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Li H, Che R, Zhu J, Yang X, Li J, Fernie AR, Yan J. Multi-omics-driven advances in the understanding of triacylglycerol biosynthesis in oil seeds. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:999-1017. [PMID: 38009661 DOI: 10.1111/tpj.16545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 11/01/2023] [Indexed: 11/29/2023]
Abstract
Vegetable oils are rich sources of polyunsaturated fatty acids and energy as well as valuable sources of human food, animal feed, and bioenergy. Triacylglycerols, which are comprised of three fatty acids attached to a glycerol backbone, are the main component of vegetable oils. Here, we review the development and application of multiple-level omics in major oilseeds and emphasize the progress in the analysis of the biological roles of key genes underlying seed oil content and quality in major oilseeds. Finally, we discuss future research directions in functional genomics research based on current omics and oil metabolic engineering strategies that aim to enhance seed oil content and quality, and specific fatty acids components according to either human health needs or industrial requirements.
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Affiliation(s)
- Hui Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Ronghui Che
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Jiantang Zhu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Xiaohong Yang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Jiansheng Li
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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2
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Tang Y, Qiu X, Hu C, Li J, Wu L, Wang W, Li X, Li X, Zhu H, Sui J, Wang J, Qiao L. Breeding of a new variety of peanut with high-oleic-acid content and high-yield by marker-assisted backcrossing. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:42. [PMID: 37313504 PMCID: PMC10248636 DOI: 10.1007/s11032-022-01313-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
Peanut (Arachis hypogaea L.) is an important crop used for oil production, and oleic acid is a major factor in determining oil quality. Alterations in the oleic acid content can improve the nutritional quality and oxidative stability and prolong the shelf life of peanut products. The objective of this study was to develop a peanut variety with a high-oleic-acid content and high yield. One elite variety, "huayu22," was hybridized with the high-oleic-acid "KN176" donor and backcrossed for four generations as the recurrent parent using fad2 marker-assisted backcross selection. Based on the Kompetitive allele-specific PCR (KASP) screening of fad2 markers, the oleic acid content of advanced generations derived by selfing was assessed by near-infrared reflectance spectroscopy and gas chromatography. The genetic background recovery rate of four BC4F4 lines showed an average of 92.34% and was confirmed by genotyping using the Axiom_Arachis 58 K SNP array. Across these superior lines in BC4F6 generations, one line with a high-oleic-acid content and high yield was detected and named "YH61." In particular, yield comparison experiments showed that YH61 exhibited high and stable yield at three different locations and was moderately resistant to leaf spot disease. The distinctness, uniformity and stability (DUS) testing for two consecutive years suggested that YH61 reached the standard for variety rights application. The use of the peanut variety YH61 contributed to the expansion of the cultivation area due to its high value in the oleic acid market and the proven economic benefits in China. This study demonstrated that the marker-assisted backcross strategy based on a cost-effective KASP assay and SNP array for the detection of mutations in fad2 and genetic background evaluation can be used to create efficient peanut breeding programs and contribute to oil quality and high-yield stability. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01313-9.
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Affiliation(s)
- Yanyan Tang
- College of Agronomy, Qingdao Agricultural University, Dry-Land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao, 266109 China
| | - Xiaochen Qiu
- College of Agronomy, Qingdao Agricultural University, Dry-Land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao, 266109 China
| | - Changli Hu
- College of Agronomy, Qingdao Agricultural University, Dry-Land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao, 266109 China
| | - Jingjing Li
- College of Agronomy, Qingdao Agricultural University, Dry-Land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao, 266109 China
| | - Lanrong Wu
- Qingdao Seed Station, Qingdao, 266071 China
| | - Weihua Wang
- College of Agronomy, Qingdao Agricultural University, Dry-Land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao, 266109 China
| | - Xin Li
- College of Agronomy, Qingdao Agricultural University, Dry-Land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao, 266109 China
| | - Xiaoting Li
