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Kim J, Scaboo A, Rainey KM, Fritschi FB, Bilyeu K. Redesigning soybean with improved oil and meal traits. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:218. [PMID: 39254853 DOI: 10.1007/s00122-024-04732-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 08/24/2024] [Indexed: 09/11/2024]
Abstract
KEY MESSAGE Soybean seed oil and meal composition traits can be combined without interference to provide additional value to the crop. Soybean [Glycine max (L.) Merr.] is an important crop worldwide; its overall value comes from seed oil and high protein meal. The development of soybean varieties with allele combinations for improved oil and meal quality is expected to provide a compositional value bundle for soybean. The high oleic and low linolenic acid seed oil trait (HOLL; > 70% oleic and < 3% linolenic acid) is targeted to optimize the health and functional properties of soybean oil. For soybean meal, metabolizable energy is improved by altering the carbohydrate profile with increased sucrose and decreased anti-nutritional factors, raffinose family of oligosaccharides (RFOs). Previous research identified four variant alleles of fatty acid desaturase (FAD) genes and two raffinose synthase (RS) genes necessary for the HOLL trait in soybean oil and Low or Ultra-Low (UL) RFO traits in soybean meal, respectively. We employed a molecular marker-assisted breeding approach to combine six alleles conferring the desired soybean oil and meal value traits. Eight environment field trials were conducted with twenty-four soybean lines to evaluate phenotypic interactions among the variant alleles of FAD and RS genes. The results indicated that the four FAD gene alleles conditioned the HOLL fatty acid profile of the seed oil regardless of the allele status of the RS genes. Independent of the allele combination of the FAD genes, soybean with two variant alleles of the RS genes had the desired RFO trait in the seeds. The results confirm the feasibility of soybean variety development with this unique combination of oil and meal traits.
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Affiliation(s)
- Jeonghwa Kim
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, USA
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA
| | - Andrew Scaboo
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, USA
| | | | - Felix B Fritschi
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, USA
| | - Kristin Bilyeu
- Plant Genetics Research Unit, USDA/ARS, Columbia, MO, USA.
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Wang L, Niu F, Wang J, Zhang H, Zhang D, Hu Z. Genome-Wide Association Studies Prioritize Genes Controlling Seed Size and Reproductive Period Length in Soybean. PLANTS (BASEL, SWITZERLAND) 2024; 13:615. [PMID: 38475461 DOI: 10.3390/plants13050615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 03/14/2024]
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.
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Affiliation(s)
- Le Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Fu'an Niu
- Institute of Crop Breeding and Cultivation, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Jinshe Wang
- National Innovation Centre for Bio-Breeding Industry, Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Hengyou Zhang
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhenbin Hu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USA
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Escamilla DM, Dietz N, Bilyeu K, Hudson K, Rainey KM. Genome-wide association study reveals GmFulb as candidate gene for maturity time and reproductive length in soybeans (Glycine max). PLoS One 2024; 19:e0294123. [PMID: 38241340 PMCID: PMC10798547 DOI: 10.1371/journal.pone.0294123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 10/25/2023] [Indexed: 01/21/2024] Open
Abstract
The ability of soybean [Glycine max (L.) Merr.] to adapt to different latitudes is attributed to genetic variation in major E genes and quantitative trait loci (QTLs) determining flowering time (R1), maturity (R8), and reproductive length (RL). Fully revealing the genetic basis of R1, R8, and RL in soybeans is necessary to enhance genetic gains in soybean yield improvement. Here, we performed a genome-wide association analysis (GWA) with 31,689 single nucleotide polymorphisms (SNPs) to detect novel loci for R1, R8, and RL using a soybean panel of 329 accessions with the same genotype for three major E genes (e1-as/E2/E3). The studied accessions were grown in nine environments and observed for R1, R8 and RL in all environments. This study identified two stable peaks on Chr 4, simultaneously controlling R8 and RL. In addition, we identified a third peak on Chr 10 controlling R1. Association peaks overlap with previously reported QTLs for R1, R8, and RL. Considering the alternative alleles, significant SNPs caused RL to be two days shorter, R1 two days later and R8 two days earlier, respectively. We identified association peaks acting independently over R1 and R8, suggesting that trait-specific minor effect loci are also involved in controlling R1 and R8. From the 111 genes highly associated with the three peaks detected in this study, we selected six candidate genes as the most likely cause of R1, R8, and RL variation. High correspondence was observed between a modifying variant SNP at position 04:39294836 in GmFulb and an association peak on Chr 4. Further studies using map-based cloning and fine mapping are necessary to elucidate the role of the candidates we identified for soybean maturity and adaptation to different latitudes and to be effectively used in the marker-assisted breeding of cultivars with optimal yield-related traits.
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Affiliation(s)
- Diana M. Escamilla
- Department of Agronomy, Purdue University, West Lafayette, Indiana, United States of America
| | - Nicholas Dietz
- Division of Plant Science and Technology, University of Missouri, Columbia, Missouri, United States of America
| | - Kristin Bilyeu
- Plant Genetics Research Unit, United States Department of Agriculture (USDA)−Agricultural Research Service (ARS), Columbia, Missouri, United States of America
| | - Karen Hudson
- USDA-ARS Crop Production and Pest Control Research Unit, West Lafayette, Indiana, United States of America
| | - Katy Martin Rainey
- Department of Agronomy, Purdue University, West Lafayette, Indiana, United States of America
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Vollmann J, Škrabišová M. Going north: adaptation of soybean to long-day environments. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2933-2936. [PMID: 37208832 DOI: 10.1093/jxb/erad105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 03/16/2023] [Indexed: 05/21/2023]
Abstract
This article comments on:
Zhu X, Leiser WL, Hahn V, Würschum T. 2023. The genetic architecture of soybean photothermal adaptation to high latitudes. Journal of Experimental Botany 74,2987–3002
In plant breeding, understanding genetic variation in the photoperiodic control of flowering time of crop plants such as soybean is a prerequisite for managing adaptation to new environments. Zhu et al. (2023) analyzed a large diversity panel of >1500 early maturity soybean lines to disclose the genetic architecture behind the timing of flowering and maturity. Their findings confirm known maturity loci and reveal new candidate genes and alleles as well as environmental interactions of individual quantitative trait loci (QTLs) for flowering and maturity time. The results shed light on the complexity of the regulatory network which controls the timing of flowering in soybean. This supports the fine-tuning of plant architectures through the combination of stem termination and flowering genes towards a better adaptation of soybean to high latitudes or other stressful environments.
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Affiliation(s)
- Johann Vollmann
- Department of Crop Sciences, University of Natural Resources and Life Sciences Vienna, 3430 Tulln an der Donau, Austria
| | - Mária Škrabišová
- Department of Biochemistry, Faculty of Science, Palacký University in Olomouc, 78371 Olomouc, Czech Republic
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Miller MJ, Song Q, Fallen B, Li Z. Genomic prediction of optimal cross combinations to accelerate genetic improvement of soybean ( Glycine max). FRONTIERS IN PLANT SCIENCE 2023; 14:1171135. [PMID: 37235007 PMCID: PMC10206060 DOI: 10.3389/fpls.2023.1171135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/17/2023] [Indexed: 05/28/2023]
Abstract
Improving yield is a primary soybean breeding goal, as yield is the main determinant of soybean's profitability. Within the breeding process, selection of cross combinations is one of most important elements. Cross prediction will assist soybean breeders in identifying the best cross combinations among parental genotypes prior to crossing, increasing genetic gain and breeding efficiency. In this study optimal cross selection methods were created and applied in soybean and validated using historical data from the University of Georgia soybean breeding program, under multiple training set compositions and marker densities utilizing multiple genomic selection models for marker evaluation. Plant materials consisted of 702 advanced breeding lines evaluated in multiple environments and genotyped using SoySNP6k BeadChips. An additional marker set, the SoySNP3k marker set, was tested in this study as well. Optimal cross selection methods were used to predict the yield of 42 previously made crosses and compared to the performance of the cross's offspring in replicated field trials. The best prediction accuracy was obtained when using Extended Genomic BLUP with the SoySNP6k marker set, consisting of 3,762 polymorphic markers, with an accuracy of 0.56 with a training set maximally related to the crosses predicted and 0.4 in a training set with minimized relatedness to predicted crosses. Prediction accuracy was most significantly impacted by training set relatedness to the predicted crosses, marker density, and the genomic model used to predict marker effects. The usefulness criterion selected had an impact on prediction accuracy within training sets with low relatedness to the crosses predicted. Optimal cross prediction provides a useful method that assists plant breeders in selecting crosses in soybean breeding.
