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Zhang H, Tang Y, Yue Y, Chen Y. Advances in the evolution research and genetic breeding of peanut. Gene 2024; 916:148425. [PMID: 38575102 DOI: 10.1016/j.gene.2024.148425] [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: 11/29/2023] [Revised: 03/15/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
Peanut is an important cash crop used in oil, food and feed in our country. The rapid development of sequencing technology has promoted the research on the related aspects of peanut genetic breeding. This paper reviews the research progress of peanut origin and evolution, genetic breeding, molecular markers and their applications, genomics, QTL mapping and genome selection techniques. The main problems of molecular genetic breeding in peanut research worldwide include: the narrow genetic resources of cultivated species, unstable genetic transformation and unclear molecular mechanism of important agronomic traits. Considering the severe challenges regarding the supply of edible oil, and the main problems in peanut production, the urgent research directions of peanut are put forward: The de novo domestication and the exploitation of excellent genes from wild resources to improve modern cultivars; Integration of multi-omics data to enhance the importance of big data in peanut genetics and breeding; Cloning the important genes related to peanut agronomic traits and analyzing their fine regulation mechanisms; Precision molecular design breeding and using gene editing technology to accurately improve the key traits of peanut.
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Affiliation(s)
- Hui Zhang
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China.
| | - Yueyi Tang
- Shandong Peanut Research Institute, Qingdao 266100, China
| | - Yunlai Yue
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Yong Chen
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China.
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2
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Guo M, Deng L, Gu J, Miao J, Yin J, Li Y, Fang Y, Huang B, Sun Z, Qi F, Dong W, Lu Z, Li S, Hu J, Zhang X, Ren L. Genome-wide association study and development of molecular markers for yield and quality traits in peanut (Arachis hypogaea L.). BMC PLANT BIOLOGY 2024; 24:244. [PMID: 38575936 PMCID: PMC10996145 DOI: 10.1186/s12870-024-04937-5] [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: 05/06/2023] [Accepted: 03/20/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND This study aims to decipher the genetic basis governing yield components and quality attributes of peanuts, a critical aspect for advancing molecular breeding techniques. Integrating genotype re-sequencing and phenotypic evaluations of seven yield components and two grain quality traits across four distinct environments allowed for the execution of a genome-wide association study (GWAS). RESULTS The nine phenotypic traits were all continuous and followed a normal distribution. The broad heritability ranged from 88.09 to 98.08%, and the genotype-environment interaction effects were all significant. There was a highly significant negative correlation between protein content (PC) and oil content (OC). The 10× genome re-sequencing of 199 peanut accessions yielded a total of 631,988 high-quality single nucleotide polymorphisms (SNPs), with 374 significant SNP loci identified in association with the nine traits of interest. Notably, 66 of these pertinent SNPs were detected in multiple environments, and 48 of them were linked to multiple traits of interest. Five loci situated on chromosome 16 (Chr16) exhibited pleiotropic effects on yield traits, accounting for 17.64-32.61% of the observed phenotypic variation. Two loci on Chr08 were found to be strongly associated with protein and oil contents, accounting for 12.86% and 14.06% of their respective phenotypic variations, respectively. Linkage disequilibrium (LD) block analysis of these seven loci unraveled five nonsynonymous variants, leading to the identification of one yield-related candidate gene and two quality-related candidate genes. The correlation between phenotypic variation and SNP loci in these candidate genes was validated by Kompetitive allele-specific PCR (KASP) marker analysis. CONCLUSIONS Overall, molecular markers were developed for genetic loci associated with yield and quality traits through a GWAS investigation of 199 peanut accessions across four distinct environments. These molecular tools can aid in the development of desirable peanut germplasm with an equilibrium of yield and quality through marker-assisted breeding.
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Affiliation(s)
- Minjie Guo
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China
| | - Li Deng
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China
| | - Jianzhong Gu
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China
| | - Jianli Miao
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China
| | - Junhua Yin
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China
| | - Yang Li
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China
| | - Yuanjin Fang
- Shennong Laboratory, Henan Provincial Key Laboratory for Oil Crops Improvement, Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Bingyan Huang
- Shennong Laboratory, Henan Provincial Key Laboratory for Oil Crops Improvement, Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Ziqi Sun
- Shennong Laboratory, Henan Provincial Key Laboratory for Oil Crops Improvement, Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Feiyan Qi
- Shennong Laboratory, Henan Provincial Key Laboratory for Oil Crops Improvement, Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Wenzhao Dong
- Shennong Laboratory, Henan Provincial Key Laboratory for Oil Crops Improvement, Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Zhenhua Lu
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China
| | - Shaowei Li
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China
| | - Junping Hu
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China
| | - Xinyou Zhang
- Shennong Laboratory, Henan Provincial Key Laboratory for Oil Crops Improvement, Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.
| | - Li Ren
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China.
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Lu Q, Huang L, Liu H, Garg V, Gangurde SS, Li H, Chitikineni A, Guo D, Pandey MK, Li S, Liu H, Wang R, Deng Q, Du P, Varshney RK, Liang X, Hong Y, Chen X. A genomic variation map provides insights into peanut diversity in China and associations with 28 agronomic traits. Nat Genet 2024; 56:530-540. [PMID: 38378864 DOI: 10.1038/s41588-024-01660-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 01/09/2024] [Indexed: 02/22/2024]
Abstract
Peanut (Arachis hypogaea L.) is an important allotetraploid oil and food legume crop. China is one of the world's largest peanut producers and consumers. However, genomic variations underlying the migration and divergence of peanuts in China remain unclear. Here we reported a genome-wide variation map based on the resequencing of 390 peanut accessions, suggesting that peanuts might have been introduced into southern and northern China separately, forming two cultivation centers. Selective sweep analysis highlights asymmetric selection between the two subgenomes during peanut improvement. A classical pedigree from South China offers a context for the examination of the impact of artificial selection on peanut genome. Genome-wide association studies identified 22,309 significant associations with 28 agronomic traits, including candidate genes for plant architecture and oil biosynthesis. Our findings shed light on peanut migration and diversity in China and provide valuable genomic resources for peanut improvement.
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Affiliation(s)
- Qing Lu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China.
| | - Lu Huang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China
| | - Hao Liu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China
| | - Vanika Garg
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Sunil S Gangurde
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Haifen Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China
| | - Annapurna Chitikineni
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Dandan Guo
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China
| | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Shaoxiong Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China
| | - Haiyan Liu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China
| | - Runfeng Wang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China
| | - Quanqing Deng
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China
| | - Puxuan Du
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China
| | - Rajeev K Varshney
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia.
| | - Xuanqiang Liang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China.
| | - Yanbin Hong
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China.
| | - Xiaoping Chen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China.
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4
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Hu P, Zhang J, Song Y, Zhao X, Jin X, Su Q, Yang Y, Wang J. Identification of Putative Quantitative Trait Loci for Improved Seed Oil Quality in Peanuts. Genes (Basel) 2024; 15:75. [PMID: 38254964 PMCID: PMC10815147 DOI: 10.3390/genes15010075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 12/31/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Improving seed oil quality in peanut (Arachis hypogaea) has long been an aim of breeding programs worldwide. The genetic resources to achieve this goal are limited. We used an advanced recombinant inbred line (RIL) population derived from JH5 × KX01-6 to explore quantitative trait loci (QTL) affecting peanut oil quality and their additive effects, epistatic effects, and QTL × environment interactions. Gas chromatography (GC) analysis suggested seven fatty acids components were obviously detected in both parents and analyzed in a follow-up QTL analysis. The major components, palmitic acid (C16:0), oleic acid (C18:1), and linoleic acid (C18:2), exhibited considerable phenotypic variation and fit the two major gene and minor gene mixed-inheritance model. Seventeen QTL explained 2.57-38.72% of the phenotypic variation in these major components, with LOD values of 4.12-37.56 in six environments, and thirty-five QTL explained 0.94-32.21% of the phenotypic variation, with LOD values of 5.99-150.38 in multiple environments. Sixteen of these QTL were detected in both individual and multiple environments. Among these, qFA_08_1 was a novel QTL with stable, valuable and major effect. Two other major-effect QTL, qFA_09_2 and qFA_19_3, share the same physical position as FAD2A and FAD2B, respectively. Eleven stable epistatic QTL involving nine loci explained 1.30-34.97% of the phenotypic variation, with epistatic effects ranging from 0.09 to 6.13. These QTL could be valuable for breeding varieties with improved oil quality.
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Affiliation(s)
| | | | | | | | | | | | - Yongqing Yang
- The Key Laboratory of Crop Genetics and Breeding of Hebei, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China; (P.H.); (J.Z.); (Y.S.); (X.Z.); (X.J.); (Q.S.)
| | - Jin Wang
- The Key Laboratory of Crop Genetics and Breeding of Hebei, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China; (P.H.); (J.Z.); (Y.S.); (X.Z.); (X.J.); (Q.S.)
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Wang J, Chen H, Li Y, Shi D, Wang W, Yan C, Yuan M, Sun Q, Chen J, Mou Y, Qu C, Shan S. Identification of Quantitative Trait Nucleotides and Development of Diagnostic Markers for Nine Fatty Acids in the Peanut. PLANTS (BASEL, SWITZERLAND) 2023; 13:16. [PMID: 38202325 PMCID: PMC10780752 DOI: 10.3390/plants13010016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024]
Abstract
The cultivated peanut (Arachis hypogaea L.) is an important oilseed crop worldwide, and fatty acid composition is a major determinant of peanut oil quality. In the present study, we conducted a genome-wide association study (GWAS) for nine fatty acid traits using the whole genome sequences of 160 representative Chinese peanut landraces and identified 6-1195 significant SNPs for different fatty acid contents. Particularly for oleic acid and linoleic acid, two peak SNP clusters on Arahy.09 and Arahy.19 were found to contain the majority of the significant SNPs associated with these two fatty acids. Additionally, a significant proportion of the candidate genes identified on Arahy.09 overlap with those identified in early studies, among which three candidate genes are of special interest. One possesses a significant missense SNP and encodes a known candidate gene FAD2A. The second gene is the gene closest to the most significant SNP for linoleic acid. It codes for an MYB protein that has been demonstrated to impact fatty acid biosynthesis in Arabidopsis. The third gene harbors a missense SNP and encodes a JmjC domain-containing protein. The significant phenotypic difference in the oleic acid/linoleic acid between the genotypes at the first and third candidate genes was further confirmed with PARMS analysis. In addition, we have also identified different candidate genes (i.e., Arahy.ZV39IJ, Arahy.F9E3EA, Arahy.X9ZZC1, and Arahy.Z0ELT9) for the remaining fatty acids. Our findings can help us gain a better understanding of the genetic foundation of peanut fatty acid contents and may hold great potential for enhancing peanut quality in the future.
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Affiliation(s)
- Juan Wang
- Shandong Peanut Research Institute, Qingdao 266100, China; (J.W.)
| | - Haoning Chen
- Shandong Peanut Research Institute, Qingdao 266100, China; (J.W.)
| | - Yuan Li
- National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, 22100 Lund, Sweden
- Department of Immunotechnology, Lund University, Medicon Village, 22100 Lund, Sweden
| | - Dachuan Shi
- Qingdao Academy of Agricultural Sciences, Qingdao 266100, China
| | - Wenjiao Wang
- Qingdao Academy of Agricultural Sciences, Qingdao 266100, China
| | - Caixia Yan
- Shandong Peanut Research Institute, Qingdao 266100, China; (J.W.)
| | - Mei Yuan
- Shandong Peanut Research Institute, Qingdao 266100, China; (J.W.)
| | - Quanxi Sun
- Shandong Peanut Research Institute, Qingdao 266100, China; (J.W.)
| | - Jing Chen
- Shandong Peanut Research Institute, Qingdao 266100, China; (J.W.)
| | - Yifei Mou
- Shandong Peanut Research Institute, Qingdao 266100, China; (J.W.)
| | - Chunjuan Qu
- Shandong Peanut Research Institute, Qingdao 266100, China; (J.W.)
| | - Shihua Shan
- Shandong Peanut Research Institute, Qingdao 266100, China; (J.W.)
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6
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Campos SB, de Oliveira Filho JG, Salgaço MK, Jesus MHD, Egea MB. Effects of Peanuts and Pistachios on Gut Microbiota and Metabolic Syndrome: A Review. Foods 2023; 12:4440. [PMID: 38137244 PMCID: PMC10743156 DOI: 10.3390/foods12244440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
There is growing evidence that the gut microbiota is associated with various aspects of human health, including immune system regulation, vitamin synthesis, short-chain fatty acid production, etc. Peanuts and pistachios are foods rich in protein, unsaturated fatty acids, vitamins, polyphenols, and other dietary components that have been shown to benefit the gut microbiota. Therefore, this review aims to describe the effects of consuming peanuts and pistachios on the gut microbiota and the potential role of these microbiota in human health. This review suggests that the consumption of peanuts or pistachios can demonstrate the potential to exert a beneficial effect on the gut microbiota by promoting the growth of beneficial gut bacteria that produce, for example, short-chain fatty acids that are beneficial for human health. In the case of peanuts, in particular, the possible modulation of the microbiota is associated with an improvement in the risk factors of metabolic syndrome and the inflammatory process triggered by a high-fat diet.