- College of Agronomy, Qingdao Agricultural University, Dry-Land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao, 266109 China
| | - Hong Zhu
- College of Agronomy, Qingdao Agricultural University, Dry-Land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao, 266109 China
| | - Jiongming Sui
- College of Agronomy, Qingdao Agricultural University, Dry-Land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao, 266109 China
| | - Jingshan Wang
- College of Agronomy, Qingdao Agricultural University, Dry-Land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao, 266109 China
| | - Lixian Qiao
- College of Agronomy, Qingdao Agricultural University, Dry-Land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao, 266109 China
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Otyama PI, Chamberlin K, Ozias-Akins P, Graham MA, Cannon EKS, Cannon SB, MacDonald GE, Anglin NL. Genome-wide approaches delineate the additive, epistatic, and pleiotropic nature of variants controlling fatty acid composition in peanut (Arachis hypogaea L.). G3-GENES GENOMES GENETICS 2021; 12:6423989. [PMID: 34751378 DOI: 10.1093/g3journal/jkab382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 10/26/2021] [Indexed: 11/12/2022]
Abstract
The fatty acid composition of seed oil is a major determinant of the flavor, shelf-life, and nutritional quality of peanuts. Major QTLs controlling high oil content, high oleic content, and low linoleic content have been characterized in several seed oil crop species. Here we employ genome-wide association approaches on a recently genotyped collection of 787 plant introduction accessions in the USDA peanut core collection, plus selected improved cultivars, to discover markers associated with the natural variation in fatty acid composition, and to explain the genetic control of fatty acid composition in seed oils. Overall, 251 single nucleotide polymorphisms (SNPs) had significant trait associations with the measured fatty acid components. Twelve SNPs were associated with two or three different traits. Of these loci with apparent pleiotropic effects, 10 were associated with both oleic (C18:1) and linoleic acid (C18:2) content at different positions in the genome. In all 10 cases, the favorable allele had an opposite effect-increasing and lowering the concentration, respectively, of oleic and linoleic acid. The other traits with pleiotropic variant control were palmitic (C16:0), behenic (C22:0), lignoceric (C24:0), gadoleic (C20:1), total saturated, and total unsaturated fatty acid content. One hundred (100) of the significantly associated SNPs were located within 1000 kbp of 55 genes with fatty acid biosynthesis functional annotations. These genes encoded, among others: ACCase carboxyl transferase subunits, and several fatty acid synthase II enzymes. With the exception of gadoleic (C20:1) and lignoceric (C24:0) acid content, which occur at relatively low abundance in cultivated peanut, all traits had significant SNP interactions exceeding a stringent Bonferroni threshold (α = 1%). We detected 7,682 pairwise SNP interactions affecting the relative abundance of fatty acid components in the seed oil. Of these, 627 SNP pairs had at least one SNP within 1000 kbp of a gene with fatty acid biosynthesis functional annotation. We evaluated 168 candidate genes underlying these SNP interactions. Functional enrichment and protein-to-protein interactions supported significant interactions (p-value < 1.0E-16) among the genes evaluated. These results show the complex nature of the biology and genes underlying the variation in seed oil fatty acid composition and contribute to an improved genotype-to-phenotype map for fatty acid variation in peanut seed oil.
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Affiliation(s)
- Paul I Otyama
- Interdepartmental Genetics and Genomics, Iowa State University, Ames, IA 50011, USA.,Agronomy Department, Iowa State University, Ames, IA 50011, USA.,ORISE Postdoctoral Fellow, Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA 50011, USA
| | - Kelly Chamberlin
- USDA-Agricultural Research Service, Stillwater, OK 740752714, USA
| | - Peggy Ozias-Akins
- Institute of Plant Breeding, Genetics, and Genomics and Department of Horticulture, University of Georgia, Tifton, GA 31793-5766, USA
| | - Michelle A Graham
- USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA
| | - Ethalinda K S Cannon
- USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA
| | - Steven B Cannon
- USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA
| | | | - Noelle L Anglin
- USDA-ARS Small Grains and Potato Research Laboratory, Aberdeen, ID 83210, USA
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Tonnis B, Wang ML, Li X, Wang J, Puppala N, Tallury S, Yu J. Peanut
FAD2
Genotype and Growing Location Interactions Significantly Affect the Level of Oleic Acid in Seeds. J AM OIL CHEM SOC 2020. [DOI: 10.1002/aocs.12401] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Brandon Tonnis
- Plant Genetic Resources Conservation Unit USDA‐ARS Griffin GA 30223 USA
| | - Ming Li Wang
