1
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Horitani M, Yamada R, Taroura K, Maeda A, Anai T, Watanabe S. Identification of Genes Responsible for the Synthesis of Glycitein Isoflavones in Soybean Seeds. PLANTS (BASEL, SWITZERLAND) 2024; 13:156. [PMID: 38256710 PMCID: PMC10818676 DOI: 10.3390/plants13020156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/23/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024]
Abstract
Soybean (Glycine max (L.) Merrill) isoflavones are among the most important secondary metabolites, with functional benefits for human health. Soybeans accumulate three aglycone forms of isoflavones: genistein, daidzein, and glycitein. Soybean landrace Kumachi-1 does not accumulate malonylglycitin at all. Gene structure analysis indicated that Glyma.11G108300 (F6H4) of Kumachi-1 has a 3.8-kbp insertion, resulting in a truncated flavonoid 6-hydroxylase (F6H) sequence compared to the wild-type sequence in Fukuyutaka. Mapping experiments using a mutant line (MUT1246) with a phenotype similar to that of Kumachi-1, with a single-nucleotide polymorphism (SNP) in F6H4, revealed co-segregation of this mutation and the absence of glycitein isoflavones. We also identified a mutant line (K01) that exhibited a change in the HPLC retention time of glycitein isoflavones, accumulating glycoside and malonylglycoside forms of 6-hydroxydaidzein. K01 contains an SNP that produces a premature stop codon in Glyma.01G004200 (IOMT3), a novel soybean isoflavone O-methyltransferase (IOMT) gene. We further analyzed transgenic hairy roots of soybeans expressing Glyma.11G108300 (F6H4) and Glyma.01G004200 (IOMT3). Those overexpressing F6H4 accumulated malonylglycoside forms of 6-hydroxydaidzein (M_6HD), and co-expression of F6H4 and IOMT3 increased the level of malonylglycitin but not of M_6HD. These results indicate that F6H4 and IOMT3 are responsible for glycitein biosynthesis in soybean seed hypocotyl.
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Affiliation(s)
- Masaki Horitani
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga 840-8502, Japan; (M.H.)
| | - Risa Yamada
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga 840-8502, Japan; (M.H.)
| | - Kanami Taroura
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga 840-8502, Japan; (M.H.)
| | - Akari Maeda
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga 840-8502, Japan; (M.H.)
| | - Toyoaki Anai
- Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan;
| | - Satoshi Watanabe
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga 840-8502, Japan; (M.H.)
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2
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Singer WM, Lee YC, Shea Z, Vieira CC, Lee D, Li X, Cunicelli M, Kadam SS, Khan MAW, Shannon G, Mian MAR, Nguyen HT, Zhang B. Soybean genetics, genomics, and breeding for improving nutritional value and reducing antinutritional traits in food and feed. THE PLANT GENOME 2023; 16:e20415. [PMID: 38084377 DOI: 10.1002/tpg2.20415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 12/22/2023]
Abstract
Soybean [Glycine max (L.) Merr.] is a globally important crop due to its valuable seed composition, versatile feed, food, and industrial end-uses, and consistent genetic gain. Successful genetic gain in soybean has led to widespread adaptation and increased value for producers, processors, and consumers. Specific focus on the nutritional quality of soybean seed composition for food and feed has further elucidated genetic knowledge and bolstered breeding progress. Seed components are historical and current targets for soybean breeders seeking to improve nutritional quality of soybean. This article reviews genetic and genomic foundations for improvement of nutritionally important traits, such as protein and amino acids, oil and fatty acids, carbohydrates, and specific food-grade considerations; discusses the application of advanced breeding technology such as CRISPR/Cas9 in creating seed composition variations; and provides future directions and breeding recommendations regarding soybean seed composition traits.
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Affiliation(s)
- William M Singer
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Yi-Chen Lee
- Department of Agriculture, Fort Hays State University, Hays, Kansas, USA
| | - Zachary Shea
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Caio Canella Vieira
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas, USA
| | - Dongho Lee
- Fisher Delta Research, Extension, and Education Center, University of Missouri, Portageville, Missouri, USA
| | - Xiaoying Li
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Mia Cunicelli
- Soybean and Nitrogen Fixation Research Unit, USDA-ARS, Raleigh, North Carolina, USA
| | - Shaila S Kadam
- Division of Plant Science and Technology, University of Missouri, Columbia, Missouri, USA
| | | | - Grover Shannon
- Fisher Delta Research, Extension, and Education Center, University of Missouri, Portageville, Missouri, USA
| | - M A Rouf Mian
- Soybean and Nitrogen Fixation Research Unit, USDA-ARS, Raleigh, North Carolina, USA
| | - Henry T Nguyen
- Division of Plant Science and Technology, University of Missouri, Columbia, Missouri, USA
| | - Bo Zhang
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
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3
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Kim JM, Seo JS, Lee JW, Lyu JI, Ryu J, Eom SH, Ha BK, Kwon SJ. QTL mapping reveals key factors related to the isoflavone contents and agronomic traits of soybean (Glycine max). BMC PLANT BIOLOGY 2023; 23:517. [PMID: 37880577 PMCID: PMC10601131 DOI: 10.1186/s12870-023-04519-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 10/10/2023] [Indexed: 10/27/2023]
Abstract
BACKGROUND Soybean is a valuable source of edible protein and oil, as well as secondary metabolites that can be used in food products, cosmetics, and medicines. However, because soybean isoflavone content is a quantitative trait influenced by polygenes and environmental interactions, its genetic basis remains unclear. RESULTS This study was conducted to identify causal quantitative trait loci (QTLs) associated with soybean isoflavone contents. A mutant-based F2 population (190 individuals) was created by crossing the Korean cultivar Hwanggeum with low isoflavone contents (1,558 µg g-1) and the soybean mutant DB-088 with high isoflavone contents (6,393 µg g-1). A linkage map (3,049 cM) with an average chromosome length of 152 cM was constructed using the 180K AXIOM® SoyaSNP array. Thirteen QTLs related to agronomic traits were mapped to chromosomes 2, 3, 11, 13, 19, and 20, whereas 29 QTLs associated with isoflavone contents were mapped to chromosomes 1, 3, 8, 11, 14, 15, and 17. Notably, the qMGLI11, qMGNI11, qADZI11, and qTI11, which located Gm11_9877690 to Gm11_9955924 interval on chromosome 11, contributed to the high isoflavone contents and explained 11.9% to 20.1% of the phenotypic variation. This QTL region included four candidate genes, encoding β-glucosidases 13, 14, 17-1, and 17-2. We observed significant differences in the expression levels of these genes at various seed developmental stages. Candidate genes within the causal QTLs were functionally characterized based on enriched GO terms and KEGG pathways, as well as the results of a co-expression network analysis. A correlation analysis indicated that certain agronomic traits (e.g., days to flowering, days to maturity, and plant height) are positively correlated with isoflavone content. CONCLUSIONS Herein, we reported that the major QTL associated with isoflavone contents was located in the interval from Gm11_9877690 to Gm11_9955924 (78 kb) on chromosome 11. Four β-glucosidase genes were identified that may be involved in high isoflavone contents of soybean DB-088. Thus, the mutant alleles from soybean DB-088 may be useful for marker-assisted selection in developing soybean lines with high isoflavone contents and superior agronomic traits.
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Affiliation(s)
- Jung Min Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
| | - Ji Su Seo
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
- Department of Applied Plant Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Jeong Woo Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
- Department of Applied Plant Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Jae Il Lyu
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Jaihyunk Ryu
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
| | - Seok Hyun Eom
- Department of Smart Farm Science, College of Life Sciences, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Bo-Keun Ha
- Department of Applied Plant Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Republic of Korea.
| | - Soon-Jae Kwon
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea.
