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Genetics and Novel Techniques for Soybean Yield Enhancement

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (30 May 2023) | Viewed by 27569

Special Issue Editors


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Guest Editor
College of Agriculture, Northeast Agricultural University, Harbin, China
Interests: soybean resources innovation; soybean molecular assisted breeding; soybean biological information
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Interests: light signal transduction; shade avoidance; photoperiodic flowering; photomorphogenesis; circadian clock; ideal plant architecture; soybean
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Soybean is a worldwide pivotal crop, providing human food, animal feed and industrial materials. Soybean also plays an important role in bio-nitrogen fixation. To meet the ever-growing globe population, more than 361.00 million metric tons soybean would be produced in recent years. With the increasing of plant area and yield of soybean, more production problem raised and had attracted the attentions of people. How to breed novel and excellent cultivar and varieties to improve the soybean yield, quality and adaptation to the environment is urgent to be addressed for human food security.

For the present, the high-quality reference genome of soybean had been released. However, numerous works are still required to dissect gene functions, signaling networks and regulation mechanisms for the improvement of agronomy traits. genomics, transcriptomics, proteomics, phenomics, and metabolomics technology had been applied to determine gene functions. However, their use in soybean breeding and modification has been limited. and there is huge space for further development and improvement of breeding, biological function detection and technology application. Compare to rice and maize, there is too many gaps need to fill for soybean. Moreover, the mechanisms of symbiosis, the specific traits of legume crop, are still largely unclear. We expect that molecular breeding approaches will be more extensively studied and used in soybean genetic improvement. This special issue will provide a forum to address this problems and present new progress in related research.

The research topic will cover basic and application-oriented basic studies that support and facilitate soybean breeding and improvement. Both research articles and review articles are welcome. The following issues will be expected to be addressed:

  • QTL mapping and marker-assisted selection;
  • GWAS and genomic selection/prediction;
  • Molecular breeding by design;
  • Germplasm application;
  • Domestication and selection signatures;
  • Genotype x environment interaction;
  • Improvement of seed quality and/or nutritional quality traits;
  • Nitrogen efficiency modification;
  • Symbiosis mechanism detection;
  • Breeding for tolerance to biotic stresses;
  • Increasing the adaption to environment.

Prof. Dr. Qingshan Chen
Prof. Dr. Bin Liu
Guest Editors

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Keywords

  • soybean
  • breeding and genetics
  • genomics
  • QTL
  • GWAS
  • genomic selection
  • seed nutrition and nutraceutical
  • disease and pest resistance
  • abiotic stress tolerance
  • G x E interaction
  • symbiosis
  • nodule
  • environment

Published Papers (11 papers)

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19 pages, 1316 KiB  
Review
Multi-Omics Techniques for Soybean Molecular Breeding
by Pan Cao, Ying Zhao, Fengjiao Wu, Dawei Xin, Chunyan Liu, Xiaoxia Wu, Jian Lv, Qingshan Chen and Zhaoming Qi
Int. J. Mol. Sci. 2022, 23(9), 4994; https://doi.org/10.3390/ijms23094994 - 30 Apr 2022
Cited by 19 | Viewed by 4266
Abstract
Soybean is a major crop that provides essential protein and oil for food and feed. Since its origin in China over 5000 years ago, soybean has spread throughout the world, becoming the second most important vegetable oil crop and the primary source of [...] Read more.
