related traits were preliminarily predicted based on functional annotations. In addition, we also compared the expression patterns of these nineteen candidate genes in different tissues of peanut, and we found that eight genes were specifically highly expressed in tender fruit, immature pericarp, or seed, so we considered these genes to be the potential candidate genes for pod-related traits. These results enriched the understanding of the genetic basis of pod-related traits and provided an important theoretical basis for subsequent gene cloning and marker-assisted selection (MAS) breeding in peanut. Full article

(This article belongs to the Special Issue Genetic Dissection of Important Agronomy Characteristics and Gene Function Analysis in Oilseed Crops)

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17 pages, 1458 KiB

Open AccessArticle

Whole-Genome Resequencing Reveals the Genetic Diversity and Selection Signatures of the Brassica juncea from the Yunnan-Guizhou Plateau

by Xiaoyan Yuan, Minglian Fu, Genze Li, Cunmin Qu, Hao Liu, Xuan Li, Yunyun Zhang, Yusong Zhang, Kaiqin Zhao, Lifan Zhang, Yanqing Luo, Jinfeng Li, Xiaoying He, Liu He and Feihu Liu

Agronomy 2023, 13(4), 1053; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy13041053 - 04 Apr 2023

Cited by 2 | Viewed by 1462

Abstract

Brassica juncea has adapted to diverse climate zones and latitudes, especially in the Yunnan-Guizhou Plateau with the complexity and diversity of the ecological types of western China. However, the genetic variations underlying the diversity of these ecotypes are poorly known. In this study, we resequenced the genome of 193 indigenous B. juncea accessions and obtained 1.04 million high-quality SNPs and 3.23 million InDels by mapping reads to the reference genomes of B. juncea var. timuda. Phenotype, population genetic, phylogenetic and principal component analyses showed considerable genetic variation including four distinct genetic groups. Selective sweep analysis and a genome-wide association study revealed the candidate genes for seed color and fatty acid biosynthesis. The results provide a comprehensive insight into the spread and improvement of B. juncea and laya foundation for accelerating rapeseed breeding by facilitating screenings of molecular markers. Full article

(This article belongs to the Special Issue Genetic Dissection of Important Agronomy Characteristics and Gene Function Analysis in Oilseed Crops)

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15 pages, 3589 KiB

Open AccessArticle

Genome-Wide Identification and Expression Analysis of GATA Gene Family under Different Nitrogen Levels in Arachis hypogaea L.

by Xiujie Li, Xiaoxu Deng, Suoyi Han, Xinyou Zhang and Tingbo Dai

Agronomy 2023, 13(1), 215; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy13010215 - 10 Jan 2023

Cited by 3 | Viewed by 1422

Abstract

Nitrogen, one of the essential elements, is a key determinant for improving peanut growth and yield. GATA zinc finger transcription factors have been found to be involved in regulation of nitrogen metabolism. However, a systematic characterization of the GATA gene family and patterns of their expression under different nitrogen levels remains elusive. In this study, a total of 45 GATA genes distributed among 17 chromosomes were identified in the peanut genome and classified into three subfamilies I, II and III with 26, 13 and 6 members, respectively, whose physicochemical characteristics, gene structures and conserved motifs were also analyzed. Furthermore, the optimal level of nitrogen fertilizer on the growth of peanut cultivar Yuhua 23 was determined by pod yield and value cost ratio from 2020 to 2022, and the results revealed that 150 kg hm⁻² nitrogen was the best for cultivation of peanut Yuhua 23 because of its highest pod yield and relatively higher VCR of more than four. In addition, expression patterns of peanut GATA genes under different nitrogen levels were detected by real-time quantitative PCR and several GATA genes were significantly changed under a nitrogen level of 150 kg hm⁻². Overall, the above results would be helpful for further understanding biological functions of the GATA gene family in cultivated peanut. Full article

(This article belongs to the Special Issue Genetic Dissection of Important Agronomy Characteristics and Gene Function Analysis in Oilseed Crops)