- Plant Genetic Resources Conservation Unit USDA‐ARS Griffin GA 30223 USA
| | - Xianran Li
- Department of Agronomy Iowa State University Ames IA 50011 USA
| | - Jianping Wang
- Agronomy Department University of Florida Gainesville FL 32610 USA
| | - Naveen Puppala
- Agronomy Department New Mexico State University Clovis NM 88101 USA
| | - Shyam Tallury
- Plant Genetic Resources Conservation Unit USDA‐ARS Griffin GA 30223 USA
| | - Jianming Yu
- Department of Agronomy Iowa State University Ames IA 50011 USA
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Tian Y, Chen K, Li X, Zheng Y, Chen F. Design of high-oleic tobacco (Nicotiana tabacum L.) seed oil by CRISPR-Cas9-mediated knockout of NtFAD2-2. BMC PLANT BIOLOGY 2020; 20:233. [PMID: 32450806 PMCID: PMC7249356 DOI: 10.1186/s12870-020-02441-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 05/11/2020] [Indexed: 05/09/2023]
Abstract
BACKGROUND Tobacco seed oil could be used as an appropriate feedstock for biodiesel production. However, the high linoleic acid content of tobacco seed oil makes it susceptible to oxidation. Altering the fatty acid profile by increasing the content of oleic acid could improve the properties of biodiesel produced from tobacco seed oil. RESULTS Four FAD2 genes, NtFAD2-1a, NtFAD2-1b, NtFAD2-2a, and NtFAD2-2b, were identified in allotetraploid tobacco genome. Phylogenetic analysis of protein sequences showed that NtFAD2-1a and NtFAD2-2a originated from N. tomentosiformis, while NtFAD2-1b and NtFAD2-2b from N. sylvestris. Expression analysis revealed that NtFAD2-2a and NtFAD2-2b transcripts were more abundant in developing seeds than in other tissues, while NtFAD2-1a and NtFAD2-1b showed low transcript levels in developing seed. Phylogenic analysis showed that NtFAD2-2a and NtFAD2-2b were seed-type FAD2 genes. Heterologous expression in yeast cells demonstrated that both NtFAD2-2a and NtFAD2-2b protein could introduce a double bond at the Δ12 position of fatty acid chain. The fatty acid profile analysis of tobacco fad2-2 mutant seeds derived from CRISPR-Cas9 edited plants showed dramatic increase of oleic acid content from 11% to over 79%, whereas linoleic acid decreased from 72 to 7%. In addition, the fatty acid composition of leaf was not affected in fad2-2 mutant plants. CONCLUSION Our data showed that knockout of seed-type FAD2 genes in tobacco could significantly increase the oleic acid content in seed oil. This research suggests that CRISPR-Cas9 system offers a rapid and highly efficient method in the tobacco seed lipid engineering programs.
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Affiliation(s)
- Yinshuai Tian
- College of Landscape and Ecological Engineering, Hebei University of Engineering, No.19 Taiji Road, Economic and technological development area, Handan, 056038, Hebei, China
- Institute of New Energy and Low-carbon Technology, Sichuan University, Chuanda Road, Shuangliu district, Chengdu, 610207, Sichuan, China
| | - Kai Chen
- College of Landscape and Ecological Engineering, Hebei University of Engineering, No.19 Taiji Road, Economic and technological development area, Handan, 056038, Hebei, China
| | - Xiao Li
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, No.29 Wangjiang Road, Wuhou district, Chengdu, 610065, Sichuan, China
| | - Yunpu Zheng
- School of Water Conservancy and Hydroelectric Power, Hebei University of Engineering, No.19 Taiji Road, Economic and technological development area, Handan, 056038, Hebei, China
| | - Fang Chen
- Institute of New Energy and Low-carbon Technology, Sichuan University, Chuanda Road, Shuangliu district, Chengdu, 610207, Sichuan, China.
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, No.29 Wangjiang Road, Wuhou district, Chengdu, 610065, Sichuan, China.
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6
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Otyama PI, Wilkey A, Kulkarni R, Assefa T, Chu Y, Clevenger J, O'Connor DJ, Wright GC, Dezern SW, MacDonald GE, Anglin NL, Cannon EKS, Ozias-Akins P, Cannon SB. Evaluation of linkage disequilibrium, population structure, and genetic diversity in the U.S. peanut mini core collection. BMC Genomics 2019; 20:481. [PMID: 31185892 PMCID: PMC6558826 DOI: 10.1186/s12864-019-5824-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 05/21/2019] [Indexed: 12/03/2022] Open
Abstract
Background Due to the recent domestication of peanut from a single tetraploidization event, relatively little genetic diversity underlies the extensive morphological and agronomic diversity in peanut cultivars today. To broaden the genetic variation in future breeding programs, it is necessary to characterize germplasm accessions for new sources of variation and to leverage the power of genome-wide association studies (GWAS) to discover markers associated with traits of interest. We report an analysis of linkage disequilibrium (LD), population structure, and genetic diversity, and examine the ability of GWA to infer marker-trait associations in the U.S. peanut mini core collection genotyped with a 58 K SNP array. Results LD persists over long distances in the