Soybean is a major crop that provides essential protein and oil for food and feed. Since its origin in China over 5000 years ago, soybean has spread throughout the world, becoming the second most important vegetable oil crop and the primary source of plant protein for global consumption. From early domestication and artificial selection through hybridization and ultimately molecular breeding, the history of soybean breeding parallels major advances in plant science throughout the centuries. Now, rapid progress in plant omics is ushering in a new era of precision design breeding, exemplified by the engineering of elite soybean varieties with specific oil compositions to meet various end-use targets. The assembly of soybean reference genomes, made possible by the development of genome sequencing technology and bioinformatics over the past 20 years, was a great step forward in soybean research. It facilitated advances in soybean transcriptomics, proteomics, metabolomics, and phenomics, all of which paved the way for an integrated approach to molecular breeding in soybean. In this review, we summarize the latest progress in omics research, highlight novel findings made possible by omics techniques, note current drawbacks and areas for further research, and suggest that an efficient multi-omics approach may accelerate soybean breeding in the future. This review will be of interest not only to soybean breeders but also to researchers interested in the use of cutting-edge omics technologies for crop research and improvement. Full article
(This article belongs to the Special Issue Genetics and Novel Techniques for Soybean Yield Enhancement)
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23 pages, 6696 KiB  
Article
Genome-Wide Identification and Expression Analysis of the Ammonium Transporter Family Genes in Soybean
by Wei Yang, Xiaoxu Dong, Zhanxin Yuan, Yan Zhang, Xia Li and Youning Wang
Int. J. Mol. Sci. 2023, 24(4), 3991; https://doi.org/10.3390/ijms24043991 - 16 Feb 2023
Cited by 5 | Viewed by 1977
Abstract
Ammonium transporters (AMTs) are responsible for ammonium absorption and utilization in plants. As a high-nitrogen-demand crop and a legume, soybean can also obtain ammonium from symbiotic root nodules in which nitrogen-fixing rhizobia convert atmospheric nitrogen (N2) into ammonium. Although increasing evidence [...] Read more.
Ammonium transporters (AMTs) are responsible for ammonium absorption and utilization in plants. As a high-nitrogen-demand crop and a legume, soybean can also obtain ammonium from symbiotic root nodules in which nitrogen-fixing rhizobia convert atmospheric nitrogen (N2) into ammonium. Although increasing evidence implicates vital roles of ammonium transport in soybean, no systematic analyses of AMTs in soybean (named GmAMTs) or functional analyses of GmAMTs are available. In this study, we aimed to identify all GmAMT family genes and gain a better understanding of the characteristics of GmAMT genes in soybean. Here, due to the improved genome assembly and annotation of soybean, we tried to generate a phylogenetic tree of 16 GmAMTs based on new information. Consistent with reported data, GmAMT family members can be divided into two subfamilies of GmAMT1 (6 genes) and GmAMT2 (10 genes). Interestingly, unlike Arabidopsis, which has only one AMT2, soybean has substantially increased the number of GmAMT2s, suggesting enhanced demand for ammonium transport. These genes were distributed on nine chromosomes, of which GmAMT1.3, GmAMT1.4, and GmAMT1.5 were three tandem repeat genes. The gene structures and conserved protein motifs of the GmAMT1 and GmAMT2 subfamilies were different. All the GmAMTs were membrane proteins with varying numbers of transmembrane domains ranging from 4 to 11. Promoter analysis found that these GmAMT genes have phytohormone-, circadian control-, and organ expression-related cis-elements in their promoters, and notably, there were nodulation-specific and nitrogen-responsive elements in the promoters of the GmAMT1 and GmAMT2 genes. Further expression data showed that these GmAMT family genes exhibited different spatiotemporal expression patterns across tissues and organs. In addition, GmAMT1.1, GmAMT1.2, GmAMT2.2, and GmAMT2.3 were responsive to nitrogen treatment, while GmAMT1.2, GmAMT1.3, GmAMT1.4, GmAMT1.5, GmAMT1.6, GmAMT2.1, GmAMT2.2, GmAMT2.3, GmAMT3.1, and GmAMT4.6 showed circadian rhythms in transcription. RT-qPCR validated the expression patterns of GmAMTs in response to different forms of nitrogen and exogenous ABA treatments. Gene expression analysis also confirmed that GmAMTs are regulated by key nodulation gene GmNINa, indicating a role of GmAMTs in symbiosis. Together, these data indicate that GmAMTs may differentially and/or redundantly regulate ammonium transport during plant development and in response to environmental factors. These findings provide a basis for future research on the functions of GmAMTs and the mechanisms through which GmAMTs regulate ammonium metabolism and nodulation in soybean. Full article
(This article belongs to the Special Issue Genetics and Novel Techniques for Soybean Yield Enhancement)
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15 pages, 6958 KiB  
Article
An Efficient Agrobacterium rhizogenes-Mediated Hairy Root Transformation Method in a Soybean Root Biology Study
by Penghui Huang, Mingyang Lu, Xiangbei Li, Huiyu Sun, Zhiyuan Cheng, Yuchen Miao, Yongfu Fu and Xiaomei Zhang
Int. J. Mol. Sci. 2022, 23(20), 12261; https://doi.org/10.3390/ijms232012261 - 14 Oct 2022
Cited by 3 | Viewed by 2766
Abstract
The stable genetic transformation of soybean is time-consuming and inefficient. As a simple and practical alternative method, hairy root transformation mediated by Agrobacterium rhizogenes is widely applied in studying root-specific processes, nodulation, biochemical and molecular functions of genes of interest, gene editing efficiency [...] Read more.