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4
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Wu D, Li D, Zhao X, Zhan Y, Teng W, Qiu L, Zheng H, Li W, Han Y. Identification of a candidate gene associated with isoflavone content in soybean seeds using genome-wide association and linkage mapping. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:950-963. [PMID: 32862479 DOI: 10.1111/tpj.14972] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 07/29/2020] [Accepted: 08/10/2020] [Indexed: 05/11/2023]
Abstract
Isoflavone, a secondary metabolite produced by Glycine max (L.) Merr. (soybean), is valuable for human and plant health. The genetic architecture of soybean isoflavone content remains unclear, however, despite several mapping studies. We generated genomic data for 200 soybean cultivars and 150 recombinant inbred lines (RILs) to localize putative loci associated with soybean seed isoflavone content. Using a genome-wide association study (GWAS), we identified 87 single-nucleotide polymorphisms (SNPs) that were significantly associated with isoflavone concentration. Using linkage mapping, we identified 37 quantitative trait loci (QTLs) underlying the content of four isoflavones found in the RILs. A major locus on chromosome 8 (qISO8-1) was co-located by both the GWAS and linkage mapping. qISO8-1 was fine mapped to a 99.5-kb region, flanked by SSR_08_1651 and SSR_08_1656, in a BC2 F5 population. GmMPK1, encoding a mitogen-activated protein kinase, was identified as the causal gene in qISO8-1, and two natural GmMPK1 polymorphisms were significantly associated with isoflavone content. Overexpression of GmMPK1 in soybean hairy roots resulted in increased isoflavone concentrations. Overexpressing GmMPK1 in transgenic soybeans had greater resistance to Phytophthora root rot, suggesting that GmMPK1 might increase soybean resistance to biotic stress by influencing isoflavone content. Our results not only increase our understanding of the genetic architecture of soybean seed isoflavone content, but also provide a framework for the future marker-assisted breeding of high isoflavone content in soybean cultivars.
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Affiliation(s)
- Depeng Wu
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030, China
| | - Dongmei Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030, China
| | - Xue Zhao
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030, China
| | - Yuhang Zhan
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030, China
| | - Weili Teng
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030, China
| | - Lijuan Qiu
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hongkun Zheng
- Bioinformatics Division, Biomarker Technologies Corporation, Beijing, 101300, China
| | - Wenbin Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030, China
| | - Yingpeng Han
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030, China
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5
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Potential Impacts of Soil Tillage System on Isoflavone Concentration of Soybean as Functional Food Ingredients. LAND 2020. [DOI: 10.3390/land9100386] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Soybean is an important natural source of isoflavones, but their concentration is likely to be influenced by external factors, such as climatic conditions and soil tillage systems. However, there is minimal information about the effects of such external factors on the isoflavone concentration in soybeans grown in Europe. Therefore, in this study, field experiments were established in Romania to investigate the potential impacts of three different soil tillage systems—conventional, minimum tillage and no-tillage—on crop yields and the isoflavone concentration of soybeans for three experimental years, 2014–2016. Our experimental results indicated that the soil tillage systems had little impact on the soybean yields each year. However, the 2016 yield was found to be higher than the 2014 and 2015 yields under all three soil systems. For every experimental year, the higher yield was recorded by the conventional system, followed by the minimum tillage system and no-tillage system under first weed control (weed control two (wct2): S-metolaclor 960 g/L, imazamox 40 g/L and propaquizafop 100 g/L). Likewise, the soil tillage system did not have a significant influence on the total isoflavone concentrations. Nevertheless, we noticed some variations in the individual isoflavone concentration (daidzin, genistin, glycitin, daidzein, genistein) in each year. Altogether, the minimum tillage and no-tillage systems may be employed as a suitable soil tillage system in soybean farming without an impact on the total isoflavone.
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6
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Sarkar MAR, Otsu W, Suzuki A, Hashimoto F, Anai T, Watanabe S. Single-base deletion in GmCHR5 increases the genistein-to-daidzein ratio in soybean seed. BREEDING SCIENCE 2020; 70:265-276. [PMID: 32714048 PMCID: PMC7372027 DOI: 10.1270/jsbbs.19134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 12/03/2019] [Indexed: 06/11/2023]
Abstract
Novel mutant alleles related to isoflavone content are useful for breeding programs to improve the disease resistance and nutritional content of soybean. However, identification of mutant alleles from high-density mutant libraries is expensive and time-consuming because soybean has a large, complicated genome. Here, we identified the gene responsible for increased genistein-to-daidzein ratio in seed of the mutant line F333ES017D9. For this purpose, we used a time- and cost-effective approach based on selective genotyping of a small number of F2 plants showing the mutant phenotype with nearest-neighboring-nucleotide substitution-high-resolution melting analysis markers, followed by alignment of short reads obtained by next-generation sequencing analysis with the identified locus. In the mutant line, GmCHR5 harbored a single-base deletion that caused a change in the substrate flow in the isoflavone biosynthetic pathway towards genistein. Mutated GmCHR5 was expressed at a lower level during seed development than wild-type GmCHR5. Ectopic overexpression of GmCHR5 increased the production of daidzein derivatives in both the wild-type and mutant plants. The present strategy will be useful for accelerating identification of mutant alleles responsible for traits of interest in agronomically important crops.
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Affiliation(s)
- Md. Abdur Rauf Sarkar
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga, Saga 840-8502, Japan
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Wakana Otsu
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga, Saga 840-8502, Japan
| | - Akihiro Suzuki
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga, Saga 840-8502, Japan
| | - Fumio Hashimoto
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Toyoaki Anai
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga, Saga 840-8502, Japan
| | - Satoshi Watanabe
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga, Saga 840-8502, Japan
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7
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Watanabe S, Yamada R, Kanetake H, Kaga A, Anai T. Identification and characterization of a major QTL underlying soybean isoflavone malonylglycitin content. BREEDING SCIENCE 2019; 69:564-572. [PMID: 31988620 PMCID: PMC6977442 DOI: 10.1270/jsbbs.19027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 06/20/2019] [Indexed: 05/27/2023]
Abstract
Isoflavones in soybean seeds are responsible for plant-microbe interactions and defend against pathogens, and are also beneficial to human health. We used two biparental populations and mini core collection of soybean germplasm to identify and validate QTLs underlying the content of isoflavone components. We identified a major QTL, qMGly_11, which regulates the content of malonylglycitin, on chromosome Gm11, in populations bred from parents with high, low, and null glycitein contents. qMGly_11 explained 44.5% of phenotypic variance in a population derived from a cross between 'Aokimame' (high) and 'Fukuyutaka' (low) and 79.9% of that in a population between 'Kumaji-1' (null) and 'Fukuyutaka' (low). The effect was observed only in the hypocotyl. We further confirmed the effect of qMGly_11 in a mini-core collection, where it explained 57.1% of the genetic diversity of glycitin production and 56.5% of malonylglycitin production. qMGly_11 increased the contents of glycitin and malonylglycitin at the expense of daidzin and malonyldaidzin in all analyzed populations. We discuss the gene responsible for this QTL and the availability of the null allele for metabolic engineering of soybean seed isoflavones.
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Affiliation(s)
- Satoshi Watanabe
- Faculty of Agriculture, Saga University,
1 Honjo-machi, Saga, Saga 840-8502,
Japan
| | - Risa Yamada
- Faculty of Agriculture, Saga University,
1 Honjo-machi, Saga, Saga 840-8502,
Japan
| | - Hazuki Kanetake
- Faculty of Agriculture, Saga University,
1 Honjo-machi, Saga, Saga 840-8502,
Japan
| | - Akito Kaga
- Soybean and Field Crop Applied Genomics Research Unit, Institute of Crop Science, NARO (National Agriculture and Food Research Organization),
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Toyoaki Anai
- Faculty of Agriculture, Saga University,
1 Honjo-machi, Saga, Saga 840-8502,
Japan
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de Camargo AC, Favero BT, Morzelle MC, Franchin M, Alvarez-Parrilla E, de la Rosa LA, Geraldi MV, Maróstica Júnior MR, Shahidi F, Schwember AR. Is Chickpea a Potential Substitute for Soybean? Phenolic Bioactives and Potential Health Benefits. Int J Mol Sci 2019; 20:E2644. [PMID: 31146372 PMCID: PMC6600242 DOI: 10.3390/ijms20112644] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 05/18/2019] [Accepted: 05/22/2019] [Indexed: 01/07/2023] Open
Abstract
Legume seeds are rich sources of protein, fiber, and minerals. In addition, their phenolic compounds as secondary metabolites render health benefits beyond basic nutrition. Lowering apolipoprotein B secretion from HepG2 cells and decreasing the level of low-density lipoprotein (LDL)-cholesterol oxidation are mechanisms related to the prevention of cardiovascular diseases (CVD). Likewise, low-level chronic inflammation and related disorders of the immune system are clinical predictors of cardiovascular pathology. Furthermore, DNA-damage signaling and repair are crucial pathways to the etiology of human cancers. Along CVD and cancer, the prevalence of obesity and diabetes is constantly increasing. Screening the ability of polyphenols in inactivating digestive enzymes is a good option in pre-clinical studies. In addition, in vivo studies support the role of polyphenols in the prevention and/or management of diabetes and obesity. Soybean, a well-recognized source of phenolic isoflavones, exerts health benefits by decreasing oxidative stress and inflammation related to the above-mentioned chronic ailments. Similar to soybeans, chickpeas are good sources of nutrients and phenolic compounds, especially isoflavones. This review summarizes the potential of chickpea as a substitute for soybean in terms of health beneficial outcomes. Therefore, this contribution may guide the industry in manufacturing functional foods and/or ingredients by using an undervalued feedstock.