collection, decaying to r2 = half decay distance at 3.78 Mb. Structure within the collection is best explained when separated into four or five groups (K = 4 and K = 5). At K = 4 and 5, accessions loosely clustered according to market type and subspecies, though with numerous exceptions. Out of 107 accessions, 43 clustered in correspondence to the main market type subgroup whereas 34 did not. The remaining 30 accessions had either missing taxonomic classification or were classified as mixed. Phylogenetic network analysis also clustered accessions into approximately five groups based on their genotypes, with loose correspondence to subspecies and market type. Genome wide association analysis was performed on these lines for 12 seed composition and quality traits. Significant marker associations were identified for arachidic and behenic fatty acid compositions, which despite having low bioavailability in peanut, have been reported to raise cholesterol levels in humans. Other traits such as blanchability showed consistent associations in multiple tests, with plausible candidate genes. Conclusions Based on GWA, population structure as well as additional simulation results, we find that the primary limitations of this collection for GWAS are a small collection size, significant remaining structure/genetic similarity and long LD blocks that limit the resolution of association mapping. These results can be used to improve GWAS in peanut in future studies – for example, by increasing the size and reducing structure in the collections used for GWAS. Electronic supplementary material The online version of this article (10.1186/s12864-019-5824-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Paul I Otyama
- Agronomy Department, Iowa State University, Ames, IA, USA
| | - Andrew Wilkey
- ORISE Fellow, Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
| | - Roshan Kulkarni
- Agronomy Department, Iowa State University, Ames, IA, USA.,ORISE Fellow, Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
| | - Teshale Assefa
- Agronomy Department, Iowa State University, Ames, IA, USA.,ORISE Fellow, Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
| | - Ye Chu
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Tifton, GA, USA
| | - Josh Clevenger
- Mars-Wrigley Confectionery, Center for Applied Genetic Technologies, Athens, GA, USA
| | | | | | | | | | | | | | - Peggy Ozias-Akins
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Tifton, GA, USA
| | - Steven B Cannon
- Corn Insects and Crop Genetics Research Unit, USDA - Agricultural Research Service, 1017 Crop Genome Lab 819 Wallace Rd, Ames, IA, 50011-4014, USA.
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Nawade B, Mishra GP, Radhakrishnan T, Dodia SM, Ahmad S, Kumar A, Kumar A, Kundu R. High oleic peanut breeding: Achievements, perspectives, and prospects. Trends Food Sci Technol 2018. [DOI: 10.1016/j.tifs.2018.05.022] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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8
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Yin DD, Li SS, Shu QY, Gu ZY, Wu Q, Feng CY, Xu WZ, Wang LS. Identification of microRNAs and long non-coding RNAs involved in fatty acid biosynthesis in tree peony seeds. Gene 2018; 666:72-82. [PMID: 29738839 DOI: 10.1016/j.gene.2018.05.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 04/20/2018] [Accepted: 05/02/2018] [Indexed: 12/27/2022]
Abstract
MicroRNAs (miRNAs) and long noncoding RNAs (lncRNAs) act as important molecular regulators in a wide range of biological processes during plant development and seed formation, including oil production. Tree peony seeds contain >90% unsaturated fatty acids (UFAs) and high proportions of α-linolenic acid (ALA, > 40%). To dissect the non-coding RNAs (ncRNAs) pathway involved in fatty acids synthesis in tree peony seeds, we construct six small RNA libraries and six transcriptome libraries from developing seeds of two cultivars (J and S) containing different content of fatty acid compositions. After deep sequencing the RNA libraries, the ncRNA expression profiles of tree peony seeds in two cultivars were systematically and comparatively analyzed. A total of 318 known and 153 new miRNAs and 22,430 lncRNAs were identified, among which 106 conserved and 9 novel miRNAs and 2785 lncRNAs were differentially expressed between the two cultivars. In addition, potential target genes of the microRNA and lncRNAs were also predicted and annotated. Among them, 9 miRNAs and 39 lncRNAs were predicted to target lipid related genes. Results showed that all of miR414, miR156b, miR2673b, miR7826, novel-m0027-5p, TR24651|c0_g1, TR24544|c0_g15, and TR27305|c0_g1 were up-regulated and expressed at a higher level in high-ALA cultivar J when compared to low-ALA cultivar S, suggesting that these ncRNAs and target genes are possibly involved in different fatty acid synthesis and lipid metabolism through post-transcriptional regulation. These results provide a better understanding of the roles of ncRNAs during fatty acid biosynthesis and metabolism in tree peony seeds.
