1
|
Gonçalves JDP, Gasparini K, Picoli EADT, Costa MDBL, Araujo WL, Zsögön A, Ribeiro DM. Metabolic control of seed germination in legumes. JOURNAL OF PLANT PHYSIOLOGY 2024; 295:154206. [PMID: 38452650 DOI: 10.1016/j.jplph.2024.154206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/19/2024] [Accepted: 02/23/2024] [Indexed: 03/09/2024]
Abstract
Seed development, dormancy, and germination are connected with changes in metabolite levels. Not surprisingly, a complex regulatory network modulates biosynthesis and accumulation of storage products. Seed development has been studied profusely in Arabidopsis thaliana and has provided valuable insights into the genetic control of embryo development. However, not every inference applies to crop legumes, as these have been domesticated and selected for high seed yield and specific metabolic profiles and fluxes. Given its enormous economic relevance, considerable work has contributed to shed light on the mechanisms that control legume seed growth and germination. Here, we summarize recent progress in the understanding of regulatory networks that coordinate seed metabolism and development in legumes.
Collapse
Affiliation(s)
- Júlia de Paiva Gonçalves
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, CEP 36570-900, Viçosa, MG, Brazil; National Institute of Science and Technology on Plant Physiology Under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil.
| | - Karla Gasparini
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, CEP 36570-900, Viçosa, MG, Brazil; National Institute of Science and Technology on Plant Physiology Under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil.
| | | | | | - Wagner Luiz Araujo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, CEP 36570-900, Viçosa, MG, Brazil; National Institute of Science and Technology on Plant Physiology Under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil.
| | - Agustin Zsögön
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, CEP 36570-900, Viçosa, MG, Brazil; National Institute of Science and Technology on Plant Physiology Under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil.
| | - Dimas Mendes Ribeiro
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, CEP 36570-900, Viçosa, MG, Brazil; National Institute of Science and Technology on Plant Physiology Under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil.
| |
Collapse
|
2
|
Bansal S, Sundararajan S, Shekhawat PK, Singh S, Soni P, Tripathy MK, Ram H. Rice lipases: a conundrum in rice bran stabilization: a review on their impact and biotechnological interventions. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:985-1003. [PMID: 37649880 PMCID: PMC10462582 DOI: 10.1007/s12298-023-01343-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 08/02/2023] [Accepted: 08/04/2023] [Indexed: 09/01/2023]
Abstract
Rice is a primary food and is one of the most important constituents of diets all around the world. Rice bran is a valuable component of rice, containing many oil-soluble vitamins, minerals, and oil. It is known for its ability to improve the economic value of rice. Further, it contains substantial quantities of minerals like potassium, calcium, magnesium, iron and antioxidants like tocopherols, tocotrienols, and γ-oryzanol, indicating that rice bran can be utilized effectively against several life-threatening disorders. It is difficult to fully utilize the necessary nutrients due to the presence of lipases in rice bran. These lipases break down lipids, specifically Triacylglycerol, into free fatty acids and glycerol. This review discusses physicochemical properties, mechanism of action, distribution, and activity of lipases in various components of rice seeds. The phylogenetic and gene expression analysis helped to understand the differential expression pattern of lipase genes at different growth phases of rice plant. Further, this review discusses various genetic and biotechnological approaches to decrease lipase activity in rice and other plants, which could potentially prevent the degradation of bran oil. The goal is to establish whether lipases are a major contributor to this issue and to develop rice varieties with improved bran stability. This information sets the stage for upcoming molecular research in this area. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01343-3.
Collapse
Affiliation(s)
- Sakshi Bansal
- National Agri-Food Biotechnology Institute, Sector 81, Mohali, 140306 India
| | - Sathish Sundararajan
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067 India
| | | | - Shivangi Singh
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Praveen Soni
- Department of Botany, University of Rajasthan, JLN Marg, Jaipur, 302004 India
| | - Manas K. Tripathy
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Hasthi Ram
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067 India
| |
Collapse
|
3
|
Padalkar G, Mandlik R, Sudhakaran S, Vats S, Kumawat S, Kumar V, Kumar V, Rani A, Ratnaparkhe MB, Jadhav P, Bhat JA, Deshmukh R, Sharma TR, Sonah H. Necessity and challenges for exploration of nutritional potential of staple-food grade soybean. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2022.105093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
4
|
Targeted Mutagenesis of the Multicopy Myrosinase Gene Family in Allotetraploid Brassica juncea Reduces Pungency in Fresh Leaves across Environments. PLANTS 2022; 11:plants11192494. [PMID: 36235360 PMCID: PMC9572489 DOI: 10.3390/plants11192494] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/08/2022] [Accepted: 09/19/2022] [Indexed: 11/17/2022]
Abstract
Recent breeding efforts in Brassica have focused on the development of new oilseed feedstock crop for biofuels (e.g., ethanol, biodiesel, bio-jet fuel), bio-industrial uses (e.g., bio-plastics, lubricants), specialty fatty acids (e.g., erucic acid), and producing low glucosinolates levels for oilseed and feed meal production for animal consumption. We identified a novel opportunity to enhance the availability of nutritious, fresh leafy greens for human consumption. Here, we demonstrated the efficacy of disarming the ‘mustard bomb’ reaction in reducing pungency upon the mastication of fresh tissue—a major source of unpleasant flavor and/or odor in leafy Brassica. Using gene-specific mutagenesis via CRISPR-Cas12a, we created knockouts of all functional copies of the type-I myrosinase multigene family in tetraploid Brassica juncea. Our greenhouse and field trials demonstrate, via sensory and biochemical analyses, a stable reduction in pungency in edited plants across multiple environments. Collectively, these efforts provide a compelling path toward boosting the human consumption of nutrient-dense, fresh, leafy green vegetables.
Collapse
|
5
|
Wallis JG, Bengtsson JD, Browse J. Molecular Approaches Reduce Saturates and Eliminate trans Fats in Food Oils. FRONTIERS IN PLANT SCIENCE 2022; 13:908608. [PMID: 35720592 PMCID: PMC9205222 DOI: 10.3389/fpls.2022.908608] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/02/2022] [Indexed: 05/29/2023]
Abstract
Vegetable oils composed of triacylglycerols (TAG) are a major source of calories in human diets. However, the fatty acid compositions of these oils are not ideal for human nutrition and the needs of the food industry. Saturated fatty acids contribute to health problems, while polyunsaturated fatty acids (PUFA) can become rancid upon storage or processing. In this review, we first summarize the pathways of fatty acid metabolism and TAG synthesis and detail the problems with the oil compositions of major crops. Then we describe how transgenic expression of desaturases and downregulation of the plastid FatB thioesterase have provided the means to lower oil saturates. The traditional solution to PUFA rancidity uses industrial chemistry to reduce PUFA content by partial hydrogenation, but this results in the production of trans fats that are even more unhealthy than saturated fats. We detail the discoveries in the biochemistry and molecular genetics of oil synthesis that provided the knowledge and tools to lower oil PUFA content by blocking their synthesis during seed development. Finally, we describe the successes in breeding and biotechnology that are giving us new, high-oleic, low PUFA varieties of soybean, canola and other oilseed crops.
Collapse
Affiliation(s)
| | | | - John Browse
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| |
Collapse
|
6
|
Silva LCC, Mayrink DB, Bueno RD, Piovesan ND, Ribeiro C, Dal-Bianco M. Reference Genes and Expression Analysis of Seed Desaturases Genes in Soybean Mutant Accessions. Biochem Genet 2022; 60:937-952. [PMID: 34554351 DOI: 10.1007/s10528-021-10135-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 09/15/2021] [Indexed: 10/20/2022]
Abstract
Soybean oil is the second most-produced vegetable oil worldwide. To enhance the nutritional quality and oxidative stability of soybean oil, many soybean breeding programs are trying to increase oleic acid content and reduce linoleic and linolenic acid contents. The fatty acid profile of soybean oil is controlled by many genes, including those which code for omega-3 and omega-6 desaturases. Mutations in GmFAD2-1 and GmFAD3 genes are widely studied and their combinations can produce soybean oil with high oleic and low linoleic and linolenic content. However, few studies evaluate the effect of these mutations on gene expression. Therefore, the present study sought to identify reference genes, evaluate the expression of GmFAD2-1 and GmFAD3 seed desaturase genes in thirteen wild-type and mutated soybean accessions, and associate the expression patterns with fatty acid composition and with the GmFAD2-1 and GmFAD3 genotypes. GmCONS7 and GmUKN2 were identified as the best reference genes for combined use to normalize data. The GmFAD2-1A mutation of PI603452 accession was associated with a decrease in gene expression of GmFAD2-1A; however, downregulation may not be due to the truncated enzyme structure alone. These results suggested that there are factors other than GmFAD2-1A and GmFAD2-1B that have a considerable effect on oleic content, at least in soybeans with mutations in these two genes.
Collapse
Affiliation(s)
- Luiz Cláudio Costa Silva
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana, BA, 44036-900, Brazil.
| | | | - Rafael Delmond Bueno
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Newton Deniz Piovesan
- Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Cleberson Ribeiro
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Maximiller Dal-Bianco
- Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| |
Collapse
|
7
|
Liu J, Dong L, Duan R, Hu L, Zhao Y, Zhang L, Wang X. Transcriptomic Analysis Reveals the Regulatory Networks and Hub Genes Controlling the Unsaturated Fatty Acid Contents of Developing Seed in Soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:876371. [PMID: 35646018 PMCID: PMC9134122 DOI: 10.3389/fpls.2022.876371] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/05/2022] [Indexed: 06/15/2023]
Abstract
Soybean [Glycine max (L.) Merr.] is one of the most important crops, which produces about 25% of the world's edible oil. The nutritional value of soybean oil depends mostly on the relative contents of three unsaturated fatty acids (UFAs), i.e., oleic acid, linoleic acid (LA), and linolenic acid. However, the biosynthetic mechanism of UFAs remains largely unknown, and there are few studies on RNA-seq analysis of developing seeds. To identify the candidate genes and related pathways involved in the regulation of UFA contents during seed development in soybean, two soybean lines with different UFA profiles were selected from 314 cultivars and landraces originated from Southern China, and RNA-seq analysis was performed in soybean seeds at three developmental stages. Using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, a series of genes and pathways related to fatty acid metabolism were identified, and 40 days after flowering (DAF) was found to be the crucial period in the formation of UFA profiles. Further, weighted gene co-expression network analysis identified three modules with six genes whose functions were highly associated with the contents of oleic and LA. The detailed functional investigation of the networks and hub genes could further improve the understanding of the underlying molecular mechanism of UFA contents and might provide some ideas for the improvement in fatty acids profiles in soybean.
