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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 (30 June 2024) | Viewed by 15803

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Prof. Dr. Haiyan Li

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Guest Editor

College of Tropical Crops, Hainan University, Haikou, China
Interests: soybean; genetics; genomics; breeding; gene discovery; molecular breeding; biotic/abiotic stresses

Prof. Dr. Yinghui Li

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Guest Editor

The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Interests: soybean; genetics; gonomics; breeding; selection; gene discovery; evolution
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Dear Colleagues,

Soybean is the world’s most important food and feed crop and the leading source of edible oil and protein. Soybean demand will likely increase over the coming decades due to the growing world population; land scarcity, unpredictable environmental conditions, biotic and abiotic stresses, and ever-decreasing affordable inputs continually challenge soybean production. Soybean genetic improvements through modern breeding techniques are necessary to break domestication bottlenecks. Conventional breeding has contributed to the advancement of soybean varieties, and a large amount of germplasm has been generated over the last 100 years; still, it faces challenges in precise selection from ample germplasm resources. Soybean is a paleopolyploid crop and has a complex genome. Therefore, it is essential to identify significant genes, their post-transcriptional regulators, and their function for creating soybean germplasm for higher yield, quality, and biotic and abiotic stress tolerance. Currently, advanced sequencing technologies coupled with sophisticated bioinformatics analysis have facilitated genetic and genomic studies, including genome assembly, omics studies (transcriptomic, metabolomics, proteomic, and epigenetic), genome-wide association studies (GWAS), gene/QTL mapping, marker-assisted selection (MAS), genomic selection (GS), and breeding by design, which has contributed to the prediction and selection of elite breeding populations, thus fast-tracking the breeding of new soybean varieties. The release of the high-quality complete reference soybean genome has significantly facilitated advances in soybean functional genomics. Similarly, genetically engineered soybean plants could result in the introgression desirable new alleles into soybean breeding programs. This Special Issue on the “Germplasm Resources and Molecular Breeding of Soybean” welcomes original research and review papers on fundamental and applied research highlighting all aspects of the genetics, breeding, GWA-study, biotechnology, evolutionary elements, genome editing, epigenetics, germplasm improvement, and any new technology or theories which can improve soybean flowering, maturity, architecture, yield, quality, and tolerance to biotic and abiotic stresses.

Prof. Dr. Haiyan Li
Prof. Dr. Yinghui Li
Guest Editors

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Keywords

soybean
genetics
epigenetics
genomics
breeding
germplasm
breeding methods
gene discovery
evolution
GWA-study
QTL mapping
biotic/abiotic stresses

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Published Papers (11 papers)

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15 pages, 2906 KiB

Open AccessArticle

Genome-Wide Association Analysis of Yield-Related Traits and Candidate Genes in Vegetable Soybean

by Hongtao Gao, Guanji Wu, Feifei Wu, Xunjun Zhou, Yonggang Zhou, Keheng Xu, Yaxin Li, Wenping Zhang, Kuan Zhao, Yan Jing, Chen Feng, Nan Wang and Haiyan Li

Plants 2024, 13(11), 1442; https://doi.org/10.3390/plants13111442 - 23 May 2024

Viewed by 1290

Abstract

Owing to the rising demand for vegetable soybean products, there is an increasing need for high-yield soybean varieties. However, the complex correlation patterns among quantitative traits with genetic architecture pose a challenge for improving vegetable soybean through breeding. Herein, a genome-wide association study (GWAS) was applied to 6 yield-related traits in 188 vegetable soybean accessions. Using a BLINK model, a total of 116 single nucleotide polymorphisms (SNPs) were identified for plant height, pod length, pod number, pod thickness, pod width, and fresh pod weight. Furthermore, a total of 220 genes were found in the 200 kb upstream and downstream regions of significant SNPs, including 11 genes encoding functional proteins. Among them, four candidate genes, Glyma.13G109100, Glyma.03G183200, Glyma.09G102200, and Glyma.09G102300 were analyzed for significant haplotype variations and to be in LD block, which encode MYB-related transcription factor, auxin-responsive protein, F-box protein, and CYP450, respectively. The relative expression of candidate genes in V030 and V071 vegetable soybean (for the plant height, pod number, and fresh pod weight of V030 were lower than those of the V071 strains) was significantly different, and these genes could be involved in plant growth and development via various pathways. Altogether, we identified four candidate genes for pod yield and plant height from vegetable soybean germplasm. This study provides insights into the genomic basis for improving soybean and crucial genomic resources that can facilitate genome-assisted high-yielding vegetable soybean breeding. Full article