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Affiliation(s)
- Stéphani Borges Campos
- Goiano Federal Institute, Campus Rio Verde, Rio Verde 75901-970, Brazil; (S.B.C.); (M.H.D.J.)
| | | | - Mateus Kawata Salgaço
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara 14800-903, Brazil; (J.G.d.O.F.); (M.K.S.)
| | - Marisa Helena De Jesus
- Goiano Federal Institute, Campus Rio Verde, Rio Verde 75901-970, Brazil; (S.B.C.); (M.H.D.J.)
| | - Mariana Buranelo Egea
- Goiano Federal Institute, Campus Rio Verde, Rio Verde 75901-970, Brazil; (S.B.C.); (M.H.D.J.)
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Bu M, Fan W, Li R, He B, Cui P. Lipid Metabolism and Improvement in Oilseed Crops: Recent Advances in Multi-Omics Studies. Metabolites 2023; 13:1170. [PMID: 38132852 PMCID: PMC10744971 DOI: 10.3390/metabo13121170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 12/23/2023] Open
Abstract
Oilseed crops are rich in plant lipids that not only provide essential fatty acids for the human diet but also play important roles as major sources of biofuels and indispensable raw materials for the chemical industry. The regulation of lipid metabolism genes is a major factor affecting oil production. In this review, we systematically summarize the metabolic pathways related to lipid production and storage in plants and highlight key research advances in characterizing the genes and regulatory factors influencing lipid anabolic metabolism. In addition, we integrate the latest results from multi-omics studies on lipid metabolism to provide a reference to better understand the molecular mechanisms underlying oil anabolism in oilseed crops.
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Affiliation(s)
- Mengjia Bu
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei Fan
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Ruonan Li
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Bing He
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Peng Cui
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
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8
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Gulten HT, Polat M, Basak M, Qureshi M, Golukcu M, Uzun B, Yol E. Molecular breeding to develop advanced lines with high oleic acid and pod yield in peanut. INDUSTRIAL CROPS AND PRODUCTS 2023; 203:117231. [DOI: 10.1016/j.indcrop.2023.117231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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9
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Pixley KV, Cairns JE, Lopez-Ridaura S, Ojiewo CO, Dawud MA, Drabo I, Mindaye T, Nebie B, Asea G, Das B, Daudi H, Desmae H, Batieno BJ, Boukar O, Mukankusi CTM, Nkalubo ST, Hearne SJ, Dhugga KS, Gandhi H, Snapp S, Zepeda-Villarreal EA. Redesigning crop varieties to win the race between climate change and food security. MOLECULAR PLANT 2023; 16:1590-1611. [PMID: 37674314 DOI: 10.1016/j.molp.2023.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 08/17/2023] [Accepted: 09/03/2023] [Indexed: 09/08/2023]
Abstract
Climate change poses daunting challenges to agricultural production and food security. Rising temperatures, shifting weather patterns, and more frequent extreme events have already demonstrated their effects on local, regional, and global agricultural systems. Crop varieties that withstand climate-related stresses and are suitable for cultivation in innovative cropping systems will be crucial to maximize risk avoidance, productivity, and profitability under climate-changed environments. We surveyed 588 expert stakeholders to predict current and novel traits that may be essential for future pearl millet, sorghum, maize, groundnut, cowpea, and common bean varieties, particularly in sub-Saharan Africa. We then review the current progress and prospects for breeding three prioritized future-essential traits for each of these crops. Experts predict that most current breeding priorities will remain important, but that rates of genetic gain must increase to keep pace with climate challenges and consumer demands. Importantly, the predicted future-essential traits include innovative breeding targets that must also be prioritized; for example, (1) optimized rhizosphere microbiome, with benefits for P, N, and water use efficiency, (2) optimized performance across or in specific cropping systems, (3) lower nighttime respiration, (4) improved stover quality, and (5) increased early vigor. We further discuss cutting-edge tools and approaches to discover, validate, and incorporate novel genetic diversity from exotic germplasm into breeding populations with unprecedented precision, accuracy, and speed. We conclude that the greatest challenge to developing crop varieties to win the race between climate change and food security might be our innovativeness in defining and boldness to breed for the traits of tomorrow.
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Affiliation(s)
- Kevin V Pixley
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico.
| | - Jill E Cairns
- International Maize and Wheat Improvement Center (CIMMYT), Harare, Zimbabwe
| | | | - Chris O Ojiewo
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | | | - Inoussa Drabo
- International Maize and Wheat Improvement Center (CIMMYT), Dakar, Senegal
| | - Taye Mindaye
- Ethiopian Institute of Agricultural Research (EIAR), Addis Ababa, Ethiopia
| | - Baloua Nebie
- International Maize and Wheat Improvement Center (CIMMYT), Dakar, Senegal
| | - Godfrey Asea
- National Agricultural Research Organization (NARO), Kampala, Uganda
| | - Biswanath Das
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Happy Daudi
- Tanzania Agricultural Research Institute (TARI), Naliendele, Tanzania
| | - Haile Desmae
- International Maize and Wheat Improvement Center (CIMMYT), Dakar, Senegal
| | - Benoit Joseph Batieno
- Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina Faso
| | - Ousmane Boukar
- International Institute of Tropicl Agriculture (IITA), Kano, Nigeria
| | | | | | - Sarah J Hearne
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Kanwarpal S Dhugga
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Harish Gandhi
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Sieglinde Snapp
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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10
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Kassie FC, Nguepjop JR, Ngalle HB, Assaha DVM, Gessese MK, Abtew WG, Tossim HA, Sambou A, Seye M, Rami JF, Fonceka D, Bell JM. An Overview of Mapping Quantitative Trait Loci in Peanut ( Arachis hypogaea L.). Genes (Basel) 2023; 14:1176. [PMID: 37372356 DOI: 10.3390/genes14061176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
Quantitative Trait Loci (QTL) mapping has been thoroughly used in peanut genetics and breeding in spite of the narrow genetic diversity and the segmental tetraploid nature of the cultivated species. QTL mapping is helpful for identifying the genomic regions that contribute to traits, for estimating the extent of variation and the genetic action (i.e., additive, dominant, or epistatic) underlying this variation, and for pinpointing genetic correlations between traits. The aim of this paper is to review the recently published studies on QTL mapping with a particular emphasis on mapping populations used as well as traits related to kernel quality. We found that several populations have been used for QTL mapping including interspecific populations developed from crosses between synthetic tetraploids and elite varieties. Those populations allowed the broadening of the genetic base of cultivated peanut and helped with the mapping of QTL and identifying beneficial wild alleles for economically important traits. Furthermore, only a few studies reported QTL related to kernel quality. The main quality traits for which QTL have been mapped include oil and protein content as well as fatty acid compositions. QTL for other agronomic traits have also been reported. Among the 1261 QTL reported in this review, and extracted from the most relevant studies on QTL mapping in peanut, 413 (~33%) were related to kernel quality showing the importance of quality in peanut genetics and breeding. Exploiting the QTL information could accelerate breeding to develop highly nutritious superior cultivars in the face of climate change.
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Affiliation(s)
- Fentanesh C Kassie
- Department of Plant Biology and Physiology, Faculty of Sciences, University of Yaounde I, Yaounde P.O. Box 337, Cameroon
- Department of Plant Science, College of Agriculture, Wolaita Sodo University, Sodo P.O. Box 138, Ethiopia
| | - Joël R Nguepjop
- UMR AGAP, CIRAD, F-34398 Montpellier, France
- AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France
- Centre d'Etudes Régional Pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS/ISRA), Route de Khombole, Thiès BP 3320, Senegal
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l'Ouest (IAVAO), CERAAS, Route de Khombole, Thiès BP 3320, Senegal
| | - Hermine B Ngalle
- Department of Plant Biology and Physiology, Faculty of Sciences, University of Yaounde I, Yaounde P.O. Box 337, Cameroon
| | - Dekoum V M Assaha
- Department of Agriculture, Higher Technical Teachers Training College, University of Buea, Kumba P.O. Box 249, Cameroon
| | - Mesfin K Gessese
- Department of Plant Science, College of Agriculture, Wolaita Sodo University, Sodo P.O. Box 138, Ethiopia
| | - Wosene G Abtew
- Department of Horticulture and Plant Science, College of Agriculture and Veterinary Medicine, Jimma University, Jimma P.O. Box 378, Ethiopia
| | - Hodo-Abalo Tossim
- Centre d'Etudes Régional Pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS/ISRA), Route de Khombole, Thiès BP 3320, Senegal
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l'Ouest (IAVAO), CERAAS, Route de Khombole, Thiès BP 3320, Senegal
| | - Aissatou Sambou
- Centre d'Etudes Régional Pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS/ISRA), Route de Khombole, Thiès BP 3320, Senegal
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l'Ouest (IAVAO), CERAAS, Route de Khombole, Thiès BP 3320, Senegal
| | - Maguette Seye
- Centre d'Etudes Régional Pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS/ISRA), Route de Khombole, Thiès BP 3320, Senegal
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l'Ouest (IAVAO), CERAAS, Route de Khombole, Thiès BP 3320, Senegal
| | - Jean-François Rami
- UMR AGAP, CIRAD, F-34398 Montpellier, France
- AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l'Ouest (IAVAO), CERAAS, Route de Khombole, Thiès BP 3320, Senegal
| | - Daniel Fonceka
- UMR AGAP, CIRAD, F-34398 Montpellier, France
- AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France
- Centre d'Etudes Régional Pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS/ISRA), Route de Khombole, Thiès BP 3320, Senegal
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l'Ouest (IAVAO), CERAAS, Route de Khombole, Thiès BP 3320, Senegal
| | - Joseph M Bell
- Department of Plant Biology and Physiology, Faculty of Sciences, University of Yaounde I, Yaounde P.O. Box 337, Cameroon
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11
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Yang Y, Li Y, Cheng Z, Su Q, Jin X, Song Y, Wang J. Genetic analysis and exploration of major effect QTLs underlying oil content in peanut. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:97. [PMID: 37027047 DOI: 10.1007/s00122-023-04328-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 02/20/2023] [Indexed: 05/13/2023]
Abstract
KEY MESSAGE AhyHOF1, likely encoding a WRI1 transcription factor, plays critical roles in peanut oil synthesis. Although increasing the oil content of peanut to meet growing demand has long been a primary aim of breeding programs worldwide, the mining of genetic resources to achieve this objective has obviously lagged behind that of other oil crops. In the present study, we developed an advanced recombinant inbred line population containing 192 F9:11 families derived from parents JH5 and KX01-6. We then constructed a high-resolution genetic map covering 3,706.382 cM, with an average length of 185.32 cM per linkage group, using 2840 polymorphic SNPs. Two stable QTLs, qCOA08_1 and qCOA08_2 having the highest contributions to genetic variation (16.1% and 20.7%, respectively), were simultaneously detected in multiple environments and closely mapped within physical intervals of approximately 2.9 Mb and 1.7 Mb, respectively, on chromosome A08. In addition, combined analysis of whole-genome and transcriptome resequencing data uncovered a strong candidate gene encoding a WRI1 transcription factor and differentially expressed between the two parents. This gene, designated as High Oil Favorable gene 1 in Arachis hypogaea (AhyHOF1), was hypothesized to play roles in oil accumulation. Examination of near-inbred lines of #AhyHOF1/#Ahyhof1 provided further evidence that AhyHOF1 increases oil content, mainly by affecting the contents of several fatty acids. Taken together, our results provide valuable information for cloning the favorable allele for oil content in peanut. In addition, the closely linked polymorphic SNP markers within qCOA08_1 and qCOA08_2 loci may be useful for accelerating marker-assisted selection breeding of peanut.
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Affiliation(s)
- Yongqing Yang
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, The Key Laboratory of Crop Genetics and Breeding of Hebei, Shijiazhuang, 050035, Hebei, China
| | - Yurong Li
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, The Key Laboratory of Crop Genetics and Breeding of Hebei, Shijiazhuang, 050035, Hebei, China
| | - Zengshu Cheng
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, The Key Laboratory of Crop Genetics and Breeding of Hebei, Shijiazhuang, 050035, Hebei, China
| | - Qiao Su
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, The Key Laboratory of Crop Genetics and Breeding of Hebei, Shijiazhuang, 050035, Hebei, China
| | - Xinxin Jin
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, The Key Laboratory of Crop Genetics and Breeding of Hebei, Shijiazhuang, 050035, Hebei, China
| | - Yahui Song
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, The Key Laboratory of Crop Genetics and Breeding of Hebei, Shijiazhuang, 050035, Hebei, China
| | - Jin Wang
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, The Key Laboratory of Crop Genetics and Breeding of Hebei, Shijiazhuang, 050035, Hebei, China.