Collapse
Affiliation(s)
- Junqi Liu
- School of Agriculture, Yunnan University, Kunming, China
| | - Liang Dong
- School of Agriculture, Yunnan University, Kunming, China
| | - Runqing Duan
- School of Agriculture, Yunnan University, Kunming, China
| | - Li Hu
- School of Agriculture, Yunnan University, Kunming, China
| | - Yinyue Zhao
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Liang Zhang
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Xianzhi Wang
- School of Agriculture, Yunnan University, Kunming, China
| |
Collapse
|
8
|
Willette A, Fallen B, Bhandari H, Sams C, Chen F, Sykes V, Smallwood C, Bilyeu K, Li Z, Pantalone V. Agronomic performance of high oleic, low linolenic soybean in Tennessee. J AM OIL CHEM SOC 2021. [DOI: 10.1002/aocs.12517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Alison Willette
- Department of Plant Sciences University of Tennessee Knoxville Tennessee USA
| | - Benjamin Fallen
- Soybean and Nitrogen Fixation Unit USDA‐ARS Raleigh North Carolina USA
| | - Hem Bhandari
- Department of Plant Sciences University of Tennessee Knoxville Tennessee USA
| | - Carl Sams
- Department of Plant Sciences University of Tennessee Knoxville Tennessee USA
| | - Feng Chen
- Department of Plant Sciences University of Tennessee Knoxville Tennessee USA
| | - Virginia Sykes
- Department of Plant Sciences University of Tennessee Knoxville Tennessee USA
| | - Chris Smallwood
- Department of Plant Sciences University of Tennessee Knoxville Tennessee USA
| | - Kristin Bilyeu
- Plant Genetics Research Unit USDA‐ARS Columbia Missouri USA
| | - Zenglu Li
- Department of Crop and Soil Sciences University of Georgia Athens Georgia USA
| | - Vincent Pantalone
- Department of Plant Sciences University of Tennessee Knoxville Tennessee USA
| |
Collapse
|
9
|
Zhao Y, Cao P, Cui Y, Liu D, Li J, Zhao Y, Yang S, Zhang B, Zhou R, Sun M, Guo X, Yang M, Xin D, Zhang Z, Li X, Lv C, Liu C, Qi Z, Xu J, Wu X, Chen Q. Enhanced production of seed oil with improved fatty acid composition by overexpressing NAD + -dependent glycerol-3-phosphate dehydrogenase in soybean. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1036-1053. [PMID: 33768659 DOI: 10.1111/jipb.13094] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
There is growing interest in expanding the production of soybean oils (mainly triacylglycerol, or TAG) to meet rising feed demand and address global energy concerns. We report that a plastid-localized glycerol-3-phosphate dehydrogenase (GPDH), encoded by GmGPDHp1 gene, catalyzes the formation of glycerol-3-phosphate (G3P), an obligate substrate required for TAG biosynthesis. Overexpression of GmGPDHp1 increases soybean seed oil content with high levels of unsaturated fatty acids (FAs), especially oleic acid (C18:1), without detectably affecting growth or seed protein content or seed weight. Based on the lipidomic analyses, we found that the increase in G3P content led to an elevated diacylglycerol (DAG) pool, in which the Kennedy pathway-derived DAG was mostly increased, followed by PC-derived DAG, thereby promoting the synthesis of TAG containing relatively high proportion of C18:1. The increased G3P levels induced several transcriptional alterations of genes involved in the glycerolipid pathways. In particular, genes encoding the enzymes responsible for de novo glycerolipid synthesis were largely upregulated in the transgenic lines, in-line with the identified biochemical phenotype. These results reveal a key role for GmGPDHp1-mediated G3P metabolism in enhancing TAG synthesis and demonstrate a strategy to modify the FA compositions of soybean oils for improved nutrition and biofuel.
Collapse
Affiliation(s)
- Ying Zhao
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| | - Pan Cao
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| | - Yifan Cui
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| | - Dongxu Liu
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| | - Jiapeng Li
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| | - Yabin Zhao
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| | - Siqi Yang
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| | - Bo Zhang
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| | - Runnan Zhou
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| | - Minghao Sun
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| | - Xuetian Guo
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| | - Mingliang Yang
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| | - Dawei Xin
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| | - Zhanguo Zhang
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| | - Xin Li
- Key Lab of Maize Genetics and Breeding, Heilongjiang Academy of Agricultural Sciences, Harbin, 150000, China
- Department of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Chen Lv
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| | - Chunyan Liu
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| | - Zhaoming Qi
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| | - Jingyu Xu
- Department of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Xiaoxia Wu
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| | - Qingshan Chen
- Department of Agriculture, Northeast Agricultural University, Harbin, 150000, China
| |
Collapse
|
10
|
Lakhssassi N, Lopes-Caitar VS, Knizia D, Cullen MA, Badad O, El Baze A, Zhou Z, Embaby MG, Meksem J, Lakhssassi A, Chen P, AbuGhazaleh A, Vuong TD, Nguyen HT, Hewezi T, Meksem K. TILLING-by-Sequencing + Reveals the Role of Novel Fatty Acid Desaturases (GmFAD2-2s) in Increasing Soybean Seed Oleic Acid Content. Cells 2021; 10:1245. [PMID: 34069320 PMCID: PMC8158723 DOI: 10.3390/cells10051245] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/15/2021] [Accepted: 05/16/2021] [Indexed: 11/17/2022] Open
Abstract
Soybean is the second largest source of oil worldwide. Developing soybean varieties with high levels of oleic acid is a primary goal of the soybean breeders and industry. Edible oils containing high level of oleic acid and low level of linoleic acid are considered with higher oxidative stability and can be used as a natural antioxidant in food stability. All developed high oleic acid soybeans carry two alleles; GmFAD2-1A and GmFAD2-1B. However, when planted in cold soil, a possible reduction in seed germination was reported when high seed oleic acid derived from GmFAD2-1 alleles were used. Besides the soybean fatty acid desaturase (GmFAD2-1) subfamily, the GmFAD2-2 subfamily is composed of five members, including GmFAD2-2A, GmFAD2-2B, GmFAD2-2C, GmFAD2-2D, and GmFAD2-2E. Segmental duplication of GmFAD2-1A/GmFAD2-1B, GmFAD2-2A/GmFAD2-2C, GmFAD2-2A/GmFAD2-2D, and GmFAD2-2D/GmFAD2-2C have occurred about 10.65, 27.04, 100.81, and 106.55 Mya, respectively. Using TILLING-by-Sequencing+ technology, we successfully identified 12, 8, 10, 9, and 19 EMS mutants at the GmFAD2-2A, GmFAD2-2B, GmFAD2-2C, GmFAD2-2D, and GmFAD2-2E genes, respectively. Functional analyses of newly identified mutants revealed unprecedented role of the five GmFAD2-2A, GmFAD2-2B, GmFAD2-2C, GmFAD2-2D, and GmFAD2-2E members in controlling the seed oleic acid content. Most importantly, unlike GmFAD2-1 members, subcellular localization revealed that members of the GmFAD2-2 subfamily showed a cytoplasmic localization, which may suggest the presence of an alternative fatty acid desaturase pathway in soybean for converting oleic acid content without substantially altering the traditional plastidial/ER fatty acid production.
Collapse
Affiliation(s)
- Naoufal Lakhssassi
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (D.K.); (M.A.C.); (O.B.); (A.E.B.); (Z.Z.)
| | | | - Dounya Knizia
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (D.K.); (M.A.C.); (O.B.); (A.E.B.); (Z.Z.)
| | - Mallory A. Cullen
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (D.K.); (M.A.C.); (O.B.); (A.E.B.); (Z.Z.)
| | - Oussama Badad
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (D.K.); (M.A.C.); (O.B.); (A.E.B.); (Z.Z.)
| | - Abdelhalim El Baze
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (D.K.); (M.A.C.); (O.B.); (A.E.B.); (Z.Z.)
| | - Zhou Zhou
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (D.K.); (M.A.C.); (O.B.); (A.E.B.); (Z.Z.)
| | - Mohamed G. Embaby
- Department of Animal Science, Food, and Nutrition, Southern Illinois University, Carbondale, IL 62901, USA; (M.G.E.); (A.A.)
| | - Jonas Meksem
- Trinity College of Arts and Sciences, Duke University, Durham, NC 27708, USA;
| | - Aicha Lakhssassi
- Faculty of Sciences and Technologies, University of Lorraine, 54506 Nancy, France;
| | - Pengyin Chen
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA; (P.C.); (T.D.V.); (H.T.N.)
| | - Amer AbuGhazaleh
- Department of Animal Science, Food, and Nutrition, Southern Illinois University, Carbondale, IL 62901, USA; (M.G.E.); (A.A.)
| | - Tri D. Vuong
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA; (P.C.); (T.D.V.); (H.T.N.)
| | - Henry T. Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA; (P.C.); (T.D.V.); (H.T.N.)
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA; (V.S.L.-C.); (T.H.)
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (D.K.); (M.A.C.); (O.B.); (A.E.B.); (Z.Z.)
| |
Collapse
|
11
|
Lakhssassi N, Zhou Z, Cullen MA, Badad O, El Baze A, Chetto O, Embaby MG, Knizia D, Liu S, Neves LG, Meksem K. TILLING-by-Sequencing + to Decipher Oil Biosynthesis Pathway in Soybeans: A New and Effective Platform for High-Throughput Gene Functional Analysis. Int J Mol Sci 2021; 22:4219. [PMID: 33921707 PMCID: PMC8073088 DOI: 10.3390/ijms22084219] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/08/2021] [Accepted: 04/13/2021] [Indexed: 12/25/2022] Open
Abstract
Reverse genetic approaches have been widely applied to study gene function in crop species; however, these techniques, including gel-based TILLING, present low efficiency to characterize genes in soybeans due to genome complexity, gene duplication, and the presence of multiple gene family members that share high homology in their DNA sequence. Chemical mutagenesis emerges as a genetically modified-free strategy to produce large-scale soybean mutants for economically important traits improvement. The current study uses an optimized high-throughput TILLING by target capture sequencing technology, or TILLING-by-Sequencing+ (TbyS+), coupled with universal bioinformatic tools to identify population-wide mutations in soybeans. Four ethyl methanesulfonate mutagenized populations (4032 mutant families) have been screened for the presence of induced mutations in targeted genes. The mutation types and effects have been characterized for a total of 138 soybean genes involved in soybean seed composition, disease resistance, and many other quality traits. To test the efficiency of TbyS+ in complex genomes, we used soybeans as a model with a focus on three desaturase gene families, GmSACPD, GmFAD2, and GmFAD3, that are involved in the soybean fatty acid biosynthesis pathway. We successfully isolated mutants from all the six gene family members. Unsurprisingly, most of the characterized mutants showed significant changes either in their stearic, oleic, or linolenic acids. By using TbyS+, we discovered novel sources of soybean oil traits, including high saturated and monosaturated fatty acids in addition to low polyunsaturated fatty acid contents. This technology provides an unprecedented platform for highly effective screening of polyploid mutant populations and functional gene analysis. The obtained soybean mutants from this study can be used in subsequent soybean breeding programs for improved oil composition traits.
Collapse
Affiliation(s)
- Naoufal Lakhssassi
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (Z.Z.); (M.A.C.); (O.B.); (A.E.B.); (O.C.); (D.K.); (S.L.)
| | - Zhou Zhou
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (Z.Z.); (M.A.C.); (O.B.); (A.E.B.); (O.C.); (D.K.); (S.L.)
| | - Mallory A. Cullen
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (Z.Z.); (M.A.C.); (O.B.); (A.E.B.); (O.C.); (D.K.); (S.L.)
| | - Oussama Badad
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (Z.Z.); (M.A.C.); (O.B.); (A.E.B.); (O.C.); (D.K.); (S.L.)
| | - Abdelhalim El Baze
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (Z.Z.); (M.A.C.); (O.B.); (A.E.B.); (O.C.); (D.K.); (S.L.)
| | - Oumaima Chetto
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (Z.Z.); (M.A.C.); (O.B.); (A.E.B.); (O.C.); (D.K.); (S.L.)
| | - Mohamed G. Embaby
- Department of Animal Science, Food, and Nutrition, Southern Illinois University, Carbondale, IL 62901, USA;
| | - Dounya Knizia
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (Z.Z.); (M.A.C.); (O.B.); (A.E.B.); (O.C.); (D.K.); (S.L.)
| | - Shiming Liu
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (Z.Z.); (M.A.C.); (O.B.); (A.E.B.); (O.C.); (D.K.); (S.L.)
| | | | - Khalid Meksem
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (Z.Z.); (M.A.C.); (O.B.); (A.E.B.); (O.C.); (D.K.); (S.L.)
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Lakhssassi N, Zhou Z, Liu S, Piya S, Cullen MA, El Baze A, Knizia D, Patil GB, Badad O, Embaby MG, Meksem J, Lakhssassi A, AbuGhazaleh A, Hewezi T, Meksem K. Soybean TILLING-by-Sequencing+ reveals the role of novel GmSACPD members in unsaturated fatty acid biosynthesis while maintaining healthy nodules. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:6969-6987. [PMID: 32898219 DOI: 10.1093/jxb/eraa402] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/27/2020] [Indexed: 05/07/2023]
Abstract
Developing soybean lines with high levels of stearic acid is a primary goal of the soybean industry. Most high-stearic-acid soybeans carry different GmSACPD-C mutated alleles. However, due to the dual role of GmSACPD-C in seeds and nodule development, all derived deleterious GmSACPD-C mutant alleles are of extremely poor agronomic value because of defective nodulation. The soybean stearoyl-acyl carrier protein desaturase (GmSACPD) gene family is composed of five members. Comparative genomics analysis indicated that SACPD genes were duplicated and derived from a common ancestor that is still present in chlorophytic algae. Synteny analysis showed the presence of segment duplications between GmSACPD-A/GmSACPD-B, and GmSACPD-C/GmSACPD-D. GmSACPD-E was not contained in any duplicated segment and may be the result of tandem duplication. We developed a TILLING by Target Capture Sequencing (Tilling-by-Sequencing+) technology, a versatile extension of the conventional TILLING by sequencing, and successfully identified 12, 14, and 18 ethyl methanesulfonate mutants at the GmSACPD-A, GmSACPD-B, and GmSACPD-D genes, respectively. Functional analysis of all identified mutants revealed an unprecedented role of GmSACPD-A, GmSACPD-B, and GmSACPD-D in unsaturated fatty acid biosynthesis without affecting nodule development and structure. This discovery will positively impact the development of high-stearic-acid lines to enhance soybean nutritional value without potential developmental tradeoffs.