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Affiliation(s)
- Mark J. Miller
- Institute of Plant Breeding, Genetics and Genomics, and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, United States Department of Agriculture - Agricultural Research Service, Beltsville, MD, United States
| | - Benjamin Fallen
- Soybean and Nitrogen Fixation Research Unit, United States Department of Agriculture - Agricultural Research Service, Raleigh, NC, United States
| | - Zenglu Li
- Institute of Plant Breeding, Genetics and Genomics, and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
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Jo H, Ha BK, Park SK, Jeong SC, Lee JD, Moon JK. Genetic Diversity of Korean Wild Soybean Core Collections and Genome-Wide Association Study for Days to Flowering. PLANTS (BASEL, SWITZERLAND) 2023; 12:1305. [PMID: 36986992 PMCID: PMC10058364 DOI: 10.3390/plants12061305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 06/19/2023]
Abstract
The utilization of wild soybean germplasms in breeding programs increases genetic diversity, and they contain the rare alleles of traits of interest. Understanding the genetic diversity of wild germplasms is essential for determining effective strategies that can improve the economic traits of soybeans. Undesirable traits make it challenging to cultivate wild soybeans. This study aimed to construct a core subset of 1467 wild soybean accessions of the total population and analyze their genetic diversity to understand their genetic variations. Genome-wild association studies were conducted to detect the genetic loci underlying the time to flowering for a core subset collection, and they revealed the allelic variation in E genes for predicting maturity using the available resequencing data of wild soybean. Based on principal component and cluster analyses, 408 wild soybean accessions in the core collection covered the total population and were explained by 3 clusters representing the collection regions, namely, Korea, China, and Japan. Most of the wild soybean collections in this study had the E1e2E3 genotype according to association mapping and a resequencing analysis. Korean wild soybean core collections can provide helpful genetic resources to identify new flowering and maturity genes near the E gene loci and genetic materials for developing new cultivars, facilitating the introgression of genes of interest from wild soybean.
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Affiliation(s)
- Hyun Jo
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
- Upland-Field Machinery Research Center, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Bo-Keun Ha
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Soo-Kwon Park
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Soon-Chun Jeong
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Jeong-Dong Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
- Department of Integrative Biology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jung-Kyung Moon
- Agricultural Genome Center, National Academy of Agricultural Sciences, Rural Development Administration, Jeonju 55365, Republic of Korea
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Kim JH, Scaboo A, Pantalone V, Li Z, Bilyeu K. Utilization of Plant Architecture Genes in Soybean to Positively Impact Adaptation to High Yield Environments. FRONTIERS IN PLANT SCIENCE 2022; 13:891587. [PMID: 35685015 PMCID: PMC9171370 DOI: 10.3389/fpls.2022.891587] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 04/20/2022] [Indexed: 05/30/2023]
Abstract
Optimization of plant architecture by modifying stem termination and timing of flowering and maturity of soybean is a promising strategy to improve its adaptability to specific production environments. Therefore, it is important to choose a proper stem termination type and to understand morphological differences between each stem termination type under various environmental conditions. Variations in abruptness of stem termination have been generally classified into three classical genetic types, indeterminate (Dt1), determinate (dt1), and semi-determinate (Dt2). However, an additional stem termination type, termed tall determinate, and its genetic symbol, dt1-t, were introduced about 25 years ago. The tall determinate soybean lines show delayed cessation of apical stem growth and about 50% taller plant heights than the typical determinate soybeans, even though the genetic control of the tall determinate phenotype was found to be allelic to dt1. Despite the potential agronomic merits of the alternative stem termination type, knowledge about the tall determinate soybean remains limited. We clarified the molecular basis of the tall determinate stem termination type and examined potential agronomic merits of the alternative stem type under three different production environments in the US. Sequence analysis of the classical tall determinate soybean lines revealed that the dt1-t allele responsible for tall determinate stem architecture is caused by two of the identified independent missense alleles of dt1, dt1-t1 (R130K), and dt1-t2 (R62S). Also, from the comparison among soybean accessions belonging to each of the genotype categories for stem termination types, soybean accessions with tall determinate alleles were found to have a high discrepancy rate in phenotyping. Newly developed tall determinate late-maturing soybean germplasm lines had taller plant heights and a greater number of nodes with a similar stem diameter and similar pod density at the apical stem compared to typical determinate soybeans having dt1 (R166W) alleles in Southern environments in the US. The phenotype of increased pod-bearing nodes with lodging resistance has the potential to improve yield, especially grown in high yield environments. This study suggests an alternative strategy to remodel the shape of soybean plants, which can possibly lead to yield improvement through the modification of soybean plant architecture.
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Affiliation(s)
- Jeong-Hwa Kim
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
| | - Andrew Scaboo
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
| | - Vincent Pantalone
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
| | - Zenglu Li
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
| | - Kristin Bilyeu
- Plant Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, University of Missouri, Columbia, MO, United States
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Dietz N, Chan YO, Scaboo A, Graef G, Hyten D, Happ M, Diers B, Lorenz A, Wang D, Joshi T, Bilyeu K. Candidate Genes Modulating Reproductive Timing in Elite US Soybean Lines Identified in Soybean Alleles of Arabidopsis Flowering Orthologs With Divergent Latitude Distribution. FRONTIERS IN PLANT SCIENCE 2022; 13:889066. [PMID: 35574141 PMCID: PMC9100572 DOI: 10.3389/fpls.2022.889066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/08/2022] [Indexed: 05/30/2023]
Abstract
Adaptation of soybean cultivars to the photoperiod in which they are grown is critical for optimizing plant yield. However, despite its importance, only the major loci conferring variation in flowering time and maturity of US soybean have been isolated. By contrast, over 200 genes contributing to floral induction in the model organism Arabidopsis thaliana have been described. In this work, putative alleles of a library of soybean orthologs of these Arabidopsis flowering genes were tested for their latitudinal distribution among elite US soybean lines developed in the United States. Furthermore, variants comprising the alleles of genes with significant differences in latitudinal distribution were assessed for amino acid conservation across disparate genera to infer their impact on gene function. From these efforts, several candidate genes from various biological pathways were identified that are likely being exploited toward adaptation of US soybean to various maturity groups.