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12
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Wang ML, Tonnis B, Li X, Morris JB. Generation of Sesame Mutant Population by Mutagenesis and Identification of High Oleate Mutants by GC Analysis. PLANTS (BASEL, SWITZERLAND) 2023; 12:1294. [PMID: 36986984 PMCID: PMC10055875 DOI: 10.3390/plants12061294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/31/2022] [Accepted: 03/10/2023] [Indexed: 06/19/2023]
Abstract
Sesame is one of the important oilseed crops in the world. Natural genetic variation exists in the sesame germplasm collection. Mining and utilizing the genetic allele variation from the germplasm collection is an important approach for seed quality improvement. The sesame germplasm accession, PI 263470, which has a significantly higher level of oleic acid (54.0%) than the average (39.5%), was identified by screening the entire USDA germplasm collection. The seeds from this accession were planted in a greenhouse. Leaf tissues and seeds were harvested from individual plants. DNA sequencing of the coding region of the fatty acid desaturase gene (FAD2) confirmed that this accession contained a natural mutation of G425A which may correspond to the deduced amino acid substitution of R142H leading to the high level of oleic acid, but it was a mixed accession with three genotypes (G/G, G/A, and A/A at the position). The genotype with A/A was selected and self-crossed for three generations. The purified seeds were used for EMS-induced mutagenesis to further enhance the level of oleic acid. A total of 635 M2 plants were generated from mutagenesis. Some mutant plants had significant morphological changes including leafy flat stems and others. M3 seeds were used for fatty acid composition analysis by gas chromatography (GC). Several mutant lines were identified with high oleic acid (70%). Six M3 mutant lines plus one control line were advanced to M7 or M8 generations. Their high oleate traits from M7 or M8 seeds harvested from M6 or M7 plants were further confirmed. The level of oleic acid from one mutant line (M7 915-2) was over 75%. The coding region of FAD2 was sequenced from these six mutants, but no mutation was identified. Additional loci may contribute to the high level of oleic acid. The mutants identified in this study can be used as breeding materials for sesame improvement and as genetic materials for forward genetic studies.
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Affiliation(s)
- Ming Li Wang
- Plant Genetic Resources Conservation Unit, USDA-ARS, 1109 Experiment Street, Griffin, GA 30223, USA
| | - Brandon Tonnis
- Plant Genetic Resources Conservation Unit, USDA-ARS, 1109 Experiment Street, Griffin, GA 30223, USA
| | - Xianran Li
- Wheat Health, Genetics, and Quality Research, USDA-ARS, 291 Clark Hall, Pullman, WA 99164, USA
| | - John Bradly Morris
- Plant Genetic Resources Conservation Unit, USDA-ARS, 1109 Experiment Street, Griffin, GA 30223, USA
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13
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Huai D, Wu J, Xue X, Hu M, Zhi C, Pandey MK, Liu N, Huang L, Bai D, Yan L, Chen Y, Wang X, Kang Y, Wang Z, Jiang H, Lei Y, Varshney RK, Liao B. Red fluorescence protein (DsRed2) promotes the screening efficiency in peanut genetic transformation. FRONTIERS IN PLANT SCIENCE 2023; 14:1123644. [PMID: 36938000 PMCID: PMC10014910 DOI: 10.3389/fpls.2023.1123644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Peanut (Arachis hypogaea L.), one of the leading oilseed crops worldwide, is an important source of vegetable oil, protein, minerals and vitamins. Peanut is widely cultivated in Asia, Africa and America, and China is the largest producer and consumer of peanut. Genetic engineering has shown great potential to alter the DNA makeup of an organism which is largely hindered by the low transformation and screening efficiency including in peanut. DsRed2 is a reporter gene widely utilized in genetic transformation to facilitate the screening of transformants, but never used in peanut genetic transformation. In this study, we have demonstrated the potential of the red fluorescence protein DsRed2 as a visual reporter to improve screening efficiency in peanut. DsRed2 was firstly expressed in protoplasts isolated from peanut cultivar Zhonhua 12 by PEG, and red fluorescence was successfully detected. Then, DsRed2 was expressed in peanut plants Zhonghua 12 driven by 35S promoter via Agrobacterium tumefaciens-mediated transformation. Red fluorescence was visually observed in calli and regenerated shoots, as well as in roots, leaves, flowers, fresh pod shells and mature seeds, suggesting that transgenic screening could be initiated at the early stage of transformation, and continued to the progeny. Upon screening with DsRed2, the positive plant rate was increased from 56.9% to 100%. The transgenic line was then used as the male parent to be crossed with Zhonghua 24, and the hybrid seeds showed red fluorescence as well, indicating that DsRed2 could be applied to hybrid plant identification very efficiently. DsRed2 was also expressed in hairy roots of Huayu 23 via Agrobacterium rhizogenes-mediated transformation, and the transgenic roots were easily selected by red fluorescence. In summary, the DsRed2 is an ideal reporter to achieve maximum screening efficiency and accuracy in peanut genetic transformation.
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Affiliation(s)
- Dongxin Huai
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Jie Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaomeng Xue
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Meiling Hu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Chenyang Zhi
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Manish K. Pandey
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute of the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Nian Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Dongmei Bai
- Institute of Industrial Crops, Shanxi Agricultural University, Taiyuan, China
| | - Liying Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yuning Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xin Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yanping Kang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Zhihui Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Rajeev K. Varshney
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute of the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- State Agricultural Biotechnology Centre, Crop Research Innovation Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
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14
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Zhou X, Luo H, Yu B, Huang L, Liu N, Chen W, Liao B, Lei Y, Huai D, Guo P, Li W, Guo J, Jiang H. Genetic dissection of fatty acid components in the Chinese peanut (Arachis hypogaea L.) mini-core collection under multi-environments. PLoS One 2022; 17:e0279650. [PMID: 36584016 PMCID: PMC9803190 DOI: 10.1371/journal.pone.0279650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 12/12/2022] [Indexed: 12/31/2022] Open
Abstract
Peanut (Arachis hypogaea L.) is an important source of edible oil and protein for human nutrition. The quality of peanut seed oil is mainly determined by the composition of fatty acids, especially the contents of oleic acid and linoleic acid. Improving the composition of fatty acids in the seed oil is one of the main objectives for peanut breeding globally. To uncover the genetic basis of fatty acids and broaden the genetic variation in future peanut breeding programs, this study used genome-wide association studies (GWAS) to identify loci associated with target traits and developed diagnostic marker. The contents of eight fatty acid components of the Chinese peanut mini-core collection were measured under four environments. Using the phenotypic information and over one hundred thousand single nucleotide polymorphisms (SNPs), GWAS were conducted to investigate the genetics basis of fatty acids under multi-environments. Overall, 75 SNPs were identified significant trait associations with fatty acid components. Nineteen associations were repeatedly identified in multiple environments, and 13 loci were co-associated with two or three traits. Three stable major associated loci were identified, including two loci for oleic acid and linoleic acid on chromosome A09 [mean phenotypic variation explained (PVE): 38.5%, 10.35%] and one for stearic acid on B06 (mean PVE: 23%). According to functional annotations, 21 putative candidate genes related to fatty acid biosynthesis were found underlying the three associations. The allelic effect of SNP A09-114690064 showed that the base variation was highly correlated with the phenotypic variation of oleic acid and linoleic acid contents, and a cost-effective Kompetitive allele-Specific PCR (KASP) diagnostic marker was developed. Furthermore, the SNP A09-114690064 was found to change the cis-element CAAT (-) in the promoter of ahFAD2A to YACT (+), leading dozens of times higher expression level. The enhancer-like activity of ahFAD2A promoter was identified that was valuable for enriching the regulation mechanism of ahFAD2A. This study improved our understanding on the genetic architecture of fatty acid components in peanut, and the new effective diagnostic marker would be useful for marker-assisted selection of high-oleic peanut breeding.
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Affiliation(s)
- Xiaojing Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Huaiyong Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Bolun Yu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Nian Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Weigang Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Dongxin Huai
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Pengxia Guo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Weitao Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Jianbing Guo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
- * E-mail:
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15
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Cheng X, Liu X, He J, Tang M, Li H, Li M. The genome wide analysis of Tryptophan Aminotransferase Related gene family, and their relationship with related agronomic traits in Brassica napus. FRONTIERS IN PLANT SCIENCE 2022; 13:1098820. [PMID: 36618649 PMCID: PMC9811149 DOI: 10.3389/fpls.2022.1098820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
Tryptophan Aminotransferase of Arabidopsis1/Tryptophan Aminotransferase-Related (TAA1/TAR) proteins are the enzymes that involved in auxin biosynthesis pathway. The TAA1/TAR gene family has been systematically characterized in several plants but has not been well reported in Brassica napus. In the present study, a total of 102 BnTAR genes with different number of introns were identified. It was revealed that these genes are distributed unevenly and occurred as clusters on different chromosomes except for A4, A5, A10 and C4 in B. napus. Most of the these BnTAR genes are conserved despite of existing of gene loss and gene gain. In addition, the segmental replication and whole-genome replication events were both play an important role in the BnTAR gene family formation. Expression profiles analysis indicated that the expression of BnTAR gene showed two patterns, part of them were mainly expressed in roots, stems and leaves of vegetative organs, and the others were mainly expressed in flowers and seeds of reproductive organs. Further analysis showed that many of BnTAR genes were located in QTL intervals of oil content or seed weight, for example BnAMI10 was located in cqOC-C5-4 and cqSW-A2-2, it indicated that some of the BnTAR genes might have relationship with these two characteristics. This study provides a multidimensional analysis of the TAA1/TAR gene family and a new insight into its biological function in B. napus.
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Affiliation(s)
- Xin Cheng
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xinmin Liu
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jianjie He
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Mi Tang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Huaixin Li
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Maoteng Li
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Molecular Biophysics, the Ministry of Education of China, Wuhan, China
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16
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Zhao S, Sun J, Sun J, Zhang X, Zhao C, Pan J, Hou L, Tian R, Wang X. Insights into the Novel FAD2 Gene Regulating Oleic Acid Accumulation in Peanut Seeds with Different Maturity. Genes (Basel) 2022; 13:2076. [PMID: 36360313 PMCID: PMC9691258 DOI: 10.3390/genes13112076] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/03/2022] [Accepted: 11/08/2022] [Indexed: 11/29/2023] Open
Abstract
AhFAD2 is a key enzyme catalyzing the conversion of oleic acid into linoleic acid. The high oleic acid characteristic of peanut mainly comes from the homozygous recessive mutation of AhFAD2A and AhFAD2B genes (aabb). However, even in high-oleic-acid varieties with the aabb genotype, the oleic acid content of seeds with different maturity varies significantly. Therefore, in addition to AhFAD2A and AhFAD2B, other FAD2 members or regulators may be involved in this process. Which FAD2 genes are involved in the regulatory processes associated with seed maturity is still unclear. In this study, four stable lines with different genotypes (AABB, aaBB, AAbb, and aabb) were used to analyze the contents of oleic acid and linoleic acid at different stages of seed development in peanut. Three new AhFAD2 genes (AhFAD2-7, AhFAD2-8, and AhFAD2-9) were cloned based on the whole-genome sequencing results of cultivated peanuts. All peanut FAD2 genes showed tissue preference in expression; however, only the expression level of AhFAD2-7 was positively correlated with the linoleic acid concentration in peanut seeds. These findings provide new insights into the regulation of oleic acid accumulation by maturity, and AhFAD2-7 plays an important role in the maturity dependent accumulation of oleic acid and linoleic acid in peanut.
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Affiliation(s)
- Shuzhen Zhao
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, China
- College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Jie Sun
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, China
- College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Jinbo Sun
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, China
| | - Xiaoqian Zhang
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, China
- College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Chuanzhi Zhao
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, China
| | - Jiaowen Pan
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, China
| | - Lei Hou
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, China
- College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Ruizheng Tian
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, China
| | - Xingjun Wang
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, China
- College of Life Sciences, Shandong Normal University, Jinan 250014, China
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17
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Andres RJ, Dunne JC. Understanding variation in oleic acid content of high-oleic virginia-type peanut. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3433-3442. [PMID: 35951034 DOI: 10.1007/s00122-022-04190-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/31/2022] [Indexed: 06/15/2023]
Abstract
Contamination at the FAD2B locus due to inadequate screening protocols is the primary cause of sporadic, insufficient oleic acid content in Virginia-type peanut. The high oleic trait in peanut is conditioned by loss-of-function mutations in a pair of homeologous enzymes and is well known to improve the shelf life of peanut products. As such, the trait is given high priority in current and future cultivars by the North Carolina State University peanut breeding program. For unknown reasons, high oleic cultivars and breeding lines intermittently failed to meet self-imposed thresholds for oleic acid content in internal testing. To determine why, a manual seed chipper, crude DNA isolation protocol, genotyping assays for both mutations, and a web-based SNP calling application were developed. The primary cause was determined to be contamination with normal oleic seeds resulting from inadequate screening protocols. In order to correct the problem, a faster screening method was acquired to accommodate a higher oleic acid threshold. Additionally, results showed the mutation in one homeolog is fixed in the program, dig date had no significant effect on oleic acid content, and minor modifiers segregating within the program explained 6% of the variation in oleic acid content.