The stable genetic transformation of soybean is time-consuming and inefficient. As a simple and practical alternative method, hairy root transformation mediated by Agrobacterium rhizogenes is widely applied in studying root-specific processes, nodulation, biochemical and molecular functions of genes of interest, gene editing efficiency of CRISPR/Cas9, and biological reactors and producers. Therefore, many laboratories have developed unique protocols to obtain hairy roots in composite plants composed of transgenic roots and wild-type shoots. However, these protocols still suffer from the shortcomings of low efficiency and time, space, and cost consumption. To address this issue, we developed a new protocol efficient regeneration and transformation of hairy roots (eR&T) in soybean, by integrating and optimizing the main current methods to achieve high efficiency in both hairy root regeneration and transformation within a shorter period and using less space. By this eR&T method, we obtained 100% regeneration of hairy roots for all explants, with an average 63.7% of transformation frequency, which promoted the simultaneous and comparative analysis of the function of several genes. The eR&T was experimentally verified Promoter:GUS reporters, protein subcellular localization, and CRISPR/Cas9 gene editing experiments. Employing this approach, we identified several novel potential regulators of nodulation, and nucleoporins of the Nup107-160 sub-complex, which showed development-dependent and tissue-dependent expression patterns, indicating their important roles in nodulation in soybean. Thus, the new eR&T method is an efficient and economical approach for investigating not only root and nodule biology, but also gene function. Full article
(This article belongs to the Special Issue Genetics and Novel Techniques for Soybean Yield Enhancement)
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12 pages, 2185 KiB  
Article
GsRSS3L, a Candidate Gene Underlying Soybean Resistance to Seedcoat Mottling Derived from Wild Soybean (Glycine soja Sieb. and Zucc)
by Shuang Song, Jing Wang, Xingqi Yang, Xuan Zhang, Xiuli Xin, Chunyan Liu, Jianan Zou, Xiaofei Cheng, Ning Zhang, Yuxi Hu, Jinhui Wang, Qingshan Chen and Dawei Xin
Int. J. Mol. Sci. 2022, 23(14), 7577; https://doi.org/10.3390/ijms23147577 - 8 Jul 2022
Cited by 3 | Viewed by 1922
Abstract
Soybeans are a major crop that produce the best vegetable oil and protein for use in food and beverage products worldwide. However, one of the most well-known viral infections affecting soybeans is the Soybean Mosaic Virus (SMV), a member of the Potyviridae family. [...] Read more.
