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Chen B, Shi Y, Sun Y, Lu L, Wang L, Liu Z, Cheng S. Innovations in functional genomics and molecular breeding of pea: exploring advances and opportunities. ABIOTECH 2024; 5:71-93. [PMID: 38576433 PMCID: PMC10987475 DOI: 10.1007/s42994-023-00129-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 12/05/2023] [Indexed: 04/06/2024]
Abstract
The garden pea (Pisum sativum L.) is a significant cool-season legume, serving as crucial food sources, animal feed, and industrial raw materials. The advancement of functional genomics over the past two decades has provided substantial theoretical foundations and progress to pea breeding. Notably, the release of the pea reference genome has enhanced our understanding of plant architecture, symbiotic nitrogen fixation (SNF), flowering time, floral organ development, seed development, and stress resistance. However, a considerable gap remains between pea functional genomics and molecular breeding. This review summarizes the current advancements in pea functional genomics and breeding while highlighting the future challenges in pea molecular breeding.
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Affiliation(s)
- Baizhi Chen
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Yan Shi
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Yuchen Sun
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Lu Lu
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Luyao Wang
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Zijian Liu
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Shifeng Cheng
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
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Xu L, Zhu X, Yi F, Liu Y, Sod B, Li M, Chen L, Kang J, Yang Q, Long R. A genome-wide study of the lipoxygenase gene families in Medicago truncatula and Medicago sativa reveals that MtLOX24 participates in the methyl jasmonate response. BMC Genomics 2024; 25:195. [PMID: 38373903 PMCID: PMC10875803 DOI: 10.1186/s12864-024-10071-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 01/31/2024] [Indexed: 02/21/2024] Open
Abstract
BACKGROUND Lipoxygenase (LOX) is a multifunctional enzyme that is primarily related to plant organ growth and development, biotic and abiotic stress responses, and production of flavor-associated metabolites. In higher plants, the LOX family encompasses several isozymes with varying expression patterns between tissues and developmental stages. These affect processes including seed germination, seed storage, seedling growth, fruit ripening, and leaf senescence. LOX family genes have multiple functions in response to hormones such as methyl jasmonate (MeJA) and salicylic acid. RESULTS In this study, we identified 30 and 95 LOX homologs in Medicago truncatula and Medicago sativa, respectively. These genes were characterized with analyses of their basic physical and chemical properties, structures, chromosomal distributions, and phylogenetic relationships to understand structural variations and their physical locations. Phylogenetic analysis was conducted for members of the three LOX subfamilies (9-LOX, type I 13-LOX, and type II 13-LOX) in Arabidopsis thaliana, Glycine max, M. truncatula, and M. sativa. Analysis of predicted promoter elements revealed several relevant cis-acting elements in MtLOX and MsLOX genes, including abscisic acid (ABA) response elements (ABREs), MeJA response elements (CGTCA-motifs), and antioxidant response elements (AREs). Cis-element data combined with transcriptomic data demonstrated that LOX gene family members in these species were most likely related to abiotic stress responses, hormone responses, and plant development. Gene expression patterns were confirmed via quantitative reverse transcription PCR. Several MtLOX genes (namely MtLOX15, MtLOX16, MtLOX20, and MtLOX24) belonging to the type I 13-LOX subfamily and other LOX genes (MtLOX7, MtLOX11, MsLOX23, MsLOX87, MsLOX90, and MsLOX94) showed significantly different expression levels in the flower tissue, suggesting roles in reproductive growth. Type I 13-LOXs (MtLOX16, MtLOX20, MtLOX21, MtLOX24, MsLOX57, MsLOX84, MsLOX85, and MsLOX94) and type II 13-LOXs (MtLOX5, MtLOX6, MtLOX9, MtLOX10, MsLOX18, MsLOX23, and MsLOX30) were MeJA-inducible and were predicted to function in the jasmonic acid signaling pathway. Furthermore, exogenous MtLOX24 expression in Arabidopsis verified that MtLOX24 was involved in MeJA responses, which may be related to insect-induced abiotic stress. CONCLUSIONS We identified six and four LOX genes specifically expressed in the flowers of M. truncatula and M. sativa, respectively. Eight and seven LOX genes were induced by MeJA in M. truncatula and M. sativa, and the LOX genes identified were mainly distributed in the type I and type II 13-LOX subfamilies. MtLOX24 was up-regulated at 8 h after MeJA induction, and exogenous expression in Arabidopsis demonstrated that MtLOX24 promoted resistance to MeJA-induced stress. This study provides valuable new information regarding the evolutionary history and functions of LOX genes in the genus Medicago.