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Affiliation(s)
- R J Andres
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, USA
| | - J C Dunne
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, USA.
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18
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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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Neelakandan AK, Subedi B, Traore SM, Binagwa P, Wright DA, He G. Base Editing in Peanut Using CRISPR/nCas9. Front Genome Ed 2022; 4:901444. [PMID: 35647579 PMCID: PMC9133374 DOI: 10.3389/fgeed.2022.901444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/22/2022] [Indexed: 12/02/2022] Open
Abstract
Peanut (Arachis hypogaea L.), an allotetraploid legume of the Fabaceae family, is able to thrive in tropical and subtropical regions and is considered as a promising oil seed crop worldwide. Increasing the content of oleic acid has become one of the major goals in peanut breeding because of health benefits such as reduced blood cholesterol level, antioxidant properties and industrial benefits such as longer shelf life. Genomic sequencing of peanut has provided evidence of homeologous AhFAD2A and AhFAD2B genes encoding Fatty Acid Desaturase2 (FAD2), which are responsible for catalyzing the conversion of monounsaturated oleic acid into polyunsaturated linoleic acid. Research studies demonstrate that mutations resulting in a frameshift or stop codon in an FAD2 gene leads to higher oleic acid content in oil. In this study, two expression vectors, pDW3873 and pDW3876, were constructed using Cas9 fused to different deaminases, which were tested as tools to induce point mutations in the promoter and the coding sequences of peanut AhFAD2 genes. Both constructs harbor the single nuclease null variant, nCas9 D10A, to which the PmCDA1 cytosine deaminase was fused to the C-terminal (pDW3873) while rAPOBEC1 deaminase and an uracil glycosylase inhibitor (UGI) were fused to the N-terminal and the C-terminal respectively (pDW3876). Three gRNAs were cloned independently into both constructs and the functionality and efficiency were tested at three target sites in the AhFAD2 genes. Both constructs displayed base editing activity in which cytosine was replaced by thymine or other bases in the targeted editing window. pDW3873 showed higher efficiency compared to pDW3876 suggesting that the former is a better base editor in peanut. This is an important step forward considering introgression of existing mutations into elite varieties can take up to 15 years making this tool a benefit for peanut breeders, farmers, industry and ultimately for consumers.
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Affiliation(s)
- Anjanasree K. Neelakandan
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, United States
| | - Binita Subedi
- Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL, United States
| | - Sy M. Traore
- Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL, United States
| | - Papias Binagwa
- Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL, United States
| | - David A. Wright
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, United States
| | - Guohao He
- Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL, United States
- *Correspondence: Guohao He,
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20
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Qi F, Sun Z, Liu H, Zheng Z, Qin L, Shi L, Chen Q, Liu H, Lin X, Miao L, Tian M, Wang X, Huang B, Dong W, Zhang X. QTL identification, fine mapping, and marker development for breeding peanut (Arachis hypogaea L.) resistant to bacterial wilt. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1319-1330. [PMID: 35059781 PMCID: PMC9033696 DOI: 10.1007/s00122-022-04033-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 12/31/2021] [Indexed: 05/26/2023]
Abstract
A major QTL, qBWA12, was fine mapped to a 216.68 kb physical region, and A12.4097252 was identified as a useful KASP marker for breeding peanut varieties resistant to bacterial wilt. Bacterial wilt, caused by Ralstonia solanacearum, is a major disease detrimental to peanut production in China. Breeding disease-resistant peanut varieties is the most economical and effective way to prevent the disease and yield loss. Fine mapping the QTLs for bacterial wilt resistance is critical for the marker-assisted breeding of disease-resistant varieties. A recombinant inbred population comprising 521 lines was used to construct a high-density genetic linkage map and to identify QTLs for bacterial wilt resistance following restriction-site-associated DNA sequencing. The genetic map, which included 5120 SNP markers, covered a length of 3179 cM with an average marker distance of 0.6 cM. Four QTLs for bacterial wilt resistance were mapped on four chromosomes. One major QTL, qBWA12, with LOD score of 32.8-66.0 and PVE of 31.2-44.8%, was stably detected in all four development stages investigated over the 3 trial years. Additionally, qBWA12 spanned a 2.7 cM region, corresponding to approximately 0.4 Mb and was fine mapped to a 216.7 kb region by applying KASP markers that were polymorphic between the two parents based on whole-genome resequencing data. In a large collection of breeding and germplasm lines, it was proved that KASP marker A12.4097252 can be applied for the marker-assisted breeding to develop peanut varieties resistant to bacterial wilt. Of the 19 candidate genes in the region covered by qBWA12, nine NBS-LRR genes should be further investigated regarding their potential contribution to the resistance of peanut against bacterial wilt.
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Affiliation(s)
- Feiyan Qi
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Science/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou, 450002, Henan, China
| | - Ziqi Sun
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Science/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou, 450002, Henan, China
| | - Hua Liu
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Science/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou, 450002, Henan, China
| | - Zheng Zheng
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Science/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou, 450002, Henan, China
| | - Li Qin
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Science/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou, 450002, Henan, China
| | - Lei Shi
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Science/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou, 450002, Henan, China
| | - Qingzheng Chen
- Hezhou Academy of Agricultural Science, Hezhou, 542899, Guangxi, China
| | - Haidong Liu
- Hezhou Academy of Agricultural Science, Hezhou, 542899, Guangxi, China
| | - Xiufang Lin
- Hezhou Academy of Agricultural Science, Hezhou, 542899, Guangxi, China
| | - Lijuan Miao
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Science/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou, 450002, Henan, China
| | - Mengdi Tian
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Science/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou, 450002, Henan, China
| | - Xiao Wang
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Science/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou, 450002, Henan, China
| | - Bingyan Huang
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Science/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou, 450002, Henan, China
| | - Wenzhao Dong
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Science/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou, 450002, Henan, China
| | - Xinyou Zhang
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Science/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou, 450002, Henan, China.
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21
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Zenda T, Liu S, Dong A, Li J, Wang Y, Liu X, Wang N, Duan H. Omics-Facilitated Crop Improvement for Climate Resilience and Superior Nutritive Value. FRONTIERS IN PLANT SCIENCE 2021; 12:774994. [PMID: 34925418 PMCID: PMC8672198 DOI: 10.3389/fpls.2021.774994] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/08/2021] [Indexed: 05/17/2023]
Abstract
Novel crop improvement approaches, including those that facilitate for the exploitation of crop wild relatives and underutilized species harboring the much-needed natural allelic variation are indispensable if we are to develop climate-smart crops with enhanced abiotic and biotic stress tolerance, higher nutritive value, and superior traits of agronomic importance. Top among these approaches are the "omics" technologies, including genomics, transcriptomics, proteomics, metabolomics, phenomics, and their integration, whose deployment has been vital in revealing several key genes, proteins and metabolic pathways underlying numerous traits of agronomic importance, and aiding marker-assisted breeding in major crop species. Here, citing several relevant examples, we appraise our understanding on the recent developments in omics technologies and how they are driving our quest to breed climate resilient crops. Large-scale genome resequencing, pan-genomes and genome-wide association studies are aiding the identification and analysis of species-level genome variations, whilst RNA-sequencing driven transcriptomics has provided unprecedented opportunities for conducting crop abiotic and biotic stress response studies. Meanwhile, single cell transcriptomics is slowly becoming an indispensable tool for decoding cell-specific stress responses, although several technical and experimental design challenges still need to be resolved. Additionally, the refinement of the conventional techniques and advent of modern, high-resolution proteomics technologies necessitated a gradual shift from the general descriptive studies of plant protein abundances to large scale analysis of protein-metabolite interactions. Especially, metabolomics is currently receiving special attention, owing to the role metabolites play as metabolic intermediates and close links to the phenotypic expression. Further, high throughput phenomics applications are driving the targeting of new research domains such as root system architecture analysis, and exploration of plant root-associated microbes for improved crop health and climate resilience. Overall, coupling these multi-omics technologies to modern plant breeding and genetic engineering methods ensures an all-encompassing approach to developing nutritionally-rich and climate-smart crops whose productivity can sustainably and sufficiently meet the current and future food, nutrition and energy demands.
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Affiliation(s)
- Tinashe Zenda
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
- Department of Crop Science, Faculty of Agriculture and Environmental Science, Bindura University of Science Education, Bindura, Zimbabwe
| | - Songtao Liu
- Academy of Agriculture and Forestry Sciences, Hebei North University, Zhangjiakou, China
| | - Anyi Dong
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Jiao Li
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Yafei Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Xinyue Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Nan Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Huijun Duan
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
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22
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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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Nayak SN, Aravind B, Malavalli SS, Sukanth BS, Poornima R, Bharati P, Hefferon K, Kole C, Puppala N. Omics Technologies to Enhance Plant Based Functional Foods: An Overview. Front Genet 2021; 12:742095. [PMID: 34858472 PMCID: PMC8631721 DOI: 10.3389/fgene.2021.742095] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/13/2021] [Indexed: 11/25/2022] Open
Abstract
Functional foods are natural products of plants that have health benefits beyond necessary nutrition. Functional foods are abundant in fruits, vegetables, spices, beverages and some are found in cereals, millets, pulses and oilseeds. Efforts to identify functional foods in our diet and their beneficial aspects are limited to few crops. Advances in sequencing and availability of different omics technologies have given opportunity to utilize these tools to enhance the functional components of the foods, thus ensuring the nutritional security. Integrated omics approaches including genomics, transcriptomics, proteomics, metabolomics coupled with artificial intelligence and machine learning approaches can be used to improve the crops. This review provides insights into omics studies that are carried out to find the active components and crop improvement by enhancing the functional compounds in different plants including cereals, millets, pulses, oilseeds, fruits, vegetables, spices, beverages and medicinal plants. There is a need to characterize functional foods that are being used in traditional medicines, as well as utilization of this knowledge to improve the staple foods in order to tackle malnutrition and hunger more effectively.
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Affiliation(s)
- Spurthi N. Nayak
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - B. Aravind
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - Sachin S. Malavalli
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - B. S. Sukanth
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - R. Poornima
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - Pushpa Bharati
- Department of Food Science and Nutrition, University of Agricultural Sciences, Dharwad, India
| | - Kathleen Hefferon
- Department of Microbiology, Cornell University, Ithaca, NY, United States
| | - Chittaranjan Kole
- President, International Phytomedomics and Nutriomics Consortium (ipnc.info), Daejeon, South Korea
| | - Naveen Puppala
- New Mexico State University-Agricultural Science Center at Clovis, New Mexico, NM, United States
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24
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Jadhav MP, Gangurde SS, Hake AA, Yadawad A, Mahadevaiah SS, Pattanashetti SK, Gowda MVC, Shirasawa K, Varshney RK, Pandey MK, Bhat RS. Genotyping-by-Sequencing Based Genetic Mapping Identified Major and Consistent Genomic Regions for Productivity and Quality Traits in Peanut. FRONTIERS IN PLANT SCIENCE 2021; 12:668020. [PMID: 34630444 PMCID: PMC8495222 DOI: 10.3389/fpls.2021.668020] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 08/25/2021] [Indexed: 06/13/2023]
Abstract
With an objective of identifying the genomic regions for productivity and quality traits in peanut, a recombinant inbred line (RIL) population developed from an elite variety, TMV 2 and its ethyl methane sulfonate (EMS)-derived mutant was phenotyped over six seasons and genotyped with genotyping-by-sequencing (GBS), Arachis hypogaea transposable element (AhTE) and simple sequence repeats (SSR) markers. The genetic map with 700 markers spanning 2,438.1 cM was employed for quantitative trait loci (QTL) analysis which identified a total of 47 main-effect QTLs for the productivity and oil quality traits with the phenotypic variance explained (PVE) of 10-52% over the seasons. A common QTL region (46.7-50.1 cM) on Ah02 was identified for the multiple traits, such as a number of pods per plant (NPPP), pod weight per plant (PWPP), shelling percentage (SP), and test weight (TW). Similarly, a QTL (7.1-18.0 cM) on Ah16 was identified for both SP and protein content (PC). Epistatic QTL (epiQTL) analysis revealed intra- and inter-chromosomal interactions for the main-effect QTLs and other genomic regions governing these productivity traits. The markers identified by a single marker analysis (SMA) mapped to the QTL regions for most of the traits. Among the five potential candidate genes identified for PC, SP and oil quality, two genes (Arahy.7A57YA and Arahy.CH9B83) were affected by AhMITE1 transposition, and three genes (Arahy.J5SZ1I, Arahy.MZJT69, and Arahy.X7PJ8H) involved functional single nucleotide polymorphisms (SNPs). With major and consistent effects, the genomic regions, candidate genes, and the associated markers identified in this study would provide an opportunity for gene cloning and genomics-assisted breeding for increasing the productivity and enhancing the quality of peanut.