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Affiliation(s)
- Dan-Dan Yin
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shan-Shan Li
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Qing-Yan Shu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhao-Yu Gu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Qian Wu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cheng-Yong Feng
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wen-Zhong Xu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Liang-Sheng Wang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Transcriptome Sequencing of Diverse Peanut (Arachis) Wild Species and the Cultivated Species Reveals a Wealth of Untapped Genetic Variability. G3-GENES GENOMES GENETICS 2016; 6:3825-3836. [PMID: 27729436 PMCID: PMC5144954 DOI: 10.1534/g3.115.026898] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
To test the hypothesis that the cultivated peanut species possesses almost no molecular variability, we sequenced a diverse panel of 22 Arachis accessions representing Arachis hypogaea botanical classes, A-, B-, and K- genome diploids, a synthetic amphidiploid, and a tetraploid wild species. RNASeq was performed on pools of three tissues, and de novo assembly was performed. Realignment of individual accession reads to transcripts of the cultivar OLin identified 306,820 biallelic SNPs. Among 10 naturally occurring tetraploid accessions, 40,382 unique homozygous SNPs were identified in 14,719 contigs. In eight diploid accessions, 291,115 unique SNPs were identified in 26,320 contigs. The average SNP rate among the 10 cultivated tetraploids was 0.5, and among eight diploids was 9.2 per 1000 bp. Diversity analysis indicated grouping of diploids according to genome classification, and cultivated tetraploids by subspecies. Cluster analysis of variants indicated that sequences of B genome species were the most similar to the tetraploids, and the next closest diploid accession belonged to the A genome species. A subset of 66 SNPs selected from the dataset was validated; of 782 SNP calls, 636 (81.32%) were confirmed using an allele-specific discrimination assay. We conclude that substantial genetic variability exists among wild species. Additionally, significant but lesser variability at the molecular level occurs among accessions of the cultivated species. This survey is the first to report significant SNP level diversity among transcripts, and may explain some of the phenotypic differences observed in germplasm surveys. Understanding SNP variants in the Arachis accessions will benefit in developing markers for selection.
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Wang Y, Zhang X, Zhao Y, Prakash C, He G, Yin D. Insights into the novel members of the FAD2 gene family involved in high-oleate fluxes in peanut. Genome 2015; 58:375-83. [DOI: 10.1139/gen-2015-0008] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The FAD2 gene family is functionally responsible for the conversion of oleic acid to linoleic acid in oilseed plants. Multiple members of the FAD gene are known to occur in several oilseed species. In this study, six novel full-length cDNA sequences (named as AhFAD2-1, -2, -3, -4, -5, and -6) were identified in peanut (Arachis hypogaea L.), an analysis of which revealed open reading frames of 379, 383, 394, or 442 amino acids. Sequence comparisons showed that AhFAD2-1 and AhFAD2-2 shared 76% identity, while AhFAD2-2, -3, and -4 displayed highly significant homology. There was only 27% identity overlap between the microsomal ω-6 fatty acid desaturase and the chloroplast ω-6 fatty acid desaturase encoded by AhFAD2-1, -2, -3, -4, and AhFAD2-5, -6, respectively. The phylogeny tree of FAD2 transcripts showed five major groups, and AhFAD2-1 was clearly separated from other groups. Analysis of AhFAD2-1 and AhFAD2-2 transcript distribution in different peanut tissues showed that the AhFAD2-1 gene showed upward of a 70-fold increase in expression of fatty acid than the AhFAD2-2 gene in peanut developing seeds, while the AhFAD2-2 gene expressed most abundantly in peanut flowers. Because the AhFAD2-1 gene played a major role in the conversion of oleic to linoleic acid during seed development, the identification of this novel member in this study would facilitate the further genetic manipulation of peanut oil quality. The implications of overall results also suggest that there may be more candidate genes controlling levels of oleate acid in developing seeds. Results also may be due to the presence of complex gene networks controlling the fluxes between the endoplasmic reticulum and the chloroplast within the peanut cells.
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Affiliation(s)
- Yun Wang
- Henan Agricultural University, Zhengzhou 450002, China
| | - Xingguo Zhang
- Henan Agricultural University, Zhengzhou 450002, China
| | - Yongli Zhao
- Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL 36088, USA
| | - C.S. Prakash
- Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL 36088, USA
| | - Guohao He
- Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL 36088, USA
| | - Dongmei Yin
- Henan Agricultural University, Zhengzhou 450002, China
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11
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Next-generation transcriptome sequencing, SNP discovery and validation in four market classes of peanut, Arachis hypogaea L. Mol Genet Genomics 2015; 290:1169-80. [PMID: 25663138 DOI: 10.1007/s00438-014-0976-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 12/06/2014] [Indexed: 10/24/2022]
Abstract
Single-nucleotide polymorphisms, which can be identified in the thousands or millions from comparisons of transcriptome or genome sequences, are ideally suited for making high-resolution genetic maps, investigating population evolutionary history, and discovering marker-trait linkages. Despite significant results from their use in human genetics, progress in identification and use in plants, and particularly polyploid plants, has lagged. As part of a long-term project to identify and use SNPs suitable for these purposes in cultivated peanut, which is tetraploid, we generated transcriptome sequences of four peanut cultivars, namely OLin, New Mexico Valencia C, Tamrun OL07 and Jupiter, which represent the four major market classes of peanut grown in the world, and which are important economically to the US southwest peanut growing region. CopyDNA libraries of each genotype were used to generate 2 × 54 paired-end reads using an Illumina GAIIx sequencer. Raw reads were mapped to a custom reference consisting of Tifrunner 454 sequences plus peanut ESTs in GenBank, compromising 43,108 contigs; 263,840 SNP and indel variants were identified among four genotypes compared to the reference. A subset of 6 variants was assayed across 24 genotypes representing four market types using KASP chemistry to assess the criteria for SNP selection. Results demonstrated that transcriptome sequencing can identify SNPs usable as selectable DNA-based markers in complex polyploid species such as peanut. Criteria for effective use of SNPs as markers are discussed in this context.