Collapse
Affiliation(s)
- Naoufal Lakhssassi
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
| | - Zhou Zhou
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
| | - Shiming Liu
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
| | - Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Mallory A Cullen
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
| | - Abdelhalim El Baze
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
| | - Dounya Knizia
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
| | - Gunvant B Patil
- Institute for Genomics of Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, USA
| | - Oussama Badad
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
| | - Mohamed G Embaby
- Department of Animal Science, Food, and Nutrition, Southern Illinois University, Carbondale, IL, USA
| | - Jonas Meksem
- Trinity College of Arts and Sciences, Duke University, Durham, NC, USA
| | - Aicha Lakhssassi
- Faculty of Sciences and Technologies, University of Lorraine, Nancy, France
| | - Amer AbuGhazaleh
- Department of Animal Science, Food, and Nutrition, Southern Illinois University, Carbondale, IL, USA
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
| |
Collapse
|
14
|
Lakhssassi N, Piya S, Knizia D, El Baze A, Cullen MA, Meksem J, Lakhssassi A, Hewezi T, Meksem K. Mutations at the Serine Hydroxymethyltransferase Impact its Interaction with a Soluble NSF Attachment Protein and a Pathogenesis-Related Protein in Soybean. Vaccines (Basel) 2020; 8:vaccines8030349. [PMID: 32629961 PMCID: PMC7563484 DOI: 10.3390/vaccines8030349] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/24/2020] [Accepted: 06/25/2020] [Indexed: 01/01/2023] Open
Abstract
Resistance to soybean cyst nematodes (SCN) in “Peking-type” resistance is bigenic, requiring Rhg4-a and rhg1-a. Rhg4-a encodes a serine hydroxymethyltransferase (GmSHMT08) and rhg1-a encodes a soluble NSF attachment protein (GmSNAP18). Recently, it has been shown that a pathogenesis-related protein, GmPR08-Bet VI, potentiates the interaction between GmSHMT08 and GmSNAP18. Mutational analysis using spontaneously occurring and ethyl methanesulfonate (EMS)-induced mutations was carried out to increase our knowledge of the interacting GmSHMT08/GmSNAP18/GmPR08-Bet VI multi-protein complex. Mutations affecting the GmSHMT08 protein structure (dimerization and tetramerization) and interaction sites with GmSNAP18 and GmPR08-Bet VI proteins were found to impact the multi-protein complex. Interestingly, mutations affecting the PLP/THF substrate binding and catalysis did not affect the multi-protein complex, although they resulted in increased susceptibility to SCN. Most importantly, GmSHMT08 and GmSNAP18 from PI88788 were shown to interact within the cell, being potentiated in the presence of GmPR08-Bet VI. In addition, we have shown the presence of incompatibility between the GmSNAP18 (rhg1-b) of PI88788 and GmSHMT08 (Rhg4-a) from Peking. Components of the reactive oxygen species (ROS) pathway were shown to be induced in the SCN incompatible reaction and were mapped to QTLs for resistance to SCN using different mapping populations.
Collapse
Affiliation(s)
- Naoufal Lakhssassi
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (D.K.); (A.E.B.); (M.A.C.)
| | - Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA; (S.P.); (T.H.)
| | - Dounya Knizia
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (D.K.); (A.E.B.); (M.A.C.)
| | - Abdelhalim El Baze
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (D.K.); (A.E.B.); (M.A.C.)
| | - Mallory A. Cullen
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (D.K.); (A.E.B.); (M.A.C.)
| | - Jonas Meksem
- Trinity College of Arts and Sciences, Duke University, Durham, NC 27708, USA;
| | - Aicha Lakhssassi
- Faculty of Sciences and Technologies, University of Lorraine, 54000 Nancy, France;
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA; (S.P.); (T.H.)
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (D.K.); (A.E.B.); (M.A.C.)
- Correspondence: ; Tel.: +1-618-453-3103
| |
Collapse
|
15
|
Li MW, Wang Z, Jiang B, Kaga A, Wong FL, Zhang G, Han T, Chung G, Nguyen H, Lam HM. Impacts of genomic research on soybean improvement in East Asia. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1655-1678. [PMID: 31646364 PMCID: PMC7214498 DOI: 10.1007/s00122-019-03462-6] [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: 07/31/2019] [Accepted: 10/15/2019] [Indexed: 05/10/2023]
Abstract
It has been commonly accepted that soybean domestication originated in East Asia. Although East Asia has the historical merit in soybean production, the USA has become the top soybean producer in the world since 1950s. Following that, Brazil and Argentina have been the major soybean producers since 1970s and 1990s, respectively. China has once been the exporter of soybean to Japan before 1990s, yet she became a net soybean importer as Japan and the Republic of Korea do. Furthermore, the soybean yield per unit area in East Asia has stagnated during the past decade. To improve soybean production and enhance food security in these East Asian countries, much investment has been made, especially in the breeding of better performing soybean germplasms. As a result, China, Japan, and the Republic of Korea have become three important centers for soybean genomic research. With new technologies, the rate and precision of the identification of important genomic loci associated with desired traits from germplasm collections or mutants have increased significantly. Genome editing on soybean is also becoming more established. The year 2019 marked a new era for crop genome editing in the commercialization of the first genome-edited plant product, which is a high-oleic-acid soybean oil. In this review, we have summarized the latest developments in soybean breeding technologies and the remarkable progress in soybean breeding-related research in China, Japan, and the Republic of Korea.
Collapse
Affiliation(s)
- Man-Wah Li
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region China
| | - Zhili Wang
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region China
| | - Bingjun Jiang
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081 China
| | - Akito Kaga
- Soybean and Field Crop Applied Genomics Research Unit, Institute of Crop Science, National Agriculture and Food Research Organization, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8518 Japan
| | - Fuk-Ling Wong
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region China
| | - Guohong Zhang
- Institute of Dryland Agriculture, Gansu Academy of Agricultural Sciences, Key Laboratory of Northwest Drought Crop Cultivation of Chinese Ministry of Agriculture, Lanzhou, 730070 China
| | - Tianfu Han
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081 China
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam 59626 Korea
| | - Henry Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 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, Hong Kong Special Administrative Region China
| |
Collapse
|
16
|
Wu N, Lu Q, Wang P, Zhang Q, Zhang J, Qu J, Wang N. Construction and Analysis of GmFAD2-1A and GmFAD2-2A Soybean Fatty Acid Desaturase Mutants Based on CRISPR/Cas9 Technology. Int J Mol Sci 2020; 21:E1104. [PMID: 32046096 PMCID: PMC7037799 DOI: 10.3390/ijms21031104] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 02/02/2020] [Accepted: 02/04/2020] [Indexed: 11/16/2022] Open
Abstract
The soybean fatty acid desaturase family is composed of seven genes, but the function of each gene has not been reported. Bioinformatics was used to analyse the structure of genes in this family, as well as the correlation between Δ12-fatty acid desaturase II (FAD2) expression and oleic acid content on different days after flowering of soybean. In the present study, CRISPR/Cas9 technology was used to construct single and double mutant knockout vectors of functional genes in the FAD2 family. Analysis of the molecular biology and expression patterns of genes in the FAD2 family, namely, GmFAD2-1A (Glyma.10G278000) and GmFAD2-2A (Glyma.19G147300), showed that they had little homology with other soybean FAD2 genes, and that their function was slightly changed. Sequencing of the target showed that the editing efficiency of the GmFAD2-1A and GmFAD2-2A genes was 95% and 55.56%, respectively, and that the double mutant editing efficiency was 66.67%. The mutations were divided into two main types, as follows: base deletion and insertion. A near-infrared grain analyser determined the following results: In the T2 generation, the oleic acid content increased from 17.10% to 73.50%; the linoleic acid content decreased from 62.91% to 12.23%; the protein content increased from 37.69% to 41.16%; in the T3 generation, the oleic acid content increased from 19.15% to 72.02%; the linoleic acid content decreased from 56.58% to 17.27%. In addition, the protein content increased from 37.52% to 40.58% compared to that of the JN38 control variety.
Collapse
Affiliation(s)
- Nan Wu
- Jilin Agricultural Science and Technology University, Jilin 132101, China
- Jilin Agricultural University, the center of plant biotechnology, Chang Chun 130118, China; (Q.Z.); (J.Z.); (J.Q.)
| | - Qiang Lu
- Institute of Agricultural College, Jilin Agricultural University, Chang Chun 130118, China;
| | - Piwu Wang
- Jilin Agricultural University, the center of plant biotechnology, Chang Chun 130118, China; (Q.Z.); (J.Z.); (J.Q.)
| | - Qi Zhang
- Jilin Agricultural University, the center of plant biotechnology, Chang Chun 130118, China; (Q.Z.); (J.Z.); (J.Q.)
| | - Jun Zhang
- Jilin Agricultural University, the center of plant biotechnology, Chang Chun 130118, China; (Q.Z.); (J.Z.); (J.Q.)
| | - Jing Qu
- Jilin Agricultural University, the center of plant biotechnology, Chang Chun 130118, China; (Q.Z.); (J.Z.); (J.Q.)
| | - Nan Wang
- Jilin Agricultural University, the center of plant biotechnology, Chang Chun 130118, China; (Q.Z.); (J.Z.); (J.Q.)
| |
Collapse
|
17
|
Darr L, Cunicelli M, Bhandari H, Bilyeu K, Chen F, Hewezi T, Li Z, Sams C, Pantalone V. Field Performance of High Oleic Soybeans with Mutant
FAD2‐1A
and
FAD2‐1B
Genes in Tennessee. J AM OIL CHEM SOC 2020. [DOI: 10.1002/aocs.12306] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Lauren Darr
- Department of Plant SciencesUniversity of Tennessee, 2431 Joe Johnson Dr. Knoxville TN 37996 USA
| | - Mia Cunicelli
- Department of Plant SciencesUniversity of Tennessee, 2431 Joe Johnson Dr. Knoxville TN 37996 USA
| | - Hem Bhandari
- Department of Plant SciencesUniversity of Tennessee, 2431 Joe Johnson Dr. Knoxville TN 37996 USA
| | - Kristin Bilyeu
- Plant Genetics Research, USDA‐ARS, 110 Waters Hall Columbia MO 65211 USA
| | - Feng Chen
- Department of Plant SciencesUniversity of Tennessee, 2431 Joe Johnson Dr. Knoxville TN 37996 USA
| | - Tarek Hewezi
- Department of Plant SciencesUniversity of Tennessee, 2431 Joe Johnson Dr. Knoxville TN 37996 USA
| | - Zenglu Li
- University of Georgia, 111 Riverbend Road Athens GA 30602 USA
| | - Carl Sams
- Department of Plant SciencesUniversity of Tennessee, 2431 Joe Johnson Dr. Knoxville TN 37996 USA
| | - Vince Pantalone
- Department of Plant SciencesUniversity of Tennessee, 2431 Joe Johnson Dr. Knoxville TN 37996 USA
| |
Collapse
|
18
|
Zhou Z, Lakhssassi N, Cullen MA, El Baz A, Vuong TD, Nguyen HT, Meksem K. Assessment of Phenotypic Variations and Correlation among Seed Composition Traits in Mutagenized Soybean Populations. Genes (Basel) 2019; 10:E975. [PMID: 31783508 PMCID: PMC6947669 DOI: 10.3390/genes10120975] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/22/2019] [Accepted: 11/22/2019] [Indexed: 01/31/2023] Open
Abstract
Soybean [Glycine max (L.) Merr.] seed is a valuable source of protein and oil worldwide. Traditionally, the natural variations were heavily used in conventional soybean breeding programs to select desired traits. However, traditional plant breeding is encumbered with low frequencies of spontaneous mutations. In mutation breeding, genetic variations from induced mutations provide abundant sources of alterations in important soybean traits; this facilitated the development of soybean germplasm with modified seed composition traits to meet the different needs of end users. In this study, a total of 2366 'Forrest'-derived M2 families were developed for both forward and reverse genetic studies. A subset of 881 M3 families was forward genetically screened to measure the contents of protein, oil, carbohydrates, and fatty acids. A total of 14 mutants were identified to have stable seed composition phenotypes observed in both M3 and M4 generations. Correlation analyses have been conducted among ten seed composition traits and compared to a collection of 103 soybean germplasms. Mainly, ethyl methanesulfonate (EMS) mutagenesis had a strong impact on the seed-composition correlation that was observed among the 103 soybean germplasms, which offers multiple benefits for the soybean farmers and industry to breed for desired multiple seed phenotypes.