Soybeans are a major crop that produce the best vegetable oil and protein for use in food and beverage products worldwide. However, one of the most well-known viral infections affecting soybeans is the Soybean Mosaic Virus (SMV), a member of the Potyviridae family. A crucial method for preventing SMV damage is the breeding of resistant soybean cultivars. Adult resistance and resistance of seedcoat mottling are two types of resistance to SMV. Most studies have focused on adult-plant resistance but not on the resistance to seedcoat mottling. In this study, chromosome segment-substituted lines derived from a cross between Suinong14 (cultivated soybean) and ZYD00006 (wild soybean) were used to identify the chromosome region and candidate genes underlying soybean resistance to seed coat mottling. Herein, two quantitative trait loci (QTLs) were found on chromosome 17, and eighteen genes were found in the QTL region. RNA-seq was used to evaluate the differentially expressed genes (DEGs) among the eighteen genes located in the QTLs. According to the obtained data, variations were observed in the expression of five genes following SMV infection. Furthermore, Nicotiana benthamiana was subjected to an Agrobacterium-mediated transient expression assay to investigate the role of the five candidate genes in SMV resistance. It has also been revealed that Glyma.17g238900 encoding a RICE SALT SENSITIVE 3-like protein (RSS3L) can inhibit the multiplication of SMV in N.benthamiana. Moreover, two nonsynonymous single-nucleotide polymorphisms (SNPs) were found in the coding sequence of Glyma.17g238900 derived from the wild soybean ZYD00006 (GsRSS3L), and the two amino acid mutants may be associated with SMV resistance. Hence, it has been suggested that GsRSS3L confers seedcoat mottling resistance, shedding light on the mechanism of soybean resistance to SMV. Full article
(This article belongs to the Special Issue Genetics and Novel Techniques for Soybean Yield Enhancement)
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13 pages, 2360 KiB  
Article
Overexpression of GmPHR1 Promotes Soybean Yield through Global Regulation of Nutrient Acquisition and Root Development
by Yanjun Li, Wenjing Ma, Kefei Zhang, Xiaoqian Wang, Ran Liu, Yingzhe Tian, Niannian Ma, Qingsong Zhao, Ruineng Xu, Yongjia Zhong and Hong Liao
Int. J. Mol. Sci. 2022, 23(23), 15274; https://doi.org/10.3390/ijms232315274 - 3 Dec 2022
Cited by 4 | Viewed by 2145
Abstract
MYB-CC transcription factors (TFs) are essential for plant growth and development. Members of the MYB-CC subfamily with long N terminal domains, such as phosphate starvation response 1 (PHR1) or PHR1-like TFs, have well documented functions, while those with short N terminal domains remain [...] Read more.
MYB-CC transcription factors (TFs) are essential for plant growth and development. Members of the MYB-CC subfamily with long N terminal domains, such as phosphate starvation response 1 (PHR1) or PHR1-like TFs, have well documented functions, while those with short N terminal domains remain less understood. In this study, we identified a nodule specific MYB-CC transcription factor 1 (GmPHR1) in soybean that is different from other canonical PHR family genes in that GmPHR1 harbors a short N terminal ahead of its MYB-CC domain and was highly induced by rhizobium infection. The overexpression of GmPHR1 dramatically increased the ratio of deformed root hairs, enhanced subsequent soybean nodulation, and promoted soybean growth in pot experiments. The growth promotion effects of GmPHR1 overexpression were further demonstrated in field trails in which two GmPHR1-OE lines yielded 10.78% and 8.19% more than the wild type line. Transcriptome analysis suggested that GmPHR1 overexpression led to global reprogramming, with 749 genes upregulated and 279 genes downregulated, especially for genes involved in MYB transcription factor activities, root growth, and nutrient acquisition. Taken together, we conclude that GmPHR1 is a key gene involved in the global regulation of nodulation, root growth, and nutrient acquisition in soybeans, and is thus a promising candidate gene to target for soybean yield enhancement. Full article
(This article belongs to the Special Issue Genetics and Novel Techniques for Soybean Yield Enhancement)
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14 pages, 2552 KiB  
Article
Identification of Genomic Regions Associated with Vine Growth and Plant Height of Soybean
by Yipeng Lu, Jiaming Zhang, Xiaoyang Guo, Jingjing Chen, Ruzhen Chang, Rongxia Guan and Lijuan Qiu
Int. J. Mol. Sci. 2022, 23(10), 5823; https://doi.org/10.3390/ijms23105823 - 22 May 2022
Cited by 3 | Viewed by 1832
Abstract
Vining growth (VG) and high plant height (PH) are the physiological traits of wild soybean that preclude their utilization for domesticated soybean breeding and improvement. To identify VG- and PH-related quantitative trait loci (QTLs) in different genetic resources, two populations of recombinant inbred [...] Read more.