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Affiliation(s)
- Nicholas Dietz
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
| | - Yen On Chan
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- MU Data Science and Informatics Institute, University of Missouri, Columbia, MO, United States
| | - Andrew Scaboo
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
| | - George Graef
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States
| | - David Hyten
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States
| | - Mary Happ
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States
| | - Brian Diers
- Department of Crop Sciences, University of Illinois, Urbana, IL, United States
| | - Aaron Lorenz
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, United States
| | - Dechun Wang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Trupti Joshi
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- MU Data Science and Informatics Institute, University of Missouri, Columbia, MO, United States
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, United States
- Department of Health Management and Informatics, School of Medicine, University of Missouri, Columbia, MO, United States
| | - Kristin Bilyeu
- USDA/ARS Plant Genetics Research Unit, Columbia, MO, United States
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Škrabišová M, Dietz N, Zeng S, Chan YO, Wang J, Liu Y, Biová J, Joshi T, Bilyeu KD. A novel Synthetic phenotype association study approach reveals the landscape of association for genomic variants and phenotypes. J Adv Res 2022; 42:117-133. [PMID: 36513408 PMCID: PMC9788956 DOI: 10.1016/j.jare.2022.04.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 02/14/2022] [Accepted: 04/08/2022] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Genome-Wide Association Studies (GWAS) identify tagging variants in the genome that are statistically associated with the phenotype because of their linkage disequilibrium (LD) relationship with the causative mutation (CM). When both low-density genotyped accession panels with phenotypes and resequenced data accession panels are available, tagging variants can assist with post-GWAS challenges in CM discovery. OBJECTIVES Our objective was to identify additional GWAS evaluation criteria to assess correspondence between genomic variants and phenotypes, as well as enable deeper analysis of the localized landscape of association. METHODS We used genomic variant positions as Synthetic phenotypes in GWAS that we named "Synthetic phenotype association study" (SPAS). The extreme case of SPAS is what we call an "Inverse GWAS" where we used CM positions of cloned soybean genes. We developed and validated the Accuracy concept as a measure of the correspondence between variant positions and phenotypes. RESULTS The SPAS approach demonstrated that the genotype status of an associated variant used as a Synthetic phenotype enabled us to explore the relationships between tagging variants and CMs, and further, that utilizing CMs as Synthetic phenotypes in Inverse GWAS illuminated the landscape of association. We implemented the Accuracy calculation for a curated accession panel to an online Accuracy calculation tool (AccuTool) as a resource for gene identification in soybean. We demonstrated our concepts on three examples of soybean cloned genes. As a result of our findings, we devised an enhanced "GWAS to Genes" analysis (Synthetic phenotype to CM strategy, SP2CM). Using SP2CM, we identified a CM for a novel gene. CONCLUSION The SP2CM strategy utilizing Synthetic phenotypes and the Accuracy calculation of correspondence provides crucial information to assist researchers in CM discovery. The impact of this work is a more effective evaluation of landscapes of GWAS associations.
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Affiliation(s)
- Mária Škrabišová
- Department of Biochemistry, Faculty of Science, Palacky University Olomouc, Olomouc 78371, Czech Republic
| | - Nicholas Dietz
- Division of Plant Sciences, University of Missouri, Columbia, MO 65201, USA
| | - Shuai Zeng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65212, USA,Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65212, USA
| | - Yen On Chan
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65212, USA,MU Data Science and Informatics Institute, University of Missouri, Columbia, MO 65212, USA
| | - Juexin Wang
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65212, USA,Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65212, USA
| | - Yang Liu
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65212, USA,MU Data Science and Informatics Institute, University of Missouri, Columbia, MO 65212, USA
| | - Jana Biová
- Department of Biochemistry, Faculty of Science, Palacky University Olomouc, Olomouc 78371, Czech Republic
| | - Trupti Joshi
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65212, USA,Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65212, USA,MU Data Science and Informatics Institute, University of Missouri, Columbia, MO 65212, USA,Department of Health Management and Informatics, School of Medicine, University of Missouri, Columbia, MO 65212, USA,Corresponding authors at: Department of Health Management and Informatics, School of Medicine, 1201 E Rollins St, 271B Life Science Center, Columbia, MO 65201, USA (T. Joshi). Plant Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, 110 Waters Hall, University of Missouri, Columbia, MO 65211, USA (K.D. Bilyeu).
| | - Kristin D. Bilyeu
- Plant Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, University of Missouri, Columbia, MO 65211, USA,Corresponding authors at: Department of Health Management and Informatics, School of Medicine, 1201 E Rollins St, 271B Life Science Center, Columbia, MO 65201, USA (T. Joshi). Plant Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, 110 Waters Hall, University of Missouri, Columbia, MO 65211, USA (K.D. Bilyeu).
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Hu B, Li Y, Wu H, Zhai H, Xu K, Gao Y, Zhu J, Li Y, Xia Z. Identification of quantitative trait loci underlying five major agronomic traits of soybean in three biparental populations by specific length amplified fragment sequencing (SLAF-seq). PeerJ 2021; 9:e12416. [PMID: 34993010 PMCID: PMC8679901 DOI: 10.7717/peerj.12416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/10/2021] [Indexed: 11/20/2022] Open
Abstract
Flowering time, plant height, branch number, node numbers of main stem and pods per plant are important agronomic traits related to photoperiodic sensitivity, plant type and yield of soybean, which are controlled by multiple genes or quantitative trait loci (QTL). The main purpose of this study is to identify new QTL for five major agronomic traits, especially for flowering time. Three biparental populations were developed by crossing cultivars from northern and central China. Specific loci amplified fragment sequencing (SLAF-seq) was used to construct linkage map and QTL mapping was carried out. A total of 10 QTL for flowering time were identified in three populations, some of which were related to E1 and E2 genes or the other reported QTL listed in Soybase. In the Y159 population (Xudou No.9 × Kenfeng No.16), QTL for flowering time on chromosome 4, qFT4_1 and qFT4_2 were new. Compared with the QTL reported in Soybase, 1 QTL for plant height (PH), 3 QTL for branch number (BR), 5 QTL for node numbers of main stem, and 3 QTL for pods per plant were new QTL. Major E genes were frequently detected in different populations indicating that major the E loci had a great effect on flowering time and adaptation of soybean. Therefore, in order to further clone minor genes or QTL, it may be of great significance to carefully select the genotypes of known loci. These results may lay a foundation for fine mapping and clone of QTL/genes related to plant-type, provided a basis for high yield breeding of soybean.
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Affiliation(s)
- Bo Hu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuqiu Li
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
| | - Hongyan Wu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
| | - Hong Zhai
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
| | - Kun Xu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
| | - Yi Gao
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinlong Zhu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
| | - Yuzhuo Li
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhengjun Xia
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
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Zimmer G, Miller MJ, Steketee CJ, Jackson SA, de Tunes LVM, Li Z. Genetic control and allele variation among soybean maturity groups 000 through IX. THE PLANT GENOME 2021; 14:e20146. [PMID: 34514734 DOI: 10.1002/tpg2.20146] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
Soybean [Glycinemax (L.) Merr.] maturity determines the growing region of a given soybean variety and is a primary factor in yield and other agronomic traits. The objectives of this research were to identify the quantitative trait loci (QTL) associated with maturity groups (MGs) and determine the genetic control of soybean maturity in each MG. Using data from 16,879 soybean accessions, genome-wide association (GWA) analyses were conducted for each paired MG and across MGs 000 through IX. Genome-wide association analyses were also performed using 184 genotypes (MGs V-IX) with days to flowering (DTF) and maturity (DTM) collected in the field. A total of 58 QTL were identified to be significantly associated with MGs in individual GWAs, which included 12 reported maturity loci and two stem termination genes. Genome-wide associations across MGs 000-IX detected a total of 103 QTL and confirmed 54 QTL identified in the individual GWAs. Of significant loci identified, qMG-5.2 had effects on the highest number (9) of MGs, followed by E2, E3, Dt2, qMG-15.5, E1, qMG-13.1, qMG-7.1, and qMG-16.1, which affected five to seven MGs. A high number of genetic loci (8-25) that affected MGs 0-V were observed. Stem termination genes Dt1 and Dt2 mainly had significant allele variation in MGs II-V. Genome-wide associations for DTF, DTM, and reproductive period (RP) in the diversity panel confirmed 15 QTL, of which seven were observed in MGs V-IX. The results generated can help soybean breeders manipulate the maturity loci for genetic improvement of soybean yield.
