Frontier Studies in Legumes Genetic Breeding and Production

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 June 2023) | Viewed by 27107

Special Issue Editors


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Guest Editor
National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing 210095, China
Interests: soybean germplasm resources; insect-resistant breeding
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
Interests: cloning and molecular mechanism of genes related to photoperiod response and plant architecture in soybean

E-Mail Website
Guest Editor
National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China
Interests: symbiosis; soybean; type III effector; genetic population
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Legumes are an important part of a sustainable farming system due to their wide use for food and feed purposes and their beneficial effect on the soil environment. To secure the food supply and meet people's increasing consumption demand, production problems have risen and have attracted the attention of researchers. The issue of how to breed novel and excellent cultivars and varieties to improve legumes’ yield, quality, and adaptation to the environment urgently needs to be addressed.

Remarkable progress has been made by scientists in the field of legume genetics, genomics, molecular biology, breeding, and biotechnology. A significant number of cultivars developed by cross breeding, genomic resources generated from whole genome sequencing, and the identification of agronomically important traits, as well as the characterization of the global legume germplasm, are in progress. However, much work is still required to dissect genes’ functions, signaling networks, and regulation mechanisms in order to stimulate the development of breeding technology for the improvement of the agronomic traits of legumes. Genomics, transcriptomics, proteomics, phenomics, and metabolomics technology have been applied to determine gene functions. However, their use in legume breeding and modification has been limited and there is huge space for further development and improvement of breeding, biological function detection, and technological application. Moreover, the mechanisms of symbiosis and the specific traits of legume crops are still largely unclear. We expect that molecular breeding approaches will be more extensively studied and used in legumes’ genetic improvement.

This Special Issue will cover basic and application-oriented studies that support and facilitate legume genetics and breeding research. Both research articles and review articles are welcome. Potential topics include, but are not limited to, the following:

  • QTL mapping and marker-assisted selection;
  • GWAS and genomic selection/prediction;
  • Molecular breeding by design;
  • Genotype × environment interaction;
  • Breeding for tolerance to abiotic and biotic stresses;
  • Nitrogen efficiency modification;
  • Symbiosis mechanism detection;
  • Varietal and agrotechnical progress;
  • Dissection of key genes regulating yield-related traits;
  • Production in various farming systems;
  • Seed quality and nutritional and fodder value;
  • Food and feed safety;
  • Crop profitability and economic aspects.

Dr. Guangnan Xing
Dr. Hong Zhai
Prof. Dr. Dawei Xin
Guest Editors

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Keywords

  • soybean
  • legumes genetics
  • genome
  • sequencing
  • mapping
  • genetic diversity
  • molecular marker
  • biotic and abiotic stress
  • seed production
  • nitrogen fixation
  • fodder value
  • food and feed safety
  • profitability of legumes cultivation

Published Papers (14 papers)

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Research

15 pages, 1816 KiB  
Article
Assessment of Yield Stability of Bambara Groundnut (Vigna subterranea (L.) Verdc.) Using Genotype and Genotype–Environment Interaction Biplot Analysis
by Rita Adaeze Linus, Oluwaseyi Samuel Olanrewaju, Olaniyi Oyatomi, Emmanuel Ohiosinmuan Idehen and Michael Abberton
Agronomy 2023, 13(10), 2558; https://doi.org/10.3390/agronomy13102558 - 4 Oct 2023
Cited by 5 | Viewed by 1356
Abstract
Biplot analysis has emerged as a crucial statistical method in plant breeding and agricultural research. The objective of this research was to identify the best-performing genotype(s) for the environments in three distinct regions of Nigeria while also examining the characteristics and magnitude of [...] Read more.