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FAD2B from a Peanut Mutant with High Oleic Acid Content Was Not Completely Dysfunctional. LECTURE NOTES IN ELECTRICAL ENGINEERING 2015. [DOI: 10.1007/978-3-662-45657-6_28] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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Pandey MK, Wang ML, Qiao L, Feng S, Khera P, Wang H, Tonnis B, Barkley NA, Wang J, Holbrook CC, Culbreath AK, Varshney RK, Guo B. Identification of QTLs associated with oil content and mapping FAD2 genes and their relative contribution to oil quality in peanut (Arachis hypogaea L.). BMC Genet 2014; 15:133. [PMID: 25491595 PMCID: PMC4278341 DOI: 10.1186/s12863-014-0133-4] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 11/20/2014] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Peanut is one of the major source for human consumption worldwide and its seed contain approximately 50% oil. Improvement of oil content and quality traits (high oleic and low linoleic acid) in peanut could be accelerated by exploiting linked markers through molecular breeding. The objective of this study was to identify QTLs associated with oil content, and estimate relative contribution of FAD2 genes (ahFAD2A and ahFAD2B) to oil quality traits in two recombinant inbred line (RIL) populations. RESULTS Improved genetic linkage maps were developed for S-population (SunOleic 97R × NC94022) with 206 (1780.6 cM) and T-population (Tifrunner × GT-C20) with 378 (2487.4 cM) marker loci. A total of 6 and 9 QTLs controlling oil content were identified in the S- and T-population, respectively. The contribution of each QTL towards oil content variation ranged from 3.07 to 10.23% in the S-population and from 3.93 to 14.07% in the T-population. The mapping positions for ahFAD2A (A sub-genome) and ahFAD2B (B sub-genome) genes were assigned on a09 and b09 linkage groups. The ahFAD2B gene (26.54%, 25.59% and 41.02% PVE) had higher phenotypic effect on oleic acid (C18:1), linoleic acid (C18:2), and oleic/linoleic acid ratio (O/L ratio) than ahFAD2A gene (8.08%, 6.86% and 3.78% PVE). The FAD2 genes had no effect on oil content. This study identified a total of 78 main-effect QTLs (M-QTLs) with up to 42.33% phenotypic variation (PVE) and 10 epistatic QTLs (E-QTLs) up to 3.31% PVE for oil content and quality traits. CONCLUSIONS A total of 78 main-effect QTLs (M-QTLs) and 10 E-QTLs have been detected for oil content and oil quality traits. One major QTL (more than 10% PVE) was identified in both the populations for oil content with source alleles from NC94022 and GT-C20 parental genotypes. FAD2 genes showed high effect for oleic acid (C18:1), linoleic acid (C18:2), and O/L ratio while no effect on total oil content. The information on phenotypic effect of FAD2 genes for oleic acid, linoleic acid and O/L ratio, and oil content will be applied in breeding selection.
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Affiliation(s)
- Manish K Pandey
- US Department of Agriculture-Agricultural Research Service, Crop Protection and Management Research Unit, Tifton, GA, USA. .,International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India. .,Department of Plant Pathology, University of Georgia, Tifton, GA, USA.
| | - Ming Li Wang
- US Department of Agriculture-Agricultural Research Service, Plant Genetic Resources Conservation Unit, Griffin, GA, USA.
| | - Lixian Qiao
- US Department of Agriculture-Agricultural Research Service, Crop Protection and Management Research Unit, Tifton, GA, USA. .,Department of Plant Pathology, University of Georgia, Tifton, GA, USA. .,College of Life Science, Qingdao Agricultural University, Qingdao, China.
| | - Suping Feng
- US Department of Agriculture-Agricultural Research Service, Crop Protection and Management Research Unit, Tifton, GA, USA. .,Department of Plant Pathology, University of Georgia, Tifton, GA, USA. .,College of Bioscience and Biotechnology, Qiongzhou University, Sanya, China.
| | - Pawan Khera
- US Department of Agriculture-Agricultural Research Service, Crop Protection and Management Research Unit, Tifton, GA, USA. .,International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India. .,Department of Plant Pathology, University of Georgia, Tifton, GA, USA.