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Affiliation(s)
- Mangesh P. Jadhav
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Sunil S. Gangurde
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Anil A. Hake
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - Arati Yadawad
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | | | | | - M. V. Channabyre Gowda
- Department of Genetics and Plant Breeding, University of Agricultural Sciences, Dharwad, India
| | - Kenta Shirasawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Chiba, Japan
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manish K. Pandey
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Ramesh S. Bhat
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
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25
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Bhunia RK, Sinha K, Kaur R, Kaur S, Chawla K. A Holistic View of the Genetic Factors Involved in Triggering Hydrolytic and Oxidative Rancidity of Rice Bran Lipids. FOOD REVIEWS INTERNATIONAL 2021. [DOI: 10.1080/87559129.2021.1915328] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Rupam Kumar Bhunia
- National Agri-Food Biotechnology Institute (NABI), Plant Tissue Culture and Genetic Engineering, Mohali, Punjab, India
| | - Kshitija Sinha
- National Agri-Food Biotechnology Institute (NABI), Plant Tissue Culture and Genetic Engineering, Mohali, Punjab, India
- Department of Biotechnology, Sector-25, Panjab University, Chandigarh, India
| | - Ranjeet Kaur
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Sumandeep Kaur
- Department of Biotechnology, Sector-25, Panjab University, Chandigarh, India
| | - Kirti Chawla
- National Agri-Food Biotechnology Institute (NABI), Plant Tissue Culture and Genetic Engineering, Mohali, Punjab, India
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Gaikwad KB, Rani S, Kumar M, Gupta V, Babu PH, Bainsla NK, Yadav R. Enhancing the Nutritional Quality of Major Food Crops Through Conventional and Genomics-Assisted Breeding. Front Nutr 2020; 7:533453. [PMID: 33324668 PMCID: PMC7725794 DOI: 10.3389/fnut.2020.533453] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 09/03/2020] [Indexed: 01/14/2023] Open
Abstract
Nutritional stress is making over two billion world population malnourished. Either our commercially cultivated varieties of cereals, pulses, and oilseed crops are deficient in essential nutrients or the soils in which these crops grow are becoming devoid of minerals. Unfortunately, our major food crops are poor sources of micronutrients required for normal human growth. To overcome the problem of nutritional deficiency, greater emphasis should be laid on the identification of genes/quantitative trait loci (QTLs) pertaining to essential nutrients and their successful deployment in elite breeding lines through marker-assisted breeding. The manuscript deals with information on identified QTLs for protein content, vitamins, macronutrients, micro-nutrients, minerals, oil content, and essential amino acids in major food crops. These QTLs can be utilized in the development of nutrient-rich crop varieties. Genome editing technologies that can rapidly modify genomes in a precise way and will directly enrich the nutritional status of elite varieties could hold a bright future to address the challenge of malnutrition.
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Affiliation(s)
- Kiran B. Gaikwad
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Sushma Rani
- Indian Council of Agricultural Research (ICAR)-National Institute for Plant Biotechnology, New Delhi, India
| | - Manjeet Kumar
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Vikas Gupta
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Prashanth H. Babu
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Naresh Kumar Bainsla
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Rajbir Yadav
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
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Sinha P, Bajaj P, Pazhamala LT, Nayak SN, Pandey MK, Chitikineni A, Huai D, Khan AW, Desai A, Jiang H, Zhuang W, Guo B, Liao B, Varshney RK. Arachis hypogaea gene expression atlas for fastigiata subspecies of cultivated groundnut to accelerate functional and translational genomics applications. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:2187-2200. [PMID: 32167667 PMCID: PMC7589347 DOI: 10.1111/pbi.13374] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 02/26/2020] [Indexed: 05/05/2023]
Abstract
Spatio-temporal and developmental stage-specific transcriptome analysis plays a crucial role in systems biology-based improvement of any species. In this context, we report here the Arachis hypogaea gene expression atlas (AhGEA) for the world's widest cultivated subsp. fastigiata based on RNA-seq data using 20 diverse tissues across five key developmental stages. Approximately 480 million paired-end filtered reads were generated followed by identification of 81 901 transcripts from an early-maturing, high-yielding, drought-tolerant groundnut variety, ICGV 91114. Further, 57 344 genome-wide transcripts were identified with ≥1 FPKM across different tissues and stages. Our in-depth analysis of the global transcriptome sheds light into complex regulatory networks namely gravitropism and photomorphogenesis, seed development, allergens and oil biosynthesis in groundnut. Importantly, interesting insights into molecular basis of seed development and nodulation have immense potential for translational genomics research. We have also identified a set of stable expressing transcripts across the selected tissues, which could be utilized as internal controls in groundnut functional genomics studies. The AhGEA revealed potential transcripts associated with allergens, which upon appropriate validation could be deployed in the coming years to develop consumer-friendly groundnut varieties. Taken together, the AhGEA touches upon various important and key features of cultivated groundnut and provides a reference for further functional, comparative and translational genomics research for various economically important traits.
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Affiliation(s)
- Pallavi Sinha
- Center of Excellence in Genomics and Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Prasad Bajaj
- Center of Excellence in Genomics and Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Lekha T. Pazhamala
- Center of Excellence in Genomics and Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Spurthi N. Nayak
- Center of Excellence in Genomics and Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
- Department of BiotechnologyUniversity of Agricultural Sciences (UAS)DharwadIndia
| | - Manish K. Pandey
- Center of Excellence in Genomics and Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Annapurna Chitikineni
- Center of Excellence in Genomics and Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Dongxin Huai
- Oil Crop Research Institute (OCRI)Chinese Academy of Agricultural Science (CAAS)WuhanChina
| | - Aamir W. Khan
- Center of Excellence in Genomics and Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Aarthi Desai
- Center of Excellence in Genomics and Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Huifang Jiang
- Oil Crop Research Institute (OCRI)Chinese Academy of Agricultural Science (CAAS)WuhanChina
| | - Weijian Zhuang
- College of Plant ProtectionFujian Agriculture and Forestry University (FAFU)FuzhouChina
| | - Baozhu Guo
- USDA‐ARS Crop Protection and Management Research Unit (CPMRU)TiftonGAUSA
| | - Boshou Liao
- Oil Crop Research Institute (OCRI)Chinese Academy of Agricultural Science (CAAS)WuhanChina
| | - Rajeev K. Varshney
- Center of Excellence in Genomics and Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
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Identification of potential QTLs and genes associated with seed composition traits in peanut (Arachis hypogaea L.) using GWAS and RNA-Seq analysis. Gene 2020; 769:145215. [PMID: 33038422 DOI: 10.1016/j.gene.2020.145215] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/03/2020] [Accepted: 10/02/2020] [Indexed: 11/21/2022]
Abstract
Cultivated peanut (Arachis hypogaea L.) is a major oilseed crop providing edible oil and protein. Oil quality is determined by fatty acid composition including the ratio of oleic acid (C18:1) and linoleic acid (C18:2). A genome-wide association study with 13,382 single nucleotide polymorphisms (SNPs) was conducted to investigate the genetics basis of oil, protein, eight fatty acid concentrations, and O/L ratio (ratio of oleic and linoleic acid) using a diverse panel of 120 genotypes mainly selected from the U.S. peanut mini core collection grown in two years. A total of 178 significant quantitative trait loci (QTLs) associated with those seed composition traits were identified with phenotypic variation explained (PVE) from 18.35% to 27.56%. RNA-Seq analysis identified 282 DEGs (differentially expressed genes) within the 1 Mb of the significant QTLs for seed composition traits. Among those 282 genes, sixteen candidate genes for seed fatty acid metabolism and protein synthesis were screened according to the gene functions.
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Wang X, Xu P, Ren Y, Yin L, Li S, Wang Y, Shi Y, Li H, Cao X, Chi X, Yu T, Pandey MK, Varshney RK, Yuan M. Genome-wide identification of meiotic recombination hot spots detected by SLAF in peanut (Arachis hypogaea L.). Sci Rep 2020; 10:13792. [PMID: 32796889 PMCID: PMC7429841 DOI: 10.1038/s41598-020-70354-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/14/2020] [Indexed: 11/10/2022] Open
Abstract
Recombination hot spots (RHP), caused by meiosis, are considered to play crucial roles in improvement and domestication of crop. Cultivated peanut is one of the most important rich-source of oil and protein crops. However, no direct scale of recombination events and RHP have been estimated for peanut. To examine the scale of recombination events and RHP in peanut, a RIL population with 200 lines and a natural population with 49 cultivars were evaluated. The precise integrated map comprises 4837 SLAF markers with genetic length of 2915.46 cM and density of 1.66 markers per cM in whole genome. An average of 30.0 crossover (2.06 cMMb−1) events was detected per RIL plant. The crossover events (CE) showed uneven distribution among B sub-genome (2.32) and A sub-genome (1.85). There were 4.34% and 7.86% of the genome contained large numbers of CE (> 50 cMMb−1) along chromosomes in F6 and natural population, respectively. High density of CE regions called RHP, showed negative relationship to marker haplotypes conservative region but positive to heatmap of recombination. The genes located within the RHP regions by GO categories showed the responding of environmental stimuli, which suggested that recombination plays a crucial role in peanut adaptation to changing environments
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Affiliation(s)
- Xiaohua Wang
- College of Agriculture and Forestry Science, Linyi University, Middle of Shuangling Road, Lanshan District, Linyi, 276000, China
| | - Ping Xu
- College of Agriculture and Forestry Science, Linyi University, Middle of Shuangling Road, Lanshan District, Linyi, 276000, China.
| | - Yan Ren
- Key Laboratory of Peanut Biology and Genetic Improvement, Ministry of Agriculture, Shandong Peanut Research Institute, No.126, Wannianquan Road, Licang District, Qingdao, 266100, China
| | - Liang Yin
- Key Laboratory of Peanut Biology and Genetic Improvement, Ministry of Agriculture, Shandong Peanut Research Institute, No.126, Wannianquan Road, Licang District, Qingdao, 266100, China
| | - Shuangling Li
- Key Laboratory of Peanut Biology and Genetic Improvement, Ministry of Agriculture, Shandong Peanut Research Institute, No.126, Wannianquan Road, Licang District, Qingdao, 266100, China
| | - Yan Wang
- College of Agriculture and Forestry Science, Linyi University, Middle of Shuangling Road, Lanshan District, Linyi, 276000, China
| | - Yanmao Shi
- Key Laboratory of Peanut Biology and Genetic Improvement, Ministry of Agriculture, Shandong Peanut Research Institute, No.126, Wannianquan Road, Licang District, Qingdao, 266100, China
| | - Hui Li
- College of Agriculture and Forestry Science, Linyi University, Middle of Shuangling Road, Lanshan District, Linyi, 276000, China
| | - Xue Cao
- College of Agriculture and Forestry Science, Linyi University, Middle of Shuangling Road, Lanshan District, Linyi, 276000, China
| | - Xiaoyuan Chi
- Key Laboratory of Peanut Biology and Genetic Improvement, Ministry of Agriculture, Shandong Peanut Research Institute, No.126, Wannianquan Road, Licang District, Qingdao, 266100, China
| | - Tianyi Yu
- Key Laboratory of Peanut Biology and Genetic Improvement, Ministry of Agriculture, Shandong Peanut Research Institute, No.126, Wannianquan Road, Licang District, Qingdao, 266100, China
| | - Manish K Pandey
- International Crops Research Institute for Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Patancheru, 502 324, India
| | - Rajeev K Varshney
- International Crops Research Institute for Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Patancheru, 502 324, India
| | - Mei Yuan
- Key Laboratory of Peanut Biology and Genetic Improvement, Ministry of Agriculture, Shandong Peanut Research Institute, No.126, Wannianquan Road, Licang District, Qingdao, 266100, China.
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Liu N, Huang L, Chen W, Wu B, Pandey MK, Luo H, Zhou X, Guo J, Chen H, Huai D, Chen Y, Lei Y, Liao B, Ren X, Varshney RK, Jiang H. Dissection of the genetic basis of oil content in Chinese peanut cultivars through association mapping. BMC Genet 2020; 21:60. [PMID: 32513099 PMCID: PMC7282078 DOI: 10.1186/s12863-020-00863-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 05/26/2020] [Indexed: 11/17/2022] Open
Abstract
Background Peanut is one of the primary sources for vegetable oil worldwide, and enhancing oil content is the main objective in several peanut breeding programs of the world. Tightly linked markers are required for faster development of high oil content peanut varieties through genomics-assisted breeding (GAB), and association mapping is one of the promising approaches for discovery of such associated markers. Results An association mapping panel consisting of 292 peanut varieties extensively distributed in China was phenotyped for oil content and genotyped with 583 polymorphic SSR markers. These markers amplified 3663 alleles with an average of 6.28 alleles per locus. The structure, phylogenetic relationship, and principal component analysis (PCA) indicated two subgroups majorly differentiating based on geographic regions. Genome-wide association analysis identified 12 associated markers including one (AGGS1014_2) highly stable association controlling up to 9.94% phenotypic variance explained (PVE) across multiple environments. Interestingly, the frequency of the favorable alleles for 12 associated markers showed a geographic difference. Two associated markers (AGGS1014_2 and AHGS0798) with 6.90–9.94% PVE were verified to enhance oil content in an independent RIL population and also indicated selection during the breeding program. Conclusion This study provided insights into the genetic basis of oil content in peanut and verified highly associated two SSR markers to facilitate marker-assisted selection for developing high-oil content breeding peanut varieties.