(This article belongs to the Special Issue Germplasm Resources and Molecular Breeding of Soybean)

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14 pages, 2497 KiB

Open AccessArticle

GWAS and WGCNA Analysis Uncover Candidate Genes Associated with Oil Content in Soybean

by Xunchao Zhao, Yan Zhang, Jie Wang, Xue Zhao, Yongguang Li, Weili Teng, Yingpeng Han and Yuhang Zhan

Plants 2024, 13(10), 1351; https://doi.org/10.3390/plants13101351 - 14 May 2024

Cited by 3 | Viewed by 1509

Abstract

Soybean vegetable oil is an important source of the human diet. However, the analysis of the genetic mechanism leading to changes in soybean oil content is still incomplete. In this study, a total of 227 soybean materials were applied and analyzed by a genome-wide association study (GWAS). There are 44 quantitative trait nucleotides (QTNs) that were identified as associated with oil content. A total of six, four, and 34 significant QTN loci were identified in Xiangyang, Hulan, and Acheng, respectively. Of those, 26 QTNs overlapped with or were near the known oil content quantitative trait locus (QTL), and 18 new QTNs related to oil content were identified. A total of 594 genes were located near the peak single nucleotide polymorphism (SNP) from three tested environments. These candidate genes exhibited significant enrichment in tropane, piperidine, and pyridine alkaloid biosynthesiss (ko00960), ABC transporters (ko02010), photosynthesis-antenna proteins (ko00196), and betalain biosynthesis (ko00965). Combined with the GWAS and weighted gene co-expression network analysis (WGCNA), four candidate genes (Glyma.18G300100, Glyma.11G221100, Glyma.13G343300, and Glyma.02G166100) that may regulate oil content were identified. In addition, Glyma.18G300100 was divided into two main haplotypes in the studied accessions. The oil content of haplotype 1 is significantly lower than that of haplotype 2. Our research findings provide a theoretical basis for improving the regulatory mechanism of soybean oil content. Full article

(This article belongs to the Special Issue Germplasm Resources and Molecular Breeding of Soybean)

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21 pages, 1852 KiB

Open AccessArticle

Ability of Genomic Prediction to Bi-Parent-Derived Breeding Population Using Public Data for Soybean Oil and Protein Content

by Chenhui Li, Qing Yang, Bingqiang Liu, Xiaolei Shi, Zhi Liu, Chunyan Yang, Tao Wang, Fuming Xiao, Mengchen Zhang, Ainong Shi and Long Yan

Plants 2024, 13(9), 1260; https://doi.org/10.3390/plants13091260 - 30 Apr 2024

Viewed by 1534

Abstract

Genomic selection (GS) is a marker-based selection method used to improve the genetic gain of quantitative traits in plant breeding. A large number of breeding datasets are available in the soybean database, and the application of these public datasets in GS will improve breeding efficiency and reduce time and cost. However, the most important problem to be solved is how to improve the ability of across-population prediction. The objectives of this study were to perform genomic prediction (GP) and estimate the prediction ability (PA) for seed oil and protein contents in soybean using available public datasets to predict breeding populations in current, ongoing breeding programs. In this study, six public datasets of USDA GRIN soybean germplasm accessions with available phenotypic data of seed oil and protein contents from different experimental populations and their genotypic data of single-nucleotide polymorphisms (SNPs) were used to perform GP and to predict a bi-parent-derived breeding population in our experiment. The average PA was 0.55 and 0.50 for seed oil and protein contents within the bi-parents population according to the within-population prediction; and 0.45 for oil and 0.39 for protein content when the six USDA populations were combined and employed as training sets to predict the bi-parent-derived population. The results showed that four USDA-cultivated populations can be used as a training set individually or combined to predict oil and protein contents in GS when using 800 or more USDA germplasm accessions as a training set. The smaller the genetic distance between training population and testing population, the higher the PA. The PA increased as the population size increased. In across-population prediction, no significant difference was observed in PA for oil and protein content among different models. The PA increased as the SNP number increased until a marker set consisted of 10,000 SNPs. This study provides reasonable suggestions and methods for breeders to utilize public datasets for GS. It will aid breeders in developing GS-assisted breeding strategies to develop elite soybean cultivars with high oil and protein contents. Full article