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15 pages, 4482 KiB

Open AccessArticle

BSA-Seq Approach Identified Candidate Region and Diagnostic Marker for Chilling Tolerance of High Oleic Acid Peanut at Germination Stage

by Hongxi Sun, Liang Ren, Feiyan Qi, Haixin Wang, Shutao Yu, Ziqi Sun, Bingyan Huang, Suoyi Han, Puxiang Shi, Yibo Wang, Xinyou Zhang and Guoqing Yu

Agronomy 2023, 13(1), 18; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy13010018 - 21 Dec 2022

Cited by 4 | Viewed by 1705

Abstract

High oleic acid peanut (HOAP) is extensively embraced in China because of its high nutritional value and enhanced oxidative stability. However, its dissemination has been severely constrained in high altitude and high latitude areas due to chilling stress during sowing, resulting in significant yield loss in these regions. Despite the lack of understanding of the molecular mechanisms underlying low temperature germination (LTG) in HOAP, discovering the quantitative trait loci (QTL) that confer this trait will undoubtedly benefit breeding efforts. In the present study, we identified putative genomic regions and single nucleotide polymorphisms (SNPs) that govern LTG tolerance of HOAP in an F₂ population derived from the cross of chilling-tolerant YH65 and chilling-sensitive FL14 using bulk segregant analysis (BSA). Analysis of ΔSNP-index and Euclidean distance (ED) value association pinpointed the overlapped region to a 2.29 Mb interval on chromosome A05. The candidate interval showed that 122 genes were significantly related to response to abiotic stress and plant–pathogen interaction. Furthermore, an SNP site associated with LTG tolerance was discovered. The SNP site was employed as a Kompetitive Allele Specific PCR (KASP) marker and validated in a universal peanut panel. These findings may provide valuable insight into the molecular mechanism underpinning LTG tolerance and facilitate marker-assisted selective breeding in HOAP. Full article

(This article belongs to the Special Issue Genetic Dissection of Important Agronomy Characteristics and Gene Function Analysis in Oilseed Crops)

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18 pages, 5655 KiB

Open AccessArticle

Comprehensive Analysis of GASA Family Members in the Peanut Genome: Identification, Characterization, and Their Expressions in Response to Pod Development

by Yue Wu, Ziqi Sun, Feiyan Qi, Mingbo Zhao, Wenzhao Dong, Bingyan Huang, Zheng Zheng and Xinyou Zhang

Agronomy 2022, 12(12), 3067; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12123067 - 03 Dec 2022

Cited by 2 | Viewed by 1617

Abstract

The gibberellic acid-stimulated Arabidopsis (GASA) gene family is essential for plant growth and development, hormone level control, and phytohormone signal transmission. Different plants have been shown to contain numerous GASA homologs. However, there is no knowledge about these proteins in peanuts. In the current study, we performed a thorough bioinformatics and expression analysis and found 20, 22, and 40 GASA genes by genome-wide analyses of A. hypogaea L., A. duranensis, and A. ipaensis, respectively. We analyzed and predicted the physical properties of these genes. Based on the results of our phylogenetic analysis, the evolutionary tree constructed from the 40 AhGASA proteins was divided into seven categories, forming a total of 14 gene pairs. According to our observations, tandem duplication is a significant factor in the expansion of the GASA gene family. AhGASA was unevenly distributed on 20 chromosomes, and 17 tandem duplicated genes were identified. A co-lineage analysis with the A/B subgenome identified 69 linear/parallel homologous gene pairs. A cis-element analysis revealed that the AhGASA protein is crucial for hormone responsiveness. In materials with different size traits at various stages of peanut pod development, transcriptomics and RT-qPCR analyses revealed that AhGASA genes are expressed at various levels and are tissue-specific. This finding suggests that some AhGASA genes may be involved in controlling peanut pod size. This study suggests that GASA genes are crucial for controlling the development of peanut pods and provides the first systematic identification and analysis of GASA genes in peanut. These findings will help future research into the function of the GASA gene in the cultivated peanut. Full article

