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Plants
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Germplasm Resources and Soybean Breeding II
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Germplasm Resources and Soybean Breeding II

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 (20 May 2023) | Viewed by 4942

Special Issue Editors

Prof. Dr. Tuanjie Zhao

E-Mail Website
Guest Editor
College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
Interests: plant genetic resources and diversity; molecular breeding; adaptation to abiotic stress
Special Issues, Collections and Topics in MDPI journals
Dr. Benjamin Karikari

E-Mail Website
Guest Editor
Department of Crop Science, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, P. O. Box TL, Tamale 1882, Ghana
Interests: germplasm characterisation and utilization; crop improvement; crop genetics and breeding
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Soybean germplasm resources include new varieties/breeding lines, genetic stocks, ancient landraces, and wild species of the Glycine genus, and their genetic variation is the material basis for trait improvement and variety development. In the past decades, great advances in germplasm research at both population and individual levels have been achieved along with the availability of the soybean genome sequence and other new techniques, and more inputs are necessary to enhance the basic and applied research on soybean genetic resources. This Special Issue of Plants will cover various aspects of soybean germplasm studies: (1) collection, preservation, and utilization of soybean germplasm; (2) evaluation and broadening of genetic diversity; (3) characterization of elite germplasm with ideal target traits; (4) gene identification and allele mining for molecular breeding; and (5) new techniques and their utilization in germplasm enhancement and variety development.

Prof. Dr. Tuanjie Zhao
Dr. Benjamin Karikari
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

  • soybean
  • genetic diversity
  • molecular marker
  • gene function
  • germplasm enhancement

Published Papers (3 papers)