Biplot analysis has emerged as a crucial statistical method in plant breeding and agricultural research. The objective of this research was to identify the best-performing genotype(s) for the environments in three distinct regions of Nigeria while also examining the characteristics and magnitude of genotype–environment interaction (GEI) effects on the yield of Bambara groundnut (BGN). The study was conducted in Ibadan, Ikenne, and Mokwa, utilizing a sample of 30 accessions. The yield of BGN was found to be significantly affected by accessions, environment, and their interaction through a combined analysis of variance, with a p-value < 0.001. Biplots were utilized to demonstrate the pattern of interaction components, specifically the genotype’s main effect and genotype–environment interaction (GEI). The initial two principal components elucidated the complete variance of the GGE model, encompassing both genetic and genotype-by-environment interaction effects (PC1 = 87.81%, PC2 = 12.19%). The accessions that exhibited superior performance in each respective environment, as determined by the “which-won-where” polygon, were identified as TVSu-2223, TVSu-2236, TVSu-2240, and TVSu-2249 in Mokwa; TVSu-2214 in Ikenne; and TVSu-2188 in Ibadan. The accessions TVSu-2207 and TVSu-2199 exhibited stability in all environments, whereas the accessions TVSu-2226, TVSu-2249, TVSu-2209, TVSu-2184, TVSu-2204, and TVSu-2236 demonstrated adaptability. In addition, the accessions TVSu-2240 and TVSu-2283 were stable and adaptable in all environments. The accessions that were chosen have been suggested as suitable parental lines for breeding programs aimed at enhancing grain yield in the agro-ecological zones that were evaluated. This study’s findings identify BGN accessions with adaptability and stability across selected environments in Nigeria, suggesting specific accessions that can serve as suitable parental lines in breeding programs to enhance grain yield, thereby holding promise for improving food security. Full article
(This article belongs to the Special Issue Frontier Studies in Legumes Genetic Breeding and Production)
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21 pages, 3433 KiB  
Article
Analysis of Phenotypic and Physiological Characteristics of Plant Height Difference in Alfalfa
by Fang Jing, Shangli Shi, Yun A, Jian Guan, Baofu Lu, Bei Wu, Wenjuan Wang, Ruihong Ma and Pan Nan
Agronomy 2023, 13(7), 1744; https://doi.org/10.3390/agronomy13071744 - 28 Jun 2023
Cited by 5 | Viewed by 1407
Abstract
Cultivating new alfalfa (Medicago sativa L.) varieties with high yield and quality is of great significance for improving alfalfa yield and promoting the development of the grass and livestock industry. Plant height is an important indicator of alfalfa yield and is closely [...] Read more.
Cultivating new alfalfa (Medicago sativa L.) varieties with high yield and quality is of great significance for improving alfalfa yield and promoting the development of the grass and livestock industry. Plant height is an important indicator of alfalfa yield and is closely related to photosynthetic capacity, harvest index and yield. However, the underlying cause of the variation in height among alfalfa plants is not clear. In this paper, we measured the phenotypic traits, photosynthetic physiology and endogenous hormone content of tall- and short-stalked alfalfa materials and analyzed the important external and internal factors that caused the difference in plant height of alfalfa. We found that the phenotypic traits of tall- and short-stalked alfalfa materials showed significant differences, and dwarf alfalfa showed significant shortening of the main stem internode length. There were also some differences in light and physiological indicators and endogenous hormone contents between tall- and short-stalked alfalfa materials. Through correlation analysis, we found that the phenotypic traits and physiological indicators significantly correlated with alfalfa plant height were the number of internodes, stem diameter, average internode length, leaf–stem ratio, leaf area, Pn (net photosynthetic rate), Tr (transpiration rate), upper leaf SP (soluble protein), Suc (sucrose) content, middle stem Sta (starch) content, middle stem ZT (zeatin) and IAA (indole-3-acetic acid). Further analysis showed that Tr, IAA and LA played a direct role in plant height, with Tr contributing the most to plant height, followed by IAA. Finally, we found that the starch content of the middle stem had a significant impact on plant height through principal component analysis. These results provide new insights into the formation and genetic improvement of plant height traits in leguminous forages such as alfalfa. Full article
(This article belongs to the Special Issue Frontier Studies in Legumes Genetic Breeding and Production)
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16 pages, 2590 KiB  
Article
Evaluating, Screening and Selecting Yardlong Bean [Vigna unguiculata subsp. sesquipedalis (L.) Verdc.] for Resistance to Common Cutworm (Spodoptera litura Fabricius)
by Tianchi Yao, Yufei Xu, Huiyan Jiang, Xinxin Chen, Xiaofeng Liu, Huatao Chen, Hongmei Zhang and Guangnan Xing
Agronomy 2023, 13(2), 502; https://doi.org/10.3390/agronomy13020502 - 9 Feb 2023
Cited by 1 | Viewed by 2193
Abstract
The yardlong bean [Vigna unguiculata subsp. sesquipedalis (L.) Verdc.] is an important vegetable crop, but it is prone to pest infestation. Therefore, breeding insect-resistant varieties is essential to reduce pesticide applications and to increase bean quality and yield. In the present study, [...] Read more.