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Affiliation(s)
- Adriano Costa de Camargo
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Casilla 306-22, Santiago, Chile.
| | - Bruno Trevenzoli Favero
- University of Copenhagen, Department of Plant and Environmental Sciences, 2630 Taastrup, Denmark.
| | - Maressa Caldeira Morzelle
- Department of Food and Nutrition, Faculty of Nutrition, Federal University of Mato Grosso, Fernando Correa Avenue, P.O. box 2367, Cuiabá, MT 78060-900, Brazil.
| | - Marcelo Franchin
- Department of Physiological Sciences, Piracicaba Dental School, University of Campinas, Piracicaba, SP 13414-903, Brazil.
| | - Emilio Alvarez-Parrilla
- Department of Chemical Biological Sciences, Universidad Autónoma de Ciudad Juárez, Anillo Envolvente del Pronaf y Estocolmo, s/n, Cd, Juárez, Chihuahua 32310, México.
| | - Laura A de la Rosa
- Department of Chemical Biological Sciences, Universidad Autónoma de Ciudad Juárez, Anillo Envolvente del Pronaf y Estocolmo, s/n, Cd, Juárez, Chihuahua 32310, México.
| | - Marina Vilar Geraldi
- Department of Food and Nutrition, University of Campinas-UNICAMP, Campinas, SP 13083-862, Brazil.
| | | | - Fereidoon Shahidi
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada.
| | - Andrés R Schwember
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Casilla 306-22, Santiago, Chile.
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9
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Cai Z, Cheng Y, Ma Z, Liu X, Ma Q, Xia Q, Zhang G, Mu Y, Nian H. Fine-mapping of QTLs for individual and total isoflavone content in soybean (Glycine max L.) using a high-density genetic map. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:555-568. [PMID: 29159422 DOI: 10.1007/s00122-017-3018-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 11/04/2017] [Indexed: 06/07/2023]
Abstract
KEY MESSAGE Fifteen stable QTLs were identified using a high-density soybean genetic map across multiple environments. One major QTL, qIF5-1, contributing to total isoflavone content explained phenotypic variance 49.38, 43.27, 46.59, 45.15 and 52.50%, respectively. Soybeans (Glycine max L.) are a major source of dietary isoflavones. To identify novel quantitative trait loci (QTL) underlying isoflavone content, and to improve the accuracy of marker-assisted breeding in soybean, a valuable mapping population comprised of 196 F7:8-10 recombinant inbred lines (RILs, Huachun 2 × Wayao) was utilized to evaluate individual and total isoflavone content in plants grown in four different environments in Guangdong. A high-density genetic linkage map containing 3469 recombination bin markers based on 0.2 × restriction site-associated DNA tag sequencing (RAD-seq) technology was used to finely map QTLs for both individual and total isoflavone contents. Correlation analyses showed that total isoflavone content, and that of five individual isoflavone, was significantly correlated across the four environments. Based on the high-density genetic linkage map, a total of 15 stable quantitative trait loci (QTLs) associated with isoflavone content across multiple environments were mapped onto chromosomes 02, 05, 07, 09, 10, 11, 13, 16, 17, and 19. Further, one of them, qIF5-1, localized to chromosomes 05 (38,434,171-39,045,620 bp) contributed to almost all isoflavone components across all environments, and explained 6.37-59.95% of the phenotypic variance, especially explained 49.38, 43.27, 46.59, 45.15 and 52.50% for total isoflavone. The results obtained in the present study will pave the way for a better understanding of the genetics of isoflavone accumulation and reveals the scope available for improvement of isoflavone content through marker-assisted selection.
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Affiliation(s)
- Zhandong Cai
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- Shofine Seed Technology Co., Ltd., Jiaxiang, 272400, Shandong, People's Republic of China
| | - Yanbo Cheng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- Shofine Seed Technology Co., Ltd., Jiaxiang, 272400, Shandong, People's Republic of China
| | - Zhuwen Ma
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, People's Republic of China
| | - Xinguo Liu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Qibin Ma
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- Shofine Seed Technology Co., Ltd., Jiaxiang, 272400, Shandong, People's Republic of China
| | - Qiuju Xia
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518086, People's Republic of China
| | - Gengyun Zhang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518086, People's Republic of China
| | - Yinghui Mu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.
- Shofine Seed Technology Co., Ltd., Jiaxiang, 272400, Shandong, People's Republic of China.
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.
- Shofine Seed Technology Co., Ltd., Jiaxiang, 272400, Shandong, People's Republic of China.
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Dwivedi SL, Upadhyaya HD, Chung IM, De Vita P, García-Lara S, Guajardo-Flores D, Gutiérrez-Uribe JA, Serna-Saldívar SO, Rajakumar G, Sahrawat KL, Kumar J, Ortiz R. Exploiting Phenylpropanoid Derivatives to Enhance the Nutraceutical Values of Cereals and Legumes. FRONTIERS IN PLANT SCIENCE 2016; 7:763. [PMID: 27375635 PMCID: PMC4891577 DOI: 10.3389/fpls.2016.00763] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 05/17/2016] [Indexed: 05/29/2023]
Abstract
Phenylpropanoids are a diverse chemical class with immense health benefits that are biosynthesized from the aromatic amino acid L-phenylalanine. This article reviews the progress for accessing variation in phenylpropanoids in germplasm collections, the genetic and molecular basis of phenylpropanoid biosynthesis, and the development of cultivars dense in seed-phenylpropanoids. Progress is also reviewed on high-throughput assays, factors that influence phenylpropanoids, the site of phenylpropanoids accumulation in seed, Genotype × Environment interactions, and on consumer attitudes for the acceptance of staple foods rich in phenylpropanoids. A paradigm shift was noted in barley, maize, rice, sorghum, soybean, and wheat, wherein cultivars rich in phenylpropanoids are grown in Europe and North and Central America. Studies have highlighted some biological constraints that need to be addressed for development of high-yielding cultivars that are rich in phenylpropanoids. Genomics-assisted breeding is expected to facilitate rapid introgression into improved genetic backgrounds by minimizing linkage drag. More research is needed to systematically characterize germplasm pools for assessing variation to support crop genetic enhancement, and assess consumer attitudes to foods rich in phenylpropanoids.