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Affiliation(s)
- Gustavo Zimmer
- Institute of Plant Breeding, Genetics, and Genomics, and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Crop Production, Federal University of Pelotas, Capão do Leão, RS, 96160-000, Brazil
| | - Mark J Miller
- Institute of Plant Breeding, Genetics, and Genomics, and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Clinton J Steketee
- Institute of Plant Breeding, Genetics, and Genomics, and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Scott A Jackson
- Institute of Plant Breeding, Genetics, and Genomics, and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
| | | | - Zenglu Li
- Institute of Plant Breeding, Genetics, and Genomics, and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
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12
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Dietz N, Combs-Giroir R, Cooper G, Stacey M, Miranda C, Bilyeu K. Geographic distribution of the E1 family of genes and their effects on reproductive timing in soybean. BMC PLANT BIOLOGY 2021; 21:441. [PMID: 34587901 PMCID: PMC8480027 DOI: 10.1186/s12870-021-03197-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/31/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Soybean is an economically important crop which flowers predominantly in response to photoperiod. Several major loci controlling the quantitative trait for reproductive timing have been identified, of which allelic combinations at three of these loci, E1, E2, and E3, are the dominant factors driving time to flower and reproductive period. However, functional genomics studies have identified additional loci which affect reproductive timing, many of which are less understood. A better characterization of these genes will enable fine-tuning of adaptation to various production environments. Two such genes, E1La and E1Lb, have been implicated in flowering by previous studies, but their effects have yet to be assessed under natural photoperiod regimes. RESULTS Natural and induced variants of E1La and E1Lb were identified and introgressed into lines harboring either E1 or its early flowering variant, e1-as. Lines were evaluated for days to flower and maturity in a Maturity Group (MG) III production environment. These results revealed that variation in E1La and E1Lb promoted earlier flowering and maturity, with stronger effects in e1-as background than in an E1 background. The geographic distribution of E1La alleles among wild and cultivated soybean revealed that natural variation in E1La likely contributed to northern expansion of wild soybean, while breeding programs in North America exploited e1-as to develop cultivars adapted to northern latitudes. CONCLUSION This research identified novel alleles of the E1 paralogues, E1La and E1Lb, which promote flowering and maturity under natural photoperiods. These loci represent sources of genetic variation which have been under-utilized in North American breeding programs to control reproductive timing, and which can be valuable additions to a breeder's molecular toolbox.
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Affiliation(s)
- Nicholas Dietz
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Rachel Combs-Giroir
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Grace Cooper
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Minviluz Stacey
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Carrie Miranda
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Kristin Bilyeu
- USDA/ARS Plant Genetics Research Unit, Columbia, MO, 65211, USA.
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13
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Li S, Su T, Wang L, Kou K, Kong L, Kong F, Lu S, Liu B, Fang C. Rapid excavating a FLOWERING LOCUS T-regulator NF-YA using genotyping-by-sequencing. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:45. [PMID: 37309386 PMCID: PMC10236035 DOI: 10.1007/s11032-021-01237-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/07/2021] [Indexed: 06/14/2023]
Abstract
Soybean (Glycine max (L.) Merrill) is one of the most important crop plants in the world as an important source of protein for both human consumption and livestock fodder. As flowering time contributes to yield, finding new QTLs and further identifying candidate genes associated with various flowering time are fundamental to enhancing soybean yield. In this study, a set of 120 recombinant inbred lines (RILs) which was developed from a cross of two soybean cultivars, Suinong4 (SN4) and ZK168, were genotyped by genotyping-by-sequencing (GBS) approach and phenotyped to expand the cognitive of flowering time by quantitative trait loci (QTL) analysis. Eventually, three stable QTLs related to flowering time which were detected separately located on chromosome 14, 18, and 19 under long-day (LD) conditions. We predicted candidate genes for each QTL and carried out association analyses between the putative causal alleles and flowering time. Moreover, a transient transfection assay was performed and showed that NUCLEAR FACTOR YA 1b (GmNF-YA1b) as a strong candidate for the QTL on chromosome 19 might affect flowering time by suppressing the expression of FLOWERING LOCUS T (GmFT) genes in soybean. QTLs detected in this study would provide fundamental resources for finding candidate genes and clarify the mechanisms of flowering which would be helpful for breeding novel high-yielding soybean cultivars. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01237-w.
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Affiliation(s)
- Shichen Li
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tong Su
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lingshuang Wang
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kun Kou
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lingping Kong
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Fanjiang Kong
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Sijia Lu
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Baohui Liu
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Chao Fang
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
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14
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Xia Z, Zhai H, Wu H, Xu K, Watanabe S, Harada K. The Synchronized Efforts to Decipher the Molecular Basis for Soybean Maturity Loci E1, E2, and E3 That Regulate Flowering and Maturity. FRONTIERS IN PLANT SCIENCE 2021; 12:632754. [PMID: 33995435 PMCID: PMC8113421 DOI: 10.3389/fpls.2021.632754] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/02/2021] [Indexed: 06/12/2023]
Abstract
The general concept of photoperiodism, i.e., the photoperiodic induction of flowering, was established by Garner and Allard (1920). The genetic factor controlling flowering time, maturity, or photoperiodic responses was observed in soybean soon after the discovery of the photoperiodism. E1, E2, and E3 were named in 1971 and, thereafter, genetically characterized. At the centennial celebration of the discovery of photoperiodism in soybean, we recount our endeavors to successfully decipher the molecular bases for the major maturity loci E1, E2, and E3 in soybean. Through systematic efforts, we successfully cloned the E3 gene in 2009, the E2 gene in 2011, and the E1 gene in 2012. Recently, successful identification of several circadian-related genes such as PRR3a, LUX, and J has enriched the known major E1-FTs pathway. Further research progresses on the identification of new flowering and maturity-related genes as well as coordinated regulation between flowering genes will enable us to understand profoundly flowering gene network and determinants of latitudinal adaptation in soybean.
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Affiliation(s)
- Zhengjun Xia
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
| | - Hong Zhai
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
| | - Hongyan Wu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
| | - Kun Xu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
| | | | - Kyuya Harada
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
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15
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Hagely K, Konda AR, Kim JH, Cahoon EB, Bilyeu K. Molecular-assisted breeding for soybean with high oleic/low linolenic acid and elevated vitamin E in the seed oil. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:3. [PMID: 37309527 PMCID: PMC10231563 DOI: 10.1007/s11032-020-01184-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 10/26/2020] [Indexed: 06/13/2023]
Abstract
The uses of vegetable oils are determined by functional properties arising from their chemical composition. Soybean oil was previously used in margarines and baked foods after partial hydrogenation to achieve heat and oxidative stability. This process, however, generates trans fats that are now excluded from food use because of cardiovascular health risks. Also present in soybean oil are the anti-oxidant tocopherols, with α-tocopherol (vitamin E) typically present as a minor component compared to γ-tocopherol. Genetic improvement of the fatty acid profile and tocopherol profile is an attractive solution to increase the functional and health qualities of soybean oil. The objective of this research was to develop resources to directly select with molecular markers for the elevated vitamin E trait in soybean oil and to use a molecular breeding approach to combine elevated vitamin E with the high oleic/low linolenic acid seed oil trait that improves oil functionality and nutrition. New soybean germplasm was developed from the molecular breeding strategy that selected for alleles of six targeted genes. Seed oil from the novel soybean germplasm was confirmed to contain increased vitamin E α-tocopherol along with a high oleic acid/low linolenic acid profile.