The yardlong bean [Vigna unguiculata subsp. sesquipedalis (L.) Verdc.] is an important vegetable crop, but it is prone to pest infestation. Therefore, breeding insect-resistant varieties is essential to reduce pesticide applications and to increase bean quality and yield. In the present study, 64 yardlong bean varieties were screened for their resistance to the common cutworm (Spodoptera litura Fabricius). In the greenhouse, leaves, pods, and seeds of yardlong beans were harmed by naturally occurring common cutworms. Seventeen insect-resistant and four insect-susceptible yardlong bean varieties were identified based on the weight of the nine-day-old larvae and 72 h weight increases of 4th instar larvae through feeding newly hatched and 4th instar larvae, respectively. Subsequent verification feeding experiments with newly hatched larvae showed that Zhuzaidou and Pingtangjiangdou’s insect resistance are the weakest and Jiangdou No.5, j-1, Zhijiangtezao No. 30, and Changcaidou have the strongest insect resistance. In 21 yardlong bean varieties, starch content and larval weight showed negative correlation and there was positive correlation between crude protein and larval weight, but almost neither of them reached significant levels. Through organ antibiotic and antixenotic experiments, it was concluded that common cutworms preferred feeding on yardlong bean leaves, and the weight increase of common cutworms feeding on leaves was higher than that of pods and seeds. These insect-resistant yardlong bean varieties warrant further investigation in basic antibiosis mechanism research in yardlong beans and can serve as germplasm resources for breeding programs engaged in reducing pesticide usage. Full article
(This article belongs to the Special Issue Frontier Studies in Legumes Genetic Breeding and Production)
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17 pages, 2827 KiB  
Article
Comparison of Trapping Effects of Different Traps and Monitoring the Occurrence Dynamics of Spodoptera litura in Soybean Fields of Dangtu, Anhui Province, China
by Yufei Xu, Zhihao Ye, Zhiyuan Xie, Di Zhang, Xiaofeng Liu, Yulu Yan, Lei Sun, Fajun Chen, Junyi Gai and Guangnan Xing
Agronomy 2023, 13(1), 47; https://doi.org/10.3390/agronomy13010047 - 23 Dec 2022
Cited by 2 | Viewed by 2323
Abstract
In order to clarify the trapping efficiency of different types of sex pheromone traps on populations of Spodoptera litura in soybean fields, three kinds of conventional traps, called YL-VT, YL-HEMT and YL-NMT, and types of traps equipped with a automatic catch monitoring mechanism, [...] Read more.
In order to clarify the trapping efficiency of different types of sex pheromone traps on populations of Spodoptera litura in soybean fields, three kinds of conventional traps, called YL-VT, YL-HEMT and YL-NMT, and types of traps equipped with a automatic catch monitoring mechanism, called AIM and AIM-lite-A, have been tested. These last two allow monitoring the diurnal and seasonal rhythms of the catches. From 5 August to 5 October 2020, each YL-VT trap caught an average of 84.4 heads of S. litura moths per day, which was significantly higher than the YL-HEMT (11.8 heads), YL-NMT (16.5 heads) and AIM (9.7 heads), which did not show significant differences between them. The half-life of pheromone attraction effect in YL-VT trap is about 17–20 days. Considering the number of trapping and the duration of pheromone attraction effect, YL-VT trap is the best. For efficient monitoring, the validity period is approximately 15 days. Among the causes that could explain its higher capture rate and efficiency, the YL-VT trap has the smallest and largest number of inlet devices, and in it, the lure core is located inside of the insect inlet device. Under different occurrence numbers of S. litura, the accuracy of the automatic count of AIM-lite-A is 90% greater than in the AIM trap. The diurnal rhythms of S. litura observed by AIM-lite-A show that S. litura have two active periods that are from 18:00 to 21:00 and from 23:00 to 4:00 at night and that the first active period may be affected by sunshine and temperature. The annual activity rhythm of S. litura monitored by AIM showed that the activity of S. litura was related to temperature, there were approximately 6 generations of S. litura in a year and that the activity peak was from August to September in Dangtu, China. AIM and AIM-lite-A can be used for the annual monitoring of S. litura population in soybean fields because of their automatic counting function. AIM can simultaneously record a variety of meteorological data, AIM-lite-A has higher accuracy and a lower cost, which can be selected according to different situations. In conventional traps, the trap YL-VT can be used for the population monitoring of S. litura in soybean fields and pest control in the field, especially in greenhouses and net rooms where organic soybeans are grown, due to its low cost and efficient trapping ability. Full article
(This article belongs to the Special Issue Frontier Studies in Legumes Genetic Breeding and Production)
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21 pages, 2933 KiB  
Article
Detection of Hub QTLs Underlying the Genetic Basis of Three Modules Covering Nine Agronomic Traits in an F2 Soybean Population
by Mengmeng Fu, Bo Qi, Shuguang Li, Haifeng Xu, Yaqi Wang, Zhixin Zhao, Xiwen Yu, Liyuan Pan and Jiayin Yang
Agronomy 2022, 12(12), 3135; https://doi.org/10.3390/agronomy12123135 - 10 Dec 2022
Viewed by 1233
Abstract
Deciphering the genetic basis underlying agronomic traits is of importance for soybean improvement. However, covariation, modulated by genetic correlations between complicated traits via hub QTLs, commonly affects the efficiency and accuracy of soybean improvement. The goals of soybean improvement have nearly all focused [...] Read more.