(This article belongs to the Special Issue Germplasm Resources and Molecular Breeding of Soybean)

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14 pages, 2383 KiB

Open AccessArticle

Integrating Genome-Wide Association Study, Transcriptome and Metabolome Reveal Novel QTL and Candidate Genes That Control Protein Content in Soybean

by Xunchao Zhao, Hanhan Zhu, Fang Liu, Jie Wang, Changjun Zhou, Ming Yuan, Xue Zhao, Yongguang Li, Weili Teng, Yingpeng Han and Yuhang Zhan

Plants 2024, 13(8), 1128; https://doi.org/10.3390/plants13081128 - 17 Apr 2024

Cited by 1 | Viewed by 1436

Abstract

Protein content (PC) is crucial to the nutritional quality of soybean [Glycine max (L.) Merrill]. In this study, a total of 266 accessions were used to perform a genome-wide association study (GWAS) in three tested environments. A total of 23,131 high-quality SNP markers (MAF ≥ 0.02, missing data ≤ 10%) were identified. A total of 40 association signals were significantly associated with PC. Among them, five novel quantitative trait nucleotides (QTNs) were discovered, and another 32 QTNs were found to be overlapping with the genomic regions of known quantitative trait loci (QTL) related to soybean PC. Combined with GWAS, metabolome and transcriptome sequencing, 59 differentially expressed genes (DEGs) that might control the change in protein content were identified. Meantime, four commonly upregulated differentially abundant metabolites (DAMs) and 29 commonly downregulated DAMs were found. Remarkably, the soybean gene Glyma.08G136900, which is homologous with Arabidopsis hydroxyproline-rich glycoproteins (HRGPs), may play an important role in improving the PC. Additionally, Glyma.08G136900 was divided into two main haplotype in the tested accessions. The PC of haplotype 1 was significantly lower than that of haplotype 2. The results of this study provided insights into the genetic mechanisms regulating protein content in soybean. Full article

(This article belongs to the Special Issue Germplasm Resources and Molecular Breeding of Soybean)

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18 pages, 4675 KiB

Open AccessArticle

Integrated Transcriptomic and Proteomic Characterization of a Chromosome Segment Substitution Line Reveals the Regulatory Mechanism Controlling the Seed Weight in Soybean

by Siming Wei, Zhenhai Yu, Fangfang Du, Fubin Cao, Mingliang Yang, Chunyan Liu, Zhaoming Qi, Qingshan Chen, Jianan Zou and Jinhui Wang

Plants 2024, 13(6), 908; https://doi.org/10.3390/plants13060908 - 21 Mar 2024

Viewed by 1260

Abstract

Soybean is the major global source of edible oils and vegetable proteins. Seed size and weight are crucial traits determining the soybean yield. Understanding the molecular regulatory mechanism underlying the seed weight and size is helpful for improving soybean genetic breeding. The molecular regulatory pathways controlling the seed weight and size were investigated in this study. The 100-seed weight, seed length, seed width, and seed weight per plant of a chromosome segment substitution line (CSSL) R217 increased compared with those of its recurrent parent ‘Suinong14’ (SN14). Transcriptomic and proteomic analyses of R217 and SN14 were performed at the seed developmental stages S15 and S20. In total, 2643 differentially expressed genes (DEGs) and 208 differentially accumulated proteins (DAPs) were detected at S15, and 1943 DEGs and 1248 DAPs were detected at S20. Furthermore, integrated transcriptomic and proteomic analyses revealed that mitogen-activated protein kinase signaling and cell wall biosynthesis and modification were potential pathways associated with seed weight and size control. Finally, 59 candidate genes that might control seed weight and size were identified. Among them, 25 genes were located on the substituted segments of R217. Two critical pathways controlling seed weight were uncovered in our work. These findings provided new insights into the seed weight-related regulatory network in soybean. Full article