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Affiliation(s)
- Katherine Hagely
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211 USA
| | - Anji Reddy Konda
- Center for Plant Science Innovation & Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588 USA
| | - Jeong-Hwa Kim
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211 USA
| | - Edgar B. Cahoon
- Center for Plant Science Innovation & Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588 USA
| | - Kristin Bilyeu
- USDA/ARS Plant Genetics Research Unit, Columbia, MO 65211 USA
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16
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Fu M, Wang Y, Ren H, Du W, Wang D, Bao R, Yang X, Tian Z, Fu L, Cheng Y, Su J, Sun B, Zhao J, Gai J. Genetic dynamics of earlier maturity group emergence in south-to-north extension of Northeast China soybeans. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1839-1857. [PMID: 32030467 DOI: 10.1007/s00122-020-03558-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 01/24/2020] [Indexed: 06/10/2023]
Abstract
KEY MESSAGE This population genetic study is characterized with direct comparisons of days to flowering QTL-allele matrices between newly evolved and originally old maturity groups of soybeans to explore its evolutionary dynamics using the RTM-GWAS procedure. The Northeast China (NEC) soybeans are the major germplasm source of modern soybean production in Americas (> 80% of the world total). NEC is a relatively new soybean area in China, expanded after its nomadic status in the seventeenth century. At nine sites of four ecoregions in NEC, 361 varieties were tested for their days to flowering (DTF), a geography-sensitive trait as an indicator for maturity groups (MGs). The DTF reduced obviously along with soybeans extended to higher latitudes, ranging in 41-83 days and MG 000-III. Using the RTM-GWAS (restricted two-stage multi-locus model genome-wide association study) procedure, 81 QTLs with 342 alleles were identified, accounting for 77.85% genetic contribution (R2 = 0.01-7.74%/locus), and other 20.75% (98.60-77.85%, h2 = 98.60%) genetic variation was due to a collective of unmapped QTLs. With soybeans northward, breeding effort made the original MG I-III evolved to MG 0-00-000. In direct comparisons of QTL-allele matrices among MGs, the genetic dynamics are identified with local exotic introduction/migration (58.48%) as the first and selection against/exclusion of positive alleles causing new recombination (40.64%) as the second, while only a few allele emergence/mutation happened (0.88%, limited in MG 0, not in MG 00-000). In new MG emergence, 24 QTLs with 19 candidate genes are the major sources. A genetic potential of further DTF shortening (13-21 days) is predicted for NEC population. The QTL detection in individual ecoregions showed various ecoregion-specific QTLs-alleles/genes after co-localization treatment (removing the random environment shifting ones).
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Affiliation(s)
- Mengmeng Fu
- Soybean Research Institute; MARA National Center for Soybean Improvement; MARA Key Laboratory of Biology and Genetic Improvement of Soybean; National Key Laboratory for Crop Genetics and Germplasm Enhancement; Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yanping Wang
- Mudanjiang Research and Development Center for Soybean; Mudanjiang Experiment Station of the National Center for Soybean Improvement, Mudanjiang Branch of Heilongjiang Academy of Agricultural Sciences, Mudanjiang, 157041, Heilongjiang, China
| | - Haixiang Ren
- Mudanjiang Research and Development Center for Soybean; Mudanjiang Experiment Station of the National Center for Soybean Improvement, Mudanjiang Branch of Heilongjiang Academy of Agricultural Sciences, Mudanjiang, 157041, Heilongjiang, China
| | - Weiguang Du
- Mudanjiang Research and Development Center for Soybean; Mudanjiang Experiment Station of the National Center for Soybean Improvement, Mudanjiang Branch of Heilongjiang Academy of Agricultural Sciences, Mudanjiang, 157041, Heilongjiang, China
| | - Deliang Wang
- Heilongjiang Academy of Land-reclamation Sciences, Jiamusi, 154007, Heilongjiang, China
| | - Rongjun Bao
- Bei'an Branch of Heilongjiang Academy of Agricultural Sciences, Bei'an, 164009, Heilongjiang, China
| | - Xingyong Yang
- Keshan Branch of Heilongjiang Academy of Agricultural Sciences, Keshan, 161606, Heilongjiang, China
| | - Zhongyan Tian
- Daqing Branch of Heilongjiang Academy of Agricultural Sciences, Daqing, 163316, Heilongjiang, China
| | - Lianshun Fu
- Tieling Academy of Agricultural Sciences, Tieling, 112616, Liaoning, China
| | - Yanxi Cheng
- Changchun Academy of Agricultural Sciences, Changchun, 130111, Jilin, China
| | - Jiangshun Su
- Baicheng Academy of Agricultural Sciences, Baicheng, 137000, Jinlin, China
| | - Bincheng Sun
- Hulunbeier Academy of Agricultural Sciences, Hulunbeier, 162650, Inner Mongolia, China
| | - Jinming Zhao
- Soybean Research Institute; MARA National Center for Soybean Improvement; MARA Key Laboratory of Biology and Genetic Improvement of Soybean; National Key Laboratory for Crop Genetics and Germplasm Enhancement; Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Mudanjiang Research and Development Center for Soybean; Mudanjiang Experiment Station of the National Center for Soybean Improvement, Mudanjiang Branch of Heilongjiang Academy of Agricultural Sciences, Mudanjiang, 157041, Heilongjiang, China
| | - Junyi Gai
- Soybean Research Institute; MARA National Center for Soybean Improvement; MARA Key Laboratory of Biology and Genetic Improvement of Soybean; National Key Laboratory for Crop Genetics and Germplasm Enhancement; Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
- Mudanjiang Research and Development Center for Soybean; Mudanjiang Experiment Station of the National Center for Soybean Improvement, Mudanjiang Branch of Heilongjiang Academy of Agricultural Sciences, Mudanjiang, 157041, Heilongjiang, China.
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17
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Beche E, Gillman JD, Song Q, Nelson R, Beissinger T, Decker J, Shannon G, Scaboo AM. Nested association mapping of important agronomic traits in three interspecific soybean populations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1039-1054. [PMID: 31974666 DOI: 10.1007/s00122-019-03529-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 12/30/2019] [Indexed: 06/10/2023]
Abstract
KEY MESSAGE Glycine soja germplasm can be used to successfully introduce new alleles with the potential to add valuable new genetic diversity to the current elite soybean gene pool. Given the demonstrated narrow genetic base of the US soybean production, it is essential to identify beneficial alleles from exotic germplasm, such as wild soybean, to enhance genetic gain for favorable traits. Nested association mapping (NAM) is an approach to population development that permits the comparison of allelic effects of the same QTL in multiple parents. Seed yield, plant maturity, plant height and plant lodging were evaluated in a NAM panel consisting of 392 recombinant inbred lines derived from three biparental interspecific soybean populations in eight environments during 2016 and 2017. Nested association mapping, combined with linkage mapping, identified three major QTL for plant maturity in chromosomes 6, 11 and 12 associated with alleles from wild soybean resulting in significant increases in days to maturity. A significant QTL for plant height was identified on chromosome 13 with the allele increasing plant height derived from wild soybean. A significant grain yield QTL was detected on chromosome 17, and the allele from Glycine soja had a positive effect of 166 kg ha-1; RIL's with the wild soybean allele yielded on average 6% more than the lines carrying the Glycine max allele. These findings demonstrate the usefulness and potential of alleles from wild soybean germplasm to enhance important agronomic traits in a soybean breeding program.