Deciphering the genetic basis underlying agronomic traits is of importance for soybean improvement. However, covariation, modulated by genetic correlations between complicated traits via hub QTLs, commonly affects the efficiency and accuracy of soybean improvement. The goals of soybean improvement have nearly all focused on agronomic traits, including yield, plant type traits, and seed-related traits especially. To decipher the hub QTLs of yield, plant type, and seed, nine pertinent traits of an F2 population (181 plants) derived from a cross between KeXin No.03 and JiDou 17, which were different in multiple traits such as plant height, seed protein, and 100-seed weight, were investigated with a high-density genetic map covering 2708.63 cM. A highly significant negative phenotypic correlation (−0.95) was found between seed protein (Pro) and seed oil (Oil). A total of 35 final QTLs after combining the ones closely linked physically were identified for eight traits explaining from 0.10% to 24.63% of the phenotypic variance explained (PVE) using composite interval mapping (CIM) and inclusive composite interval mapping (ICIM) procedures, and 13 QTLs were novel genes. A genomic region on chromosome 14 (qPro14, qOil14.2, and qSw14) was associated with three seed-related traits based on the relationship within and among the three trait modules. In addition, four genomic regions were detected as hub QTLs which linked to the seed-related module and plant-type model, including the E loci (E1 and E2). From the QTL results, 31 candidate genes were annotated, including the verified genes E1, E2, and QNE1, and they were grouped into three categories of biological processes. These results illustrate the genetic architecture as correlations among various soybean traits, and the hub QTLs should provide insights into the genetic improvement of complex traits in soybean. Full article
(This article belongs to the Special Issue Frontier Studies in Legumes Genetic Breeding and Production)
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19 pages, 2965 KiB  
Article
Effects of Fertilizer Level and Intercropping Planting Pattern with Corn on the Yield-Related Traits and Insect Community of Soybean
by Likun Li, Fajun Chen and Guangnan Xing
Agronomy 2022, 12(12), 3080; https://doi.org/10.3390/agronomy12123080 - 5 Dec 2022
Cited by 2 | Viewed by 1810
Abstract
Intercropping of corn and soybean is widely practiced in agricultural production. However, few studies have investigated the effect of intercropping and fertilizer reduction on soybean yield. In the present study, corn and soybean were interplanted in 2:2, 2:3 and 2:4 ratios. Two fertilizer [...] Read more.