| | - Hui Wang
- US Department of Agriculture-Agricultural Research Service, Crop Protection and Management Research Unit, Tifton, GA, USA. .,Department of Plant Pathology, University of Georgia, Tifton, GA, USA. .,Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, China.
| | - Brandon Tonnis
- US Department of Agriculture-Agricultural Research Service, Plant Genetic Resources Conservation Unit, Griffin, GA, USA.
| | - Noelle A Barkley
- US Department of Agriculture-Agricultural Research Service, Plant Genetic Resources Conservation Unit, Griffin, GA, USA.
| | - Jianping Wang
- Department of Agronomy, University of Florida, Gainesville, FL, USA.
| | - C Corley Holbrook
- US Department of Agriculture-Agricultural Research Service, Crop Genetics and Breeding Research Unit, Tifton, GA, USA.
| | | | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
| | - Baozhu Guo
- US Department of Agriculture-Agricultural Research Service, Crop Protection and Management Research Unit, Tifton, GA, USA. .,Department of Plant Pathology, University of Georgia, Tifton, GA, USA.
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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]
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Thambugala D, Duguid S, Loewen E, Rowland G, Booker H, You FM, Cloutier S. Genetic variation of six desaturase genes in flax and their impact on fatty acid composition. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:2627-41. [PMID: 23928861 PMCID: PMC3782649 DOI: 10.1007/s00122-013-2161-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Accepted: 07/12/2013] [Indexed: 05/09/2023]
Abstract
Flax (Linum usitatissimum L.) is one of the richest plant sources of omega-3 fatty acids praised for their health benefits. In this study, the extent of the genetic variability of genes encoding stearoyl-ACP desaturase (SAD), and fatty acid desaturase 2 (FAD2) and 3 (FAD3) was determined by sequencing the six paralogous genes from 120 flax accessions representing a broad range of germplasm including some EMS mutant lines. A total of 6 alleles for sad1 and sad2, 21 for fad2a, 5 for fad2b, 15 for fad3a and 18 for fad3b were identified. Deduced amino acid sequences of the alleles predicted 4, 2, 3, 4, 6 and 7 isoforms, respectively. Allele frequencies varied greatly across genes. Fad3a, with 110 SNPs and 19 indels, and fad3b, with 50 SNPs and 5 indels, showed the highest levels of genetic variations. While most of the SNPs and all the indels were silent mutations, both genes carried nonsense SNP mutations resulting in premature stop codons, a feature not observed in sad and fad2 genes. Some alleles and isoforms discovered in induced mutant lines were absent in the natural germplasm. Correlation of these genotypic data with fatty acid composition data of 120 flax accessions phenotyped in six field experiments revealed statistically significant effects of some of the SAD and FAD isoforms on fatty acid composition, oil content and iodine value. The novel allelic variants and isoforms identified for the six desaturases will be a resource for the development of oilseed flax with unique and useful fatty acid profiles.
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Affiliation(s)
- Dinushika Thambugala
- Department of Plant Science, University of Manitoba, 66 Dafoe Rd, Winnipeg, MB R3T 2N2 Canada
| | - Scott Duguid
- Morden Research Station, Agriculture and Agri-Food Canada, 101 Route 100, Unit 100, Morden, MB R6M 1Y5 Canada
| | - Evelyn Loewen
- Morden Research Station, Agriculture and Agri-Food Canada, 101 Route 100, Unit 100, Morden, MB R6M 1Y5 Canada
| | - Gordon Rowland
- Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Helen Booker
- Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Frank M. You
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Rd, Winnipeg, MB R3T 2M9 Canada
| | - Sylvie Cloutier
- Department of Plant Science, University of Manitoba, 66 Dafoe Rd, Winnipeg, MB R3T 2N2 Canada
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Rd, Winnipeg, MB R3T 2M9 Canada
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Thambugala D, Duguid S, Loewen E, Rowland G, Booker H, You FM, Cloutier S. Genetic variation of six desaturase genes in flax and their impact on fatty acid composition. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:2627-2641. [PMID: 23928861 DOI: 10.1007/s00122-013-2161-2162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Accepted: 07/12/2013] [Indexed: 05/24/2023]
Abstract
Flax (Linum usitatissimum L.) is one of the richest plant sources of omega-3 fatty acids praised for their health benefits. In this study, the extent of the genetic variability of genes encoding stearoyl-ACP desaturase (SAD), and fatty acid desaturase 2 (FAD2) and 3 (FAD3) was determined by sequencing the six paralogous genes from 120 flax accessions representing a broad range of germplasm including some EMS mutant lines. A total of 6 alleles for sad1 and sad2, 21 for fad2a, 5 for fad2b, 15 for fad3a and 18 for fad3b were identified. Deduced amino acid sequences of the alleles predicted 4, 2, 3, 4, 6 and 7 isoforms, respectively. Allele frequencies varied greatly across genes. Fad3a, with 110 SNPs and 19 indels, and fad3b, with 50 SNPs and 5 indels, showed the highest levels of genetic variations. While most of the SNPs and all the indels were silent mutations, both genes carried nonsense SNP mutations resulting in premature stop codons, a feature not observed in sad and fad2 genes. Some alleles and isoforms discovered in induced mutant lines were absent in the natural germplasm. Correlation of these genotypic data with fatty acid composition data of 120 flax accessions phenotyped in six field experiments revealed statistically significant effects of some of the SAD and FAD isoforms on fatty acid composition, oil content and iodine value. The novel allelic variants and isoforms identified for the six desaturases will be a resource for the development of oilseed flax with unique and useful fatty acid profiles.