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Affiliation(s)
- Lei Xu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Xiaoxi Zhu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Fengyan Yi
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, 010031, China
| | - Yajiao Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Bilig Sod
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Mingna Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lin Chen
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Junmei Kang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Qingchuan Yang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Ruicai Long
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Bhowmik P, Yan W, Hodgins C, Polley B, Warkentin T, Nickerson M, Ro DK, Marsolais F, Domoney C, Shariati-Ievari S, Aliani M. CRISPR/Cas9-mediated lipoxygenase gene-editing in yellow pea leads to major changes in fatty acid and flavor profiles. FRONTIERS IN PLANT SCIENCE 2023; 14:1246905. [PMID: 37810390 PMCID: PMC10552856 DOI: 10.3389/fpls.2023.1246905] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 08/23/2023] [Indexed: 10/10/2023]
Abstract
Introduction Although pulses are nutritious foods containing high amounts of protein, fiber and phytochemicals, their consumption and use in the food industry have been limited due to the formation of unappealing flavors/aromas described as beany, green, and grassy. Lipoxygenase (LOX) enzymes are prevalent among pulse seeds, and their activity can lead to the formation of specific volatile organic compounds (VOCs) from certain polyunsaturated fatty acids (PUFAs). As a widespread issue in legumes, including soybean, these VOCs have been linked to certain unappealing taste perception of foods containing processed pulse seeds. Methods To address this problem in pea and as proof of principle to promote the wider use of pulses, a Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) construct was designed to create null alleles (knockouts) of PsLOX2 which had been implicated in the generation of VOCs in peas. Results and discussion Successful CRISPR/Cas9-mediated LOX gene editing of stable transgenic pea lines (TGP) was confirmed by DNA sequencing of the wild type (WT) and TGP pslox2 mutant lines. These lines were also assessed for LOX activity, PUFA levels, and VOCs. Compared to WT peas, the TGP lines showed a significant reduction (p < 0.05) in LOX activity and in the concentration of key VOCs, including hexanal, 2-hexenal, heptanal, (E)-2-heptenal, (E,E)-2,4-heptadienal, 1-octen-3-ol, octanal, (E)-2-octenal (E,E)-2,4-nonadienal and furan-2-pentyl. The content of two essential PUFAs, linoleic and α-linolenic acids, the known substrates of LOX in plants, was higher in TGP flours, indicating the efficacy of the CRISPR-mediated gene editing in minimizing their oxidation and the further modification of PUFAs and their products. The collection of VOCs from the headspace of ground pea seeds, using a portable eNose also distinguished the TGP and WT lines. Multiple regression analysis showed that LOX activity correlated with the two VOCs, heptanal and (E,E)-2,4-heptadienal in pea flours. Partial Least Squares Regression (PLS-R) plot for selected PUFAs, VOCs, and sensor responses in WT and TGP lines showed distinct clusters for WT and TGP lines. Together this data demonstrates the utility of CRISPR mediated mutagenesis of PsLOX2 to quickly improve aroma and fatty acid (FA) profiles of pea seeds of an elite Canadian variety.