Intercropping of corn and soybean is widely practiced in agricultural production. However, few studies have investigated the effect of intercropping and fertilizer reduction on soybean yield. In the present study, corn and soybean were interplanted in 2:2, 2:3 and 2:4 ratios. Two fertilizer levels (normal: 600 kg/ha VS. reduced: 375 kg/ha) were set. The effects of fertilizer levels and intercropping planting patterns on the growth and yield of intercropping soybeans were studied based on the changes in enzyme activities related to nitrogen metabolism and insect community in the field. The results show that fertilizer reduction significantly reduced the biomass, 100-seed weight and yield of soybean. Intercropping also reduced these yield-related traits; a decreasing trend was more obvious with a decrease in soybean ratio. Intercropping had greater effect on soybean plant biomass, 100-seed weight and yield than fertilizer reduction. Reduction in fertilizer reduced the activities of nitrogen-metabolism-related enzymes in soybean. In addition to increased NR (nitrate reductase) enzyme activity in R5, intercropping planting pattern also had negative effect on the activities of nitrogen-metabolism-related enzymes in soybean. Reduced fertilizer only significantly reduced the Pielou evenness index. Reduced fertilizer application was beneficial with respect to the outbreak of greenhouse whitefly. However, an intercropping planting pattern can significantly increase the number of species, as well as the Shannon–Wiener diversity index and the Pielou evenness index of the insect community, and significantly reduce the Simpson dominance index and the population of the important pest, green leafhopper. In conclusion, C2S4 (two corn rows with four rows of soybean) is a scientific intercropping planting pattern that can reduce the occurrence of pests through ecological regulation and does not significantly reduce the activity of enzymes-related to nitrogen metabolism in most cases, ensuring soybean yield. Full article
(This article belongs to the Special Issue Frontier Studies in Legumes Genetic Breeding and Production)
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15 pages, 3248 KiB  
Article
Genome-Wide Identification of Phytophthora sojae-Associated microRNAs and Network in a Resistant and a Susceptible Soybean Germplasm
by Na Guo, Ammara Tahir, Xiaoxia Cui, Jianyu Xu, Jutao Sun, Nannan Zhang, Ruidong Sun, Sushuang Deng, Han Xing and Jinming Zhao
Agronomy 2022, 12(12), 2922; https://doi.org/10.3390/agronomy12122922 - 23 Nov 2022
Cited by 2 | Viewed by 1351
Abstract
Phytophthora root rot, caused by Phytophthora sojae (P. sojae), is one of the most devastating diseases limiting soybean production worldwide. microRNAs (miRNAs) play major roles in regulating plant defense against pathogens. To understand the roles of soybean miRNAs during P. sojae [...] Read more.
Phytophthora root rot, caused by Phytophthora sojae (P. sojae), is one of the most devastating diseases limiting soybean production worldwide. microRNAs (miRNAs) play major roles in regulating plant defense against pathogens. To understand the roles of soybean miRNAs during P. sojae infection, we analyzed four small RNA libraries from two soybean germplasms before and after P. sojae isolate JS08-12 infection. The cultivar Nannong 10-1 was resistant to JS08-12, whereas the 06-070583 line was susceptible to JS08-12. In total, 528 known and 555 putative novel miRNAs in soybean were identified from 97 million reads; 74 known miRNAs and 75 novel miRNAs that might be specifically related to Nannong10-1 responses to P. sojae; and 55 known and 43 novel miRNAs expressed before and after infection in the susceptible line 06-070583. qRT-PCR provided similar miRNA expression patterns to those obtained by the small-RNA sequencing of the four libraries. Then, the potential target genes of these differentially expressed miRNA were predicted, which encoded transcriptional factors, resistance proteins and transporters. Finally, we focused on the targets of the three legume-specific miRNAs (gma-miR1508, gma-miR1509, and gma-miR1510) and charted the miRNA–target interactions and networks based on the published degradome data. Full article
(This article belongs to the Special Issue Frontier Studies in Legumes Genetic Breeding and Production)
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20 pages, 5887 KiB  
Article
The Effect of Neutral Salt and Alkaline Stress with the Same Na+ Concentration on Root Growth of Soybean (Glycine max (L.) Merr.) Seedlings
by Guangda Wang, Wanzheng Shen, Zhaoning Zhang, Shuang Guo, Jiachen Hu, Ruiqi Feng, Qiang Zhao, Jidao Du and Yanli Du
Agronomy 2022, 12(11), 2708; https://doi.org/10.3390/agronomy12112708 - 1 Nov 2022
Cited by 2 | Viewed by 1921
Abstract
Salt stress is a common abiotic stress that negatively affects crop growth and yield. However, there have been significant differences found on the effect degree and management mechanism in plants under neutral salt stress and alkaline stress. In this study, two soybean cultivars, [...] Read more.