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Affiliation(s)
- Dinushika Thambugala
- Department of Plant Science, University of Manitoba, 66 Dafoe Rd, Winnipeg, MB, R3T 2N2, Canada
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Wang ML, Chen CY, Tonnis B, Barkley NA, Pinnow DL, Pittman RN, Davis J, Holbrook CC, Stalker HT, Pederson GA. Oil, fatty acid, flavonoid, and resveratrol content variability and FAD2A functional SNP genotypes in the U.S. peanut mini-core collection. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:2875-82. [PMID: 23379758 DOI: 10.1021/jf305208e] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Peanut seeds contain high amounts of oil and protein as well as some useful bioactive phytochemicals which can contribute to human health. The U.S. peanut mini-core collection is an important genetic resource for improving seed quality and developing new cultivars. Variability of seed chemical composition within the mini-core was evaluated from freshly harvested seeds for two years. Oil, fatty acid composition, and flavonoid/resveratrol content were quantified by NMR, GC, and HPLC, respectively. Significant variability was detected in seed chemical composition among accessions and botanical varieties. Accessions were further genotyped with a functional SNP marker from the FAD2A gene using real-time PCR and classified into three genotypes with significantly different O/L ratios: wild type (G/G with a low O/L ratio <1.7), heterozygote (G/A with O/L ratio >1.4 but <1.7), and mutant (A/A with a high O/L ratio >1.7). The results from real-time PCR genotyping and GC fatty acid analysis were consistent. Accessions with high amounts of oil, quercetin, high seed weight, and O/L ratio were identified. The results from this study may be useful not only for peanut breeders, food processors, and product consumers to select suitable accessions or cultivars but also for curators to potentially expand the mini-core collection.
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Affiliation(s)
- Ming Li Wang
- USDA-ARS , Plant Genetic Resources Conservation Unit, Griffin, Georgia 30223, United States
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Osuji GO, Brown TK, South SM, Johnson D, Hyllam S. Molecular modeling of metabolism for allergen-free low linoleic acid peanuts. Appl Biochem Biotechnol 2012; 168:805-23. [PMID: 22918723 PMCID: PMC3470683 DOI: 10.1007/s12010-012-9821-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Accepted: 08/01/2012] [Indexed: 11/28/2022]
Abstract
It is necessary to eliminate linoleic acid and allergenic arachins from peanuts for good health reasons. Virginia-type peanuts, harvested from plots treated with mineral salts combinations that mimic the subunit compositions of glutamate dehydrogenase (GDH) were analyzed for fatty acid and arachin compositions by HPLC and polyacrylamide gel electrophoresis, respectively. Fatty acid desaturase and arachin encoding mRNAs were analyzed by Northern hybridization using the homologous RNAs synthesized by peanut GDH as probes. There were 70–80 % sequence similarities between the GDH-synthesized RNAs and the mRNAs encoding arachins, fatty acid desaturases, glutamate synthase, and nitrate reductase, which similarities induced permutation of the metabolic pathways at the mRNA level. Modeling of mRNAs showed there were 210, 3,150, 1,260, 2,520, and 4,200 metabolic permutations in the control, NPKS-, NS-, Pi-, NH4Cl-, and PK-treated peanuts, respectively. The mRNA cross-talks decreased the arachin to almost zero percent in the NPKS- and PK-treated peanuts, and linoleate to ∼18 % in the PK-treated peanut. The mRNA cross-talks may account for the vastly reported environmentally induced variability in the linoleate contents of peanut genotypes. These results have quantitatively unified molecular biology and metabolic pathways into one simple biotechnology for optimizing peanut quality and may encourage small-scale industry to produce arachin-free low linoleate peanuts.
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Affiliation(s)
- Godson O Osuji
- CARC, Prairie View A&M University, P.O. Box 519-2008, Prairie View, TX 77446, USA.
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