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Affiliation(s)
- Pankaj Bhowmik
- Aquatic and Crop Resource Development Centre, National Research Council Canada, Saskatoon, SK, Canada
| | - Wei Yan
- Aquatic and Crop Resource Development Centre, National Research Council Canada, Saskatoon, SK, Canada
| | - Connor Hodgins
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Brittany Polley
- Aquatic and Crop Resource Development Centre, National Research Council Canada, Saskatoon, SK, Canada
| | - Tom Warkentin
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Michael Nickerson
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Dae-Kyun Ro
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Frédéric Marsolais
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Claire Domoney
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Shiva Shariati-Ievari
- Division of Neurodegenerative Diseases (DND), St Boniface Hospital Research Center, Winnipeg, MB, Canada
| | - Michel Aliani
- Division of Neurodegenerative Diseases (DND), St Boniface Hospital Research Center, Winnipeg, MB, Canada
- Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, MB, Canada
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Robinson GHJ, Domoney C. Perspectives on the genetic improvement of health- and nutrition-related traits in pea. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 158:353-362. [PMID: 33250319 PMCID: PMC7801860 DOI: 10.1016/j.plaphy.2020.11.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 11/15/2020] [Indexed: 05/27/2023]
Abstract
Pea (Pisum sativum L.) is a widely grown pulse crop that is a source of protein, starch and micronutrients in both human diets and livestock feeds. There is currently a strong global focus on making agriculture and food production systems more sustainable, and pea has one of the smallest carbon footprints of all crops. Multiple genetic loci have been identified that influence pea seed protein content, but protein composition is also important nutritionally. Studies have previously identified gene families encoding individual seed protein classes, now documented in a reference pea genome assembly. Much is also known about loci affecting starch metabolism in pea, with research especially focusing on improving concentrations of resistant starch, which has a positive effect on maintaining blood glucose homeostasis. Diversity in natural germplasm for micronutrient concentrations and mineral hyperaccumulation mutants have been discovered, with quantitative trait loci on multiple linkage groups identified for seed micronutrient concentrations. Antinutrients, which affect nutrient bioavailability, must also be considered; mutants in which the concentrations of important antinutrients including phytate and trypsin inhibitors are reduced have already been discovered. Current knowledge on the genetics of nutritional traits in pea will greatly assist with crop improvement for specific end uses, and further identification of genes involved will help advance our knowledge of the control of the synthesis of seed compounds.
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Affiliation(s)
- Gabriel H J Robinson
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, United Kingdom
| | - Claire Domoney
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, United Kingdom.
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Warsame A, Michael N, O’Sullivan DM, Tosi P. Identification and Quantification of Major Faba Bean Seed Proteins. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:8535-8544. [PMID: 32678595 PMCID: PMC7458416 DOI: 10.1021/acs.jafc.0c02927] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Faba bean (Vicia faba L.) holds great importance for human and animal nutrition for its high protein content. However, better understanding of its seed protein composition is required in order to develop cultivars that meet market demands for plant proteins with specific quality attributes. In this study, we screened 35 diverse Vicia faba genotypes by employing the one-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis (1D SDS-PAGE) method, and 35 major protein bands obtained from three genotypes with contrasting seed protein profiles were further analyzed by mass spectrometry (MS). Twenty-five of these protein bands (MW range: ∼ 9-107 kDa) had significant (p ≤ 0.05) matches to polypeptides in protein databases. MS analysis showed that most of the analyzed protein bands contained more than one protein type and, in total, over 100 proteins were identified. These included major seed storage proteins such as legumin, vicilin, and convicilin, as well as other protein classes like lipoxygenase, heat shock proteins, sucrose-binding proteins, albumin, and defensin. Furthermore, seed protein extracts were separated by size-exclusion high-performance liquid chromatography (SE-HPLC), and percentages of the major protein classes were determined. On average, legumin and vicilin/convicilin accounted for 50 and 27% of the total protein extract, respectively. However, the proportions of these proteins varied considerably among genotypes, with the ratio of legumin:vicilin/convicilin ranging from 1:1 to 1:3. In addition, there was a significant (p < 0.01) negative correlation between the contents of these major fractions (r = -0.83). This study significantly extends the number of identified Vicia faba seed proteins and reveals new qualitative and quantitative variation in seed protein composition, filling a significant gap in the literature. Moreover, the germplasm and screening methods presented here are expected to contribute in selecting varieties with improved protein content and quality.