(This article belongs to the Special Issue Germplasm Resources and Molecular Breeding of Soybean)

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20 pages, 3403 KiB

Open AccessArticle

Genome-Wide Association Studies Prioritize Genes Controlling Seed Size and Reproductive Period Length in Soybean

by Le Wang, Fu’an Niu, Jinshe Wang, Hengyou Zhang, Dan Zhang and Zhenbin Hu

Plants 2024, 13(5), 615; https://doi.org/10.3390/plants13050615 - 23 Feb 2024

Cited by 1 | Viewed by 1872

Abstract

Hundred-seed weight (HSW) and reproductive period length (RPL) are two major agronomic traits critical for soybean production and adaptation. However, both traits are quantitatively controlled by multiple genes that have yet to be comprehensively elucidated due to the lack of major genes; thereby, the genetic basis is largely unknown. In the present study, we conducted comprehensive genome-wide association analyses (GWAS) of HSW and RPL with multiple sets of accessions that were phenotyped across different environments. The large-scale analysis led to the identification of sixty-one and seventy-four significant QTLs for HSW and RPL, respectively. An ortholog-based search analysis prioritized the most promising candidate genes for the QTLs, including nine genes (TTG2, BZR1, BRI1, ANT, KLU, EOD1/BB, GPA1, ABA2, and ABI5) for HSW QTLs and nine genes (such as AGL8, AGL9, TOC1, and COL4) and six known soybean flowering time genes (E2, E3, E4, Tof11, Tof12, and FT2b) for RPL QTLs. We also demonstrated that some QTLs were targeted during domestication to drive the artificial selection of both traits towards human-favored traits. Local adaptation likely contributes to the increased genomic diversity of the QTLs underlying RPL. The results provide additional insight into the genetic basis of HSW and RPL and prioritize a valuable resource of candidate genes that merits further investigation to reveal the complex molecular mechanism and facilitate soybean improvement. Full article

(This article belongs to the Special Issue Germplasm Resources and Molecular Breeding of Soybean)

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10 pages, 2434 KiB

Open AccessArticle

Genetic and Phenotypic Characterization of Soybean Landraces Collected from the Zhejiang Province in China

by Xiaomin Yu, Xujun Fu, Qinghua Yang, Hangxia Jin, Longming Zhu and Fengjie Yuan

Plants 2024, 13(3), 353; https://doi.org/10.3390/plants13030353 - 25 Jan 2024

Cited by 1 | Viewed by 1452

Abstract

The soybean is an important feed, industrial raw material, and food crop in the world due to its rich components. There is a long history of soybean cultivation with different types and rich resources in the Zhejiang province of China. It is important to understand genetic diversity as well as phenotypic variation for soybean breeding. The objective of this study was to analyze both genetic and phenotypic characteristics of the 78 soybean landraces collected, and to explore a potential advantage of germplasm resources for further application. These 78 autumn-type soybean landraces have been propagated, identified, and evaluated in both 2021 and 2022. There were agronomic, quality, and genetic variations according to the comprehensive analyses. There was a good consistency between seed size and seed coat color. There were significant differences of seed protein, fat, and sugar contents based upon the seed coat color. These soybean landraces were genotyped using 42 simple sequence repeat markers and then clustered into two groups. The two groups had a consistency with the seed coat color. This study gave us a combined understanding of both the phenotypic variation and the genetic diversity of the soybean landraces. Therefore, the reasonable crossing between different soybean types is highly recommended. Full article

(This article belongs to the Special Issue Germplasm Resources and Molecular Breeding of Soybean)

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18 pages, 3351 KiB

Open AccessArticle

Transcriptome Profiling of a Soybean Mutant with Salt Tolerance Induced by Gamma-ray Irradiation

by Byeong Hee Kang, Sreeparna Chowdhury, Se-Hee Kang, Seo-Young Shin, Won-Ho Lee, Hyeon-Seok Lee and Bo-Keun Ha