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Affiliation(s)
- Sangam L. Dwivedi
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Hari D. Upadhyaya
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
- Department of Agronomy, Kansas State UniversityManhattan, KS, USA
- UWA Institute of Agriculture, University of Western AustraliaCrawley, WA, Australia
| | - Ill-Min Chung
- Department of Applied Life Science, College of Life and Environmental Science, Konkuk UniversitySeoul, Korea
| | - Pasquale De Vita
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per la CerealicolturaFoggia, Italy
| | - Silverio García-Lara
- Tecnológico de Monterrey, Centro de Biotecnología-FEMSA, Escuela de Ingeniería y CienciasMonterrey, Mexico
| | - Daniel Guajardo-Flores
- Tecnológico de Monterrey, Centro de Biotecnología-FEMSA, Escuela de Ingeniería y CienciasMonterrey, Mexico
| | - Janet A. Gutiérrez-Uribe
- Tecnológico de Monterrey, Centro de Biotecnología-FEMSA, Escuela de Ingeniería y CienciasMonterrey, Mexico
| | - Sergio O. Serna-Saldívar
- Tecnológico de Monterrey, Centro de Biotecnología-FEMSA, Escuela de Ingeniería y CienciasMonterrey, Mexico
| | - Govindasamy Rajakumar
- Department of Applied Life Science, College of Life and Environmental Science, Konkuk UniversitySeoul, Korea
| | - Kanwar L. Sahrawat
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | | | - Rodomiro Ortiz
- Swedish University of Agricultural SciencesAlnarp, Sweden
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11
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Wang Y, Han Y, Zhao X, Li Y, Teng W, Li D, Zhan Y, Li W. Mapping isoflavone QTL with main, epistatic and QTL × environment effects in recombinant inbred lines of soybean. PLoS One 2015; 10:e0118447. [PMID: 25738957 PMCID: PMC4349890 DOI: 10.1371/journal.pone.0118447] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 01/16/2015] [Indexed: 12/16/2022] Open
Abstract
Soybean (Glycine max (L.) Merr.) isoflavone is important for human health and plant defense system. To identify novel quantitative trait loci (QTL) and epistatic QTL underlying isoflavone content in soybean, F5:6, F5:7 and F5:8 populations of 130 recombinant inbred (RI) lines, derived from the cross of soybean cultivar 'Zhong Dou 27' (high isoflavone) and 'Jiu Nong 20' (low isoflavone), were analyzed with 95 new SSR markers. A new linkage map including 194 SSR markers and covering 2,312 cM with mean distance of about 12 cM between markers was constructed. Thirty four QTL for both individual and total seed isoflavone contents of soybean were identified. Six, seven, ten and eleven QTL were associated with daidzein (DZ), glycitein (GC), genistein (GT) and total isoflavone (TI), respectively. Of them 23 QTL were newly identified. The qTIF_1 between Satt423 and Satt569 shared the same marker Satt569 with qDZF_2, qGTF_1 and qTIF_2. The qGTD2_1 between Satt186 and Satt226 was detected in four environments and explained 3.41%-10.98% of the phenotypic variation. The qGTA2_1, overlapped with qGCA2_1 and detected in four environments, was close to the previously identified major QTL for GT, which were responsible for large a effects. QTL (qDZF_2, qGTF_1 and qTIF_2) between Satt144-Satt569 were either clustered or pleiotropic. The qGCM_1, qGTM_1 and qTIM_1 between Satt540-Sat_244 explained 2.02%-9.12% of the phenotypic variation over six environments. Moreover, the qGCE_1 overlapped with qGTE_1 and qTIE_1, the qTIH_2 overlapped with qGTH_1, qGCI_1 overlapped with qDZI_1, qTIL_1 overlapped with qGTL_1, and qTIO_1 overlapped with qGTO_1. In this study, some of unstable QTL were detected in different environments, which were due to weak expression of QTL, QTL by environment interaction in the opposite direction to a effects, and/or epistasis. The markers identified in multi-environments in this study could be applied in the selection of soybean cultivars for higher isoflavone content and in the map-based gene cloning.
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Affiliation(s)
- Yan Wang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, Heilongjiang Province, People’s Republic of China; Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, Heilongjiang Province, People’s Republic of China
| | - Yingpeng Han
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, Heilongjiang Province, People’s Republic of China; Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, Heilongjiang Province, People’s Republic of China
| | - Xue Zhao
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, Heilongjiang Province, People’s Republic of China; Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, Heilongjiang Province, People’s Republic of China
| | - Yongguang Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, Heilongjiang Province, People’s Republic of China; Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, Heilongjiang Province, People’s Republic of China
| | - Weili Teng
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, Heilongjiang Province, People’s Republic of China; Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, Heilongjiang Province, People’s Republic of China
| | - Dongmei Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, Heilongjiang Province, People’s Republic of China; Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, Heilongjiang Province, People’s Republic of China
| | - Yong Zhan
- Agricultural Science Academy of Shi He Zi, Xinjiang Province, People’s Republic of China
| | - Wenbin Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, Heilongjiang Province, People’s Republic of China; Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, Heilongjiang Province, People’s Republic of China
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12
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Li B, Tian L, Zhang J, Huang L, Han F, Yan S, Wang L, Zheng H, Sun J. Construction of a high-density genetic map based on large-scale markers developed by specific length amplified fragment sequencing (SLAF-seq) and its application to QTL analysis for isoflavone content in Glycine max. BMC Genomics 2014; 15:1086. [PMID: 25494922 PMCID: PMC4320444 DOI: 10.1186/1471-2164-15-1086] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 11/26/2014] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Quantitative trait locus (QTL) mapping is an efficient approach to discover the genetic architecture underlying complex quantitative traits. However, the low density of molecular markers in genetic maps has limited the efficiency and accuracy of QTL mapping. In this study, specific length amplified fragment sequencing (SLAF-seq), a new high-throughput strategy for large-scale SNP discovery and genotyping based on next generation sequencing (NGS), was employed to construct a high-density soybean genetic map using recombinant inbred lines (RILs, Luheidou2×Nanhuizao, F5:8). With this map, the consistent QTLs for isoflavone content across various environments were identified. RESULTS In total, 23 Gb of data containing 87,604,858 pair-end reads were obtained. The average coverage for each SLAF marker was 11.20-fold for the female parent, 12.51-fold for the male parent, and an average of 3.98-fold for individual RILs. Among the 116,216 high-quality SLAFs obtained, 9,948 were polymorphic. The final map consisted of 5,785 SLAFs on 20 linkage groups (LGs) and spanned 2,255.18 cM in genome size with an average distance of 0.43 cM between adjacent markers. Comparative genomic analysis revealed a relatively high collinearity of 20 LGs with the soybean reference genome. Based on this map, 41 QTLs were identified that contributed to the isoflavone content. The high efficiency and accuracy of this map were evidenced by the discovery of genes encoding isoflavone biosynthetic enzymes within these loci. Moreover, 11 of these 41 QTLs (including six novel loci) were associated with isoflavone content across multiple environments. One of them, qIF20-2, contributed to a majority of isoflavone components across various environments and explained a high amount of phenotypic variance (8.7%-35.3%). This represents a novel major QTL underlying isoflavone content across various environments in soybean. CONCLUSIONS Herein, we reported a high-density genetic map for soybean. This map exhibited high resolution and accuracy. It will facilitate the identification of genes and QTLs underlying essential agronomic traits in soybean. The novel major QTL for isoflavone content is useful not only for further study on the genetic basis of isoflavone accumulation, but also for marker-assisted selection (MAS) in soybean breeding in the future.
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Affiliation(s)
- Bin Li
- />The National Key Facility for Crop Gene Resources and Genetic Improvement, NFCRI, MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081 China
| | - Ling Tian
- />The National Key Facility for Crop Gene Resources and Genetic Improvement, NFCRI, MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081 China
| | - Jingying Zhang
- />The National Key Facility for Crop Gene Resources and Genetic Improvement, NFCRI, MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081 China
| | - Long Huang
- />Biomarker Technologies Corporation, Beijing, 101300 China
| | - Fenxia Han
- />The National Key Facility for Crop Gene Resources and Genetic Improvement, NFCRI, MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081 China
| | - Shurong Yan
- />The National Key Facility for Crop Gene Resources and Genetic Improvement, NFCRI, MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081 China
| | - Lianzheng Wang
- />The National Key Facility for Crop Gene Resources and Genetic Improvement, NFCRI, MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081 China
| | - Hongkun Zheng
- />Biomarker Technologies Corporation, Beijing, 101300 China
| | - Junming Sun
- />The National Key Facility for Crop Gene Resources and Genetic Improvement, NFCRI, MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081 China
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13
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Wang Y, Han Y, Teng W, Zhao X, Li Y, Wu L, Li D, Li W. Expression quantitative trait loci infer the regulation of isoflavone accumulation in soybean (Glycine max L. Merr.) seed. BMC Genomics 2014; 15:680. [PMID: 25124843 PMCID: PMC4138391 DOI: 10.1186/1471-2164-15-680] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 07/30/2014] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Mapping expression quantitative trait loci (eQTL) of targeted genes represents a powerful and widely adopted approach to identify putative regulatory variants. Linking regulation differences to specific genes might assist in the identification of networks and interactions. The objective of this study is to identify eQTL underlying expression of four gene families encoding isoflavone synthetic enzymes involved in the phenylpropanoid pathway, which are phenylalanine ammonia-lyase (PAL; EC 4.3.1.5), chalcone synthase (CHS; EC 2.3.1.74), 2-hydroxyisoflavanone synthase (IFS; EC1.14.13.136) and flavanone 3-hydroxylase (F3H; EC 1.14.11.9). A population of 130 recombinant inbred lines (F5:11), derived from a cross between soybean cultivar 'Zhongdou 27' (high isoflavone) and 'Jiunong 20' (low isoflavone), and a total of 194 simple sequence repeat (SSR) markers were used in this study. Overlapped loci of eQTLs and phenotypic QTLs (pQTLs) were analyzed to identify the potential candidate genes underlying the accumulation of isoflavone in soybean seed. RESULTS Thirty three eQTLs (thirteen cis-eQTLs and twenty trans-eQTLs) underlying the transcript abundance of the four gene families were identified on fifteen chromosomes. The eQTLs between Satt278-Sat_134, Sat_134-Sct_010 and Satt149-Sat_234 underlie the expression of both IFS and CHS genes. Five eQTL intervals were overlapped with pQTLs. A total of eleven candidate genes within the overlapped eQTL and pQTL were identified. CONCLUSIONS These results will be useful for the development of marker-assisted selection to breed soybean cultivars with high or low isoflavone contents and for map-based cloning of new isoflavone related genes.