Collapse
Affiliation(s)
- Zhou Zhou
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (Z.Z.); (N.L.); (M.A.C.); (A.E.B.)
| | - Naoufal Lakhssassi
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (Z.Z.); (N.L.); (M.A.C.); (A.E.B.)
| | - Mallory A. Cullen
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (Z.Z.); (N.L.); (M.A.C.); (A.E.B.)
| | - Abdelhalim El Baz
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (Z.Z.); (N.L.); (M.A.C.); (A.E.B.)
| | - Tri D. Vuong
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA; (T.D.V.); (H.T.N.)
| | - Henry T. Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA; (T.D.V.); (H.T.N.)
| | - Khalid Meksem
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (Z.Z.); (N.L.); (M.A.C.); (A.E.B.)
| |
Collapse
|
19
|
Rani A, Kumar V, Mourya V, Tayalkar T. Genomic Regions Governing the Biosynthesis of Unsaturated Fatty Acids in Recombinant Inbred Lines of Soybean Raised across Multiple Growing Years. J AM OIL CHEM SOC 2019. [DOI: 10.1002/aocs.12298] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Anita Rani
- Crop Improvement Section, ICAR—Indian Institute of Soybean Research Indore Madhya Pradesh 452001 India
| | - Vineet Kumar
- Crop Improvement Section, ICAR—Indian Institute of Soybean Research Indore Madhya Pradesh 452001 India
| | - Vaishali Mourya
- Crop Improvement Section, ICAR—Indian Institute of Soybean Research Indore Madhya Pradesh 452001 India
| | - Trupti Tayalkar
- Crop Improvement Section, ICAR—Indian Institute of Soybean Research Indore Madhya Pradesh 452001 India
| |
Collapse
|
20
|
Xie D, Dai Z, Yang Z, Tang Q, Deng C, Xu Y, Wang J, Chen J, Zhao D, Zhang S, Zhang S, Su J. Combined genome-wide association analysis and transcriptome sequencing to identify candidate genes for flax seed fatty acid metabolism. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 286:98-107. [PMID: 31300147 DOI: 10.1016/j.plantsci.2019.06.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/31/2019] [Accepted: 06/01/2019] [Indexed: 05/11/2023]
Abstract
Flax seeds have a high oil content and are rich in unsaturated fatty acids, which have advantageous effects in preventing chronic diseases, such as cardiovascular diseases. At present, flax seeds are mainly developed for oil. Therefore, it is of practical significance to identify the candidate genes of fatty acid metabolism in flax seeds for breeding flax seeds with high oil content. In the present study, a natural population of flax containing 224 samples planted in 3 different environments was studied. The genome-wide association analysis (GWAS) of seed fatty acid content was conducted based on specific length amplified fragment sequencing (SLAF-seq) data. Transcriptome sequencing (RNA-seq) of samples from 3 different periods (14 d, 21 d and 28 d after anthesis) during seed development of the low oil variety Shuangya 4 and the high oil variety NEW was performed. The candidate genes for seed fatty acid metabolism were identified by combined analysis of these 2 methods. GWAS detected 16 SNP loci significantly associated with seed fatty acid content, and RNA-seq analysis identified 11,802 differentially expressed genes between high and low oil samples. Pathway enrichment analysis revealed that some differentially expressed genes were classified into fatty acid-related pathways. After comparison of these differentially expressed genes with the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, 20 genes homologous to other species were obtained. After analysis, 10 candidate genes were screened by GWAS and RNA-seq screening. Of these 10 genes, qRT-PCR assays using flax seeds in 5 different developmental stages showed that the expression levels of 6 candidate genes were significantly correlated with 5 fatty acid contents in seeds of the high oil variety NEW. Through metabolic pathway analysis found that 6 genes were involved in important fatty acid metabolic pathways, and some of them also have upstream and downstream regulation relations. The present study combined GWAS and RNA-seq methods to identify candidate genes for fatty acid metabolism in flax seeds, which provided reference for screening of candidate genes with complex traits.
Collapse
Affiliation(s)
- Dongwei Xie
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, China; Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.
| | - Zhigang Dai
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.
| | - Zemao Yang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.
| | - Qing Tang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.
| | - Canhui Deng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.
| | - Ying Xu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.
| | - Jing Wang
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, China.
| | - Jing Chen
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, China.
| | - Debao Zhao
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, China.
| | - Shuli Zhang
- Wuchang Rice Research Institute, Heilongjiang Academy of Agricultural Sciences, Wuchang, China.
| | - Shuquan Zhang
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, China.
| | - Jianguang Su
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.
| |
Collapse
|
21
|
Do PT, Nguyen CX, Bui HT, Tran LTN, Stacey G, Gillman JD, Zhang ZJ, Stacey MG. Demonstration of highly efficient dual gRNA CRISPR/Cas9 editing of the homeologous GmFAD2-1A and GmFAD2-1B genes to yield a high oleic, low linoleic and α-linolenic acid phenotype in soybean. BMC PLANT BIOLOGY 2019; 19:311. [PMID: 31307375 PMCID: PMC6632005 DOI: 10.1186/s12870-019-1906-8] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 06/25/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND CRISPR/Cas9 gene editing is now revolutionizing the ability to effectively modify plant genomes in the absence of efficient homologous recombination mechanisms that exist in other organisms. However, soybean is allotetraploid and is commonly viewed as difficult and inefficient to transform. In this study, we demonstrate the utility of CRISPR/Cas9 gene editing in soybean at relatively high efficiency. This was shown by specifically targeting the Fatty Acid Desaturase 2 (GmFAD2) that converts the monounsaturated oleic acid (C18:1) to the polyunsaturated linoleic acid (C18:2), therefore, regulating the content of monounsaturated fats in soybean seeds. RESULTS We designed two gRNAs to guide Cas9 to simultaneously cleave two sites, spaced 1Kb apart, within the second exons of GmFAD2-1A and GmFAD2-1B. In order to test whether the Cas9 and gRNAs would perform properly in transgenic soybean plants, we first tested the CRISPR construct we developed by transient hairy root transformation using Agrobacterium rhizogenesis strain K599. Once confirmed, we performed stable soybean transformation and characterized ten, randomly selected T0 events. Genotyping of CRISPR/Cas9 T0 transgenic lines detected a variety of mutations including large and small DNA deletions, insertions and inversions in the GmFAD2 genes. We detected CRISPR- edited DNA in all the tested T0 plants and 77.8% of the events transmitted the GmFAD2 mutant alleles to T1 progenies. More importantly, null mutants for both GmFAD2 genes were obtained in 40% of the T0 plants we genotyped. The fatty acid profile analysis of T1 seeds derived from CRISPR-edited plants homozygous for both GmFAD2 genes showed dramatic increases in oleic acid content to over 80%, whereas linoleic acid decreased to 1.3-1.7%. In addition, transgene-free high oleic soybean homozygous genotypes were created as early as the T1 generation. CONCLUSIONS Overall, our data showed that dual gRNA CRISPR/Cas9 system offers a rapid and highly efficient method to simultaneously edit homeologous soybean genes, which can greatly facilitate breeding and gene discovery in this important crop plant.
Collapse
Affiliation(s)
- Phat T. Do
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211 USA
- Present address: Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Cuong X. Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211 USA
| | - Hien T. Bui
- Plant Biotechnology Innovation Laboratory, Division of Plant Sciences, University of Missouri, Columbia, MO 65211 USA
| | - Ly T. N. Tran
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211 USA
| | - Gary Stacey
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211 USA
- Division of Biochemistry, University of Missouri, Columbia, MO 65211 USA
| | | | - Zhanyuan J. Zhang
- Plant Biotechnology Innovation Laboratory, Division of Plant Sciences, University of Missouri, Columbia, MO 65211 USA
| | - Minviluz G. Stacey
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211 USA
| |
Collapse
|
22
|
Islam N, Bates PD, Maria John KM, Krishnan HB, J Zhang Z, Luthria DL, Natarajan SS. Quantitative Proteomic Analysis of Low Linolenic Acid Transgenic Soybean Reveals Perturbations of Fatty Acid Metabolic Pathways. Proteomics 2019; 19:e1800379. [PMID: 30784187 DOI: 10.1002/pmic.201800379] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 02/06/2019] [Indexed: 12/15/2022]
Abstract
To understand the effect of fatty acid desaturase gene (GmFAD3) silencing on perturbation of fatty acid (FA) metabolic pathways, the changes are compared in protein profiling in control and low linolenic acid transgenic soybeans using tandem mass tag based mass spectrometry. Protein profiling of the transgenic line unveiled changes in several key enzymes of FA metabolism. This includes enzymes of lower abundance; fabH, fabF, and thioestrase associated with FA initiation, elongation, and desaturation processes and LOX1_5, ACOX, ACAA1, MFP2 associated with β-oxidation of α-linolenic acids pathways. In addition, the GmFAD3 silencing results in a significant reduction in one of the major allergens, Gly m 4 (C6T3L5). These results are important for exploring how plants adjust in their biological processes when certain changes are induced in the genetic makeup. A complete understanding of these processes will aid researchers to alter genes for developing value-added soybeans.
Collapse
Affiliation(s)
- Nazrul Islam
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, 20705, USA
| | - Philip D Bates
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164, USA
| | - K M Maria John
- Food Composition and Methods Development Laboratory, BHNRC, USDA-ARS, Beltsville, MD, 20705, USA
| | - Hari B Krishnan
- Plant Genetics Research Unit, USDA-ARS, University of Missouri, Columbia, MO, 65211, USA
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Zhanyuan J Zhang
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Devanand L Luthria
- Food Composition and Methods Development Laboratory, BHNRC, USDA-ARS, Beltsville, MD, 20705, USA
| | | |
Collapse
|
23
|
Bai S, Engelen S, Denolf P, Wallis JG, Lynch K, Bengtsson JD, Van Thournout M, Haesendonckx B, Browse J. Identification, characterization and field testing of Brassica napus mutants producing high-oleic oils. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:33-41. [PMID: 30536486 PMCID: PMC6604813 DOI: 10.1111/tpj.14195] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/16/2018] [Accepted: 11/30/2018] [Indexed: 05/05/2023]
Abstract
Producing healthy, high-oleic oils and eliminating trans-fatty acids from foods are two goals that can be addressed by reducing activity of the oleate desaturase, FAD2, in oilseeds. However, it is essential to understand the consequences of reducing FAD2 activity on the metabolism, cell biology and physiology of oilseed crop plants. Here, we translate knowledge from studies of fad2 mutants in Arabidopsis (Arabidopsis thaliana) to investigate the limits of non-GMO approaches to maximize oleic acid in the seed oil of canola (Brassica napus), a species that expresses three active FAD2 isozymes. A series of hypomorphic and null mutations in the FAD2.A5 isoform were characterized in yeast (Saccharomyes cerevisiae). Then, four of these were combined with null mutations in the other two isozymes, FAD2.C5 and FAD2.C1. The resulting mutant lines contained 71-87% oleic acid in their seed oil, compared with 62% in wild-type controls. All the mutant lines grew well in a greenhouse, but in field experiments we observed a clear demarcation in plant performance. Mutant lines containing less than 80% oleate in the seed oil were indistinguishable from wild-type controls in growth parameters and seed oil content. By contrast, lines with more than 80% oleate in the seed oil had significantly lower seedling establishment and vigor, delayed flowering and reduced plant height at maturity. These lines also had 7-11% reductions in seed oil content. Our results extend understanding of the B. napusFAD2 isozymes and define the practical limit to increasing oil oleate content in this crop species.