Plants 2024, 13(2), 254; https://doi.org/10.3390/plants13020254 - 16 Jan 2024

Viewed by 1686

Abstract

Salt stress is a significant abiotic stress that reduces crop yield and quality globally. In this study, we utilized RNA sequencing (RNA-Seq) to identify differentially expressed genes (DEGs) in response to salt stress induced by gamma-ray irradiation in a salt-tolerant soybean mutant. The total RNA library samples were obtained from the salt-sensitive soybean cultivar Kwangan and the salt-tolerant mutant KA-1285. Samples were taken at three time points (0, 24, and 72 h) from two tissues (leaves and roots) under 200 mM NaCl. A total of 967,719,358 clean reads were generated using the Illumina NovaSeq 6000 platform, and 94.48% of these reads were mapped to 56,044 gene models of the soybean reference genome (Glycine_max_Wm82.a2.v1). The DEGs with expression values were compared at each time point within each tissue between the two soybeans. As a result, 296 DEGs were identified in the leaves, while 170 DEGs were identified in the roots. In the case of the leaves, eight DEGs were related to the phenylpropanoid biosynthesis pathway; however, in the roots, Glyma.03G171700 within GmSalt3, a major QTL associated with salt tolerance in soybean plants, was differentially expressed. Overall, these differences may explain the mechanisms through which mutants exhibit enhanced tolerance to salt stress, and they may provide a basic understanding of salt tolerance in soybean plants. Full article

(This article belongs to the Special Issue Germplasm Resources and Molecular Breeding of Soybean)

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15 pages, 4571 KiB

Open AccessArticle

No Pairwise Interactions of GmSNAP18, GmSHMT08 and AtPR1 with Suppressed AtPR1 Expression Enhance the Susceptibility of Arabidopsis to Beet Cyst Nematode

by Liuping Zhang, Jie Zhao, Lingan Kong, Wenkun Huang, Huan Peng, Deliang Peng, Khalid Meksem and Shiming Liu

Plants 2023, 12(24), 4118; https://doi.org/10.3390/plants12244118 - 9 Dec 2023

Viewed by 1086

Abstract

GmSNAP18 and GmSHMT08 are two major genes conferring soybean cyst nematode (SCN) resistance in soybean. Overexpression of either of these two soybean genes would enhance the susceptibility of Arabidopsis to beet cyst nematode (BCN), while overexpression of either of their corresponding orthologs in Arabidopsis, AtSNAP2 and AtSHMT4, would suppress it. However, the mechanism by which these two pairs of orthologous genes boost or inhibit BCN susceptibility of Arabidopsis still remains elusive. In this study, Arabidopsis with simultaneously overexpressed GmSNAP18 and GmSHMT0 suppressed the growth of underground as well as above-ground parts of plants. Furthermore, Arabidopsis that simultaneously overexpressed GmSNAP18 and GmSHMT08 substantially stimulated BCN susceptibility and remarkably suppressed expression of AtPR1 in the salicylic acid signaling pathway. However, simultaneous overexpression of GmSNAP18 and GmSHMT08 did not impact the expression of AtJAR1 and AtHEL1 in the jasmonic acid and ethylene signaling pathways. GmSNAP18, GmSHMT08, and a pathogenesis-related (PR) protein, GmPR08-Bet VI, in soybean, and AtSNAP2, AtSHMT4, and AtPR1 in Arabidopsis could interact pair-wisely for mediating SCN and BCN resistance in soybean and Arabidopsis, respectively. Both AtSNAP2 and AtPR1 were localized on the plasma membrane, and AtSHMT4 was localized both on the plasma membrane and in the nucleus of cells. Nevertheless, after interactions, AtSNAP2 and AtPR1 could partially translocate into the cell nucleus. GmSNAP18 interacted with AtSHMT4, and GmSHMT4 interacted with AtSNAP2. However, neither GmSNAP18 nor GmSHMT08 interacted with AtPR1. Thus, no pairwise interactions among α-SNAPs, SHMTs, and AtPR1 occurred in Arabidopsis overexpressing either GmSNAP18 or GmSHMT08, or both of them. Transgenic Arabidopsis overexpressing either GmSNAP18 or GmSHMT08 substantially suppressed AtPR1 expression, while transgenic Arabidopsis overexpressing either AtSNAP2 or AtSHMT4 remarkably enhanced it. Taken together, no pairwise interactions of GmSNAP18, GmSHMT08, and AtPR1 with suppressed expression of AtPR1 enhanced BCN susceptibility in Arabidopsis. This study may provide a clue that nematode-resistant or -susceptible functions of plant genes likely depend on both hosts and nematode species. Full article