Vining growth (VG) and high plant height (PH) are the physiological traits of wild soybean that preclude their utilization for domesticated soybean breeding and improvement. To identify VG- and PH-related quantitative trait loci (QTLs) in different genetic resources, two populations of recombinant inbred lines (RILs) were developed by crossing a cultivated soybean, Zhonghuang39 (ZH39), with two wild soybean accessions, NY27-38 and NY36-87. Each line from the two crosses was evaluated for VG and PH. Three QTLs for VG and three for PH, detected in the ZH39 × NY27-38 population of the RILs, co-located on chromosomes 2, 17 and 19. The VG- and PH-related QTL in the ZH39 × NY36-87 population co-located on chromosome 19. A common QTL shared by the two populations was located on chromosome 19, suggesting that this major QTL was consistently selected for in different genetic backgrounds. The results suggest that different loci are involved in the domestication or adaptations of soybean of various genetic backgrounds. The molecular markers presented here would benefit the fine mapping and cloning of candidate genes underlying the VG and PH co-localized regions and thus facilitate the utilization of wild resources in breeding by avoiding undesirable traits. Full article
(This article belongs to the Special Issue Genetics and Novel Techniques for Soybean Yield Enhancement)
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17 pages, 4547 KiB  
Article
Functional Characterization of a (E)-β-Ocimene Synthase Gene Contributing to the Defense against Spodoptera litura
by Taotao Han, Yan Shao, Ruifang Gao, Jinshan Gao, Yu Jiang, Yue Yang, Yanan Wang, Siqi Yang, Xiang Gao, Li Wang and Yueqing Li
Int. J. Mol. Sci. 2023, 24(8), 7182; https://doi.org/10.3390/ijms24087182 - 13 Apr 2023
Cited by 2 | Viewed by 2070
Abstract
Soybean is a worldwide crop that offers valuable proteins, fatty acids, and phytonutrients to humans but is always damaged by insect pests or pathogens. Plants have captured sophisticated defense mechanisms in resisting the attack of insects and pathogens. How to protect soybean in [...] Read more.
Soybean is a worldwide crop that offers valuable proteins, fatty acids, and phytonutrients to humans but is always damaged by insect pests or pathogens. Plants have captured sophisticated defense mechanisms in resisting the attack of insects and pathogens. How to protect soybean in an environment- or human-friendly way or how to develop plant-based pest control is a hotpot. Herbivore-induced plant volatiles that are released by multiple plant species have been assessed in multi-systems against various insects, of which (E)-β-ocimene has been reported to show anti-insect function in a variety of plants, including soybean. However, the responsible gene in soybean is unknown, and its mechanism of synthesis and anti-insect properties lacks comprehensive assessment. In this study, (E)-β-ocimene was confirmed to be induced by Spodoptera litura treatment. A plastidic localized monoterpene synthase gene, designated as GmOCS, was identified to be responsible for the biosynthesis of (E)-β-ocimene through genome-wide gene family screening and in vitro and in vivo assays. Results from transgenic soybean and tobacco confirmed that (E)-β-ocimene catalyzed by GmOCS had pivotal roles in repelling a S. litura attack. This study advances the understanding of (E)-β-ocimene synthesis and its function in crops, as well as provides a good candidate for further anti-insect soybean improvement. Full article
(This article belongs to the Special Issue Genetics and Novel Techniques for Soybean Yield Enhancement)
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19 pages, 6474 KiB  
Article
Identifying the Soybean microRNAs Related to Phytophthora sojae Based on RNA Sequencing and Bioinformatics Analysis
by Zhanguo Zhang, Song Jin, Huilin Tian, Zhihao Wang, Rui Jiang, Chunyan Liu, Dawei Xin, Xiaoxia Wu, Qingshan Chen and Rongsheng Zhu
Int. J. Mol. Sci. 2023, 24(10), 8546; https://doi.org/10.3390/ijms24108546 - 10 May 2023
Cited by 1 | Viewed by 1370
Abstract
Phytophthora root rot in soybeans is caused by a pathogen called Phytophthora sojae (P. sojae), which results in a significant decrease in soybean production within affected regions. MicroRNAs (miRNAs) are a class of small non-coding RNA molecules that play a key [...] Read more.