Collapse
Affiliation(s)
- Shuangyi Bai
- Institute of Biological Chemistry, Clark Hall, Washington State University, Pullman, WA 99164-6340, USA
| | - Steven Engelen
- BASF Agricultural Solutions Belgium N.V., Technologiepark 101, B-9052 Ghent, Belgium
| | - Peter Denolf
- BASF Agricultural Solutions Belgium N.V., Technologiepark 101, B-9052 Ghent, Belgium
| | - James G. Wallis
- Institute of Biological Chemistry, Clark Hall, Washington State University, Pullman, WA 99164-6340, USA
| | - Katherine Lynch
- Institute of Biological Chemistry, Clark Hall, Washington State University, Pullman, WA 99164-6340, USA
| | - Jesse D. Bengtsson
- Institute of Biological Chemistry, Clark Hall, Washington State University, Pullman, WA 99164-6340, USA
| | - Michel Van Thournout
- BASF Agricultural Solutions Belgium N.V., Technologiepark 101, B-9052 Ghent, Belgium
| | - Boris Haesendonckx
- BASF Agricultural Solutions Belgium N.V., Technologiepark 101, B-9052 Ghent, Belgium
| | - John Browse
- Institute of Biological Chemistry, Clark Hall, Washington State University, Pullman, WA 99164-6340, USA
- For correspondence ()
| |
Collapse
|
24
|
Zhao X, Jiang H, Feng L, Qu Y, Teng W, Qiu L, Zheng H, Han Y, Li W. Genome-wide association and transcriptional studies reveal novel genes for unsaturated fatty acid synthesis in a panel of soybean accessions. BMC Genomics 2019; 20:68. [PMID: 30665360 PMCID: PMC6341525 DOI: 10.1186/s12864-019-5449-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 01/11/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The nutritional value of soybean oil is largely influenced by the proportions of unsaturated fatty acids (FAs), including oleic acid (OA, 18:1), linoleic acid (LLA, 18:2), and linolenic acid (LNA, 18:3). Genome-wide association (GWAS) studies along with gene expression studies in soybean [Glycine max (L.) Merr.] were leveraged to dissect the genetics of unsaturated FAs. RESULTS A association panel of 194 diverse soybean accessions were phenotyped in 2013, 2014 and 2015 to identify Single Nucleotide Polymorphisms (SNPs) associated with OA, LLA, and LNA content, and determine putative candidate genes responsible for regulating unsaturated FAs composition. 149 SNPs that represented 73 genomic regions were found to be associated with the unsaturated FA contents in soybean seeds according to the results of GWAS. Twelve novel genes were predicted to be involved in unsaturated FA synthesis in soybean. The relationship between expression pattern of the candidate genes and the accumulation of unsaturated FAs revealed that multiple genes might be involved in unsaturated FAs regulation simultaneously but work in very different ways: Glyma.07G046200 and Glyma.20G245500 promote the OA accumulation in soybean seed in all the tested accessions; Glyma.13G68600 and Glyma.16G200200 promote the OA accumulation only in high OA germplasms; Glyma.07G151300 promotes OA accumulation in higher OA germplasms and suppresses that in lower OA germplasms; Glyma.16G003500 has the effect of increasing LLA accumulation in higher LA germplasms; Glyma.07G254500 suppresses the accumulation of LNA in lower OA germplasms; Glyma.14G194300 might be involved in the accumulation of LNA content in lower LNA germplasms. CONCLUSIONS The beneficial alleles and candidate genes identified might be valuable for improving marker-assisted breeding efficiency and exploring the molecular mechanisms underlying unsaturated fatty acid of soybean.
Collapse
Affiliation(s)
- 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, 150030, Harbin, China
| | - Haipeng Jiang
- 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, 150030, Harbin, China
| | - Lei Feng
- 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, 150030, Harbin, China
| | - Yingfan Qu
- 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, 150030, Harbin, 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, 150030, Harbin, 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
| | - 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, 150030, Harbin, 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, 150030, Harbin, China
| |
Collapse
|
25
|
Pichler H, Emmerstorfer-Augustin A. Modification of membrane lipid compositions in single-celled organisms – From basics to applications. Methods 2018; 147:50-65. [DOI: 10.1016/j.ymeth.2018.06.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 05/18/2018] [Accepted: 06/16/2018] [Indexed: 12/12/2022] Open
|
26
|
Genomics-Assisted Identification and Characterization of the Genetic Variants Underlying Differential Nitrogen Use Efficiencies in Allotetraploid Rapeseed Genotypes. G3-GENES GENOMES GENETICS 2018; 8:2757-2771. [PMID: 29967053 PMCID: PMC6071586 DOI: 10.1534/g3.118.200481] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Nitrogen (N) is a non-mineral macronutrient essential for plant growth and development. Oilseed rape (AnAnCnCn, 2n = 4x = 38) has a high requirement for N nutrients whereas showing the lowest N use efficiency (NUE) among crops. The mechanisms underlying NUE regulation in Brassica napus remain unclear because of genome complexity. In this study, we performed high-depth and -coverage whole-genome re-sequencing (WGS) of an N-efficient (higher NUE) genotype “XY15” and an N-inefficient (lower NUE) genotype “814” of rapeseed. More than 687 million 150-bp paired-end reads were generated, which provided about 93% coverage and 50× depth of the rapeseed genome. Applying stringent parameters, we identified a total of 1,449,157 single-nucleotide polymorphisms (SNPs), 335,228 InDels, 175,602 structure variations (SVs) and 86,280 copy number variations (CNVs) between the N-efficient and -inefficient genotypes. The largest proportion of various DNA polymorphisms occurred in the inter-genic regions. Unlike CNVs, the SNP/InDel and SV polymorphisms showed variation bias of the An and Cn subgenomes, respectively. Gene ontology analysis showed the genetic variants were mapped onto the genes involving N compound transport and ATPase complex metabolism, but not including N assimilation-related genes. On basis of identification of N-starvation responsive genes through high-throughput expression profiling, we also mapped these variants onto some key NUE-regulating genes, and validated their significantly differential expression between the N-efficient and -inefficient genotypes through qRT-PCR assays. Our data provide genome-wide high resolution DNA variants underlying NUE divergence in allotetraploid rapeseed genotypes, which would expedite the effective identification and functional validation of key NUE-regulating genes through genomics-assisted improvement of crop nutrient efficiency.
Collapse
|
27
|
Silva LCC, Bueno RD, da Matta LB, Pereira PHS, Mayrink DB, Piovesan ND, Sediyama CS, Fontes EPB, Cardinal AJ, Dal-Bianco M. Characterization of a new GmFAD3A allele in Brazilian CS303TNKCA soybean cultivar. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:1099-1110. [PMID: 29397403 DOI: 10.1007/s00122-018-3061-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 01/19/2018] [Indexed: 06/07/2023]
Abstract
KEY MESSAGE We molecularly characterized a new mutation in the GmFAD3A gene associated with low linolenic content in the Brazilian soybean cultivar CS303TNKCA and developed a molecular marker to select this mutation. Soybean is one of the most important crops cultivated worldwide. Soybean oil has 13% palmitic acid, 4% stearic acid, 20% oleic acid, 55% linoleic acid and 8% linolenic acid. Breeding programs are developing varieties with high oleic and low polyunsaturated fatty acids (linoleic and linolenic) to improve the oil oxidative stability and make the varieties more attractive for the soy industry. The main goal of this study was to characterize the low linoleic acid trait in CS303TNKCA cultivar. We sequenced CS303TNKCA GmFAD3A, GmFAD3B and GmFAD3C genes and identified an adenine point deletion in the GmFAD3A exon 5 (delA). This alteration creates a premature stop codon, leading to a truncated protein with just 207 residues that result in a non-functional enzyme. Analysis of enzymatic activity by heterologous expression in yeast support delA as the cause of low linolenic acid content in CS303TNKCA. Thus, we developed a TaqMan genotyping assay to associate delA with low linolenic acid content in segregating populations. Lines homozygous for delA had a linolenic acid content of 3.3 to 4.4%, and the variation at this locus accounted for 50.83 to 73.70% of the phenotypic variation. This molecular marker is a new tool to introgress the low linolenic acid trait into elite soybean cultivars and can be used to combine with high oleic trait markers to produce soybean with enhanced economic value. The advantage of using CS303TNKCA compared to other lines available in the literature is that this cultivar has good agronomic characteristics and is adapted to Brazilian conditions.
Collapse
Affiliation(s)
- Luiz Claudio Costa Silva
- Laboratório de Bioquímica Genética de Plantas, 212, BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
| | - Rafael Delmond Bueno
- Laboratório de Bioquímica Genética de Plantas, 212, BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
| | | | | | - Danyelle Barbosa Mayrink
- Laboratório de Bioquímica Genética de Plantas, 212, BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
| | - Newton Deniz Piovesan
- Laboratório de Bioquímica Genética de Plantas, 212, BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
| | | | | | - Andrea J Cardinal
- Crop Science Department, North Carollina State University, Raleigh, NC, 27695, USA
- Syngenta Biotechnology, Inc, 3054 Cornwallis Rd., Research Triangle Park, NC, 27709, USA
| | - Maximiller Dal-Bianco
- Laboratório de Bioquímica Genética de Plantas, 212, BIOAGRO and Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil.
| |
Collapse
|
28
|
Kulkarni KP, Patil G, Valliyodan B, Vuong TD, Shannon JG, Nguyen HT, Lee JD. Comparative genome analysis to identify SNPs associated with high oleic acid and elevated protein content in soybean. Genome 2018; 61:217-222. [PMID: 29365289 DOI: 10.1139/gen-2017-0158] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
The objective of this study was to determine the genetic relationship between the oleic acid and protein content. The genotypes having high oleic acid and elevated protein (HOEP) content were crossed with five elite lines having normal oleic acid and average protein (NOAP) content. The selected accessions were grown at six environments in three different locations and phenotyped for protein, oil, and fatty acid components. The mean protein content of parents, HOEP, and NOAP lines was 34.6%, 38%, and 34.9%, respectively. The oleic acid concentration of parents, HOEP, and NOAP lines was 21.7%, 80.5%, and 20.8%, respectively. The HOEP plants carried both FAD2-1A (S117N) and FAD2-1B (P137R) mutant alleles contributing to the high oleic acid phenotype. Comparative genome analysis using whole-genome resequencing data identified six genes having single nucleotide polymorphism (SNP) significantly associated with the traits analyzed. A single SNP in the putative gene Glyma.10G275800 was associated with the elevated protein content, and palmitic, oleic, and linoleic acids. The genes from the marker intervals of previously identified QTL did not carry SNPs associated with protein content and fatty acid composition in the lines used in this study, indicating that all the genes except Glyma.10G278000 may be the new genes associated with the respective traits.
Collapse
Affiliation(s)
- Krishnanand P Kulkarni
- a School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Gunvant Patil
- b Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Babu Valliyodan
- b Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Tri D Vuong
- b Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - J Grover Shannon
- b Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Henry T Nguyen
- b Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Jeong-Dong Lee
- a School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| |
Collapse
|
29
|
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
| |
Collapse
|
30
|
Poggetti L, Ferfuia C, Chiabà C, Testolin R, Baldini M. Kernel oil content and oil composition in walnut (Juglans regia L.) accessions from north-eastern Italy. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2018; 98:955-962. [PMID: 28703854 DOI: 10.1002/jsfa.8542] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/06/2017] [Accepted: 07/09/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Walnut oil use is currently limited by its poor oxidative stability due to the high percentage of polyunsaturated fatty acids. Modifying the oil composition may be a goal in walnut breeding to increase interest in this crop. Exploring natural variability and identifying the main environmental factors affecting oil quality are necessary in crop selection. Therefore 190 wild accessions were collected and evaluated during 2013 and 2014 for oil content and its fatty acid profile and compared with five commercial cultivars as references. RESULTS High variation in kernel oil content and fatty acid composition was found in the native walnut. Kernel oil content ranged from 54.2 to 72.2% (w/w). The major fatty acids were linoleic (range 46.9-68.6%), oleic (10.0-25.1%), linolenic (6.9-17.6%), palmitic (3.9-11.4%) and stearic (1.1-5.2%) acids. Some accessions had oil with a fatty acid ratio very different from the reference commercial cultivars, especially the oleic acid/polyunsaturated fatty acid (PUFA) ratio. A significant linear relationship and positive correlation between the daily minimum temperature and oleic acid content was observed in the wild walnuts. CONCLUSION The wide variation in fatty acid content and composition allows superior accessions to be selected for diffusion among growers. A suitable strategy would be to make a selection against PUFA content rather than just for high oleic acid. In addition, the selected high oleic accessions, before being utilized per se or as donor parents in breeding programs, have to demonstrate they are not adversely affected by the environment. © 2017 Society of Chemical Industry.