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Affiliation(s)
- Ahmed
O. Warsame
- School
of Agriculture, Policy and Development, University of Reading, Reading RG6 6AH, United Kingdom
| | - Nicholas Michael
- School
of Chemistry, Food and Pharmacy, University
of Reading, Reading RG6 6UR, United Kingdom
| | - Donal M. O’Sullivan
- School
of Agriculture, Policy and Development, University of Reading, Reading RG6 6AH, United Kingdom
| | - Paola Tosi
- School
of Agriculture, Policy and Development, University of Reading, Reading RG6 6AH, United Kingdom
- . Tel.: +44 (0) 118 378 8119
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Breeding of lipoxygenase-1-less malting barley variety ‘SouthernStar’ and evaluation of malting and brewing quality. J Cereal Sci 2018. [DOI: 10.1016/j.jcs.2018.07.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Kosterin OE. Abyssnian pea (Lathyrus schaeferi Kosterin pro Pisum abyssinicum A. Br.) – a problematic taxon. ACTA BIOLOGICA SIBIRICA 2017. [DOI: 10.14258/abs.v3i3.3621] [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
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Clemente A, Arques MC, Dalmais M, Le Signor C, Chinoy C, Olias R, Rayner T, Isaac PG, Lawson DM, Bendahmane A, Domoney C. Eliminating anti-nutritional plant food proteins: the case of seed protease inhibitors in pea. PLoS One 2015; 10:e0134634. [PMID: 26267859 PMCID: PMC4534040 DOI: 10.1371/journal.pone.0134634] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 07/11/2015] [Indexed: 12/03/2022] Open
Abstract
Several classes of seed proteins limit the utilisation of plant proteins in human and farm animal diets, while plant foods have much to offer to the sustainable intensification of food/feed production and to human health. Reduction or removal of these proteins could greatly enhance seed protein quality and various strategies have been used to try to achieve this with limited success. We investigated whether seed protease inhibitor mutations could be exploited to enhance seed quality, availing of induced mutant and natural Pisum germplasm collections to identify mutants, whilst acquiring an understanding of the impact of mutations on activity. A mutant (TILLING) resource developed in Pisum sativum L. (pea) and a large germplasm collection representing Pisum diversity were investigated as sources of mutations that reduce or abolish the activity of the major protease inhibitor (Bowman-Birk) class of seed protein. Of three missense mutations, predicted to affect activity of the mature trypsin / chymotrypsin inhibitor TI1 protein, a C77Y substitution in the mature mutant inhibitor abolished inhibitor activity, consistent with an absolute requirement for the disulphide bond C77-C92 for function in the native inhibitor. Two further classes of mutation (S85F, E109K) resulted in less dramatic changes to isoform or overall inhibitory activity. The alternative strategy to reduce anti-nutrients, by targeted screening of Pisum germplasm, successfully identified a single accession (Pisum elatius) as a double null mutant for the two closely linked genes encoding the TI1 and TI2 seed protease inhibitors. The P. elatius mutant has extremely low seed protease inhibitory activity and introgression of the mutation into cultivated germplasm has been achieved. The study provides new insights into structure-function relationships for protease inhibitors which impact on pea seed quality. The induced and natural germplasm variants identified provide immediate potential for either halving or abolishing the corresponding inhibitory activity, along with associated molecular markers for breeding programmes. The potential for making large changes to plant protein profiles for improved and sustainable food production through diversity is illustrated. The strategy employed here to reduce anti-nutritional proteins in seeds may be extended to allergens and other seed proteins with negative nutritional effects. Additionally, the novel variants described for pea will assist future studies of the biological role and health-related properties of so-called anti-nutrients.
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Affiliation(s)
- Alfonso Clemente
- Department of Physiology and Biochemistry of Animal Nutrition, Estación Experimental del Zaidín (CSIC), Profesor Albareda 1, 18008 Granada, Spain
| | - Maria C. Arques
- Department of Physiology and Biochemistry of Animal Nutrition, Estación Experimental del Zaidín (CSIC), Profesor Albareda 1, 18008 Granada, Spain
| | - Marion Dalmais
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165—CNRS 8114—UEVE 2, Rue Gaston Crémieux—CP 5708—F-91000 Evry cedex, France
| | - Christine Le Signor
- UMR 1347 Agroécologie AgroSup/INRA/uB, Pôle Génétique & Ecophysiologie GEAPSI, 17 rue Sully BP 86510, 21065 Dijon cedex, France
| | - Catherine Chinoy
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Raquel Olias
- Department of Physiology and Biochemistry of Animal Nutrition, Estación Experimental del Zaidín (CSIC), Profesor Albareda 1, 18008 Granada, Spain
| | - Tracey Rayner
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Peter G. Isaac
- IDna Genetics Ltd, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - David M. Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Abdelhafid Bendahmane