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Affiliation(s)
- Nian Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Weigang Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Bei Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), 502324, Hyderabad, India
| | - Huaiyong Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Xiaojing Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Jianbin Guo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Haiwen Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Dongxin Huai
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Yuning Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Xiaoping Ren
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), 502324, Hyderabad, India
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China.
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Nayak SN, Hebbal V, Bharati P, Nadaf HL, Naidu GK, Bhat RS. Profiling of Nutraceuticals and Proximates in Peanut Genotypes Differing for Seed Coat Color and Seed Size. Front Nutr 2020; 7:45. [PMID: 32351969 PMCID: PMC7174653 DOI: 10.3389/fnut.2020.00045] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 03/23/2020] [Indexed: 11/13/2022] Open
Abstract
A total of 60 genotypes of peanut comprising 46 genotypes selected from ICRISAT mini core collection and 14 elite cultivars with differing kernel color and size were used to profile the nutritional parameters such as proximates (moisture, fat, ash, crude protein, crude fiber, carbohydrate content) and nutraceuticals (total polyphenol content and total antioxidant activity). The genotypes showed varied kernel color ranging from white to purple. Kernel skin color was quantified using colorimetry, and the color parameters were expressed as CIELAB color parameters. In total, nine morphological traits, six yield related traits, eight nutritional traits and eleven color parameters were observed across 60 genotypes. The sixty genotypes were grouped into ten clusters based on the color strength. Among them, Cluster-III with dark red seeds had the maximum fat content and total polyphenol content (TPC). Cluster-VI with light pink colored seeds had high antioxidant activity (AOA) and Cluster-X with white colored seeds had highest moisture and crude protein content. Color strength (K/S) was found to be positively correlated with TPC. Another color parameter, redness/greenness (a*) was found to be positively correlated with AOA. However, seed size was positively correlated with the crude protein content, but not with any other nutritional traits under study. The population studies based on the genotypic data indicated two distinct groups pertaining to botanical types of peanut. The marker-trait association (MTA) using single marker analysis indicated 75 major MTAs for most of the nutritional traits except for moisture content. The markers associated with nutritional parameters and other important yield related traits can further be utilized for genomics-assisted breeding for nutrient-rich peanuts.
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Affiliation(s)
- Spurthi N Nayak
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - Viresh Hebbal
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - Pushpa Bharati
- Department of Food Science and Nutrition, University of Agricultural Sciences, Dharwad, India
| | - Hajisab L Nadaf
- Department of Genetics and Plant Breeding, University of Agricultural Sciences, Dharwad, India
| | - Gopalkrishna K Naidu
- Department of Genetics and Plant Breeding, University of Agricultural Sciences, Dharwad, India
| | - Ramesh S Bhat
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
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Berestovoy MA, Pavlenko OS, Goldenkova-Pavlova IV. Plant Fatty Acid Desaturases: Role in the Life of Plants and Biotechnological Potential. ACTA ACUST UNITED AC 2020. [DOI: 10.1134/s2079086420020024] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Antioxidant and anti-isomerization effects of sesamol and resveratrol on high oleic acid peanut oil. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.109077] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Ojiewo CO, Janila P, Bhatnagar-Mathur P, Pandey MK, Desmae H, Okori P, Mwololo J, Ajeigbe H, Njuguna-Mungai E, Muricho G, Akpo E, Gichohi-Wainaina WN, Variath MT, Radhakrishnan T, Dobariya KL, Bera SK, Rathnakumar AL, Manivannan N, Vasanthi RP, Kumar MVN, Varshney RK. Advances in Crop Improvement and Delivery Research for Nutritional Quality and Health Benefits of Groundnut ( Arachis hypogaea L.). FRONTIERS IN PLANT SCIENCE 2020; 11:29. [PMID: 32153601 PMCID: PMC7046547 DOI: 10.3389/fpls.2020.00029] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 01/13/2020] [Indexed: 05/28/2023]
Abstract
Groundnut is an important global food and oil crop that underpins agriculture-dependent livelihood strategies meeting food, nutrition, and income security. Aflatoxins, pose a major challenge to increased competitiveness of groundnut limiting access to lucrative markets and affecting populations that consume it. Other drivers of low competitiveness include allergens and limited shelf life occasioned by low oleic acid profile in the oil. Thus grain off-takers such as consumers, domestic, and export markets as well as processors need solutions to increase profitability of the grain. There are some technological solutions to these challenges and this review paper highlights advances in crop improvement to enhance groundnut grain quality and nutrient profile for food, nutrition, and economic benefits. Significant advances have been made in setting the stage for marker-assisted allele pyramiding for different aflatoxin resistance mechanisms-in vitro seed colonization, pre-harvest aflatoxin contamination, and aflatoxin production-which, together with pre- and post-harvest management practices, will go a long way in mitigating the aflatoxin menace. A breakthrough in aflatoxin control is in sight with overexpression of antifungal plant defensins, and through host-induced gene silencing in the aflatoxin biosynthetic pathway. Similarly, genomic and biochemical approaches to allergen control are in good progress, with the identification of homologs of the allergen encoding genes and development of monoclonal antibody based ELISA protocol to screen for and quantify major allergens. Double mutation of the allotetraploid homeologous genes, FAD2A and FAD2B, has shown potential for achieving >75% oleic acid as demonstrated among introgression lines. Significant advances have been made in seed systems research to bridge the gap between trait discovery, deployment, and delivery through innovative partnerships and action learning.
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Affiliation(s)
- Chris O. Ojiewo
- Research Program – Genetic Gains, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Nairobi, Kenya
| | - Pasupuleti Janila
- Research Program – Genetic Gains, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Pooja Bhatnagar-Mathur
- Research Program – Genetic Gains, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manish K. Pandey
- Research Program – Genetic Gains, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Haile Desmae
- Research Program – West and Central Africa, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Bamako, Mali
| | - Patrick Okori
- Research Program – Eastern and Southern Africa, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Lilongwe, Malawi
| | - James Mwololo
- Research Program – Eastern and Southern Africa, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Lilongwe, Malawi
| | - Hakeem Ajeigbe
- Research Program – West and Central Africa, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Kano, Nigeria
| | - Esther Njuguna-Mungai
- Research Program – Genetic Gains, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Nairobi, Kenya
| | - Geoffrey Muricho
- Research Program – Genetic Gains, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Nairobi, Kenya
| | - Essegbemon Akpo
- Research Program – Genetic Gains, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Nairobi, Kenya
| | - Wanjiku N. Gichohi-Wainaina
- Research Program – Eastern and Southern Africa, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Lilongwe, Malawi
| | - Murali T. Variath
- Research Program – Genetic Gains, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Thankappan Radhakrishnan
- Indian Council of Agricultural Research - Directorate of Groundnut Research (ICAR-DGR), Junagadh, India
| | - Kantilal L. Dobariya
- Main Oilseeds Research Station, Junagadh Agricultural University (JAU), Junagadh, India
| | - Sandip Kumar Bera
- Indian Council of Agricultural Research - Directorate of Groundnut Research (ICAR-DGR), Junagadh, India
| | | | - Narayana Manivannan
- National Pulses Research Center, Tamil Nadu Agricultural University (TNAU), Pudukkottai, India
| | - Ragur Pandu Vasanthi
- Regional Agricultural Research Station, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, India
| | - Mallela Venkata Nagesh Kumar
- Department of Genetics and Plant Breeding, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Hyderabad, India
| | - Rajeev K. Varshney
- Research Program – Genetic Gains, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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Shasidhar Y, Variath MT, Vishwakarma MK, Manohar SS, Gangurde SS, Sriswathi M, Sudini HK, Dobariya KL, Bera SK, Radhakrishnan T, Pandey MK, Janila P, Varshney RK. Improvement of three popular Indian groundnut varieties for foliar disease resistance and high oleic acid using SSR markers and SNP array in marker-assisted backcrossing. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.cj.2019.07.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Liu N, Guo J, Zhou X, Wu B, Huang L, Luo H, Chen Y, Chen W, Lei Y, Huang Y, Liao B, Jiang H. High-resolution mapping of a major and consensus quantitative trait locus for oil content to a ~ 0.8-Mb region on chromosome A08 in peanut (Arachis hypogaea L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:37-49. [PMID: 31559527 PMCID: PMC6952344 DOI: 10.1007/s00122-019-03438-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 09/17/2019] [Indexed: 05/24/2023]
Abstract
KEY MESSAGE: ddRAD-seq-based high-density genetic map comprising 2595 loci identified a major and consensus QTL with a linked marker in a 0.8-Mb physical interval for oil content in peanut. Enhancing oil content is an important breeding objective in peanut. High-resolution mapping of quantitative trait loci (QTLs) with linked markers could facilitate marker-assisted selection in breeding for target traits. In the present study, a recombined inbred line population (Xuhua 13 × Zhonghua 6) was used to construct a genetic map based on double-digest restriction-site-associated DNA sequencing (ddRAD-seq). The resulting high-density genetic map contained 2595 loci, and spanned a length of 2465.62 cM, with an average distance of 0.95 cM/locus. Seven QTLs for oil content were identified on five linkage groups, including the major and stable QTL qOCA08.1 on chromosome A08 with 10.14-27.19% phenotypic variation explained. The physical interval of qOCA08.1 was further delimited to a ~ 0.8-Mb genomic region where two genes affecting oil synthesis had been annotated. The marker SNPOCA08 was developed targeting the SNP loci associated with oil content and validated in peanut cultivars with diverse oil contents. The major and stable QTL identified in the present study could be further dissected for gene discovery. Furthermore, the tightly linked marker for oil content would be useful in marker-assisted breeding in peanut.
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Affiliation(s)
- Nian Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Jianbin Guo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Xiaojing Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Bei Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Huaiyong Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Yuning Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Weigang Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Yi Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China.
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Steady expression of high oleic acid in peanut bred by marker-assisted backcrossing for fatty acid desaturase mutant alleles and its effect on seed germination along with other seedling traits. PLoS One 2019; 14:e0226252. [PMID: 31830093 PMCID: PMC6910123 DOI: 10.1371/journal.pone.0226252] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 11/22/2019] [Indexed: 12/16/2022] Open
Abstract
Peanut (Arachis hypogaea L.) is an important nutrient-rich food legume and valued for its good quality cooking oil. The fatty acid content is the major determinant of the quality of the edible oil. The oils containing higher monounsaturated fatty acid are preferred for improved shelf life and potential health benefits. Therefore, a high oleic/linoleic fatty acid ratio is the target trait in an advanced breeding program. The two mutant alleles, ahFAD2A (on linkage group a09) and ahFAD2B (on linkage group b09) control fatty acid composition for higher oleic/linoleic ratio in peanut. In the present study, marker-assisted backcrossing was employed for the introgression of two FAD2 mutant alleles from SunOleic95R into the chromosome of ICGV06100, a high oil content peanut breeding line. In the marker-assisted backcrossing-introgression lines, a 97% increase in oleic acid, and a 92% reduction in linoleic acid content was observed in comparison to the recurrent parent. Besides, the oleic/linoleic ratio was increased to 25 with respect to the recurrent parent, which was only 1.2. The most significant outcome was the stable expression of oil-content, oleic acid, linoleic acid, and palmitic acid in the marker-assisted backcrossing-introgression lines over the locations. No significant difference was observed between high oleic and normal oleic in peanuts for seedling traits except germination percentage. In addition, marker-assisted backcrossing-introgression lines exhibited higher yield and resistance to foliar fungal diseases, i.e., late leaf spot and rust.