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Affiliation(s)
- Yan Wang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030 China
| | - Yingpeng Han
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030 China
| | - Weili Teng
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030 China
| | - Xue Zhao
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030 China
| | - Yongguang Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030 China
| | - Lin Wu
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030 China
| | - Dongmei Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030 China
| | - Wenbin Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030 China
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14
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Zhang HJ, Li JW, Liu YJ, Jiang WZ, Du XL, Li L, Li XW, Su LT, Wang QY, Wang Y. Quantitative trait loci analysis of individual and total isoflavone contents in soybean seeds. J Genet 2014; 93:331-8. [PMID: 25189227 DOI: 10.1007/s12041-014-0371-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Soybean isoflavones play diverse roles in human health, including cancers, osteoporosis, heart disease, menopausal symptoms and pabulums. The objective of this study was to identify the quantitative trait loci (QTL) associated with the isoflavones daidzein (DC), genistein (GeC), glycitein (GlC) and total isoflavone contents (TIC) in soybean seeds. A population of 184 F2:10 recombinant inbred lines derived from a 'Xiaoheidou' x 'GR8836' cross was planted in pot and field conditions to evaluate soybean isoflavones. Twenty-one QTL were detected by composite interval mapping. Several QTL were associated with the traits for DC, GeC, GlC and TIC only. QDGeGlTIC4_1 and QDGlTIC12_1 are reported first in this study and were associated with the DC, GeC, GlC and TIC traits simultaneously. The QTL identified have potential value for marker-assisted selection to develop soybean varieties with desirable isoflavone content.
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Affiliation(s)
- Hai Jun Zhang
- College of Plant Science, Jilin University, Changchun 130062, Jinlin, People's Republic of China.
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Akond M, Liu S, Kantartzi SK, Meksem K, Bellaloui N, Lightfoot DA, Yuan J, Wang D, Kassem MA. Quantitative trait loci for seed isoflavone contents in 'MD96-5722' by 'Spencer' recombinant inbred lines of soybean. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:1464-8. [PMID: 24499298 DOI: 10.1021/jf4040173] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Isoflavones from soybeans [ Glycine max (L.) Merr.] have a significant impact on human health to reduce the risk of several major diseases. Breeding soybean for high isoflavone content in the seed is possible through marker-assisted selection (MAS) which can be based on quantitative trait loci (QTL). The objective of this study was to identify QTL controlling isoflavone content in a set of 'MD96-5722' by 'Spencer' recombinant inbred line (RIL) populations of soybean. Wide variations were found for seed concentrations of daidzein, glycitein, genistein, and total isoflavones among the RIL populations. Three QTL were identified on three different linkage groups (LG) represented by three different chromosomes (Chr). One QTL that controlled daidzein content was identified on LG A1 (Chr 5), and two QTL that underlay glycitein content were identified on LG K (Chr 9) and LG B2 (Chr 14). Identified QTL could be functional in developing soybean with preferable isoflavone concentrations in the seeds through MAS.
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Affiliation(s)
- Masum Akond
- Plant Genomics and Biotechnology Laboratory, Department of Biological Sciences, Fayetteville State University , Fayetteville, North Carolina 28301-4298, United States
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16
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Ragin B, Akond M, Kantartzi S, Meksem K, Herrera H, Akbay C, Lightfoot DA, Kassem MA. Effect of Row Spacing on Seed Isoflavone Contents in Soybean [Glycine max (L.) Merr.]. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/ajps.2014.526418] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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17
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Zhang J, Lazarenko OP, Wu X, Tong Y, Blackburn ML, Gomez-Acevedo H, Shankar K, Badger TM, Ronis MJJ, Chen JR. Differential effects of short term feeding of a soy protein isolate diet and estrogen treatment on bone in the pre-pubertal rat. PLoS One 2012; 7:e35736. [PMID: 22536432 PMCID: PMC3335011 DOI: 10.1371/journal.pone.0035736] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 03/20/2012] [Indexed: 11/19/2022] Open
Abstract
Background Previous reports suggest that beneficial effects of soy on bone quality are due to the estrogenic actions of isoflavone phytochemicals associated with the protein. However, mechanistic studies comparing the effects of soy diet and estrogens on bone, particularly in rapidly growing animals are lacking. Methodology and Principal Findings We studied the effects of short term feeding of soy protein isolate (SPI) on bone in comparison to the effects of 17β-estradiol (E2) in pre-pubertal rats. Female rats were weaned to one of 4 treatments: 1) a control casein-based diet (CAS); 2) CAS with subcutaneous E2 (10 µg/kg/d) (CAS+E2); 3) a SPI-containing diet (SPI); or 4) SPI with subcutaneous E2 (SPI) or SPI with 10 µg/kg/d E2 (SPI+E2) for 14 days beginning on postnatal day 20. SPI increased while E2 decreased bone turnover compared to CAS. In contrast, both treatments decreased serum sclerostin levels. Microarray analysis of RNA isolated from bone revealed 652 genes regulated by SPI, 491 genes regulated by E2, and 266 genes regulated by both SPI diet and E2 compared to CAS. The expression of caveolin-1, a protein localized in the cell membrane, was down-regulated (p<0.05) in rats fed SPI, but not by E2 compared to rats fed casein. Down-regulation of caveolin-1 by SPI was associated with increased BMP2, Smad and Runx2 expression in bone and osteoblasts (p<0.05). Conclusions/Significance These results suggest SPI and E2 have different effects on bone turnover prior to puberty. Approximately half of the genes are regulated in the same direction by E2 or SPI, but in combination, SPI blocks the estrogen effects and returns the profile towards control levels. In addition, there are E2 specific and SPI-specific gene changes related to regulation of bone formation.