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165—CNRS 8114—UEVE 2, Rue Gaston Crémieux—CP 5708—F-91000 Evry cedex, France
| | - Claire Domoney
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
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Shin JH, Van K, Kim KD, Lee YH, Jun TH, Lee SH. Molecular sequence variations of the lipoxygenase-2 gene in soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:613-22. [PMID: 22083354 DOI: 10.1007/s00122-011-1733-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Accepted: 10/14/2011] [Indexed: 05/31/2023]
Abstract
Soybean lipoxygenase genes comprise a multi-gene family, with the seed lipoxygenase isozymes LOX1, LOX2, and LOX3 present in soybean seeds. Among these, the LOX2 isozyme is primarily responsible for the "beany" flavor of most soybean seeds. The variety, Jinpumkong 2, having null alleles (lx1, lx2, and lx3) lacks the three seed lipoxygenases; so, sequence variations between the lipoxygenase-2 genes of Pureunkong (Lx2) and Jinpumkong 2 (lx2) cultivars were examined. One indel, four single nucleotide polymorphisms (SNPs), a 175-bp fragment in the 5'-flanking sequence, and a missense mutation within the coding region were found in Jinpumkong 2. The distribution of the sequence variations was investigated among 90 recombinant inbred lines (RILs) derived from a cross of Pureunkong × Jinpumkong 2 and in 480 germplasm accessions with various origins and maturity groups. Evidence for a genetic bottleneck was observed: the 175-bp fragment was rare in Glycine max, but present in the majority of the G. soja accessions. Furthermore, the 175-bp fragment was not detected in the 5' upstream region of the Lx2 gene on chromosome (Chr) 13 in Williams 82; instead, a similar 175-bp fragment was positioned in the homeologous region on Chr 15. The findings indicated that the novel fragment identified was originally present in the Lx2 region prior to the recent genome duplication in soybean, but became rare in the G. max gene pool. The missense mutation of the conserved histidine residue of the lx2 allele was developed into a single nucleotide-amplified polymorphism (SNAP) marker. The missense mutation showed a perfect correlation with the LOX2-lacking phenotype, so the SNAP marker is expected to facilitate breeding of soybean cultivars which lack the LOX2 isozyme.
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Affiliation(s)
- Jin Hee Shin
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, San 56-1, Sillim-dong, Gwanak-gu, Seoul, 151-921, The Republic of Korea
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Shin JH, Van K, Kim DH, Kim KD, Jang YE, Choi BS, Kim MY, Lee SH. The lipoxygenase gene family: a genomic fossil of shared polyploidy between Glycine max and Medicago truncatula. BMC PLANT BIOLOGY 2008; 8:133. [PMID: 19105811 PMCID: PMC2644698 DOI: 10.1186/1471-2229-8-133] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2008] [Accepted: 12/23/2008] [Indexed: 05/04/2023]
Abstract
BACKGROUND Soybean lipoxygenases (Lxs) play important roles in plant resistance and in conferring the distinct bean flavor. Lxs comprise a multi-gene family that includes GmLx1, GmLx2 and GmLx3, and many of these genes have been characterized. We were interested in investigating the relationship between the soybean lipoxygenase isozymes from an evolutionary perspective, since soybean has undergone two rounds of polyploidy. Here we report the tetrad genome structure of soybean Lx regions produced by ancient and recent polyploidy. Also, comparative genomics with Medicago truncatula was performed to estimate Lxs in the common ancestor of soybean and Medicago. RESULTS Two Lx regions in Medicago truncatula showing synteny with soybean were analyzed. Differential evolutionary rates between soybean and Medicago were observed and the median Ks values of Mt-Mt, Gm-Mt, and Gm-Gm paralogs were determined to be 0.75, 0.62, and 0.46, respectively. Thus the comparison of Gm-Mt paralogs (Ks = 0.62) and Gm-Mt orthologs (Ks = 0.45) supports the ancient duplication of Lx regions in the common ancestor prior to the Medicago-Glycine split. After speciation, no Lx regions generated by another polyploidy were identified in Medicago. Instead tandem duplication of Lx genes was observed. On the other hand, a lineage-specific duplication occurred in soybean resulting in two pairs of Lx regions. Each pair of soybean regions was co-orthologous to one Lx region in Medicago. A total of 34 Lx genes (15 MtLxs and 19 GmLxs) were divided into two groups by phylogenetic analysis. Our study shows that the Lx gene family evolved from two distinct Lx genes in the most recent common ancestor. CONCLUSION This study analyzed two pairs of Lx regions generated by two rounds of polyploidy in soybean. Each pair of soybean homeologous regions is co-orthologous to one region of Medicago, demonstrating the quartet structure of the soybean genome. Differential evolutionary rates between soybean and Medicago were observed; thus optimized rates of Ks per year should be applied for accurate estimation of coalescence times to each case of comparison: soybean-soybean, soybean-Medicago, or Medicago-Medicago. In conclusion, the soybean Lx gene family expanded by ancient polyploidy prior to taxon divergence, followed by a soybean- specific duplication and tandem duplications, respectively.