Salt stress is a common abiotic stress that negatively affects crop growth and yield. However, there have been significant differences found on the effect degree and management mechanism in plants under neutral salt stress and alkaline stress. In this study, two soybean cultivars, Heihe 49 (HH49, saline-alkali stress tolerant) and Henong 95 (HN95, saline-alkali stress sensitive), were hydroponically cultured and treated with salt solutions of 25, 50, and 75 mM Na+ in the form of NaCl, Na2SO4, NaHCO3, and Na2CO3. Plants treated with alkaline stress (NaHCO3 and Na2CO3) showed a greater decrease in root growth and root activity of both soybean cultivar seedlings than that under neutral salt stresses (NaCl and Na2SO4) with 25–75 mM Na+ concentration. Alkaline stress (25–50 mM Na+ content) activated a higher ability of antioxidant defense (by enhancing the activists of superoxide dismutase (SOD), peroxidase (POD), and ascorbate peroxidase (APX)) and increased the content of soluble sugars to a higher level than that under neutral salt stresses. However, 75 mM Na+ content salt treatments reduced antioxidant enzyme activities and osmotic regulating substance content. Furthermore, alkaline salt and neutral salt stress was able to induce DNA damage and cell cycle arrest in HH49 and HN95 seedling roots. Treatment with Na2CO3 induced the least random amplification polymorphic DNA (RAPD) polymorphism in soybean seedling roots among all salt treatments, which could have been related to the early cell cycle arrest. Full article
(This article belongs to the Special Issue Frontier Studies in Legumes Genetic Breeding and Production)
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16 pages, 2564 KiB  
Article
Comparative Transcriptome Analyses between Resistant and Susceptible Varieties in Response to Soybean Mosaic Virus Infection
by Yuanyuan Chen, Ying Shen, Boyu Chen, Lijun Xie, Yanmin Xiao, Zheng Chong, Han Cai, Guangnan Xing, Haijian Zhi and Kai Li
Agronomy 2022, 12(8), 1785; https://doi.org/10.3390/agronomy12081785 - 28 Jul 2022
Cited by 2 | Viewed by 1595
Abstract
Soybean mosaic virus (SMV) is a worldwide and hardly controlled virus disease in soybean. Kefeng-1 is an elite variety resistant to SMV in China. In order to discover resistance genes and regulation networks in Kefeng-1, we analyzed transcriptome data of resistant (Kefeng-1) and [...] Read more.
Soybean mosaic virus (SMV) is a worldwide and hardly controlled virus disease in soybean. Kefeng-1 is an elite variety resistant to SMV in China. In order to discover resistance genes and regulation networks in Kefeng-1, we analyzed transcriptome data of resistant (Kefeng-1) and susceptible (NN1138-2) soybean varieties in response to infection of the SMV strain SC18 at 0, 6, and 48 hours post-inoculation (hpi) and 5 days post-inoculation (dpi). Many differentially expressed genes (DEGs) were identified with Kefeng-1 and NN 1138-2. Based on the enrichment analysis for gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, we found that 48 hpi was the best time point for the defense response of the two soybean varieties in response to the SMV infection. The expression of seven candidate genes was further verified by qRT-PCR and was relatively consistent with the results of RNA-Seq. The expression of genes for Glyma.11G239000 and Glyma.18G018400, members of the ethylene-insensitive 3/ethylene-insensitive3-like (EIN3/EIL) protein family involved in ETH, were downregulated in NN1138-2 but not in Kefeng-1 and the expression of Glyma.14G041500 was upregulated in Kefeng-1 at 5 dpi. The expression of jasmonic acid repressor genes (TIFY/JAZ) was downregulated in NN1138-2 but not in Kefeng-1. NPR1 involved in the salicylic acid signaling pathway was downregulated in NN1138-2 at 48 hpi but upregulated in Kefeng-1. It shows that ethylene, jasmonic acid, and salicylic acid signaling pathways may be involved in the disease resistance process to the SMV strain SC18. Our findings would help to understand the molecular mechanism of soybean resistance to SMV. Full article
(This article belongs to the Special Issue Frontier Studies in Legumes Genetic Breeding and Production)
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18 pages, 4552 KiB  
Article
Genome-Wide Identification and Characterization of the Abiotic-Stress-Responsive LACS Gene Family in Soybean (Glycine max)
by Jie Wang, Xiaoxue Li, Xunchao Zhao, Chen Na, Hongliang Liu, Huanran Miao, Jinghang Zhou, Jialei Xiao, Xue Zhao and Yingpeng Han
Agronomy 2022, 12(7), 1496; https://doi.org/10.3390/agronomy12071496 - 22 Jun 2022
Cited by 4 | Viewed by 1727
Abstract
Long-chain acyl-CoA synthases (LACSs) are a key factor in the formation of acyl-CoA after fatty acid hydrolysis and play an important role in plant stress resistance. This gene family has not been research in soybeans. In this study, the soybean (Glycine max [...] Read more.