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Affiliation(s)
- Jian Zhang
- Arkansas Children's Nutrition Center, Little Rock, Arkansas, United States of America
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Oxana P. Lazarenko
- Arkansas Children's Nutrition Center, Little Rock, Arkansas, United States of America
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Xianli Wu
- Arkansas Children's Nutrition Center, Little Rock, Arkansas, United States of America
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Yudong Tong
- Arkansas Children's Nutrition Center, Little Rock, Arkansas, United States of America
| | - Michael L. Blackburn
- Arkansas Children's Nutrition Center, Little Rock, Arkansas, United States of America
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Horatio Gomez-Acevedo
- Arkansas Children's Nutrition Center, Little Rock, Arkansas, United States of America
| | - Kartik Shankar
- Arkansas Children's Nutrition Center, Little Rock, Arkansas, United States of America
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Thomas M. Badger
- Arkansas Children's Nutrition Center, Little Rock, Arkansas, United States of America
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Martin J. J. Ronis
- Arkansas Children's Nutrition Center, Little Rock, Arkansas, United States of America
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
- Department of Pharmacology and Toxicology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Jin-Ran Chen
- Arkansas Children's Nutrition Center, Little Rock, Arkansas, United States of America
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
- * E-mail:
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Novel major quantitative trait loci regulating the content of isoflavone in soybean seeds. Genes Genomics 2011. [DOI: 10.1007/s13258-011-0043-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Liu X, Liu S, Jamai A, Bendahmane A, Lightfoot DA, Mitchum MG, Meksem K. Soybean cyst nematode resistance in soybean is independent of the Rhg4 locus LRR-RLK gene. Funct Integr Genomics 2011; 11:539-49. [PMID: 21541782 DOI: 10.1007/s10142-011-0225-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 04/04/2011] [Accepted: 04/05/2011] [Indexed: 01/08/2023]
Abstract
To test the function of candidate genes in soybean for resistance to the soybean cyst nematode (SCN), a large collection of EMS-mutants from the SCN-resistant soybean cultivar "Forrest" was developed for Targeting Induced Local Lesions IN Genomes (TILLING). Additionally, due to the complexity of the soybean genome, an integrated set of genomic and genetic analysis tools was employed to complement the TILLING approach. The efficiency of this integrated set of tools was tested using a candidate soybean gene for resistance to SCN, encoding a leucine-rich repeat receptor-like kinase (LRR-RLK) that was identified by map-based cloning at the Rhg4 locus. The Rhg4 locus is one of the major quantitative trait loci controlling soybean resistance against SCN race 3 (HG type 0) in cv. Forrest, but the gene(s) sequence for resistance remains to be determined. Using TILLING, a Forrest mutant containing a nonsense mutation in the LRR domain of the candidate resistance protein was identified and confirmed; however, the SCN-resistant phenotype of the mutant was not altered. Haplotyping and EcoTILLING of recombinant inbred lines along with complementation analysis corroborated the TILLING result and ruled out the possibility of functional redundancy by a second copy of the LRR-RLK gene identified in the soybean genome. This study validates the use of TILLING, in combination with an integrated set of genomic tools, as an efficient means of testing candidate genes for SCN resistance in soybean.
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Affiliation(s)
- Xiaohong Liu
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
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20
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Gutierrez-Gonzalez JJ, Vuong TD, Zhong R, Yu O, Lee JD, Shannon G, Ellersieck M, Nguyen HT, Sleper DA. Major locus and other novel additive and epistatic loci involved in modulation of isoflavone concentration in soybean seeds. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:1375-85. [PMID: 21850478 DOI: 10.1007/s00122-011-1673-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2011] [Accepted: 07/26/2011] [Indexed: 05/08/2023]
Abstract
Seeds of soybean [Glycine max (L.) Merr.] accumulate more isoflavones than any tissue of any plant species. In other plant parts, isoflavones are usually released to counteract the effects of various biotic and abiotic stresses. Because of the benefits to the plant and positive implications that consumption may have on human health, increasing isoflavones is a goal of many soybean breeding programs. However, altering isoflavone levels through marker-assisted selection (MAS) has been impractical due to the small and often environmentally variable contributions that each individual quantitative trait locus (QTL) has on total isoflavones. In this study, we developed a Magellan × PI 437654 F(7)-RIL population to construct a highly saturated non-redundant linkage map that encompassed 451 SNP and SSR molecular markers and used it to locate genomic regions that govern accumulation of isoflavones in the seeds of soybean. Five QTLs were found that contribute to the concentration of isoflavones, having single or multiple additive effects on isoflavone component traits. We also validated a major locus which alone accounted for up to 10% of the phenotypic variance for glycitein, and 35-37% for genistein, daidzein and the sum of all three soybean isoflavones. This QTL was consistently associated with increased concentration of isoflavones across different locations, years and crosses. It was the most important QTL in terms of net increased amounts of all isoflavone forms. Our results suggest that this locus would be an excellent candidate to target for MAS. Also, several minor QTLs were identified that interacted in an additive-by-additive epistatic manner, to increase isoflavone concentration.
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Affiliation(s)
- Juan J Gutierrez-Gonzalez
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211, USA
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LIANG HZ, YU YL, WANG SF, LIAN Y, WANG TF, WEI YL, GONG PT, LIU XY, FANG XJ, ZHANG MC. QTL Mapping of Isoflavone, Oil and Protein Contents in Soybean (Glycine max L. Merr.). ACTA ACUST UNITED AC 2010. [DOI: 10.1016/s1671-2927(09)60197-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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22
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Gutierrez-Gonzalez JJ, Wu X, Zhang J, Lee JD, Ellersieck M, Shannon JG, Yu O, Nguyen HT, Sleper DA. Genetic control of soybean seed isoflavone content: importance of statistical model and epistasis in complex traits. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 119:1069-83. [PMID: 19626310 PMCID: PMC2755750 DOI: 10.1007/s00122-009-1109-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2009] [Accepted: 06/25/2009] [Indexed: 05/07/2023]
Abstract
A major objective for geneticists is to decipher genetic architecture of traits associated with agronomic importance. However, a majority of such traits are complex, and their genetic dissection has been traditionally hampered not only by the number of minor-effect quantitative trait loci (QTL) but also by genome-wide interacting loci with little or no individual effect. Soybean (Glycine max [L.] Merr.) seed isoflavonoids display a broad range of variation, even in genetically stabilized lines that grow in a fixed environment, because their synthesis and accumulation are affected by many biotic and abiotic factors. Due to this complexity, isoflavone QTL mapping has often produced conflicting results especially with variable growing conditions. Herein, we comparatively mapped soybean seed isoflavones genistein, daidzein, and glycitein by using several of the most commonly used mapping approaches: interval mapping, composite interval mapping, multiple interval mapping and a mixed-model based composite interval mapping. In total, 26 QTLs, including many novel regions, were found bearing additive main effects in a population of RILs derived from the cross between Essex and PI 437654. Our comparative approach demonstrates that statistical mapping methodologies are crucial for QTL discovery in complex traits. Despite a previous understanding of the influence of additive QTL on isoflavone production, the role of epistasis is not well established. Results indicate that epistasis, although largely dependent on the environment, is a very important genetic component underlying seed isoflavone content, and suggest epistasis as a key factor causing the observed phenotypic variability of these traits in diverse environments.
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Affiliation(s)
- Juan Jose Gutierrez-Gonzalez
- Division of Plant Sciences, National Center for Soybean Biotechnology, University of Missouri, Life Sciences Building, Columbia, MO 65201 USA
| | - Xiaolei Wu
- Division of Plant Sciences, National Center for Soybean Biotechnology, University of Missouri, Life Sciences Building, Columbia, MO 65201 USA
| | - Juan Zhang
- Donald Danforth Plant Science Center, 975 North Warson Road, Saint Louis, MO 63132 USA
| | - Jeong-Dong Lee
- Division of Plant Sciences, National Center for Soybean Biotechnology, University of Missouri, Life Sciences Building, Columbia, MO 65201 USA
| | - Mark Ellersieck
- Department of Statistics, University of Missouri, 146 Middlebush Hall, Columbia, MO 65211 USA
| | - J. Grover Shannon
- Division of Plant Sciences, National Center for Soybean Biotechnology, University of Missouri, Life Sciences Building, Columbia, MO 65201 USA
| | - Oliver Yu
- Donald Danforth Plant Science Center, 975 North Warson Road, Saint Louis, MO 63132 USA
| | - Henry T. Nguyen
- Division of Plant Sciences, National Center for Soybean Biotechnology, University of Missouri, Life Sciences Building, Columbia, MO 65201 USA
| | - David A. Sleper
- Division of Plant Sciences, National Center for Soybean Biotechnology, University of Missouri, Life Sciences Building, Columbia, MO 65201 USA
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Zeng G, Li D, Han Y, Teng W, Wang J, Qiu L, Li W. Identification of QTL underlying isoflavone contents in soybean seeds among multiple environments. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 118:1455-63. [PMID: 19266178 DOI: 10.1007/s00122-009-0994-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2008] [Accepted: 02/13/2009] [Indexed: 05/08/2023]
Abstract
Soybean isoflavones are valued in certain medicines, cosmetics, foods and feeds. Selection for high-isoflavone content in seeds along with agronomic traits is a goal of many soybean breeders. The aim of the study was to identify the quantitative trait loci (QTL) underlying seed isoflavone content in soybean among seven environments in China. A cross was made between 'Zhongdou 27', a soybean cultivar with higher mean isoflavone content in the seven environments (daidzein, DZ, 1,865 microg g(-1); genistein, GT, 1,614 microg g(-1); glycitein, GC, 311 microg g(-1) and total isoflavone, TI, 3,791 microg g(-1)) and 'Jiunong 20', a soybean cultivar with lower isoflavone content (DZ, 844 microg g(-1); GT, 1,046 microg g(-1); GC, 193 microg g(-1) and TI, 2,061 microg g(-1)). Through single-seed-descent, 130 F(5)-derived F(6) recombinant inbred lines were advanced. A total of 99 simple-sequence repeat markers were used to construct a genetic linkage map. Seed isoflavone contents were analyzed using high-performance liquid chromatography for multiple years and locations (Harbin in 2005, 2006 and 2007, Hulan in 2006 and 2007, and Suihua in 2006 and 2007). Three QTL were associated with DZ content, four with GT content, three with GC content, and five with TI content. For all QTL detected the beneficial allele was from Zhongdou 27. QTL were located on three (DZ), three (GC), four (GT) and five (TI) molecular linkage groups (LG). A novel QTL was detected with marker Satt144 on LG F that was associated with DZ (0.0014 > P > 0.0001, 5% < R (2) < 11%; 254 < DZ < 552 microg g(-1)), GT (0.0027 > P > 0.0001; 4% < R (2) < 9%; 262 < GT < 391 microg g(-1)), and TI (0.0011 > P > 0.0001; 4% < R (2) < 15%; 195 < TI < 871 microg g(-1)) across the various environments. A previously reported QTL on LG M detected by Satt540 was associated with TI across four environments and TI mean (0.0022 > P > 0.0001; 3% < R (2) < 8%; 182 < TI < 334 microg g(-1)) in China. Because both beneficial alleles were from Zhongdou 27, it was concluded that these two QTL would have the greatest potential value for marker-assisted selection for high-isoflavone content in soybean seed in China.