Collapse
Affiliation(s)
- Luca Poggetti
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Claudio Ferfuia
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Cristina Chiabà
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Raffaele Testolin
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Mario Baldini
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| |
Collapse
|
31
|
Mutlu C, Arslan-Tontul S, Candal C, Kilic O, Erbas M. Physicochemical, Thermal, and Sensory Properties of Blue Corn (Zea Mays L.). J Food Sci 2017; 83:53-59. [PMID: 29278653 DOI: 10.1111/1750-3841.14014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 11/09/2017] [Accepted: 11/18/2017] [Indexed: 10/18/2022]
Abstract
The aim of this study was to investigate some physicochemical and sensory properties of blue corn cultivated in Turkey. The length and width of the cob with kernels, hectoliter, and 1000-kernel weight of blue corn were measured as 7.66, 2.02 mm, 84.40 kg/100 L, and 44.27 g, respectively. The gelatinization onset, peak, and end temperatures were measured as 61.12 °C, 64.35 °C, and 75.65 °C, respectively. The water activity, moisture content, total protein, lipid, and crude fiber contents of the blue corn sample were detected as 0.44, 9.39%, 13.13%, 4.30%, and 2.68%, respectively. Total starch and resistant starch contents of blue corn were determined as 63.94% and 8.89%, respectively. Also, total monomeric anthocyanin content and antioxidant capacity of blue corn were detected as 915.43 mg CGE/kg and 7.99 μmol TE/g, respectively. Additionally, the major fatty acids detected in blue corn samples were palmitic, stearic, oleic, and linoleic acids. PRACTICAL APPLICATION Blue corn can be utilized in the production of enjoyable and healthier snacks, such as popcorn and chips, because of its color and high phenolic, anthocyanin, and fiber contents.
Collapse
Affiliation(s)
- Ceren Mutlu
- Dept. of Food Engineering, Faculty of Engineering, Akdeniz Univ., 07058 Antalya, Turkey.,Dept. of Food Engineering, Faculty of Engineering, Balikesir Univ., 10145 Balikesir, Turkey
| | - Sultan Arslan-Tontul
- Dept. of Food Engineering, Faculty of Engineering, Akdeniz Univ., 07058 Antalya, Turkey
| | - Cihadiye Candal
- Dept. of Food Engineering, Faculty of Engineering, Akdeniz Univ., 07058 Antalya, Turkey.,Dept. of Nutrition and Dietetics, Faculty of Health Sciences, Artvin Coruh Univ., 08100 Artvin, Turkey
| | - Ozlem Kilic
- Dept. of Food Engineering, Faculty of Engineering, Akdeniz Univ., 07058 Antalya, Turkey.,Dept. of Food Technology, Applied Science School of Kadirli, Osmaniye Korkut Ata Univ., 80000 Adana, Turkey
| | - Mustafa Erbas
- Dept. of Food Engineering, Faculty of Engineering, Akdeniz Univ., 07058 Antalya, Turkey
| |
Collapse
|
32
|
Kulkarni KP, Kim M, Song JT, Bilyeu KD, Lee JD. Genetic Improvement of the Fatty Acid Biosynthesis System to Alter the ω-6/ω-3 Ratio in the Soybean Seed. J AM OIL CHEM SOC 2017. [DOI: 10.1007/s11746-017-3049-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
33
|
Tian Y, He X, Liu S, Dong J. Comparative analysis of lipid profile and in vitro cytotoxic activity of fermented and unfermented soybean extracted by supercritical CO 2 extraction. J Funct Foods 2017. [DOI: 10.1016/j.jff.2017.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
|
34
|
Rauf S, Jamil N, Tariq SA, Khan M, Kausar M, Kaya Y. Progress in modification of sunflower oil to expand its industrial value. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2017; 97:1997-2006. [PMID: 28093767 DOI: 10.1002/jsfa.8214] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 01/09/2017] [Accepted: 01/11/2017] [Indexed: 05/20/2023]
Abstract
Increasing the sunflower seed oil content as well as improving its quality makes it compatible for industrial demands. This is an important breeding objective of sunflower which increases its market value and ensures high returns for the producers. The present review focuses on determining the progress of improving sunflower seed oil content and modifying its quality by empirical and advanced molecular breeding methods. It is known that the sunflower oil content and quality have been altered through empirical selection methods and mutation breeding programmes in various parts of the world. Further improvement in seed oil content and its components (such as phytosterols, tocopherols and modified fatty acid profile) has been slowed down due to low genetic variation in elite germplasm and complex of hereditary traits. Introgression from wild species can be carried out to modify the fatty acids profile and tocopherol contents with linkage drags. Different transgenes introduced through biotechnological methods may produce novel long-chain fatty acids within sunflower oil. Bio-engineering of sunflower oil could allow it to be used in diverse industrial products such as bio-diesel or bio-plastics. These results showed that past and current trends of modifying sunflower oil quality are essential for its further expansion as an oilseed crop. © 2017 Society of Chemical Industry.
Collapse
Affiliation(s)
- Saeed Rauf
- Department of Plant Breeding & Genetics, University College of Agriculture, University of Sargodha, Pakistan
| | - Nazia Jamil
- Department of Microbiology and Molecular Genetics University of the Punjab, Quaid-e-Campus, Lahore, Pakistan
| | - Sultan Ali Tariq
- National Agriculture Research Institute, Murre Road, Islamabad, Pakistan
| | - Maria Khan
- Department of Plant Breeding & Genetics, University College of Agriculture, University of Sargodha, Pakistan
| | - Maria Kausar
- Department of Plant Breeding & Genetics, University College of Agriculture, University of Sargodha, Pakistan
| | - Yalcin Kaya
- Department of Genetic and Bioengineering, Engineering Faculty, Trakya University, Edirne, Turkey
| |
Collapse
|
35
|
Sturtevant D, Horn P, Kennedy C, Hinze L, Percy R, Chapman K. Lipid metabolites in seeds of diverse Gossypium accessions: molecular identification of a high oleic mutant allele. PLANTA 2017; 245:595-610. [PMID: 27988885 DOI: 10.1007/s00425-016-2630-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 11/30/2016] [Indexed: 05/12/2023]
Abstract
Genetically diverse cottonseeds show altered compositions and spatial distributions of phosphatidylcholines and triacylglycerols. Lipidomics profiling led to the discovery of a novel FAD2 - 1 allele, fad2 - 1D - 1 , resulting in a high oleic phenotype. The domestication and breeding of cotton for elite, high-fiber cultivars have led to reduced variation of seed constituents within currently cultivated upland cotton genotypes. However, a recent screen of the genetically diverse U.S. National Cotton Germplasm Collection identified Gossypium accessions with marked differences in seed oil and protein content. Here, several of these accessions representing substantial variation in seed oil content were analyzed for quantitative and spatial differences in lipid compositions by mass spectrometric approaches. Results indicate considerable variation in amount and spatial distribution of pathway metabolites for triacylglycerol biosynthesis in embryos across Gossypium accessions, suggesting that this variation might be exploited by breeders for seed composition traits. By way of example, these lipid metabolite differences led to the identification of a mutant allele of the D-subgenome homolog of the delta-12 desaturase (fad2-1D-1) in a wild accession of G. barbadense that has a high oil and high oleic seed phenotype. This mutation is a 90-bp insertion in the 3' end of the FAD2-1D coding sequence and a modification of the 3' end of the gene beyond the coding sequence leading to the introduction of a premature stop codon. Given the large amounts of cottonseed produced around the world that is currently not processed into higher value products, these efforts might be one avenue to raise the overall value of the cotton crop for producers.
Collapse
Affiliation(s)
- Drew Sturtevant
- Department of Biological Sciences, Center for Plant Lipid Research, BioDiscovery Institute, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203-5217, USA
| | - Patrick Horn
- Department of Biological Sciences, Center for Plant Lipid Research, BioDiscovery Institute, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203-5217, USA
- U.S. Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
| | - Christopher Kennedy
- Department of Biological Sciences, Center for Plant Lipid Research, BioDiscovery Institute, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203-5217, USA
| | - Lori Hinze
- USDA/ARS, Southern Plains Agricultural Research Center, College Station, TX, 77845, USA
| | - Richard Percy
- USDA/ARS, Southern Plains Agricultural Research Center, College Station, TX, 77845, USA
| | - Kent Chapman
- Department of Biological Sciences, Center for Plant Lipid Research, BioDiscovery Institute, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203-5217, USA.
| |
Collapse
|
36
|
Patil G, Chaudhary J, Vuong TD, Jenkins B, Qiu D, Kadam S, Shannon GJ, Nguyen HT. Development of SNP Genotyping Assays for Seed Composition Traits in Soybean. INTERNATIONAL JOURNAL OF PLANT GENOMICS 2017; 2017:6572969. [PMID: 28630621 PMCID: PMC5463095 DOI: 10.1155/2017/6572969] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 03/20/2017] [Accepted: 03/30/2017] [Indexed: 05/20/2023]
Abstract
Seed composition is one of the most important determinants of the economic values in soybean. The quality and quantity of different seed components, such as oil, protein, and carbohydrates, are crucial ingredients in food, feed, and numerous industrial products. Soybean researchers have successfully developed and utilized a diverse set of molecular markers for seed trait improvement in soybean breeding programs. It is imperative to design and develop molecular assays that are accurate, robust, high-throughput, cost-effective, and available on a common genotyping platform. In the present study, we developed and validated KASP (Kompetitive allele-specific polymerase chain reaction) genotyping assays based on previously known functional mutant alleles for the seed composition traits, including fatty acids, oligosaccharides, trypsin inhibitor, and lipoxygenase. These assays were validated on mutant sources as well as mapping populations and precisely distinguish the homozygotes and heterozygotes of the mutant genes. With the obvious advantages, newly developed KASP assays in this study can substitute the genotyping assays that were previously developed for marker-assisted selection (MAS). The functional gene-based assay resource developed using common genotyping platform will be helpful to accelerate efforts to improve soybean seed composition traits.
Collapse
Affiliation(s)
- Gunvant Patil
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
- Department of Agronomy and Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Juhi Chaudhary
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Tri D. Vuong
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Brian Jenkins
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Dan Qiu
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Suhas Kadam
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Grover J. Shannon
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Henry T. Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
- *Henry T. Nguyen:
| |
Collapse
|
37
|
Lakhssassi N, Zhou Z, Liu S, Colantonio V, AbuGhazaleh A, Meksem K. Characterization of the FAD2 Gene Family in Soybean Reveals the Limitations of Gel-Based TILLING in Genes with High Copy Number. FRONTIERS IN PLANT SCIENCE 2017; 8:324. [PMID: 28348573 PMCID: PMC5346563 DOI: 10.3389/fpls.2017.00324] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 02/23/2017] [Indexed: 05/21/2023]
Abstract
Soybean seed oil typically contains 18-20% oleic acid. Increasing the content of oleic acid is beneficial for health and biodiesel production. Mutations in FAD2-1 genes have been reported to increase seed oleic acid content. A subset of 1,037 mutant families from a mutagenized soybean cultivar (cv.) Forrest population was screened using reverse genetics (TILLING) to identify mutations within FAD2 genes. Although no fad2 mutants were identified using gel-based TILLING, four fad2-1A and one fad2-1B mutants were identified to have high seed oleic acid content using forward genetic screening and subsequent target sequencing. TILLING has been successfully used as a non-transgenic reverse genetic approach to identify mutations in genes controlling important agronomic traits. However, this technique presents limitations in traits such as oil composition due to gene copy number and similarities within the soybean genome. In soybean, FAD2 are present as two copies, FAD2-1 and FAD2-2. Two FAD2-1 members: FAD2-1A and FAD2-1B; and three FAD2-2 members: FAD2-2A, FAD2-2B, and FAD2-2C have been reported. Syntenic, phylogenetic, and in silico analysis revealed two additional members constituting the FAD2 gene family: GmFAD2-2D and GmFAD2-2E, located on chromosomes 09 and 15, respectively. They are presumed to have diverged from other FAD2-2 members localized on chromosomes 19 (GmFAD2-2A and GmFAD2-2B) and 03 (GmFAD2-2C). This work discusses alternative solutions to the limitations of gel-based TILLING in functional genomics due to high copy number and multiple paralogs of the FAD2 gene family in soybean.