Phytophthora root rot in soybeans is caused by a pathogen called Phytophthora sojae (P. sojae), which results in a significant decrease in soybean production within affected regions. MicroRNAs (miRNAs) are a class of small non-coding RNA molecules that play a key post-transcriptional regulatory role in eukaryotes. In this paper, the miRNAs that respond to P. sojae were analyzed from the gene level to complement the study of molecular resistance mechanisms in soybean. The study utilized high-throughput sequencing of soybean data to predict miRNAs that respond to P. sojae, analyze their specific functions, and verify regulatory relationships using qRT-PCR. The results showed that the miRNAs in soybean respond to P. sojae infection. MiRNAs can be transcribed independently, suggesting the presence of transcription factor binding sites in the promoter regions. Additionally, we performed an evolutionary analysis on conserved miRNAs that respond to P. sojae. Finally, we investigated the regulatory relationships among miRNAs, genes, and transcription factors, and identified five regulatory patterns. These findings lay the groundwork for future studies on the evolution of miRNAs responsive to P. sojae. Full article
(This article belongs to the Special Issue Genetics and Novel Techniques for Soybean Yield Enhancement)
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12 pages, 4494 KiB  
Article
Novel Seed Size: A Novel Seed-Developing Gene in Glycine max
by Mingxia Zhang, Rui Dong, Penghui Huang, Mingyang Lu, Xianzhong Feng, Yongfu Fu and Xiaomei Zhang
Int. J. Mol. Sci. 2023, 24(4), 4189; https://doi.org/10.3390/ijms24044189 - 20 Feb 2023
Cited by 3 | Viewed by 1667
Abstract
Soybean-seed development is controlled in multiple ways, as in many known regulating genes. Here, we identify a novel gene, Novel Seed Size (NSS), involved in seed development, by analyzing a T-DNA mutant (S006). The S006 mutant is a random [...] Read more.
Soybean-seed development is controlled in multiple ways, as in many known regulating genes. Here, we identify a novel gene, Novel Seed Size (NSS), involved in seed development, by analyzing a T-DNA mutant (S006). The S006 mutant is a random mutant of the GmFTL4pro:GUS transgenic line, with phenotypes with small and brown seed coats. An analysis of the metabolomics and transcriptome combined with RT-qPCR in the S006 seeds revealed that the brown coat may result from the increased expression of chalcone synthase 7/8 genes, while the down-regulated expression of NSS leads to small seed size. The seed phenotypes and a microscopic observation of the seed-coat integument cells in a CRISPR/Cas9-edited mutant nss1 confirmed that the NSS gene conferred small phenotypes of the S006 seeds. As mentioned in an annotation on the Phytozome website, NSS encodes a potential DNA helicase RuvA subunit, and no such genes were previously reported to be involved in seed development. Therefore, we identify a novel gene in a new pathway controlling seed development in soybeans. Full article
(This article belongs to the Special Issue Genetics and Novel Techniques for Soybean Yield Enhancement)
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14 pages, 3993 KiB  
Article
Quantitative Trait Loci (QTL) Analysis of Seed Protein and Oil Content in Wild Soybean (Glycine soja)
by Woon Ji Kim, Byeong Hee Kang, Chang Yeok Moon, Sehee Kang, Seoyoung Shin, Sreeparna Chowdhury, Man-Soo Choi, Soo-Kwon Park, Jung-Kyung Moon and Bo-Keun Ha
Int. J. Mol. Sci. 2023, 24(4), 4077; https://doi.org/10.3390/ijms24044077 - 17 Feb 2023
Cited by 6 | Viewed by 1780
Abstract
Soybean seeds consist of approximately 40% protein and 20% oil, making them one of the world’s most important cultivated legumes. However, the levels of these compounds are negatively correlated with each other and regulated by quantitative trait loci (QTL) that are controlled by [...] Read more.