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Affiliation(s)
- Eduardo Beche
- Division of Plant Science, University of Missouri, Columbia, MO, USA
| | | | - Qijian Song
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, USA
| | - Randall Nelson
- Department of Crop Sciences, University of Illinois, 1101 W. Peabody Dr, Urbana, IL, 61801, USA
- USDA-Agricultural Research Service, 1101 W. Peabody Dr, Urbana, IL, 61801, USA
| | - Tim Beissinger
- Center for Integrated Breeding Research, Georg-August-Universität, Göttingen, Germany
| | - Jared Decker
- Division of Animal Science, University of Missouri, Columbia, MO, USA
| | - Grover Shannon
- Division of Plant Science, University of Missouri, Columbia, MO, USA
| | - Andrew M Scaboo
- Division of Plant Science, University of Missouri, Columbia, MO, USA.
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18
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Miranda C, Scaboo A, Cober E, Denwar N, Bilyeu K. The effects and interaction of soybean maturity gene alleles controlling flowering time, maturity, and adaptation in tropical environments. BMC PLANT BIOLOGY 2020; 20:65. [PMID: 32033536 PMCID: PMC7006184 DOI: 10.1186/s12870-020-2276-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 02/03/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Soybean is native to the temperate zones of East Asia. Poor yields of soybean in West African countries may be partially attributed to inadequate adaptation of soybean to tropical environments. Adaptation will require knowledge of the effects of allelic combinations of major maturity genes (E1, E2, and E3) and stem architecture. The long juvenile trait (J) influences soybean flowering time in short, ~ 12 h days, which characterize tropical latitudes. Soybean plant architecture includes determinate or indeterminate stem phenotypes controlled by the Dt1 gene. Understanding the influence of these genetic components on plant development and adaptation is key to optimize phenology and improve soybean yield potential in tropical environments. RESULTS Soybean lines from five recombinant inbred populations were developed that varied in their combinations of targeted genes. The soybean lines were field tested in multiple environments and characterized for days to flowering (DTF), days to maturity (DTM), and plant height in locations throughout northern Ghana, and allelic combinations were determined for each line for associating genotype with phenotype. The results revealed significant differences based on genotype for DTF and DTM and allowed the comparison of different variant alleles of those genes. The mutant alleles of J and E1 had significant impact on DTF and DTM, and alleles of those genes interacted with each other for DTF but not DTM. The Dt1 gene significantly influenced plant height but not DTF or DTM. CONCLUSIONS This research identified major and minor effect alleles of soybean genes that can be combined to control DTF, DTM, and plant height in short day tropical environments in Ghana. These phenotypes contribute to adaptation to a low latitude environment that can be optimized in a soybean breeding program with targeted selection of desired allele combinations. The knowledge of the genetic control of these traits will enhance molecular breeding to produce optimally adapted soybean varieties targeted to tropical environments.
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Affiliation(s)
- Carrie Miranda
- USDA/ARS Plant Genetics Research Unit, 110 Waters Hall, University of Missouri, Columbia, MO 65211 USA
| | - Andrew Scaboo
- Division of Plant Sciences, 110 Waters Hall, University of Missouri, Columbia, MO 65211 USA
| | - Elroy Cober
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario K1A 0C6 Canada
| | - Nicholas Denwar
- CSIR-Savanna Agricultural Research Institute, P. O. Box 52, Tamale, Ghana
| | - Kristin Bilyeu
- USDA/ARS Plant Genetics Research Unit, 110 Waters Hall, University of Missouri, Columbia, MO 65211 USA
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19
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Bruce RW, Torkamaneh D, Grainger C, Belzile F, Eskandari M, Rajcan I. Genome-wide genetic diversity is maintained through decades of soybean breeding in Canada. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:3089-3100. [PMID: 31384959 DOI: 10.1007/s00122-019-03408-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 07/24/2019] [Indexed: 05/20/2023]
Abstract
KEY MESSAGE Genetic diversity in Canadian soybean is maintained over decades of selection in two public breeding programs. Breeders have used a portion of the genetic diversity available in germplasm collections. Both public and private breeding efforts have been critical for the development of soybean cultivars grown around the world. Global genetic diversity of soybean has been well characterized; however, this diversity is not well studied at the breeding program scale. The objective of this study was to characterize genetic diversity over decades of breeding in two public soybean breeding programs at the University of Guelph, Canada. To address this objective, a pedigree-related panel combining 296 soybean accessions from the Ridgetown and Guelph Campus breeding programs was studied. The accessions were genotyped using genotyping-by-sequencing, imputed using the GmHapMap reference genotypes resulting in more than 3.8M SNPs, further filtered to 77k SNPs. Population structure analysis did not identify structure between the breeding programs and historical germplasm. The linkage disequilibrium decay ranged from 400 to 600 kb on average in euchromatic regions. Nucleotide diversity over decades of breeding shows that historical accessions had the highest nucleotide diversity, with significant decreases corresponding to the initial breeding activity in Canada; however, genetic diversity has increased in the last 20 years in both breeding programs. Maturity gene E2 was nearly fixed for e2 in Ridgetown accessions, while unfixed in Guelph accessions. Comparison of the breeding programs to the USDA germplasm collection reveals that breeders have only used a portion of the available genetic diversity, allowing future breeders to exploit this untapped resource. The approach used in this study may be of interest to other breeding programs for evaluating changes in genetic diversity resulting from breeding activities.
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Affiliation(s)
- Robert W Bruce
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Davoud Torkamaneh
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | | | - François Belzile
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Milad Eskandari
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Istvan Rajcan
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada.
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20
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Kumawat G, Yadav A, Satpute GK, Gireesh C, Patel R, Shivakumar M, Gupta S, Chand S, Bhatia VS. Genetic relationship, population structure analysis and allelic characterization of flowering and maturity genes E1, E2, E3 and E4 among 90 Indian soybean landraces. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2019; 25:387-398. [PMID: 30956422 PMCID: PMC6419859 DOI: 10.1007/s12298-018-0615-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 10/03/2018] [Accepted: 10/08/2018] [Indexed: 06/03/2023]
Abstract
A set of 90 Indian soybean landraces were analysed for polymorphism at 43 SSRs and five allele specific markers of four major genes involved in regulating flowering and photoperiod response. A total of 42 polymorphic SSRs had amplified 126 alleles which served as raw data for estimation of genetic relationship and population structure among 90 accessions. Rare alleles of four and three SSRs were detected in accessions IC18768 and IC15089, respectively. Gene diversity in the population ranges from 0.065 to 0.717 with a mean value of 0.411. The polymorphism information content of 42 SSRs varied from 0.063 to 0.668. Hierarchical clustering based on neighbour-joining method identified three major clusters among 90 soybean accessions. Model based population structure analysis divided the 90 soybean accessions into four populations (K = 4). Mean value of Fst for different populations ranged between 0.4143 and 0.7239. Genotyping of 90 accessions with allele specific markers had identified accession IC15089 as triple recessive mutant of flowering genes E1, E2 and photoperiod sensitivity gene E3. The triple mutant IC15089 (e1, e3, e3) had been characterized phenotypically and identified as early maturing (88 days) and photoperiod insensitive genotype under extended photoperiod. The present study characterized genetic relationship among 90 Indian soybean landraces and had identified a few diverse and unique genotypes for utilization in soybean breeding programmes targeting development of short duration and photoperiod insensitive varieties through marker assisted selection.