Long-chain acyl-CoA synthases (LACSs) are a key factor in the formation of acyl-CoA after fatty acid hydrolysis and play an important role in plant stress resistance. This gene family has not been research in soybeans. In this study, the soybean (Glycine max (L.) Merr.) whole genome was identified, the LACS family genes of soybean were screened, and the bioinformatics, tissue expression, abiotic stress, drought stress and co-expression of transcription factors of the gene family were analyzed to preliminarily clarify the function of the LACS family of soybean. A total of 17 LACS genes were screened from soybean genome sequencing data. A bioinformatics analysis of the GmLACS gene was carried out from the aspects of phylogeny, gene structure, conserved sequence and promoter homeopathic element. The transcription spectra of GmLACSs in different organs and abiotic stresses were used by qRT-PCR. The GmLACS genes, which co-expresses the significant response of the analysis of drought stress and transcription factors. The results showed that all soybean LACS have highly conserved AMP-binding domains, and all soybean LACS genes were divided into 6 subfamilies. Transcriptome analysis indicated that the gene-encoding expression profiles under alkali, low temperature, and drought stress. The expression of GmLACS9/15/17 were significantly upregulated under alkali, low temperature and drought stress. Co-expression analysis showed that there was a close correlation between transcription factors and genes that significantly responded to LACS under drought stress. These results provide a theoretical and empirical basis for clarifying the function of LACS family genes and abiotic stress response mechanism of soybean. Full article
(This article belongs to the Special Issue Frontier Studies in Legumes Genetic Breeding and Production)
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11 pages, 2594 KiB  
Article
GWAS and Identification of Candidate Genes Associated with Seed Soluble Sugar Content in Vegetable Soybean
by Wenjing Xu, Hui Liu, Songsong Li, Wei Zhang, Qiong Wang, Hongmei Zhang, Xiaoqing Liu, Xiaoyan Cui, Xin Chen, Wei Tang, Yanzhe Li, Yuelin Zhu and Huatao Chen
Agronomy 2022, 12(6), 1470; https://doi.org/10.3390/agronomy12061470 - 18 Jun 2022
Cited by 6 | Viewed by 2516
Abstract
Total soluble sugar (TSS) is an important component in vegetable soybean seeds during the R6 stage and greatly impacts fresh soybean flavor. Increasing the TSS content is thus one of the most important breeding objectives for the creation of high-quality vegetable soybean germplasm. [...] Read more.
Total soluble sugar (TSS) is an important component in vegetable soybean seeds during the R6 stage and greatly impacts fresh soybean flavor. Increasing the TSS content is thus one of the most important breeding objectives for the creation of high-quality vegetable soybean germplasm. To better understand the genetic basis of the TSS at the R6 stage, we investigated 264 germplasm accessions in two environments. We obtained five associations with 27 significant SNPs using GWAS. The significant SNPs S15_10810881–S15_10843821 and S06_12044239–S06_12048607 were identified in both environments. We then conducted candidate gene analysis and uncovered nine candidate genes as potential regulators of TSS content in vegetable soybean seeds using RT-PCR. These genes may be involved in the regulation of soluble sugar content in soybean seeds. This study provides new knowledge for the understanding of the genetic basis of TSS at the R6 stage and will help improve regulation of TSS in vegetable soybean using molecular breeding. Full article
(This article belongs to the Special Issue Frontier Studies in Legumes Genetic Breeding and Production)
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13 pages, 3635 KiB  
Article
Genome-Wide Identification and Analysis of the NF-Y Transcription Factor Family in Medicago sativa L.
by Tingting Song, Jiawei Li, Yuying Yuan, Jinqiu Yu, Yuqi Cao, Hua Cai and Guowen Cui
Agronomy 2022, 12(5), 1237; https://doi.org/10.3390/agronomy12051237 - 23 May 2022
Viewed by 2051
Abstract
The nuclear factor Y (NF-Y) gene family is an important transcription factor family consisting of three subfamilies, NF-YA, NF-YB and NF-YC, which are widely involved in plant growth and development, stress responses and other processes. In this study, we identified 64 members of [...] Read more.