Soybean seeds consist of approximately 40% protein and 20% oil, making them one of the world’s most important cultivated legumes. However, the levels of these compounds are negatively correlated with each other and regulated by quantitative trait loci (QTL) that are controlled by several genes. In this study, a total of 190 F2 and 90 BC1F2 plants derived from a cross of Daepung (Glycine max) with GWS-1887 (G. soja, a source of high protein), were used for the QTL analysis of protein and oil content. In the F2:3 populations, the average protein and oil content was 45.52% and 11.59%, respectively. A QTL associated with protein levels was detected at Gm20_29512680 on chr. 20 with a likelihood of odds (LOD) of 9.57 and an R2 of 17.2%. A QTL associated with oil levels was also detected at Gm15_3621773 on chr. 15 (LOD: 5.80; R2: 12.2%). In the BC1F2:3 populations, the average protein and oil content was 44.25% and 12.14%, respectively. A QTL associated with both protein and oil content was detected at Gm20_27578013 on chr. 20 (LOD: 3.77 and 3.06; R2 15.8% and 10.7%, respectively). The crossover to the protein content of BC1F3:4 population was identified by SNP marker Gm20_32603292. Based on these results, two genes, Glyma.20g088000 (S-adenosyl-l-methionine-dependent methyltransferases) and Glyma.20g088400 (oxidoreductase, 2-oxoglutarate-Fe(II) oxygenase family protein), in which the amino acid sequence had changed and a stop codon was generated due to an InDel in the exon region, were identified. Full article
(This article belongs to the Special Issue Genetics and Novel Techniques for Soybean Yield Enhancement)
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26 pages, 57067 KiB  
Article
Machine-Learning-Based Genome-Wide Association Studies for Uncovering QTL Underlying Soybean Yield and Its Components
by Mohsen Yoosefzadeh-Najafabadi, Milad Eskandari, Sepideh Torabi, Davoud Torkamaneh, Dan Tulpan and Istvan Rajcan
Int. J. Mol. Sci. 2022, 23(10), 5538; https://doi.org/10.3390/ijms23105538 - 16 May 2022
Cited by 19 | Viewed by 4293
Abstract
A genome-wide association study (GWAS) is currently one of the most recommended approaches for discovering marker-trait associations (MTAs) for complex traits in plant species. Insufficient statistical power is a limiting factor, especially in narrow genetic basis species, that conventional GWAS methods are suffering [...] Read more.
A genome-wide association study (GWAS) is currently one of the most recommended approaches for discovering marker-trait associations (MTAs) for complex traits in plant species. Insufficient statistical power is a limiting factor, especially in narrow genetic basis species, that conventional GWAS methods are suffering from. Using sophisticated mathematical methods such as machine learning (ML) algorithms may address this issue and advance the implication of this valuable genetic method in applied plant-breeding programs. In this study, we evaluated the potential use of two ML algorithms, support-vector machine (SVR) and random forest (RF), in a GWAS and compared them with two conventional methods of mixed linear models (MLM) and fixed and random model circulating probability unification (FarmCPU), for identifying MTAs for soybean-yield components. In this study, important soybean-yield component traits, including the number of reproductive nodes (RNP), non-reproductive nodes (NRNP), total nodes (NP), and total pods (PP) per plant along with yield and maturity, were assessed using a panel of 227 soybean genotypes evaluated at two locations over two years (four environments). Using the SVR-mediated GWAS method, we were able to discover MTAs colocalized with previously reported quantitative trait loci (QTL) with potential causal effects on the target traits, supported by the functional annotation of candidate gene analyses. This study demonstrated the potential benefit of using sophisticated mathematical approaches, such as SVR, in a GWAS to complement conventional GWAS methods for identifying MTAs that can improve the efficiency of genomic-based soybean-breeding programs. Full article
(This article belongs to the Special Issue Genetics and Novel Techniques for Soybean Yield Enhancement)
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