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Affiliation(s)
- Guoliang Zeng
- Soybean Research Institute (Key Laboratory of Soybean Biology in Chinese Ministry of Education), Northeast Agricultural University, 150030, Harbin, China
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CHEN QS, ZHANG ZC, LIU CY, XIN DW, QIU HM, SHAN DP, SHAN CY, HU GH. QTL Analysis of Major Agronomic Traits in Soybean. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/s1671-2927(07)60062-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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25
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Shultz JL, Kazi S, Bashir R, Afzal JA, Lightfoot DA. The development of BAC-end sequence-based microsatellite markers and placement in the physical and genetic maps of soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 114:1081-90. [PMID: 17287974 DOI: 10.1007/s00122-007-0501-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2006] [Accepted: 01/07/2007] [Indexed: 05/07/2023]
Abstract
The composite map of soybean shared among Soybase, LIS and SoyGD (March 2006) contained 3,073 DNA markers in the "Locus" class. Among the markers were 1,019 class I microsatellite markers with 2-3 bp simple sequence repeats (SSRs) of >10 iterations (BARC-SSR markers). However, there were few class II SSRs (2-5 bp repeats with <10 iterations; mostly SIUC-Satt markers). The aims here were to increase the number of classes I and II SSR markers and to integrate bacterial artificial chromosome (BAC) clones onto the soybean physical map using the markers. Used was 10 Mb of BAC-end sequence (BES) derived from 13,473 reads from 7,050 clones constituting minimum tile path 2 of the soybean physical map ( http://www.soybeangenome.siu.edu ; SoyGD). Identified were 1,053 1-6 bp motif, repeat sequences, 333 from class I (>10 repeats) and 720 from class II (<10 repeats). Potential markers were shown on the MTP_SSR track at Gbrowse. Primers were designed as 20-24 bp oligomers that had Tm of 55 +/- 1 C that would generate 100-500 bp amplicons. About 853 useful primer pairs were established. Motifs were not randomly distributed with biases toward AT rich motifs. Strong biases against the GC motif and all tetra-nucleotide repeats were found. The markers discovered were useful. Among the first 135 targeted for use in genetic map improvement about 60% of class II markers and 75% of class I markers were polymorphic among on the parents of four recombinant inbred line (RIL) populations. Many of the BES-based SSRs were located on the soybean genetic map in regions with few BARC-SSR markers. Therefore, BES-based SSRs represent useful tools for genetic map development in soybean. New members of a consortium to map the markers in additional populations are invited.
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Affiliation(s)
- Jeffry L Shultz
- Genomics Core Facility and Center of Excellence in Soybean Research, Teaching and Outreach, and Department of Plant, Soil and Agricultural Systems, Southern Illinois University at Carbondale, Carbondale, IL 62901, USA
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26
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Kassem MA, Shultz J, Meksem K, Cho Y, Wood AJ, Iqbal MJ, Lightfoot DA. An updated 'Essex' by 'Forrest' linkage map and first composite interval map of QTL underlying six soybean traits. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 113:1015-26. [PMID: 16953420 DOI: 10.1007/s00122-006-0361-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2006] [Accepted: 06/26/2006] [Indexed: 05/11/2023]
Abstract
DNA marker maps based on single populations are the basis for gene, loci and genomic analyses. Individual maps can be integrated to produce composite maps with higher marker densities if shared marker orders are consistent. However, estimates of marker order in composite maps must include sets of markers that were not polymorphic in multiple populations. Often some of the pooled markers were not codominant, or were not correctly scored. The soybean composite map was composed of data from five separate populations based on northern US germplasm but does not yet include 'Essex' by 'Forrest' recombinant inbred line (RIL) population (E x F) or any southern US soybean cultivars. The objectives were, to update the E x F map with codominant markers, to compare marker orders among this map, the Forrest physical map and the composite soybean map and to compare QTL identified by composite interval maps to the earlier interval maps. Two hundred and thirty seven markers were used to construct the core of the E x F map. The majority of marker orders were consistent between the maps. However, 19 putative marker inversions were detected on 12 of 20 linkage groups (LG). Eleven marker distance compressions were also found. The number of inverted markers ranged from 1 to 2 per LG. Thus, marker order inversions may be common in southern compared to northern US germplasm. A total of 61 QTL among 37 measures of six traits were detected by composite interval maps, interval maps and single point analysis. Seventeen of the QTL found in composite intervals had previously been detected among the 29 QTL found in simple interval maps. The genomic locations of the known QTL were more closely delimited. A genome sequencing project to compare Southern and Northern US soybean cultivars would catalog and delimit inverted regions and the associated QTL. Gene introgression in cultivar development programs would be accelerated.
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Affiliation(s)
- M A Kassem
- Plant Biotechnology and Genomics Core-Facility, Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA
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González-Martínez SC, Robledo-Arnuncio JJ, Collada C, Díaz A, Williams CG, Alía R, Cervera MT. Cross-amplification and sequence variation of microsatellite loci in Eurasian hard pines. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 109:1125-32. [PMID: 14985972 DOI: 10.1007/s00122-004-1739-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2003] [Accepted: 01/05/2004] [Indexed: 05/20/2023]
Abstract
Microsatellite transfer across coniferous species is a valued methodology because de novo development for each species is costly and there are many species with only a limited commodity value. Cross-species amplification of orthologous microsatellite regions provides valuable information on mutational and evolutionary processes affecting these loci. We tested 19 nuclear microsatellite markers from Pinus taeda L. (subsection Australes) and three from P. sylvestris L. (subsection Pinus) on seven Eurasian hard pine species ( P. uncinata Ram., P. sylvestris L., P. nigra Arn., P. pinaster Ait., P. halepensis Mill., P. pinea L. and P. canariensis Sm.). Transfer rates to species in subsection Pinus (36-59%) were slightly higher than those to subsections Pineae and Pinaster (32-45%). Half of the trans-specific microsatellites were found to be polymorphic over evolutionary times of approximately 100 million years (ten million generations). Sequencing of three trans-specific microsatellites showed conserved repeat and flanking regions. Both a decrease in the number of perfect repeats in the non-focal species and a polarity for mutation, the latter defined as a higher substitution rate in the flanking sequence regions close to the repeat motifs, were observed in the trans-specific microsatellites. The transfer of microsatellites among hard pine species proved to be useful for obtaining highly polymorphic markers in a wide range of species, thereby providing new tools for population and quantitative genetic studies.