(This article belongs to the Special Issue Genetic Dissection of Important Agronomy Characteristics and Gene Function Analysis in Oilseed Crops)

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10 pages, 2100 KiB

Open AccessArticle

SNP and Haplotype Variability in the BnP5CR2 Gene and Association with Resistance and Susceptible Cultivars for Sclerotinia sclerotiorum in Brassica napus

by Yu Zhang, Yu Wang, Dong Wu, Dong Qu, Xiaomin Sun and Xiaojuan Zhang

Agronomy 2022, 12(12), 2956; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12122956 - 25 Nov 2022

Viewed by 1083

Abstract

Sclerotinia sclerotiorum is a serious disease of oil crop. The P5CR gene is the first gene reported to be associated with resistance to Sclerotinia infection in soybeans, and its closest homologs are located on chromosomes A10 and C09 of Brassica napus. We named these BnP5CR1 and BnP5CR2, respectively. The purpose of this study was to examine the single-nucleotide polymorphism (SNP) and haplotype diversity (Hd) of BnP5CR2 among canola cultivars with different levels of resistance to S. sclerotiorum as well as the expression patterns of BnP5CR2 via an association analysis using resistant and susceptible cultivars of B. napus. The results can thus provide information for future research on the mechanisms of disease resistance to S. sclerotiorum and the breeding of resistant canola cultivars. A total of 95 and 12 polymorphic sites were detected in 1870 and 678 SNP sites in 16 BnP5CR2 and their coding DNA sequence (CDS) population, respectively. A total of six different haplotypes (H1–H6) were inferred from the 16 BnP5CR2 gene-CDS that contributed to the high level of polymorphism. Hd was equal to 0.617, and H1 shared by 10 cultivars was the dominant haplotype, suggesting that H1 is an ancient haplotype among the BnP5CR2 genes. H6 and H5 haplotpypes were present in Nan12R and ZhongYou821, respectively. The expression level in vitro of the BnP5CR2 between Nan12R and ZhongYou821 was significantly different. The upregulated expression of BnP5CR2 in resistant cultivars was higher than that of susceptible cultivars under 6 h, 12 h, 24 h, and 36 h treatments of pathogen stress, among which the expression level was significantly increased at 6 h, 12 h and 36 h in resistant cultivars, and the difference reached a highly significant level at 6 h (p < 0.01). The two cultivars with clear differences in expression features possessed different BnP5CR2 gene-CDS-haplotypes, indicating that gene-CDS-haplotype diversity may have greater power than SNPs for the detection of causal genes for quantitative traits. Full article

(This article belongs to the Special Issue Genetic Dissection of Important Agronomy Characteristics and Gene Function Analysis in Oilseed Crops)

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15 pages, 1654 KiB

Open AccessArticle

Dissecting the Genetic Mechanisms of Hemicellulose Content in Rapeseed Stalk

by Yinhai Xu, Yuting Yang, Wenkai Yu, Liezhao Liu, Qiong Hu, Wenliang Wei and Jia Liu

Agronomy 2022, 12(11), 2886; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12112886 - 18 Nov 2022

Cited by 1 | Viewed by 1304

Abstract

Polysaccharides such as hemicellulose in rapeseed can be used as an abundant resource to develop biomass energy. In the present study, the hemicellulose content in the middle stalk and taproot of a rapeseed core population of 139 accessions in Guizhou, Hubei and Anhui provinces was determined. Genotyping of the core population was carried out by a 60 K single nucleotide polymorphism chip, and a genome-wide association study (GWAS) was performed to reveal the associated sites of hemicellulose content in rapeseed. The results of the GWAS showed that 28 SNPs (p ≤ 0.001) were significantly associated with hemicellulose content, and revealed that three sites—qHCs.C02 (contribution rate = 17.20%), qHCs.C05 (10.62%), and qHCs.C08 (8.80%)—are significantly associated with hemicellulose content in the stalk and three sites—qHCt.A09 (9.49%), qHCt.C05 (9.18%) and qHCt.C08 (13.10%)—are significantly associated with hemicellulose content in the taproot. Seven candidate genes associated with hemicellulose synthesis were identified in these major loci. Further RNA-seq analysis showed that two key differentially expressed genes (BnaC05G0092200ZS and BnaC05G0112400ZS) involved in hemicellulose synthesis were identified as having underlying QTL. This study excavated the key loci and candidate genes for regulating hemicellulose synthesis, providing a theoretical basis for developing rapeseed varieties with high hemicellulose content. At the same time, our results will be helpful in producing rapeseed cultivars with high lodging-resistance as well as highlighting the value of rapeseed as a resources for the bioenergy industry. Full article

