Genomic Dissection in Soybean

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Crop Physiology and Crop Production".

Deadline for manuscript submissions: closed (30 November 2022) | Viewed by 6399

Special Issue Editors

Chinese Academy of Agricultural Sciences, Beijing, China
Interests: soybean biology; plant genetics and genomics; crop genetic diversity and domestication; molecular breeding; flowering and maturity
Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
Interests: genome; domestication; quantitative trait locus; flowering; agriculture; soybean
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Soybean (Glycine max (L.) Merr.) is a widely cultivated crop of global economic and ecological significance due to its high dietary oil and protein content as well as its ability to fix atmospheric nitrogen into biologically available forms. With these characteristics, soybean plays important roles in sustainable agriculture and plant-based diets. Soybean has been domesticated for thousands of years to satisfy our demand. However, further improvement of soybean production is stymied by the lack of thorough understanding of the soybean genome. With the advance in high-throughput sequencing technologies, dozens of soybean reference genomes and tons of soybean sequence data have been released. Diving into these data creates new knowledge, potentially beneficial to soybean breeding and improvement. Furthermore, genome information is also laying a foundation for precision genome editing, bringing a new era of soybean molecular breeding. This Special Issue of Plants will highlight genomic research of soybean, the dissection of the genomic basis of important soybean traits, and gene–gene and gene–environment interactions of soybean.

Dr. Bingjun Jiang
Dr. Man-Wah Li
Guest Editors

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Keywords

  • soybean
  • glycine max
  • glycine soja
  • genome
  • sequencing
  • molecular breeding
  • mapping

Published Papers (3 papers)

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Research

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13 pages, 2605 KiB  
Article
Novel QTL for Low Seed Cadmium Accumulation in Soybean
Plants 2022, 11(9), 1146; https://doi.org/10.3390/plants11091146 - 24 Apr 2022
Cited by 1 | Viewed by 1509
Abstract
Soybean is a valuable crop, used in animal feed and for human consumption. Selecting soybean cultivars with low seed cadmium (Cd) concentration is important for the purpose of minimizing the transfer of Cd into the human body. To ensure international trade, farmers need [...] Read more.
Soybean is a valuable crop, used in animal feed and for human consumption. Selecting soybean cultivars with low seed cadmium (Cd) concentration is important for the purpose of minimizing the transfer of Cd into the human body. To ensure international trade, farmers need to produce soybean that meets the European Union (EU) Cd limit of 0.2 mg kg−1. In this study, we evaluated two populations of recombinant inbred lines (RILs), X5154 and X4050, for seed Cd accumulation. Linkage maps were constructed with 325 and 280 polymorphic simple sequence repeat (SSR) markers, respectively, and used to identify a novel minor quantitative trait locus (QTL) on chromosome 13 in the X4050 population between SSR markers Satt522 and Satt218. Based on a gene ontology search within the QTL region, seven genes were identified as candidates responsible for low seed Cd accumulation, including Glyma.13G308700 and Glyma.13G309100. In addition, we confirmed the known major gene, Cda1, in the X5154 population and developed KASP and CAPS/dCAPS allele-specific markers for efficient marker-assisted breeding for Cda1. Full article
(This article belongs to the Special Issue Genomic Dissection in Soybean)
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16 pages, 5319 KiB  
Article
Comprehensive Genomic Survey, Evolution, and Expression Analysis of GIF Gene Family during the Development and Metal Ion Stress Responses in Soybean
Plants 2022, 11(4), 570; https://doi.org/10.3390/plants11040570 - 21 Feb 2022
Cited by 3 | Viewed by 1947
Abstract
The GIF gene family is one of the plant transcription factors specific to seed plants. The family members are expressed in all lateral organs produced by apical and floral meristems and contribute to the development of leaves, shoots, flowers, and seeds. This study [...] Read more.
The GIF gene family is one of the plant transcription factors specific to seed plants. The family members are expressed in all lateral organs produced by apical and floral meristems and contribute to the development of leaves, shoots, flowers, and seeds. This study identified eight GIF genes in the soybean genome and clustered them into three groups. Analyses of Ka/Ks ratios and divergence times indicated that they had undergone purifying selection during species evolution. RNA-sequence and relative expression patterns of these GmGIF genes tended to be conserved, while different expression patterns were also observed between the duplicated GIF members in soybean. Numerous cis-regulatory elements related to plant hormones, light, and stresses were found in the promoter regions of these GmGIF genes. Moreover, the expression patterns of GmGIF members were confirmed in soybean roots under cadmium (Cd) and copper (Cu) stress, indicating their potential functions in the heavy metal response in soybean. Our research provides valuable information for the functional characterization of each GmGIF gene in different legumes in the future. Full article
(This article belongs to the Special Issue Genomic Dissection in Soybean)
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Review

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13 pages, 654 KiB  
Review
Progress and Prospects of the Molecular Basis of Soybean Cold Tolerance
Plants 2023, 12(3), 459; https://doi.org/10.3390/plants12030459 - 19 Jan 2023
Cited by 3 | Viewed by 2381
Abstract
Cold stress is a major factor influencing the geographical distribution of soybean growth and causes immense losses in productivity. Understanding the molecular mechanisms that the soybean has undergone to survive cold temperatures will have immense value in improving soybean cold tolerance. This review [...] Read more.
Cold stress is a major factor influencing the geographical distribution of soybean growth and causes immense losses in productivity. Understanding the molecular mechanisms that the soybean has undergone to survive cold temperatures will have immense value in improving soybean cold tolerance. This review focuses on the molecular mechanisms involved in soybean response to cold. We summarized the recent studies on soybean cold-tolerant quantitative trait loci (QTLs), transcription factors, associated cold-regulated (COR) genes, and the regulatory pathways in response to cold stress. Cold-tolerant QTLs were found to be overlapped with the genomic region of maturity loci of E1, E3, E4, pubescence color locus of T, stem growth habit gene locus of Dt1, and leaf shape locus of Ln, indicating that pleiotropic loci may control multiple traits, including cold tolerance. The C-repeat responsive element binding factors (CBFs) are evolutionarily conserved across species. The expression of most GmDREB1s was upregulated by cold stress and overexpression of GmDREB1B;1 in soybean protoplast, and transgenic Arabidopsis plants can increase the expression of genes with the DRE core motif in their promoter regions under cold stress. Other soybean cold-responsive regulators, such as GmMYBJ1, GmNEK1, GmZF1, GmbZIP, GmTCF1a, SCOF-1 and so on, enhance cold tolerance by regulating the expression of COR genes in transgenic Arabidopsis. CBF-dependent and CBF-independent pathways are cross-talking and work together to activate cold stress gene expression. Even though it requires further dissection for precise understanding, the function of soybean cold-responsive transcription factors and associated COR genes studied in Arabidopsis shed light on the molecular mechanism of cold responses in soybeans and other crops. Furthermore, the findings may also provide practical applications for breeding cold-tolerant soybean varieties in high-latitude and high-altitude regions. Full article
(This article belongs to the Special Issue Genomic Dissection in Soybean)
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