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Lu Q, Hong Y, Li S, Liu H, Li H, Zhang J, Lan H, Liu H, Li X, Wen S, Zhou G, Varshney RK, Jiang H, Chen X, Liang X. Genome-wide identification of microsatellite markers from cultivated peanut (Arachis hypogaea L.). BMC Genomics 2019; 20:799. [PMID: 31675924 PMCID: PMC6824139 DOI: 10.1186/s12864-019-6148-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 09/29/2019] [Indexed: 12/03/2022] Open
Abstract
Background Microsatellites, or simple sequence repeats (SSRs), represent important DNA variations that are widely distributed across the entire plant genome and can be used to develop SSR markers, which can then be used to conduct genetic analyses and molecular breeding. Cultivated peanut (A. hypogaea L.), an important oil crop worldwide, is an allotetraploid (AABB, 2n = 4× = 40) plant species. Because of its complex genome, genomic marker development has been very challenging. However, sequencing of cultivated peanut genome allowed us to develop genomic markers and construct a high-density physical map. Results A total of 8,329,496 SSRs were identified, including 3,772,653, 4,414,961, and 141,882 SSRs that were distributed in subgenome A, B, and nine scaffolds, respectively. Based on the flanking sequences of the identified SSRs, a total of 973,984 newly developed SSR markers were developed in subgenome A (462,267), B (489,394), and nine scaffolds (22,323), with an average density of 392.45 markers per Mb. In silico PCR evaluation showed that an average of 88.32% of the SSR markers generated only one in silico-specific product in two tetraploid A. hypogaea varieties, Tifrunner and Shitouqi. A total of 39,599 common SSR markers were identified among the two A. hypogaea varieties and two progenitors, A. duranensis and A. ipaensis. Additionally, an amplification effectiveness of 44.15% was observed by real PCR validation. Moreover, a total of 1276 public SSR loci were integrated with the newly developed SSR markers. Finally, a previously known leaf spot quantitative trait locus (QTL), qLLS_T13_A05_7, was determined to be in a 1.448-Mb region on chromosome A05. In this region, a total of 819 newly developed SSR markers were located and 108 candidate genes were detected. Conclusions The availability of these newly developed and public SSR markers both provide a large number of molecular markers that could potentially be used to enhance the process of trait genetic analyses and improve molecular breeding strategies for cultivated peanut.
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Affiliation(s)
- Qing Lu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory for Crop Genetic Improvement, Guangzhou, 510640, China
| | - Yanbin Hong
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory for Crop Genetic Improvement, Guangzhou, 510640, China
| | - Shaoxiong Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory for Crop Genetic Improvement, Guangzhou, 510640, China
| | - Hao Liu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory for Crop Genetic Improvement, Guangzhou, 510640, China
| | - Haifen Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory for Crop Genetic Improvement, Guangzhou, 510640, China
| | - Jianan Zhang
- MolBreeding Biotechnology Co., Ltd., Shijiazhuang, China
| | - Haofa Lan
- MolBreeding Biotechnology Co., Ltd., Shijiazhuang, China
| | - Haiyan Liu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory for Crop Genetic Improvement, Guangzhou, 510640, China
| | - Xingyu Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory for Crop Genetic Improvement, Guangzhou, 510640, China
| | - Shijie Wen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory for Crop Genetic Improvement, Guangzhou, 510640, China
| | - Guiyuan Zhou
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory for Crop Genetic Improvement, Guangzhou, 510640, China
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Xiaoping Chen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory for Crop Genetic Improvement, Guangzhou, 510640, China.
| | - Xuanqiang Liang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory for Crop Genetic Improvement, Guangzhou, 510640, China.
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Desmae H, Janila P, Okori P, Pandey MK, Motagi BN, Monyo E, Mponda O, Okello D, Sako D, Echeckwu C, Oteng‐Frimpong R, Miningou A, Ojiewo C, Varshney RK. Genetics, genomics and breeding of groundnut ( Arachis hypogaea L.). PLANT BREEDING = ZEITSCHRIFT FUR PFLANZENZUCHTUNG 2019; 138:425-444. [PMID: 31598026 PMCID: PMC6774334 DOI: 10.1111/pbr.12645] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 04/10/2018] [Accepted: 07/13/2018] [Indexed: 05/04/2023]
Abstract
Groundnut is an important food and oil crop in the semiarid tropics, contributing to household food consumption and cash income. In Asia and Africa, yields are low attributed to various production constraints. This review paper highlights advances in genetics, genomics and breeding to improve the productivity of groundnut. Genetic studies concerning inheritance, genetic variability and heritability, combining ability and trait correlations have provided a better understanding of the crop's genetics to develop appropriate breeding strategies for target traits. Several improved lines and sources of variability have been identified or developed for various economically important traits through conventional breeding. Significant advances have also been made in groundnut genomics including genome sequencing, marker development and genetic and trait mapping. These advances have led to a better understanding of the groundnut genome, discovery of genes/variants for traits of interest and integration of marker-assisted breeding for selected traits. The integration of genomic tools into the breeding process accompanied with increased precision of yield trialing and phenotyping will increase the efficiency and enhance the genetic gain for release of improved groundnut varieties.
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Affiliation(s)
- Haile Desmae
- International Crop Research Institute for the Semi‐Arid Tropics (ICRISAT)BamakoMali
| | | | | | | | | | | | - Omari Mponda
- Division of Research and Development (DRD)Tanzania Agricultural Research Institute (TARI) ‐ NaliendeleMtwaraTanzania
| | - David Okello
- National Agricultural Research Organization (NARO)EntebbeUganda
| | | | | | | | - Amos Miningou
- Institut National d'Environnement et de Recherches Agricoles (INERA)OuagadougouBurkina Faso
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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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Huang B, Qi F, Sun Z, Miao L, Zhang Z, Liu H, Fang Y, Dong W, Tang F, Zheng Z, Zhang X. Marker-assisted backcrossing to improve seed oleic acid content in four elite and popular peanut ( Arachis hypogaea L.) cultivars with high oil content. BREEDING SCIENCE 2019; 69:234-243. [PMID: 31481832 PMCID: PMC6711728 DOI: 10.1270/jsbbs.18107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 01/02/2019] [Indexed: 05/08/2023]
Abstract
High oleic acid composition is an important determinant of seed quality in peanut (Arachis hypogaea) in regard to its nutritional benefits for human health and prolonged shelf-life for peanut products. To improve the oleic acid content of popular peanut cultivars in China, four peanut cultivars of different market types were hybridized with high-oleic-acid donors and backcrossed for four generations as recurrent parents using fad2 marker-assisted backcross selection. Seed quality traits in advanced generations derived by selfing were assessed using near-infrared reflectance spectroscopy for detection of oleic acid and Kompetitive allele-specific PCR (KASP) screening of fad2 mutant markers. Twenty-four high-oleic-acid lines of BC4F4 and BC4F5 populations, with morphological features and agronomic traits similar to those of the recurrent parents, were obtained within 5 years. The genetic backgrounds of BC4F5 lines were estimated using the KASP assay, which revealed the genetic background recovery rate was 79.49%-92.31%. The superior lines raised are undergoing a multi-location test for cultivar registration and release. To our knowledge, this is the first application of single nucleotide polymorphism markers based on the high-throughput and cost-effective KASP assay for detection of fad2 mutations and genetic background evaluation in a peanut breeding program.
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Affiliation(s)
- Bingyan Huang
- Key Laboratory of Oil Crops in Huanghuaihai Plains, Industrial Crops Research Institute, Henan Academy of Agricultural Sciences,
116 Huayuan Road, 450002, Zhengzhou,
China
| | - Feiyan Qi
- Key Laboratory of Oil Crops in Huanghuaihai Plains, Industrial Crops Research Institute, Henan Academy of Agricultural Sciences,
116 Huayuan Road, 450002, Zhengzhou,
China
| | - Ziqi Sun
- Henan Provincial Key Laboratory for Oil Crops Improvement,
116 Huayuan Road, 450002, Zhengzhou,
China
| | - Lijuan Miao
- Key Laboratory of Oil Crops in Huanghuaihai Plains, Industrial Crops Research Institute, Henan Academy of Agricultural Sciences,
116 Huayuan Road, 450002, Zhengzhou,
China
| | - Zhongxin Zhang
- Key Laboratory of Oil Crops in Huanghuaihai Plains, Industrial Crops Research Institute, Henan Academy of Agricultural Sciences,
116 Huayuan Road, 450002, Zhengzhou,
China
| | - Hua Liu
- Henan Provincial Key Laboratory for Oil Crops Improvement,
116 Huayuan Road, 450002, Zhengzhou,
China
| | - Yuanjin Fang
- Key Laboratory of Oil Crops in Huanghuaihai Plains, Industrial Crops Research Institute, Henan Academy of Agricultural Sciences,
116 Huayuan Road, 450002, Zhengzhou,
China
| | - Wenzhao Dong
- Key Laboratory of Oil Crops in Huanghuaihai Plains, Industrial Crops Research Institute, Henan Academy of Agricultural Sciences,
116 Huayuan Road, 450002, Zhengzhou,
China
| | - Fengshou Tang
- Key Laboratory of Oil Crops in Huanghuaihai Plains, Industrial Crops Research Institute, Henan Academy of Agricultural Sciences,
116 Huayuan Road, 450002, Zhengzhou,
China
| | - Zheng Zheng
- Key Laboratory of Oil Crops in Huanghuaihai Plains, Industrial Crops Research Institute, Henan Academy of Agricultural Sciences,
116 Huayuan Road, 450002, Zhengzhou,
China
| | - Xinyou Zhang
- Key Laboratory of Oil Crops in Huanghuaihai Plains, Industrial Crops Research Institute, Henan Academy of Agricultural Sciences,
116 Huayuan Road, 450002, Zhengzhou,
China
- Corresponding author (e-mail: )
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Nawade B, Mishra GP, Radhakrishnan T, Sangh C, Dobariya JR, Kundu R. Development of high oleic peanut lines through marker-assisted introgression of mutant ahFAD2 alleles and its fatty acid profiles under open-field and controlled conditions. 3 Biotech 2019; 9:243. [PMID: 31168436 DOI: 10.1007/s13205-019-1774-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 05/20/2019] [Indexed: 12/13/2022] Open
Abstract
Peanut is one of the most important oilseed crops grown worldwide. In this study, the mutant ahFAD2 alleles conferring high oleic (HO) content are introgressed into an elite Indian cultivar GPBD4 which is also resistant to the foliar fungal diseases like rust and late leaf spot (LLS). The allele-specific PCR (AS-PCR) and cleaved amplified polymorphic sequences (CAPS) assays were used for the marker-assisted backcross (MABC) approach and 64 HO introgression lines (ILs) were generated. These ILs were tested for the FA compositions under the glasshouse and field conditions. The oleic acid and linoleic acid contents in the ILs were recorded to be between 68.94-82.33% and 1.74-10.87%, respectively, under glasshouse and 67.04-81.71% and 2.00-15.66%, respectively, under field conditions. The increase in the oleic acid content of the ILs over its recurrent parent (RP) was recorded to the tune of 28.78-53.80% and 33.70-62.96% under glasshouse and field conditions, respectively, indicating the stable expression of ahFAD2B gene in two different environments. On the contrary, linoleic acid showed 56.47-93.03% and 40.02-92.34% reduction in the ILs over its RP under glasshouse and field conditions, respectively. These ILs with a healthy FA profile can meet not only the nutritional requirements of a health-conscious society but also the industrial demands for better shelf life of oil and its products.
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Affiliation(s)
- Bhagwat Nawade
- 1Department of Biotechnology, Directorate of Groundnut Research, Junagadh, Gujarat 362001 India
- 2Department of Biosciences, Saurashtra University, Rajkot, 360005 India
| | - Gyan P Mishra
- 1Department of Biotechnology, Directorate of Groundnut Research, Junagadh, Gujarat 362001 India
- 3Division of Genetics, Indian Agricultural Research Institute, Pusa, New Delhi, 110012 India
| | - T Radhakrishnan
- 1Department of Biotechnology, Directorate of Groundnut Research, Junagadh, Gujarat 362001 India
| | - Chandramohan Sangh
- 1Department of Biotechnology, Directorate of Groundnut Research, Junagadh, Gujarat 362001 India
| | - J R Dobariya
- 1Department of Biotechnology, Directorate of Groundnut Research, Junagadh, Gujarat 362001 India
| | - Rahul Kundu
- 2Department of Biosciences, Saurashtra University, Rajkot, 360005 India
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The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication. Nat Genet 2019; 51:865-876. [PMID: 31043757 PMCID: PMC7188672 DOI: 10.1038/s41588-019-0402-2] [Citation(s) in RCA: 282] [Impact Index Per Article: 56.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 03/22/2019] [Indexed: 11/09/2022]
Abstract
High oil and protein content make tetraploid peanut a leading oil and food legume. Here we report a high-quality peanut genome sequence, comprising 2.54 Gb with 20 pseudomolecules and 83,709 protein-coding gene models. We characterize gene functional groups implicated in seed size evolution, seed oil content, disease resistance and symbiotic nitrogen fixation. The peanut B subgenome has more genes and general expression dominance, temporally associated with long-terminal-repeat expansion in the A subgenome that also raises questions about the A-genome progenitor. The polyploid genome provided insights into the evolution of Arachis hypogaea and other legume chromosomes. Resequencing of 52 accessions suggests that independent domestications formed peanut ecotypes. Whereas 0.42-0.47 million years ago (Ma) polyploidy constrained genetic variation, the peanut genome sequence aids mapping and candidate-gene discovery for traits such as seed size and color, foliar disease resistance and others, also providing a cornerstone for functional genomics and peanut improvement.