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Affiliation(s)
- Giriraj Kumawat
- ICAR-Indian Institute of Soybean Research, Indore, Madhya Pradesh 452001 India
| | - Arti Yadav
- School of Life Sciences, Devi Ahilya Vishwavidyalaya, Indore, Madhya Pradesh 452001 India
| | - Gyanesh K. Satpute
- ICAR-Indian Institute of Soybean Research, Indore, Madhya Pradesh 452001 India
| | - C. Gireesh
- ICAR-Indian Institute of Soybean Research, Indore, Madhya Pradesh 452001 India
| | - Rakesh Patel
- ICAR-Indian Institute of Soybean Research, Indore, Madhya Pradesh 452001 India
| | - M. Shivakumar
- ICAR-Indian Institute of Soybean Research, Indore, Madhya Pradesh 452001 India
| | - Sanjay Gupta
- ICAR-Indian Institute of Soybean Research, Indore, Madhya Pradesh 452001 India
| | - Suresh Chand
- School of Life Sciences, Devi Ahilya Vishwavidyalaya, Indore, Madhya Pradesh 452001 India
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Li MW, Liu W, Lam HM, Gendron JM. Characterization of Two Growth Period QTLs Reveals Modification of PRR3 Genes During Soybean Domestication. PLANT & CELL PHYSIOLOGY 2019; 60:407-420. [PMID: 30418611 DOI: 10.1093/pcp/pcy215] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 11/01/2018] [Indexed: 06/09/2023]
Abstract
Soybean yield is largely dependent on growth period. We characterized two growth period quantitative trait loci, Gp11 and Gp12, from a recombinant inbred population generated from a cross of wild (W05) and cultivated (C08) soybean. Lines carrying Gp11C08 and Gp12C08 tend to have a shorter growth period and higher expression of GmFT2a and GmFT5a. Furthermore, multiple interval mapping suggests that Gp11 and Gp12 may be genetically interacting with the E2 locus. This is consistent with the observation that GmFT2a and GmFT5a are activated by Gp11C08 and Gp12C08 at ZT4 in the recessive e2 but not the dominant E2 background. Gp11 and Gp12 are duplicated genomic regions each containing a copy of the soybean ortholog of PSEUDO RESPONSE REGULATOR 3 (GmPRR3A and GmPRR3B). GmPRR3A and GmPRR3B from C08 carry mutations that delete the CCT domain in the encoded proteins. These mutations were selected during soybean improvement and they alter the subcellular localization of GmPRR3A and GmPRR3B. Furthermore, GmPRR3A and GmPRR3B can interact with TOPLESS-related transcription factors, suggesting that they function in a transcription repressor complex. This study addresses previously unexplored components of the genetic network that probably controls the growth period of soybean and puts these loci into context with the well-characterized growth period-regulating E loci.
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Affiliation(s)
- Man-Wah Li
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Wei Liu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Hon-Ming Lam
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR
| | - Joshua M Gendron
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
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Li Y, Dong Y, Wu H, Hu B, Zhai H, Yang J, Xia Z. Positional Cloning of the Flowering Time QTL qFT12-1 Reveals the Link Between the Clock Related PRR Homolog With Photoperiodic Response in Soybeans. FRONTIERS IN PLANT SCIENCE 2019; 10:1303. [PMID: 31681389 PMCID: PMC6803524 DOI: 10.3389/fpls.2019.01303] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 09/18/2019] [Indexed: 05/10/2023]
Abstract
Flowering time and maturity are important agronomic traits for soybean cultivars to adapt to different latitudes and achieve maximal yield. Genetic studies on genes and quantitative trait loci (QTL) that control flowering time and maturity are extensive. In particular, the molecular bases of E1-E4, E6, E9, E10, and J have been deciphered. For a better understanding of regulation of flowering time gene networks, we need to understand if more molecular factors carrying different biological functions are also involved in the regulation of flowering time in soybeans. We developed a population derived from a cross between a landrace Jilincailihua (male) and a Chinese cultivar Chongnong16 (female). Both parents carry the same genotypes of E1e2E3HaE4 at E1, E2, E3, and E4 loci. Nighty-six individuals of the F2 population were genotyped with Illumina SoySNP8k iSelect BeadChip. A total of 2,407 polymorphic single nucleotide polymorphism (SNP) markers were used to construct a genetic linkage map. One major QTL, qFT12-1, was mapped to an approximately 567-kB region on chromosome 12. Genotyping and phenotyping of recombinant plant whose recombination events were occurring within the QTL region allowed us to narrow down the QTL region to 56.4 kB, in which four genes were annotated. Allelism and association analysis indicated Glyma.12G073900, a PRR7 homolog, is the strongest candidate gene for qFT12-1. The findings of this study disclosed the possible involvement of circadian clock gene in flowering time regulation of soybeans.
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Affiliation(s)
- Yuqiu Li
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
- Soybean Research Institute, Jilin Academy Agricultural of Science, Changchun, China
| | - Yingshan Dong
- Soybean Research Institute, Jilin Academy Agricultural of Science, Changchun, China
| | - Hongyan Wu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
| | - Bo Hu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hong Zhai
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
| | - Jiayin Yang
- Crop Development Center, Huaiyin Institute of Agricultural Sciences in Xuhuai Region of Jiangsu Province, Huaian, China
| | - Zhengjun Xia
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
- *Correspondence: Zheng-jun Xia,
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Nagatoshi Y, Fujita Y. Accelerating Soybean Breeding in a CO2-Supplemented Growth Chamber. PLANT & CELL PHYSIOLOGY 2019; 60:77-84. [PMID: 30219921 PMCID: PMC6343635 DOI: 10.1093/pcp/pcy189] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 09/07/2018] [Indexed: 05/13/2023]
Abstract
Soybean (Glycine max) is the most important dicot crop worldwide, and is increasingly used as a model legume due to the wide availability of genomic soybean resources; however, the slow generation times of soybean plants are currently a major hindrance to research. Here, we demonstrate a method for accelerating soybean breeding in compact growth chambers, which greatly shortens the generation time of the plants and accelerates breeding and research projects. Our breeding method utilizes commonly used fluorescent lamps (220 µmol m-2 s-1 at the canopy level), a 14 h light (30°C)/10 h dark (25°C) cycle and carbon dioxide (CO2) supplementation at >400 p.p.m. Using this approach, the generation time of the best-characterized elite Japanese soybean cultivar, Enrei, was shortened from 102-132 d reported in the field to just 70 d, thereby allowing up to 5 generations per year instead of the 1-2 generations currently possible in the field and/or greenhouse. The method also facilitates the highly efficient and controlled crossing of soybean plants. Our method uses CO2 supplementation to promote the growth and yield of plants, appropriate light and temperature conditions to reduce the days to flowering, and the reaping and sowing of immature seeds to shorten the reproductive period greatly. Thus, the appropriate parameters enable acceleration of soybean breeding in the compact growth chambers commonly used for laboratory research. The parameters used in our method could therefore be optimized for other species, cultivars, accessions and experimental designs to facilitate rapid breeding in a wide range of crops.
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Affiliation(s)
- Yukari Nagatoshi
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, Japan
| | - Yasunari Fujita
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
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Salentijn EMJ, Petit J, Trindade LM. The Complex Interactions Between Flowering Behavior and Fiber Quality in Hemp. FRONTIERS IN PLANT SCIENCE 2019; 10:614. [PMID: 31156677 PMCID: PMC6532435 DOI: 10.3389/fpls.2019.00614] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/25/2019] [Indexed: 05/05/2023]
Abstract
Hemp, Cannabis sativa L., is a sustainable multipurpose fiber crop with high nutrient and water use efficiency and with biomass of excellent quality for textile fibers and construction materials. The yield and quality of hemp biomass are largely determined by the genetic background of the hemp cultivar but are also strongly affected by environmental factors, such as temperature and photoperiod. Hemp is a facultative short-day plant, characterized by a strong adaptation to photoperiod and a great influence of environmental factors on important agronomic traits such as "flowering-time" and "sex determination." This sensitivity of hemp can cause a considerable degree of heterogeneity, leading to unforeseen yield reductions. Fiber quality for instance is influenced by the developmental stage of hemp at harvest. Also, male and female plants differ in stature and produce fibers with different properties and quality. Next to these causes, there is evidence for specific genotypic variation in fiber quality among hemp accessions. Before improved hemp cultivars can be developed, with specific flowering-times and fiber qualities, and adapted to different geographical regions, a better understanding of the molecular mechanisms controlling important phenological traits such as "flowering-time" and "sex determination" in relation to fiber quality in hemp is required. It is well known that genetic factors play a major role in the outcome of both phenological traits, but the major molecular factors involved in this mechanism are not characterized in hemp. Genome sequences and transcriptome data are available but their analysis mainly focused on the cannabinoid pathway for medical purposes. Herein, we review the current knowledge of phenotypic and genetic data available for "flowering-time," "sex determination," and "fiber quality" in short-day and dioecious crops, respectively, and compare them with the situation in hemp. A picture emerges for several controlling key genes, for which natural genetic variation may lead to desired flowering behavior, including examples of pleiotropic effects on yield quality and on carbon partitioning. Finally, we discuss the prospects for using this knowledge for the molecular breeding of this sustainable crop via a candidate gene approach.