(This article belongs to the Special Issue Genetic Dissection of Important Agronomy Characteristics and Gene Function Analysis in Oilseed Crops)

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18 pages, 355 KiB

Open AccessArticle

Identification of SSR Markers Associated with Yield-Related Traits and Heterosis Effect in Winter Oilseed Rape (Brassica Napus L.)

by Joanna Wolko, Agnieszka Łopatyńska, Łukasz Wolko, Jan Bocianowski, Katarzyna Mikołajczyk and Alina Liersch

Agronomy 2022, 12(7), 1544; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12071544 - 28 Jun 2022

Cited by 6 | Viewed by 1761

Abstract

The identification of markers responsible for regulating important agronomic traits in rapeseed supports breeding and increases the seed yield. Microsatellite (SSR) markers are mainly used as ‘neutral’ genetic markers but are also linked with many biological functions. The objective of this study was identification of microsatellite markers associated with important agronomic traits affecting the seed yield of winter oilseed rape and with the heterosis effect for these traits. The plant material consists of four parental lines, 60 doubled haploid (DH) lines, 60 single cross hybrids, and 60 three-way cross hybrids. The association between molecular markers and observed traits was estimated using regression analysis. Among 89 SSR markers, 43 were polymorphic, and 15 were selected for mapping because they demonstrated stability in both years of observation. These markers were physically mapped in the rapeseed reference genomes and their immediate vicinity was searched to identify candidate genes associated with the studied traits. Six markers (BrGMS3837, BnEMS1119, BrGMS2901, BnGMS0509, BrGMS3688, BrGMS4057), which showed a positive estimation effect in our association analysis, and thus increased the value of a given trait or heterosis effect, turned out to be linked with genes that could be responsible for the development and growth of plants. Full article

(This article belongs to the Special Issue Genetic Dissection of Important Agronomy Characteristics and Gene Function Analysis in Oilseed Crops)

Review

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22 pages, 5069 KiB

Open AccessReview

Application of CRISPR/Cas9 in Rapeseed for Gene Function Research and Genetic Improvement

by Qing Tian, Baojun Li, Yizhen Feng, Weiguo Zhao, Jinyong Huang and Hongbo Chao

Agronomy 2022, 12(4), 824; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12040824 - 28 Mar 2022

Cited by 5 | Viewed by 5150

Abstract

Brassica napus L. provides high-quality edible oil and clean energy for humans. For a long time, rapeseed breeders have tried to breed improved varieties through traditional breeding strategies. However, B. napus is an allotetraploid species containing many repetitive sequences. It is very inefficient to change traits through traditional genetic methods such as hybridization and random mutagenesis due to gene redundancy. Today, the burgeoning CRISPR/Cas9 technology has been applied in polyploid rapeseed for gene function research and targeted genetic improvement because of its unique advantages of high efficiency and simplicity. This review summarizes current reports about the application of CRISPR/Cas9 system for gene function research and genetic improvement in rapeseed, involving important agronomic traits such as yield, oil content, and fatty acid composition. The application status of emerging precise genome editing technology in plants and several potential limitations and technical bottlenecks in rapeseed gene editing is discussed, which will provide confidence for researchers in rapeseed gene function research and genetic improvement through genome editing technology. Full article

(This article belongs to the Special Issue Genetic Dissection of Important Agronomy Characteristics and Gene Function Analysis in Oilseed Crops)

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