The nuclear factor Y (NF-Y) gene family is an important transcription factor family consisting of three subfamilies, NF-YA, NF-YB and NF-YC, which are widely involved in plant growth and development, stress responses and other processes. In this study, we identified 64 members of the NF-Y gene family in the M. sativa L. (Xinjiang Daye) genome, including 11 MsNF-YAs, 33 MsNF-YBs and 20 MsNF-YCs. Analysis of conserved motifs indicated that each unit included unique compounds of motifs, although certain members lost some motifs. Conserved functional domain analysis showed that each subunit contained a specific set of functional domains. Analysis of cis-acting elements in the promoter region of the MsNF-Y genes identified a series of cis-acting elements associated with stress responses. In addition, the transcriptome data and qRT-PCR analysis showed that MsNF-Y genes were significantly induced or downregulated by alkali treatment. The results of this study may help to establish a basis for further cloning and functional studies of NF-Y genes in Medicago sativa and other related legume species. Full article
(This article belongs to the Special Issue Frontier Studies in Legumes Genetic Breeding and Production)
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16 pages, 936 KiB  
Article
Evolutionary Variation of Accumulative Day Length and Accumulative Active Temperature Required for Growth Periods in Global Soybeans
by Can Wang, Xueqin Liu, Xiaoshuai Hao, Yongpeng Pan, Chunmei Zong, Weiying Zeng, Wubin Wang, Guangnan Xing, Jianbo He and Junyi Gai
Agronomy 2022, 12(4), 962; https://doi.org/10.3390/agronomy12040962 - 15 Apr 2022
Cited by 2 | Viewed by 1770
Abstract
Soybean (Glycine max (L.) Merr.) is a typical short-day and thermophilic crop. This study aimed to reveal the required accumulative day length (ADL) and accumulative active temperature (AAT) for DSF (days of sowing to flowering) and DFM (days of flowering to maturity) [...] Read more.
Soybean (Glycine max (L.) Merr.) is a typical short-day and thermophilic crop. This study aimed to reveal the required accumulative day length (ADL) and accumulative active temperature (AAT) for DSF (days of sowing to flowering) and DFM (days of flowering to maturity) in global soybeans. A sample consisted of 354 varieties from 27 countries in five geographic regions, which were tested in Nanjing, China in two spring-sowing and two summer-sowing seasons. The ADL and AAT were calculated from the climatological data provided by the Public Service of Nanjing Meteorological Bureau. The results showed that the average DSF and DFM of global soybeans were 41.0 d and 83.3 d, which required ADLDSF of 606.6 d·h and AATDSF of 1185.9 d·°C, ADLDFM of 1126.7 d·h and AATDFM of 2145.1 d·°C, respectively, all with a wide variation among/within geographic and MG(maturity-group)-set subpopulations. From the multiple regression of DSF and DFM on required ADL and AAT, the ADL, AAT and ADL×AAT contributed 38.5%, 44.79% and 17.10% to DSF variation and 86.98%, 11.42% and 0.54% to DFM variation, respectively, and their relative importance to DSF and DFM varied among the geographic and MG subpopulations. The geographic subpopulations matched only partially with the genomic marker clusters, indicating multiple genetic sources of each subpopulation and that genetic exchange happened among subpopulations. Full article
(This article belongs to the Special Issue Frontier Studies in Legumes Genetic Breeding and Production)
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15 pages, 1969 KiB  
Article
Genome-Wide Association Studies of Plant Architecture-Related Traits in the Chinese Soybean Mini Core Collection
by Wentao Ding, Xiaoli Zhang, Dandan Liu, Chen Li, Congcong Wang, Ruidong Sun, Xiangpei Jin, Na Guo, Jinming Zhao and Han Xing
Agronomy 2022, 12(4), 817; https://doi.org/10.3390/agronomy12040817 - 28 Mar 2022
Viewed by 2327
Abstract
Plant architecture traits are closely related to plant biomass, lodging, and photosynthetic efficiency, which in turn affect soybean yield. In this study, we investigated a Chinese soybean mini core collection consisting of 224 germplasm accessions for four plant architecture-related traits (plant height (PH), [...] Read more.
Plant architecture traits are closely related to plant biomass, lodging, and photosynthetic efficiency, which in turn affect soybean yield. In this study, we investigated a Chinese soybean mini core collection consisting of 224 germplasm accessions for four plant architecture-related traits (plant height (PH), number of nodes on main stem (NN), branch number (BN), and stem diameter (DI)) under three environments and conducted a genome-wide association study (GWAS) based on 1514 single nucleotide polymorphisms (SNPs). A total of 41 SNPs were found to be significantly associated with PH, NN, BN, and DI in two or more environments. Among these SNPs, 15 were located in regions in which plant architecture-related QTLs had been reported in previous studies, and 26 were new genetic loci. In addition, 18 potential candidate genes for plant architecture-related traits were obtained by predicting the genes in the interval of four large-effect markers (BARC-017097-02199, Map-2213, BARC-014639-01604, and Map-2223). This research will help to illuminate the genetic basis of soybean plant architecture-related traits and accelerate the process of plant architecture breeding by molecular marker-assisted selection in soybean. Full article
(This article belongs to the Special Issue Frontier Studies in Legumes Genetic Breeding and Production)
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