Collapse
Affiliation(s)
- Naoufal Lakhssassi
- Department of Plant, Soil and Agricultural Systems, Southern Illinois UniversityCarbondale, IL, USA
| | - Zhou Zhou
- Department of Plant, Soil and Agricultural Systems, Southern Illinois UniversityCarbondale, IL, USA
| | - Shiming Liu
- Department of Plant, Soil and Agricultural Systems, Southern Illinois UniversityCarbondale, IL, USA
| | - Vincent Colantonio
- Department of Plant, Soil and Agricultural Systems, Southern Illinois UniversityCarbondale, IL, USA
| | - Amer AbuGhazaleh
- Department of Animal Science, Food and Nutrition, Southern Illinois UniversityCarbondale, IL, USA
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois UniversityCarbondale, IL, USA
- *Correspondence: Khalid Meksem
| |
Collapse
|
38
|
Kumawat G, Gupta S, Ratnaparkhe MB, Maranna S, Satpute GK. QTLomics in Soybean: A Way Forward for Translational Genomics and Breeding. FRONTIERS IN PLANT SCIENCE 2016; 7:1852. [PMID: 28066449 PMCID: PMC5174554 DOI: 10.3389/fpls.2016.01852] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/23/2016] [Indexed: 05/19/2023]
Abstract
Food legumes play an important role in attaining both food and nutritional security along with sustainable agricultural production for the well-being of humans globally. The various traits of economic importance in legume crops are complex and quantitative in nature, which are governed by quantitative trait loci (QTLs). Mapping of quantitative traits is a tedious and costly process, however, a large number of QTLs has been mapped in soybean for various traits albeit their utilization in breeding programmes is poorly reported. For their effective use in breeding programme it is imperative to narrow down the confidence interval of QTLs, to identify the underlying genes, and most importantly allelic characterization of these genes for identifying superior variants. In the field of functional genomics, especially in the identification and characterization of gene responsible for quantitative traits, soybean is far ahead from other legume crops. The availability of genic information about quantitative traits is more significant because it is easy and effective to identify homologs than identifying shared syntenic regions in other crop species. In soybean, genes underlying QTLs have been identified and functionally characterized for phosphorous efficiency, flowering and maturity, pod dehiscence, hard-seededness, α-Tocopherol content, soybean cyst nematode, sudden death syndrome, and salt tolerance. Candidate genes have also been identified for many other quantitative traits for which functional validation is required. Using the sequence information of identified genes from soybean, comparative genomic analysis of homologs in other legume crops could discover novel structural variants and useful alleles for functional marker development. The functional markers may be very useful for molecular breeding in soybean and harnessing benefit of translational research from soybean to other leguminous crops. Thus, soybean crop can act as a model crop for translational genomics and breeding of quantitative traits in legume crops. In this review, we summarize current status of identification and characterization of genes underlying QTLs for various quantitative traits in soybean and their significance in translational genomics and breeding of other legume crops.
Collapse
Affiliation(s)
- Giriraj Kumawat
- Crop Improvement Section, ICAR—Indian Institute of Soybean ResearchIndore, India
| | | | | | | | | |
Collapse
|
39
|
Rajwade AV, Joshi RS, Kadoo NY, Gupta VS. Sequence characterization and in silico structure prediction of fatty acid desaturases in linseed varieties with differential fatty acid composition. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2016; 96:4896-4906. [PMID: 27109704 DOI: 10.1002/jsfa.7775] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Revised: 04/20/2016] [Accepted: 04/21/2016] [Indexed: 05/24/2023]
Abstract
BACKGROUND Linseed is the richest agricultural source of α-linolenic acid (ALA), an ω-3 fatty acid (FA) that offers several nutritional benefits. In the present study, sequence characterization of six desaturase genes (SAD1, SAD2, FAD2, FAD2-2, FAD3A and FAD3B) and 3D structure prediction of their proteins from ten Indian linseed varieties differing in ALA content were performed to determine whether the nucleotide and amino acid (AA) sequence variants have any functional implications in differential accumulation of ALA or other FAs in linseed. RESULTS The SAD and FAD2 genes exhibited few sequence variations among the ten varieties, forming only one or two protein isoforms. In contrast, the FAD3A and FAD3B genes showed more sequence variations and three or four protein isoforms. Interestingly, the two high-ALA varieties NL260 and Padmini had the same FAD3B nucleotide and protein isoforms, which differed from all other varieties. Surprisingly, no AA changes altered the 3D structures of the desaturase proteins. CONCLUSION Several nucleotide and AA sequence variations in desaturase genes were observed; however, they did not alter the 3D structure of any desaturase protein and were not correlated with FA levels among the ten linseed varieties, which had different ALA contents. This suggests a complex regulatory process of biosynthesis of FAs in linseed. © 2016 Society of Chemical Industry.
Collapse
Affiliation(s)
- Ashwini V Rajwade
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411 008, India
| | - Rakesh S Joshi
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411 008, India
| | - Narendra Y Kadoo
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411 008, India.
| | - Vidya S Gupta
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411 008, India.
| |
Collapse
|
40
|
Chiquito-Almanza E, Ochoa-Zarzosa A, López-Meza JE, Pecina-Quintero V, Nuñez-Colín CA, Anaya-López JL. A new allele of γ-kafirin gene coding for a protein with high lysine content in Mexican white sorghum germplasm. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2016; 96:3342-3350. [PMID: 26526074 DOI: 10.1002/jsfa.7513] [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: 03/09/2015] [Revised: 08/01/2015] [Accepted: 10/28/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND Low protein digestibility and lysine content of white sorghum grain limit its use as a foodstuff. The increase in γ-kafirin cross-linking, has an important role in the reduction of protein digestibility. The objective of this study was to characterize the γ-kafirin gene in 12 Mexican tannin-free white sorghum genotypes and its relationship with protein digestibility and lysine content. RESULTS Two alleles of γ-kafirin gene were identified: alleles 1 and 7. The predicted amino acid sequence of allele 7 showed seven point mutations; six were silent, and one missense (C235G), causing the substitution P79A in the deduced amino acid sequence. In silico analysis showed that γ-kafirin codified by allele 1 has five α-helixes without disulfide bonds, while γ-kafirin coding by allele 7 has four α-helixes and three disulfide bonds. Genotypes with allele 7 had higher lysine content than those with allele 1, showing no differences in the kafirin electrophoretic profile, neither a correlation with the protein content nor the in vitro pepsin digestibility. CONCLUSIONS Mexican tannin-free white sorghum genotypes showed two γ-kafirin alleles, 1 and 7. Allele 7 was associated with higher lysine content; in silico analysis showed that the substitution of P79A in this allele could modify γ-kafirin secondary structure. © 2015 Society of Chemical Industry.
Collapse
Affiliation(s)
- Elizabeth Chiquito-Almanza
- Centro Multidisciplinario de Estudios en Biotecnología-Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo, C.P. 58893, Morelia, Michoacán, México
| | - Alejandra Ochoa-Zarzosa
- Centro Multidisciplinario de Estudios en Biotecnología-Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo, C.P. 58893, Morelia, Michoacán, México
| | - Joel E López-Meza
- Centro Multidisciplinario de Estudios en Biotecnología-Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo, C.P. 58893, Morelia, Michoacán, México
| | - Víctor Pecina-Quintero
- Unidad de Biotecnología, Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, Campo Experimental Bajío. C.P. 38110, Celaya, Guanajuato, México
| | - Carlos A Nuñez-Colín
- Programa de Biotecnología, Universidad de Guanajuato, Mutualismo #303, Col. La Suiza, C.P. 38060, Celaya, Guanajuato, México
| | - José L Anaya-López
- Unidad de Biotecnología, Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, Campo Experimental Bajío. C.P. 38110, Celaya, Guanajuato, México
| |
Collapse
|
41
|
Goettel W, Ramirez M, Upchurch RG, An YQC. Identification and characterization of large DNA deletions affecting oil quality traits in soybean seeds through transcriptome sequencing analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1577-93. [PMID: 27179525 PMCID: PMC4943983 DOI: 10.1007/s00122-016-2725-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 04/28/2016] [Indexed: 05/11/2023]
Abstract
KEY MESSAGE Identification and characterization of a 254-kb genomic deletion on a duplicated chromosome segment that resulted in a low level of palmitic acid in soybean seeds using transcriptome sequencing. A large number of soybean genotypes varying in seed oil composition and content have been identified. Understanding the molecular mechanisms underlying these variations is important for breeders to effectively utilize them as a genetic resource. Through design and application of a bioinformatics approach, we identified nine co-regulated gene clusters by comparing seed transcriptomes of nine soybean genotypes varying in oil composition and content. We demonstrated that four gene clusters in the genotypes M23, Jack and N0304-303-3 coincided with large-scale genome rearrangements. The co-regulated gene clusters in M23 and Jack mapped to a previously described 164-kb deletion and a copy number amplification of the Rhg1 locus, respectively. The coordinately down-regulated gene clusters in N0304-303-3 were caused by a 254-kb deletion containing 19 genes including a fatty acyl-ACP thioesterase B gene (FATB1a). This deletion was associated with reduced palmitic acid content in seeds and was the molecular cause of a previously reported nonfunctional FATB1a allele, fap nc . The M23 and N0304-304-3 deletions were located in duplicated genome segments retained from the Glycine-specific whole genome duplication that occurred 13 million years ago. The homoeologous genes in these duplicated regions shared a strong similarity in both their encoded protein sequences and transcript accumulation levels, suggesting that they may have conserved and important functions in seeds. The functional conservation of homoeologous genes may result in genetic redundancy and gene dosage effects for their associated seed traits, explaining why the large deletion did not cause lethal effects or completely eliminate palmitic acid in N0304-303-3.
Collapse
Affiliation(s)
- Wolfgang Goettel
- US Department of Agriculture, Agricultural Research Service, Midwest Area, Plant Genetics Research Unit, Donald Danforth Plant Science Center, 975 N. Warson Rd, St. Louis, MO, 63132, USA
| | - Martha Ramirez
- US Department of Agriculture, Agricultural Research Service, Soybean and Nitrogen Fixation Research, 2417 Gardner Hall, Raleigh, NC, 27695, USA
| | - Robert G Upchurch
- US Department of Agriculture, Agricultural Research Service, Soybean and Nitrogen Fixation Research, 2417 Gardner Hall, Raleigh, NC, 27695, USA
| | - Yong-Qiang Charles An
- US Department of Agriculture, Agricultural Research Service, Midwest Area, Plant Genetics Research Unit, Donald Danforth Plant Science Center, 975 N. Warson Rd, St. Louis, MO, 63132, USA.
| |
Collapse
|
42
|
Nguyen QT, Kisiala A, Andreas P, Neil Emery R, Narine S. Soybean Seed Development: Fatty Acid and Phytohormone Metabolism and Their Interactions. Curr Genomics 2016; 17:241-60. [PMID: 27252591 PMCID: PMC4869011 DOI: 10.2174/1389202917666160202220238] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 07/27/2015] [Accepted: 08/04/2015] [Indexed: 12/20/2022] Open
Abstract
Vegetable oil utilization is determined by its fatty acid composition. In soybean and other grain crops, during the seed development oil accumulation is important trait for value in food or industrial applications. Seed development is relatively short and sensitive to unfavorable abiotic conditions. These stresses can lead to a numerous undesirable qualitative as well as quantitative changes in fatty acid production. Fatty acid manipulation which targets a higher content of a specific single fatty acid for food or industrial application has gained more attention. Despite several successes in modifying the ratio of endogenous fatty acids in most domesticated oilseed crops, numerous obstacles in FA manipulation of seed maturation are yet to be overcome. Remarkably, connections with plant hormones have not been well studied despite their critical roles in the regulation and promotion of a plethora of processes in plant growth and development. While activities of phytohormones during the reproductive phase have been partially clarified in seed physiology, the biological role of plant hormones in oil accumulation during seed development has not been investigated. In this review seed development and numerous effects of abiotic stresses are discussed. After describing fatty acid and phytohormone metabolism and their interactions, we postulate that the endogenous plant hormones play important roles in fatty acid production in soybean seeds.