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Research

22 pages, 6977 KiB  
Article
Genetic Dissection of Extreme Seed-Flooding Tolerance in a Wild Soybean PI342618B by Linkage Mapping and Candidate Gene Analysis
by Zhe-Ping Yu, Wen-Huan Lv, Ripa Akter Sharmin, Jie-Jie Kong and Tuan-Jie Zhao
Plants 2023, 12(12), 2266; https://doi.org/10.3390/plants12122266 - 10 Jun 2023
Cited by 2 | Viewed by 1063
Abstract
Seed-flooding stress is one of major abiotic constraints that adversely affects soybean production worldwide. Identifying tolerant germplasms and revealing the genetic basis of seed-flooding tolerance are imperative goals for soybean breeding. In the present study, high-density linkage maps of two inter-specific recombinant inbred [...] Read more.
Seed-flooding stress is one of major abiotic constraints that adversely affects soybean production worldwide. Identifying tolerant germplasms and revealing the genetic basis of seed-flooding tolerance are imperative goals for soybean breeding. In the present study, high-density linkage maps of two inter-specific recombinant inbred line (RIL) populations, named NJIRNP and NJIR4P, were utilized to identify major quantitative trait loci (QTLs) for seed-flooding tolerance using three parameters viz., germination rate (GR), normal seedling rate (NSR), and electrical conductivity (EC). A total of 25 and 18 QTLs were detected by composite interval mapping (CIM) and mixed-model-based composite interval mapping (MCIM), respectively, and 12 common QTLs were identified through both methods. All favorable alleles for the tolerance are notably from the wild soybean parent. Moreover, four digenic epistatic QTL pairs were identified, and three of them showed no main effects. In addition, the pigmented soybean genotypes exhibited high seed-flooding tolerance compared with yellow seed coat genotypes in both populations. Moreover, out of five identified QTLs, one major region containing multiple QTLs associated with all three traits was identified on Chromosome 8, and most of the QTLs within this hotspot were major loci (R2 > 10) and detectable in both populations and multiple environments. Based on the gene expression and functional annotation information, 10 candidate genes from QTL “hotspot 8-2” were screened for further analysis. Furthermore, the results of qRT-PCR and sequence analysis revealed that only one gene, GmDREB2 (Glyma.08G137600), was significantly induced under flooding stress and displayed a TTC tribasic insertion mutation of the nucleotide sequence in the tolerant wild parent (PI342618B). GmDREB2 encodes an ERF transcription factor, and the subcellular localization analysis using green fluorescent protein (GFP) revealed that GmDREB2 protein was localized in the nucleus and plasma membrane. Furthermore, overexpression of GmDREB2 significantly promoted the growth of soybean hairy roots, which might indicate its critical role in seed-flooding stress. Thus, GmDREB2 was considered as the most possible candidate gene for seed-flooding tolerance. Full article
(This article belongs to the Special Issue Germplasm Resources and Soybean Breeding II)
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15 pages, 7469 KiB  
Article
Genetic Diversity and Population Structure of European Soybean Germplasm Revealed by Single Nucleotide Polymorphism
by Zoe Andrijanić, Nelson Nazzicari, Hrvoje Šarčević, Aleksandra Sudarić, Paolo Annicchiarico and Ivan Pejić
Plants 2023, 12(9), 1837; https://doi.org/10.3390/plants12091837 - 29 Apr 2023
Cited by 2 | Viewed by 1248
Abstract
Soybean is the most grown high-protein crop in the world. Despite the rapid increase of acreage and production volume, European soybean production accounts for only 34% of its consumption in Europe. This study aims to support the optimal exploitation of genetic resources by [...] Read more.
Soybean is the most grown high-protein crop in the world. Despite the rapid increase of acreage and production volume, European soybean production accounts for only 34% of its consumption in Europe. This study aims to support the optimal exploitation of genetic resources by European breeding programs by investigating the genetic diversity and the genetic structure of 207 European cultivars or American introductions registered in Europe, which were genotyped by the SoySNP50K array. The expected heterozygosity (He) was 0.34 for the entire collection and ranged among countries from 0.24 for Swiss cultivars to 0.32 for American cultivars (partly reflecting differences in sample size between countries). Cluster analysis grouped all genotypes into two main clusters with eight subgroups that corresponded to the country of origin of cultivars and their maturity group. Pairwise Fst values between countries of origin showed the highest differentiation of Swiss cultivars from the rest of the European gene pool, while the lowest mean differentiation was found between American introductions and all other European countries. On the other hand, Fst values between maturity groups were much lower compared to those observed between countries. In analysis of molecular variance, the total genetic variation was partitioned either by country of origin or by maturity group, explaining 9.1% and 3.5% of the total genetic variance, respectively. On the whole, our results suggest that the European soybean gene pool still has sufficient diversity due to the different historical breeding practices in western and eastern countries and the relatively short period of breeding in Europe. Full article
(This article belongs to the Special Issue Germplasm Resources and Soybean Breeding II)
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20 pages, 7708 KiB  
Article
Identification of Genomic Loci and Candidate Genes Related to Seed Tocopherol Content in Soybean
by Suprio Ghosh, Shengrui Zhang, Muhammad Azam, Kwadwo Gyapong Agyenim-Boateng, Jie Qi, Yue Feng, Yecheng Li, Jing Li, Bin Li and Junming Sun
Plants 2022, 11(13), 1703; https://doi.org/10.3390/plants11131703 - 27 Jun 2022
Cited by 3 | Viewed by 1995
Abstract
Soybean seeds are primary sources of natural tocopherols used by the food and pharmaceutical industries, owing to their beneficial impacts on human health. Selection for higher tocopherol contents in seeds along with other desirable traits is an important goal in soybean breeding. In [...] Read more.
Soybean seeds are primary sources of natural tocopherols used by the food and pharmaceutical industries, owing to their beneficial impacts on human health. Selection for higher tocopherol contents in seeds along with other desirable traits is an important goal in soybean breeding. In order to identify the genomic loci and candidate genes controlling tocopherol content in soybean seeds, the bulked-segregant analysis technique was performed using a natural population of soybean consisting of 1525 accessions. We constructed the bulked-segregant analysis based on 98 soybean accessions that showed extreme phenotypic variation for the target trait, consisting of 49 accessions with extremely-high and 49 accessions with extremely-low tocopherol content. A total of 144 variant sites and 109 predicted genes related to tocopherol content were identified, in which a total of 83 genes were annotated by the gene ontology functions. Furthermore, 13 enriched terms (p < 0.05) were detected, with four of them found to be highly enriched: response to lipid, response to abscisic acid, transition metal ion transmembrane transporter activity, and double-stranded DNA binding. Especially, six candidate genes were detected at 41.8–41.9 Mb genomic hotspots on chromosome 5 based on ANNOtate VARiation analysis. Among the genes, only Glyma.05G243400 carried a non-synonymous mutation that encodes a “translation elongation factor EF1A or initiation factor IF2gamma family protein” was identified. The haplotype analysis confirmed that Glyma.05G243400 exhibited highly significant variations in terms of tocopherol content across multiple experimental locations, suggesting that it can be the key candidate gene regulating soybean seed tocopherols. The present findings provide novel gene resources related to seed tocopherols for further validation by genome editing, functional characterization, and genetic improvement targeting enhanced tocopherol composition in soybean molecular breeding. Full article
(This article belongs to the Special Issue Germplasm Resources and Soybean Breeding II)
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