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González-Martínez SC, Robledo-Arnuncio JJ, Collada C, Díaz A, Williams CG, Alía R, Cervera MT. Cross-amplification and sequence variation of microsatellite loci in Eurasian hard pines. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 109:103-11. [PMID: 14985972 DOI: 10.1007/s00122-004-1596-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2003] [Accepted: 01/05/2004] [Indexed: 05/23/2023]
Abstract
Microsatellite transfer across coniferous species is a valued methodology because de novo development for each species is costly and there are many species with only a limited commodity value. Cross-species amplification of orthologous microsatellite regions provides valuable information on mutational and evolutionary processes affecting these loci. We tested 19 nuclear microsatellite markers from Pinus taeda L. (subsection Australes) and three from P. sylvestris L. (subsection Pinus) on seven Eurasian hard pine species ( P. uncinata Ram., P. sylvestris L., P. nigra Arn., P. pinaster Ait., P. halepensis Mill., P. pinea L. and P. canariensis Sm.). Transfer rates to species in subsection Pinus (36-59%) were slightly higher than those to subsections Pineae and Pinaster (32-45%). Half of the trans-specific microsatellites were found to be polymorphic over evolutionary times of approximately 100 million years (ten million generations). Sequencing of three trans-specific microsatellites showed conserved repeat and flanking regions. Both a decrease in the number of perfect repeats in the non-focal species and a polarity for mutation, the latter defined as a higher substitution rate in the flanking sequence regions close to the repeat motifs, were observed in the trans-specific microsatellites. The transfer of microsatellites among hard pine species proved to be useful for obtaining highly polymorphic markers in a wide range of species, thereby providing new tools for population and quantitative genetic studies.
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Kassem MA, Meksem K, Iqbal MJ, Njiti VN, Banz WJ, Winters TA, Wood A, Lightfoot DA. Definition of Soybean Genomic Regions That Control Seed Phytoestrogen Amounts. J Biomed Biotechnol 2004; 2004:52-60. [PMID: 15123888 PMCID: PMC545653 DOI: 10.1155/s1110724304304018] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2003] [Revised: 10/08/2003] [Accepted: 11/07/2003] [Indexed: 11/18/2022] Open
Abstract
Soybean seeds contain large amounts of isoflavones or phytoestrogens such as genistein, daidzein, and glycitein that display biological effects when ingested by humans and animals. In seeds, the total amount, and amount of each type, of isoflavone varies by 5 fold between cultivars and locations. Isoflavone content and quality are one key to the biological effects of soy foods, dietary supplements, and nutraceuticals. Previously we had identified 6 loci (QTL) controlling isoflavone content using 150 DNA markers. This study aimed to identify and delimit loci underlying heritable variation in isoflavone content with additional DNA markers. We used a recombinant inbred line (RIL) population ( $n=100$ ) derived from the cross of Essex by Forrest, two cultivars that contrast for isoflavone content. Seed isoflavone content of each RIL was determined by HPLC and compared against 240 polymorphic microsatellite markers by one-way analysis of variance. Two QTL that underlie seed isoflavone content were newly discovered. The additional markers confirmed and refined the positions of the six QTL already reported. The first new region anchored by the marker BARC-Satt063 was significantly associated with genistein ( $P=0.009$, $Rcirc;2=29.5\%$ ) and daidzein ( $P=0.007$, $Rcirc;2=17.0\%$ ). The region is located on linkage group B2 and derived the beneficial allele from Essex. The second new region defined by the marker BARC-Satt129 was significantly associated with total glycitein ( $P=0.0005$, $Rcirc;2=32.0\%$ ). The region is located on linkage group D1a+Q and also derived the beneficial allele from Essex. Jointly the eight loci can explain the heritable variation in isoflavone content. The loci may be used to stabilize seed isoflavone content by selection and to isolate the underlying genes.
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Affiliation(s)
- My A. Kassem
- Center for Excellence in Soybean Research, Teaching, and Outreach,
Department of Plant, Soil, and Agricultural Systems, Southern
Illinois University at Carbondale, Carbondale, IL 62901-4415, USA
| | - K. Meksem
- Center for Excellence in Soybean Research, Teaching, and Outreach,
Department of Plant, Soil, and Agricultural Systems, Southern
Illinois University at Carbondale, Carbondale, IL 62901-4415, USA
| | - M. J. Iqbal
- Center for Excellence in Soybean Research, Teaching, and Outreach,
Department of Plant, Soil, and Agricultural Systems, Southern
Illinois University at Carbondale, Carbondale, IL 62901-4415, USA
| | - V. N. Njiti
- Center for Biotechnology and Genomics, Alcorn State University,
Alcorn, MS 39096, USA
| | - W. J. Banz
- Center for Excellence in Soybean Research, Teaching, and Outreach,
Department of Animal Science, Food, and Nutrition, Southern
Illinois University at Carbondale, Carbondale, IL 62901-4417, USA
| | - T. A. Winters
- Center for Excellence in Soybean Research, Teaching, and Outreach,
Department of Animal Science, Food, and Nutrition, Southern
Illinois University at Carbondale, Carbondale, IL 62901-4417, USA
| | - A. Wood
- Center for Excellence in Soybean Research, Teaching, and Outreach,
Department of Plant Biology, 420 Life Science II, Southern
Illinois University at Carbondale, Carbondale, IL 62901-6509, USA
| | - D. A. Lightfoot
- Center for Excellence in Soybean Research, Teaching, and Outreach,
Department of Plant, Soil, and Agricultural Systems, Southern
Illinois University at Carbondale, Carbondale, IL 62901-4415, USA
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Dhaubhadel S, McGarvey BD, Williams R, Gijzen M. Isoflavonoid biosynthesis and accumulation in developing soybean seeds. PLANT MOLECULAR BIOLOGY 2003; 53:733-43. [PMID: 15082922 DOI: 10.1023/b:plan.0000023666.30358.ae] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Isoflavonoids are biologically active natural products that accumulate in soybean seeds during development. The amount of isoflavonoids present in soybean seed is variable, depending on genetic and environmental factors that are not fully understood. Experiments were conducted to determine whether isoflavonoids are synthesized within seed tissues during development, or made in other plant organs and transported to the seeds where they accumulate. An analysis of isoflavonoids by HPLC detected the compounds in all organs of soybean plant, but the amount of isoflavonoids present varied depending on the tissue and developmental stage. The greatest concentrations were found in mature seeds and leaves. The 2-hydroxyisoflavanone synthase genes IFS1 and IFS2 were studied to determine their pattern of expression in different tissues and developmental stages. The highest level of expression of IFS1 was observed in the root and seed coat, while IFS2 was most highly expressed in embryos and pods, and in elicitor-treated or pathogen-challenged tissues. Incorporation of radiolabel into isoflavonoids was observed when developing embryos and other plant organs were fed with [(14)C]phenylalanine. Embryos excised from developing soybean seeds also accumulated isoflavonoids from a synthetic medium. A maternal effect on seed isoflavonoid content was noted in reciprocal crosses between soybean cultivars that differ in seed isoflavonoids. From these results, we propose that developing soybean embryos have an ability to synthesize isoflavonoids de novo, but that transport from maternal tissues may in part contribute to the accumulation of these natural products in the seed.
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Affiliation(s)
- Sangeeta Dhaubhadel
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario, Canada N5V 4T3
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31
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Vyn TJ, Yin X, Bruulsema TW, Jackson CJC, Rajcan I, Brouder SM. Potassium fertilization effects on isoflavone concentrations in soybean [Glycine max (L.) Merr.]. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2002; 50:3501-6. [PMID: 12033818 DOI: 10.1021/jf0200671] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Soybean isoflavone concentrations vary widely, but the contribution of soil fertility and nutrient management to this variability is unknown. Field experiments from 1998 to 2000 on soils with low to high exchangeable potassium (K) concentrations evaluated K application and placement effects on isoflavone concentrations and composition of soybean in various tillage and row-width systems. Soybean seed yield and concentrations of daidzein, genistein, glycitein, leaf K, and seed K were measured. Significant increases in daidzein, genistein, and total isoflavone were observed with direct deep-banded K or residual surface-applied K on low-K soils. Positive effects of K fertilization on isoflavones were less frequent on medium- to high-testing K soils. Both individual and total isoflavones were often positively correlated with seed yield, leaf K, and seed K on low-K soils. Appropriate K management could be an effective approach to increase isoflavone concentrations for soybeans produced on low- to medium-K soils.
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Affiliation(s)
- Tony J Vyn
- Department of Agronomy, Purdue University, 1150 Lilly Hall, West Lafayette, Indiana 47907-1150, USA.
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