(This article belongs to the Special Issue Germplasm Resources and Molecular Breeding of Soybean)

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15 pages, 2282 KiB

Open AccessArticle

The Assessment of Natural Cross Pollination Properties of a Novel Male-Sterile–Female-Fertile Mutation ms_LC01 in Soybean

by Wen Wang, Xiaojie Zhu, Yu Zhang, Huawei Gao, Zeru Zhang, Chunyan Yang, Yuhong Zheng, Qianqian Yu, Yixin Zhu, Yating Geng, Shulei Wang and Like Liu

Plants 2023, 12(20), 3538; https://doi.org/10.3390/plants12203538 - 11 Oct 2023

Viewed by 1096

Abstract

The value of a novel soybean male-sterile mutation ms_LC01 in breeding practice was determined by its outcrossing properties. Then, the effects of different planting arrangements on the pod set characteristics of male-sterile plants were assessed by using orthogonal experiments at two sites. At the same time, the effects of ms_LC01 male sterility on other traits were assessed in two C₂F₂ populations. In addition, the nectar secretion and natural outcross of male-sterile plants from four ms_LC01 lines were compared with one ms1 line and one ms6 line. The results of the orthogonal experiment showed that the pod numbers and pod set rates of male-sterile plants were decisively different between the two experimental sites but not between the two levels of the other factors. Both increasing the ratio of paternal parent to maternal parent and planting the parental seeds in a mixed way, the proportion of seeds pollinated by the target parent pollen could be increased. Except for the pod number per plant trait, there was no significant difference between male-sterile plants and their fertile siblings. The amount of nectar significantly differed among the lines. Compared with ms1 and ms6 male-sterile plants, the four ms_LC01 lines possessed significantly more or similar numbers of pod sets. The results of this study lay a foundation for the future use of this mutant in soybean breeding. Full article

(This article belongs to the Special Issue Germplasm Resources and Molecular Breeding of Soybean)

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6 pages, 589 KiB

Open AccessBrief Report

GmHs1-1 and GmqHS1 Simultaneously Contribute to the Domestication of Soybean Hard-Seededness

by Huifang Yan, Daicai Tian, Qian Zhang, Jiangqi Wen, Zeng-Yu Wang and Maofeng Chai

Plants 2024, 13(15), 2061; https://doi.org/10.3390/plants13152061 - 26 Jul 2024

Viewed by 656

Abstract

Seed physical dormancy (hard-seededness) is an interesting ecological phenomenon and important agronomic trait. The loss of seed coat impermeability/hard-seededness is a key target trait during the domestication of leguminous crops which allows seeds to germinate rapidly and uniformly. In this study, we examined the mutation of quantitative trait locus (QTL) genes, GmHs1-1 and GmqHS1, in 18 wild soybean (G. soja) and 23 cultivated soybean (G. max) accessions. The sequencing results indicate that a G-to-T substitution in GmqHS1 and a C-to-T substitution in GmHs1-1 occurred in all 23 cultivated soybean accessions but not in any of the 18 wild soybean accessions. The mutations in the two genes led to increased seed coat permeability in cultivated soybean. Therefore, we provide evidence that two genes, GmHs1-1 and GmqHS1, simultaneously contribute to the domestication of hard-seededness in soybeans. This finding is of great significance for genetic analysis and improved utilization of the soybean hard-seededness trait. Full article

(This article belongs to the Special Issue Germplasm Resources and Molecular Breeding of Soybean)

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