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Affiliation(s)
- Jin Hee Shin
- Department of Plant Science, Seoul National University, Seoul 151-921, Korea
| | - Kyujung Van
- Department of Plant Science, Seoul National University, Seoul 151-921, Korea
| | - Dong Hyun Kim
- Department of Plant Science, Seoul National University, Seoul 151-921, Korea
| | - Kyung Do Kim
- Department of Plant Science, Seoul National University, Seoul 151-921, Korea
| | - Young Eun Jang
- Department of Plant Science, Seoul National University, Seoul 151-921, Korea
| | - Beom-Soon Choi
- National Instrumentation Center for Environmental Management, Seoul National University, Seoul 151-921, Korea
| | - Moon Young Kim
- Department of Plant Science, Seoul National University, Seoul 151-921, Korea
- Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Suk-Ha Lee
- Department of Plant Science, Seoul National University, Seoul 151-921, Korea
- National Instrumentation Center for Environmental Management, Seoul National University, Seoul 151-921, Korea
- Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
- Plant Genomic and Breeding Research Institute, Seoul National University, Seoul, 151-921, Korea
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Jing R, Johnson R, Seres A, Kiss G, Ambrose MJ, Knox MR, Ellis THN, Flavell AJ. Gene-based sequence diversity analysis of field pea (Pisum). Genetics 2007; 177:2263-75. [PMID: 18073431 PMCID: PMC2219474 DOI: 10.1534/genetics.107.081323] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2007] [Accepted: 10/11/2007] [Indexed: 11/18/2022] Open
Abstract
Sequence diversity of 39 dispersed gene loci was analyzed in 48 diverse individuals representative of the genus Pisum. The different genes show large variation in diversity parameters, suggesting widely differing levels of selection and a high overall diversity level for the species. The data set yields a genetic diversity tree whose deep branches, involving wild samples, are preserved in a tree derived from a polymorphic retrotransposon insertions in an identical sample set. Thus, gene regions and intergenic "junk DNA" share a consistent picture for the genomic diversity of Pisum, despite low linkage disequilibrium in wild and landrace germplasm, which might be expected to allow independent evolution of these very different DNA classes. Additional lines of evidence indicate that recombination has shuffled gene haplotypes efficiently within Pisum, despite its high level of inbreeding and widespread geographic distribution. Trees derived from individual gene loci show marked differences from each other, and genetic distance values between sample pairs show high standard deviations. Sequence mosaic analysis of aligned sequences identifies nine loci showing evidence for intragenic recombination. Lastly, phylogenetic network analysis confirms the non-treelike structure of Pisum diversity and indicates the major germplasm classes involved. Overall, these data emphasize the artificiality of simple tree structures for representing genomic sequence variation within Pisum and emphasize the need for fine structure haplotype analysis to accurately define the genetic structure of the species.
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Affiliation(s)
- Runchun Jing
- Plant Research Unit, University of Dundee at Scotish Crop Research Institute, United Kingdom
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Casey R, Hughes RK. Recombinant Lipoxygenases and Oxylipin Metabolism in Relation to Food Quality. FOOD BIOTECHNOL 2007. [DOI: 10.1081/fbt-200025673] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Wang TL, Domoney C, Hedley CL, Casey R, Grusak MA. Can we improve the nutritional quality of legume seeds? PLANT PHYSIOLOGY 2003; 131:886-91. [PMID: 12644641 PMCID: PMC1540288 DOI: 10.1104/pp.102.017665] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Affiliation(s)
- Trevor L Wang
- John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, United Kingdom.
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