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Miladinović J, Ćeran M, Đorđević V, Balešević-Tubić S, Petrović K, Đukić V, Miladinović D. Allelic Variation and Distribution of the Major Maturity Genes in Different Soybean Collections. FRONTIERS IN PLANT SCIENCE 2018; 9:1286. [PMID: 30233624 PMCID: PMC6131654 DOI: 10.3389/fpls.2018.01286] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 08/16/2018] [Indexed: 05/20/2023]
Abstract
Soybean time of flowering and maturity are genetically controlled by E genes. Different allelic combinations of these genes determine soybean adaptation to a specific latitude. The paper describes the first attempt to assess adaptation of soybean genotypes developed and realized at Institute of Field and Vegetable Crops, Novi Sad, Serbia [Novi Sad (NS) varieties and breeding lines] based on E gene variation, as well as to comparatively assess E gene variation in North-American (NA), Chinese, and European genotypes, as most of the studies published so far deal with North-American and Chinese cultivars and breeding material. Allelic variation and distribution of the major maturity genes (E1, E2, E3, and E4) has been determined in 445 genotypes from soybean collections of NA ancestral lines, Chinese germplasm, and European varieties, as well as NS varieties and breeding lines. The study showed that allelic combinations of E1-E4 genes significantly determined the adaptation of varieties to different geographical regions, although they have different impacts on maturity. In general, each collection had one major E genotype haplogroup, comprising over 50% of the lines. The exceptions were European varieties that had two predominant haplogroups and NA ancestral lines distributed almost evenly among several haplogroups. As e1-as/e2/E3/E4 was the most common genotype in NS population, present in the best-performing genotypes in terms of yield, this specific allele combination was proposed as the optimal combination for the environments of Central-Eastern Europe.
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Affiliation(s)
- Jegor Miladinović
- Soybean Department, Institute of Field and Vegetable Crops, Novi Sad, Serbia
| | - Marina Ćeran
- Soybean Department, Institute of Field and Vegetable Crops, Novi Sad, Serbia
| | - Vuk Đorđević
- Soybean Department, Institute of Field and Vegetable Crops, Novi Sad, Serbia
| | | | - Kristina Petrović
- Soybean Department, Institute of Field and Vegetable Crops, Novi Sad, Serbia
| | - Vojin Đukić
- Soybean Department, Institute of Field and Vegetable Crops, Novi Sad, Serbia
| | - Dragana Miladinović
- Industrial Crops Department, Institute of Field and Vegetable Crops, Novi Sad, Serbia
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26
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Wang YY, Li YQ, Wu HY, Hu B, Zheng JJ, Zhai H, Lv SX, Liu XL, Chen X, Qiu HM, Yang J, Zong CM, Han DZ, Wen ZX, Wang DC, Xia ZJ. Genotyping of Soybean Cultivars With Medium-Density Array Reveals the Population Structure and QTNs Underlying Maturity and Seed Traits. FRONTIERS IN PLANT SCIENCE 2018; 9:610. [PMID: 29868067 PMCID: PMC5954420 DOI: 10.3389/fpls.2018.00610] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 04/17/2018] [Indexed: 05/08/2023]
Abstract
Soybean was domesticated about 5,000 to 6,000 years ago in China. Although genotyping technologies such as genotyping by sequencing (GBS) and high-density array are available, it is convenient and economical to genotype cultivars or populations using medium-density SNP array in genetic study as well as in molecular breeding. In this study, 235 cultivars, collected from China, Japan, USA, Canada and some other countries, were genotyped using SoySNP8k iSelect BeadChip with 7,189 single nucleotide polymorphisms (SNPs). In total, 4,471 polymorphic SNP markers were used to analyze population structure and perform genome-wide association study (GWAS). The most likely K value was 7, indicating this population can be divided into 7 subpopulations, which is well in accordance with the geographic origins of cultivars or accession studied. The LD decay rate was estimated at 184 kb, where r2 dropped to half of its maximum value (0.205). GWAS using FarmCPU detected a stable quantitative trait nucleotide (QTN) for hilum color and seed color, which is consistent with the known loci or genes. Although no universal QTNs for flowering time and maturity were identified across all environments, a total of 30 consistent QTNs were detected for flowering time (R1) or maturity (R7 and R8) on 16 chromosomes, most of them were corresponding to known E1 to E4 genes or QTL region reported in SoyBase (soybase.org). Of 16 consistent QTNs for protein and oil contents, 11 QTNs were detected having antagonistic effects on protein and oil content, while 4 QTNs soly for oil content, and one QTN soly for protein content. The information gained in this study demonstrated that the usefulness of the medium-density SNP array in genotyping for genetic study and molecular breeding.
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Affiliation(s)
- Ya-ying Wang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu-qiu Li
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Hong-yan Wu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Bo Hu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jia-jia Zheng
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hong Zhai
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Shi-xiang Lv
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Xin-lei Liu
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Xin Chen
- Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Hong-mei Qiu
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Jiayin Yang
- Huaiyin Institute of Agricultural Sciences in Xuhuai Region of Jiangsu Province, Huaian, China
| | - Chun-mei Zong
- Mudanjiang Branch of Heilongjiang Academy of Agricultural Sciences, Mudanjiang, China
| | - De-zhi Han
- Heihe Branch of Heilongjiang Academy of Agricultural Sciences, Heihe, China
| | - Zi-xiang Wen
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - De-chun Wang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Zheng-jun Xia
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
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Bilyeu K, Škrabišová M, Allen D, Rajcan I, Palmquist DE, Gillen A, Mian R, Jo H. The Interaction of the Soybean Seed High Oleic Acid Oil Trait With Other Fatty Acid Modifications. J AM OIL CHEM SOC 2018. [DOI: 10.1002/aocs.12025] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Kristin Bilyeu
- USDA/ARS Plant Genetics Research Unit; University of Missouri; Columbia MO 65211 USA
| | - Mária Škrabišová
- Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science; Palacký University in Olomouc; Olomouc Czech Republic, 783 71
| | - Doug Allen
- USDA/ARS Plant Genetics Research Unit; Donald Danforth Plant Science Center; St Louis MO 63132 USA
| | - Istvan Rajcan
- Department of Plant Agriculture; University of Guelph; Guelph ON N1G 2W1 Canada
| | | | - Anne Gillen
- USDA/ARS Crop Genetics Research Unit; Stoneville MS 38776 USA
| | - Rouf Mian
- USDA/ARS Soybean and Nitrogen Fixation Research Unit; Raleigh NC 27607 USA
| | - Hyun Jo
- Division of Plant Sciences; University of Missouri; Columbia MO 65211 USA
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