Collapse
Affiliation(s)
- Quoc Thien. Nguyen
- Environmental & Life Sciences Graduate Program, Trent University, Peterborough, Ontario,Canada
| | - Anna Kisiala
- Department of Biology, Trent University, Peterborough, Ontario, Canada
| | - Peter Andreas
- Department of Biology, Trent University, Peterborough, Ontario, Canada
| | - R.J. Neil Emery
- Department of Biology, Trent University, Peterborough, Ontario, Canada
| | - Suresh Narine
- Trent Centre for Biomaterials Research, Departments of Physics & Astronomy and Chemistry, Trent University, Peterborough,Ontario, Canada
| |
Collapse
|
43
|
Mehra P, Pandey BK, Giri J. Genome-wide DNA polymorphisms in low Phosphate tolerant and sensitive rice genotypes. Sci Rep 2015; 5:13090. [PMID: 26278778 PMCID: PMC4538390 DOI: 10.1038/srep13090] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 07/17/2015] [Indexed: 12/30/2022] Open
Abstract
Soil Phosphorus (P) deficiency is one of the major challenges to rice crop world-wide. Modern rice genotypes are highly P-responsive and rely on high input of P fertilizers. However, low P tolerant traditional cultivars and landraces have genetic potential to sustain well under low P. Identification of high resolution DNA polymorphisms (SNPs and InDels) in such contrasting genotypes is largely missing for low P response at gene levels. Here, we report high quality DNA polymorphisms in low P sensitive genotype, PB1 and tolerant traditional genotype, Dular. We performed whole genome resequencing using Illumina NGS platform and identified a total of 5,157,939 sequence variants in PB1 and Dular with reference to Nipponbare genome. We have identified approximately 2.3 million and 2.9 million high quality polymorphisms in PB1 and Dular, respectively, with an average read depth of ≥24X. We further mapped several DNA polymorphisms (non-synonymous and regulatory variants) having potential functional significance to key Phosphate Starvation Responsive (PSR) and root architecture genes in Dular and Kasalath using a compiled list of low P responsive genes. These identified variants can serve as a useful source of genetic variability for improving low P tolerance and root architecture of high yielding modern genotypes.
Collapse
Affiliation(s)
- Poonam Mehra
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Bipin K Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Jitender Giri
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| |
Collapse
|
44
|
Cheng J, Salentijn EMJ, Huang B, Denneboom C, Qi W, Dechesne AC, Krens FA, Visser RGF, van Loo EN. Detection of induced mutations in CaFAD2 genes by next-generation sequencing leading to the production of improved oil composition in Crambe abyssinica. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:471-81. [PMID: 25393152 DOI: 10.1111/pbi.12269] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 08/10/2014] [Accepted: 08/20/2014] [Indexed: 05/09/2023]
Abstract
Crambe abyssinica is a hexaploid oil crop for industrial applications. An increase of erucic acid (C22:1) and reduction of polyunsaturated fatty acid (PUFA) contents in crambe oil is a valuable improvement. An increase in oleic acid (C18:1), a reduction in PUFA and possibly an increase in C22:1 can be obtained by down-regulating the expression of fatty acid desaturase2 genes (CaFAD2), which code for the enzyme that converts C18:1 into C18:2. We conducted EMS-mutagenesis in crambe, followed by Illumina sequencing, to screen mutations in three expressed CaFAD2 genes. Two novel analysis strategies were used to detect mutation sites. In the first strategy, mutation detection targeted specific sequence motifs. In the second strategy, every nucleotide position in a CaFAD2 fragment was tested for the presence of mutations. Seventeen novel mutations were detected in 1100 one-dimensional pools (11 000 individuals) in three expressed CaFAD2 genes, including non-sense mutations and mis-sense mutations in CaFAD2-C1, -C2 and -C3. The homozygous non-sense mutants for CaFAD2-C3 resulted in a 25% higher content of C18:1 and 25% lower content of PUFA compared to the wild type. The mis-sense mutations only led to small changes in oil composition. Concluding, targeted mutation detection using NGS in a polyploid was successfully applied and it was found that a non-sense mutation in even a single CaFAD2 gene can lead to changes in crambe oil composition. Stacking the mutations in different CaFAD2 may gain additional changes in C18:1 and PUFA contents.
Collapse
Affiliation(s)
- Jihua Cheng
- Wageningen UR Plant Breeding, Wageningen, The Netherlands; College of Life Science, Hubei University, Hubei, China
| | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Chaudhary J, Patil GB, Sonah H, Deshmukh RK, Vuong TD, Valliyodan B, Nguyen HT. Expanding Omics Resources for Improvement of Soybean Seed Composition Traits. FRONTIERS IN PLANT SCIENCE 2015; 6:1021. [PMID: 26635846 PMCID: PMC4657443 DOI: 10.3389/fpls.2015.01021] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 11/05/2015] [Indexed: 05/19/2023]
Abstract
Food resources of the modern world are strained due to the increasing population. There is an urgent need for innovative methods and approaches to augment food production. Legume seeds are major resources of human food and animal feed with their unique nutrient compositions including oil, protein, carbohydrates, and other beneficial nutrients. Recent advances in next-generation sequencing (NGS) together with "omics" technologies have considerably strengthened soybean research. The availability of well annotated soybean genome sequence along with hundreds of identified quantitative trait loci (QTL) associated with different seed traits can be used for gene discovery and molecular marker development for breeding applications. Despite the remarkable progress in these technologies, the analysis and mining of existing seed genomics data are still challenging due to the complexity of genetic inheritance, metabolic partitioning, and developmental regulations. Integration of "omics tools" is an effective strategy to discover key regulators of various seed traits. In this review, recent advances in "omics" approaches and their use in soybean seed trait investigations are presented along with the available databases and technological platforms and their applicability in the improvement of soybean. This article also highlights the use of modern breeding approaches, such as genome-wide association studies (GWAS), genomic selection (GS), and marker-assisted recurrent selection (MARS) for developing superior cultivars. A catalog of available important resources for major seed composition traits, such as seed oil, protein, carbohydrates, and yield traits are provided to improve the knowledge base and future utilization of this information in the soybean crop improvement programs.
Collapse
|
46
|
Chen Z, Tonnis B, Morris B, Wang RB, Zhang AL, Pinnow D, Wang ML. Variation in seed fatty acid composition and sequence divergence in the FAD2 gene coding region between wild and cultivated sesame. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:11706-11710. [PMID: 25386691 DOI: 10.1021/jf503648b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Sesame germplasm harbors genetic diversity which can be useful for sesame improvement in breeding programs. Seven accessions with different levels of oleic acid were selected from the entire USDA sesame germplasm collection (1232 accessions) and planted for morphological observation and re-examination of fatty acid composition. The coding region of the FAD2 gene for fatty acid desaturase (FAD) in these accessions was also sequenced. Cultivated sesame accessions flowered and matured earlier than the wild species. The cultivated sesame seeds contained a significantly higher percentage of oleic acid (40.4%) than the seeds of the wild species (26.1%). Nucleotide polymorphisms were identified in the FAD2 gene coding region between wild and cultivated species. Some nucleotide polymorphisms led to amino acid changes, one of which was located in the enzyme active site and may contribute to the altered fatty acid composition. Based on the morphology observation, chemical analysis, and sequence analysis, it was determined that two accessions were misnamed and need to be reclassified. The results obtained from this study are useful for sesame improvement in molecular breeding programs.
Collapse
Affiliation(s)
- Zhenbang Chen
- Department of Crop and Soil Sciences, University of Georgia , Griffin, Georgia 30223, United States
| | | | | | | | | | | | | |
Collapse
|
47
|
Haun W, Coffman A, Clasen BM, Demorest ZL, Lowy A, Ray E, Retterath A, Stoddard T, Juillerat A, Cedrone F, Mathis L, Voytas DF, Zhang F. Improved soybean oil quality by targeted mutagenesis of the fatty acid desaturase 2 gene family. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:934-40. [PMID: 24851712 DOI: 10.1111/pbi.12201] [Citation(s) in RCA: 232] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 03/27/2014] [Accepted: 04/24/2014] [Indexed: 05/03/2023]
Abstract
Soybean oil is high in polyunsaturated fats and is often partially hydrogenated to increase its shelf life and improve oxidative stability. The trans-fatty acids produced through hydrogenation pose a health threat. Soybean lines that are low in polyunsaturated fats were generated by introducing mutations in two fatty acid desaturase 2 genes (FAD2-1A and FAD2-1B), which in the seed convert the monounsaturated fat, oleic acid, to the polyunsaturated fat, linoleic acid. Transcription activator-like effector nucleases (TALENs) were engineered to recognize and cleave conserved DNA sequences in both genes. In four of 19 transgenic soybean lines expressing the TALENs, mutations in FAD2-1A and FAD2-1B were observed in DNA extracted from leaf tissue; three of the four lines transmitted heritable FAD2-1 mutations to the next generation. The fatty acid profile of the seed was dramatically changed in plants homozygous for mutations in both FAD2-1A and FAD2-1B: oleic acid increased from 20% to 80% and linoleic acid decreased from 50% to under 4%. Further, mutant plants were identified that lacked the TALEN transgene and only carried the targeted mutations. The ability to create a valuable trait in a single generation through targeted modification of a gene family demonstrates the power of TALENs for genome engineering and crop improvement.
Collapse
Affiliation(s)
- William Haun
- Cellectis plant sciences Inc., New Brighton, MN, USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Bioinformatics study of delta-12 fatty acid desaturase 2 (FAD2) gene in oilseeds. Mol Biol Rep 2014; 41:5077-87. [DOI: 10.1007/s11033-014-3373-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 01/16/2014] [Indexed: 10/25/2022]
|
49
|
Radovanovic N, Thambugala D, Duguid S, Loewen E, Cloutier S. Functional Characterization of Flax Fatty Acid Desaturase FAD2 and FAD3 Isoforms Expressed in Yeast Reveals a Broad Diversity in Activity. Mol Biotechnol 2014; 56:609-20. [DOI: 10.1007/s12033-014-9737-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
50
|
Guo HH, Li QQ, Wang TT, Hu Q, Deng WH, Xia XL, Gao HB. XsFAD2 gene encodes the enzyme responsible for the high linoleic acid content in oil accumulated in Xanthoceras sorbifolia seeds. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2014; 94:482-488. [PMID: 23775588 DOI: 10.1002/jsfa.6273] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Revised: 05/25/2013] [Accepted: 06/17/2013] [Indexed: 06/02/2023]
Abstract
BACKGROUND Xanthoceras sorbifolia Bunge is a valuable oilseed tree that has linoleic acid-rich seed oil. Microsomal oleate desaturase (FAD2; EC 1.3.1.35) is responsible for the conversion of oleic acid to linoleic acid during fatty acid synthesis. In this study, XsFAD2 was cloned from developing embryos of X. sorbifolia. RESULTS XsFAD2 contained three histidine boxes, a C-terminal endoplasmic reticulum retrieval motif, and five putative transmembrane domains representing the characteristics of membrane-bound fatty acid desaturase. XsFAD2 expression in yeast cells resulted in linoleic acid (18:2) and palmitolinoleic acid (16:2) production, confirming the biological activity of the enzyme encoded by XsFAD2. These fatty acids are not normally present in wild-type yeast. Phylogenetic analysis indicated that XsFAD2 is located in a subgroup of FAD2 enzymes specifically or highly expressed in developing seeds. The expression level of XsFAD2 in seeds was much higher than those in leaves and petals. Furthermore, XsFAD2 expression pattern correlated well with linoleic acid accumulated in seeds. CONCLUSION Results suggested that XsFAD2 is responsible for the high linoleic acid content in X. sorbifolia seed oil. This study provides insight on the regulation mechanism of fatty acid synthesis in X. sorbifolia seeds and a valuable gene for improving the oil quality in oilseed trees.
Collapse
Affiliation(s)
- Hui-Hong Guo
- College of Biological Sciences and Biotechnology, Beijing Forestry University, National Engineering Laboratory for Tree Breeding; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of State Forestry Administration, No. 35, Tsing Hua East Road, Haidian District, Beijing, 100083, China
| | | | | | | | | | | | | |
Collapse
|