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Wu P, Zhang L, Feng T, Lu W, Zhao H, Li J, Lü S. A Conserved Glycine Is Identified to be Essential for Desaturase Activity of IpFAD2s by Analyzing Natural Variants from Idesia polycarpa. Int J Mol Sci 2018; 19:E3932. [PMID: 30544564 PMCID: PMC6321622 DOI: 10.3390/ijms19123932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 12/02/2018] [Accepted: 12/05/2018] [Indexed: 11/25/2022] Open
Abstract
High amounts of polyunsaturated fatty acids (PUFAs) in vegetable oil are not desirable for biodiesel or food oil due to their lower oxidative stability. The oil from Idesia polycarpa fruit contains 65⁻80% (mol%) linoleic acid (C18:2). Therefore, development of Idesia polycarpa cultivars with low PUFAs is highly desirable for Idesia polycarpa oil quality. Fatty acid desaturase 2 (FAD2) is the key enzyme converting oleic acid (C18:1) to C18:2. We isolated four FAD2 homologs from the fruit of Idesia polycarpa. Yeast transformed with IpFAD2-1, IpFAD2-2 and IpFAD2-3 can generate appreciable amounts of hexadecadienoic acid (C16:2) and C18:2, which are not present in wild-type yeast cells, revealing that the proteins encoded by these genes have Δ12 desaturase activity. Only trace amounts of C18:2 and little C16:2 were detected in yeast cells transformed with IpFAD2-4, suggesting IpFAD2-4 displays low activity. We also analyzed the activity of several FAD2 natural variants of Idesia polycarpa in yeast and found that a highly conserved Gly376 substitution caused the markedly reduced products catalyzed by IpFAD2-3. This glycine is also essential for the activity of IpFAD2-1 and IpFAD2-2, but its replacement in other plant FAD2 proteins displays different effects on the desaturase activity, suggesting its distinct roles across plant FAD2s proteins.
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Affiliation(s)
- Pan Wu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Lingling Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
| | - Tao Feng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
| | - Wenying Lu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Huayan Zhao
- Applied Biotechnology Center, Wuhan Institute of Bioengineering, Wuhan 430415, China.
| | - Jianzhong Li
- Tianjin Garrison hangu farm, Tianjin 300480, China.
| | - Shiyou Lü
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China.
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45
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Khera P, Pandey MK, Mallikarjuna N, Sriswathi M, Roorkiwal M, Janila P, Sharma S, Shilpa K, Sudini H, Guo B, Varshney RK. Genetic imprints of domestication for disease resistance, oil quality, and yield component traits in groundnut (Arachis hypogaea L.). Mol Genet Genomics 2018; 294:365-378. [PMID: 30467595 DOI: 10.1007/s00438-018-1511-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 11/08/2018] [Indexed: 11/29/2022]
Abstract
Ploidy difference between wild Arachis species and cultivated genotypes hinder transfer of useful alleles for agronomically important traits. To overcome this genetic barrier, two synthetic tetraploids, viz., ISATGR 1212 (A. duranensis ICG 8123 × A. ipaensis ICG 8206) and ISATGR 265-5A (A. kempff-mercadoi ICG 8164 × A. hoehnei ICG 8190), were used to generate two advanced backcross (AB) populations. The AB-populations, namely, AB-pop1 (ICGV 91114 × ISATGR 1212) and AB-pop2, (ICGV 87846 × ISATGR 265-5A) were genotyped with DArT and SSR markers. Genetic maps were constructed for AB-pop1 and AB-pop2 populations with 258 loci (1415.7 cM map length and map density of 5.5 cM/loci) and 1043 loci (1500.8 cM map length with map density of 1.4 cM/loci), respectively. Genetic analysis identified large number of wild segments in the population and provided a good source of diversity in these populations. Phenotyping of these two populations identified several introgression lines with good agronomic, oil quality, and disease resistance traits. Quantitative trait locus (QTL) analysis showed that the wild genomic segments contributed favourable alleles for foliar disease resistance while cultivated genomic segments mostly contributed favourable alleles for oil quality and yield component traits. These populations, after achieving higher stability, will be useful resource for genetic mapping and QTL discovery for wild species segments in addition to using population progenies in breeding program for diversifying the gene pool of cultivated groundnut.
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Affiliation(s)
- Pawan Khera
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Nalini Mallikarjuna
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manda Sriswathi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manish Roorkiwal
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Pasupuleti Janila
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Shivali Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Krishna Shilpa
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Harikishan Sudini
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Baozhu Guo
- Crop Protection and Management Research Unit, US Department of Agriculture-Agricultural Research Service, Tifton, USA
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
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46
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Agarwal G, Clevenger J, Pandey MK, Wang H, Shasidhar Y, Chu Y, Fountain JC, Choudhary D, Culbreath AK, Liu X, Huang G, Wang X, Deshmukh R, Holbrook CC, Bertioli DJ, Ozias‐Akins P, Jackson SA, Varshney RK, Guo B. High-density genetic map using whole-genome resequencing for fine mapping and candidate gene discovery for disease resistance in peanut. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1954-1967. [PMID: 29637729 PMCID: PMC6181220 DOI: 10.1111/pbi.12930] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/28/2018] [Accepted: 03/25/2018] [Indexed: 05/04/2023]
Abstract
Whole-genome resequencing (WGRS) of mapping populations has facilitated development of high-density genetic maps essential for fine mapping and candidate gene discovery for traits of interest in crop species. Leaf spots, including early leaf spot (ELS) and late leaf spot (LLS), and Tomato spotted wilt virus (TSWV) are devastating diseases in peanut causing significant yield loss. We generated WGRS data on a recombinant inbred line population, developed a SNP-based high-density genetic map, and conducted fine mapping, candidate gene discovery and marker validation for ELS, LLS and TSWV. The first sequence-based high-density map was constructed with 8869 SNPs assigned to 20 linkage groups, representing 20 chromosomes, for the 'T' population (Tifrunner × GT-C20) with a map length of 3120 cM and an average distance of 1.45 cM. The quantitative trait locus (QTL) analysis using high-density genetic map and multiple season phenotyping data identified 35 main-effect QTLs with phenotypic variation explained (PVE) from 6.32% to 47.63%. Among major-effect QTLs mapped, there were two QTLs for ELS on B05 with 47.42% PVE and B03 with 47.38% PVE, two QTLs for LLS on A05 with 47.63% and B03 with 34.03% PVE and one QTL for TSWV on B09 with 40.71% PVE. The epistasis and environment interaction analyses identified significant environmental effects on these traits. The identified QTL regions had disease resistance genes including R-genes and transcription factors. KASP markers were developed for major QTLs and validated in the population and are ready for further deployment in genomics-assisted breeding in peanut.
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Affiliation(s)
- Gaurav Agarwal
- Crop Protection and Management Research UnitUSDA‐ARSTiftonGAUSA
- Department of Plant PathologyUniversity of GeorgiaTiftonGAUSA
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Josh Clevenger
- Center for Applied Genetic TechnologiesMars Wrigley ConfectioneryAthensGAUSA
- Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGAUSA
| | - Manish K. Pandey
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Hui Wang
- Crop Protection and Management Research UnitUSDA‐ARSTiftonGAUSA
- Department of Plant PathologyUniversity of GeorgiaTiftonGAUSA
| | - Yaduru Shasidhar
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Ye Chu
- Department of Horticulture and Institute of Plant Breeding & GenomicsUniversity of GeorgiaTiftonGAUSA
| | - Jake C. Fountain
- Crop Protection and Management Research UnitUSDA‐ARSTiftonGAUSA
- Department of Plant PathologyUniversity of GeorgiaTiftonGAUSA
| | - Divya Choudhary
- Crop Protection and Management Research UnitUSDA‐ARSTiftonGAUSA
- Department of Plant PathologyUniversity of GeorgiaTiftonGAUSA
| | | | | | | | - Xingjun Wang
- Shandong Academy of Agricultural SciencesBiotechnology Research CenterJinanChina
| | | | | | - David J. Bertioli
- Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGAUSA
| | - Peggy Ozias‐Akins
- Department of Horticulture and Institute of Plant Breeding & GenomicsUniversity of GeorgiaTiftonGAUSA
| | - Scott A. Jackson
- Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGAUSA
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Baozhu Guo
- Crop Protection and Management Research UnitUSDA‐ARSTiftonGAUSA
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47
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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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48
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Wen S, Liu H, Li X, Chen X, Hong Y, Li H, Lu Q, Liang X. TALEN-mediated targeted mutagenesis of fatty acid desaturase 2 (FAD2) in peanut (Arachis hypogaea L.) promotes the accumulation of oleic acid. PLANT MOLECULAR BIOLOGY 2018; 97:177-185. [PMID: 29700675 DOI: 10.1007/s11103-018-0731-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 04/16/2018] [Indexed: 06/08/2023]
Abstract
A first creation of high oleic acid peanut varieties by using transcription activator-like effecter nucleases (TALENs) mediated targeted mutagenesis of Fatty Acid Desaturase 2 (FAD2). Transcription activator like effector nucleases (TALENs), which allow the precise editing of DNA, have already been developed and applied for genome engineering in diverse organisms. However, they are scarcely used in higher plant study and crop improvement, especially in allopolyploid plants. In the present study, we aimed to create targeted mutagenesis by TALENs in peanut. Targeted mutations in the conserved coding sequence of Arachis hypogaea fatty acid desaturase 2 (AhFAD2) were created by TALENs. Genetic stability of AhFAD2 mutations was identified by DNA sequencing in up to 9.52 and 4.11% of the regeneration plants at two different targeted sites, respectively. Mutation frequencies among AhFAD2 mutant lines were significantly correlated to oleic acid accumulation. Genetically, stable individuals of positive mutant lines displayed a 0.5-2 fold increase in the oleic acid content compared with non-transgenic controls. This finding suggested that TALEN-mediated targeted mutagenesis could increase the oleic acid content in edible peanut oil. Furthermore, this was the first report on peanut genome editing event, and the obtained high oleic mutants could serve for peanut breeding project.
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Affiliation(s)
- Shijie Wen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China
| | - Hao Liu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China
| | - Xingyu Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China
| | - Xiaoping Chen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China
| | - Yanbin Hong
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China
| | - Haifen Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China
| | - Qing Lu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China
| | - Xuanqiang Liang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China.
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49
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Hu XH, Zhang SZ, Miao HR, Cui FG, Shen Y, Yang WQ, Xu TT, Chen N, Chi XY, Zhang ZM, Chen J. High-Density Genetic Map Construction and Identification of QTLs Controlling Oleic and Linoleic Acid in Peanut using SLAF-seq and SSRs. Sci Rep 2018; 8:5479. [PMID: 29615772 PMCID: PMC5883025 DOI: 10.1038/s41598-018-23873-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 03/20/2018] [Indexed: 11/08/2022] Open
Abstract
The cultivated peanut, A. hypogaea L., is an important oil and food crop globally.High-density genetic linkage mapping is a valuable and effective method for exploring complex quantitative traits. In this context, a recombinant inbred line (RIL) of 146 lines was developed by crossing Huayu28 and P76. We developed 433,679 high-quality SLAFs, of which 29,075 were polymorphic. 4,817 SLAFs were encoded and grouped into different segregation patterns. A high-resolution genetic map containing 2,334 markers (68 SSRs and 2,266 SNPs) on 20 linkage groups (LGs) spanning 2586.37 cM was constructed for peanut. The average distance between adjacent markers was 2.25 cM. Based on phenotyping in seven environments, QTLs for oleic acid (C18:1), linoleic acid (C18:2) and the ratio of oleic acid to linoleic acid (O/L) were identified and positioned on linkage groups A03, A04, A09, B09 and B10. Marker2575339 and Marker2379598 in B09 were associated with C18:1, C18:2 and O/L in seven environments, Marker4391589 and Marker4463600 in A09 were associated with C18:1, C18:2 and O/L in six environments. This map exhibits high resolution and accuracy, which will facilitate QTL discovery for essential agronomic traits in peanut.
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Affiliation(s)
- X H Hu
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China
| | - S Z Zhang
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China
| | - H R Miao
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China
| | - F G Cui
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China
| | - Y Shen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P.R. China
| | - W Q Yang
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China
| | - T T Xu
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China
| | - N Chen
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China
| | - X Y Chi
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China
| | - Z M Zhang
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China
| | - J Chen
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China.
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50
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Wang X, Xu P, Yin L, Ren Y, Li S, Shi Y, Alcock TD, Xiong Q, Qian W, Chi X, Pandey MK, Varshney RK, Yuan M. Genomic and Transcriptomic Analysis Identified Gene Clusters and Candidate Genes for Oil Content in Peanut (Arachis hypogaea L.). PLANT MOLECULAR BIOLOGY REPORTER 2018; 36:518-529. [PMID: 30100671 PMCID: PMC6061501 DOI: 10.1007/s11105-018-1088-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Peanut (Arachis hypogaea), a major source of vegetable oil in many Asian countries, has become an integral part of human diet globally due to its high nutritional properties and option to consume in different forms. In order to meet the demand of vegetable oil, many peanut breeding programs of China have intensified their efforts in increasing oil content in newly bred varieties for reducing the import of edible oils in China. In this context, transcriptome sequencing data generated on 49 peanut cultivars were analyzed to identify candidate genes and develop molecular markers for seed oil content across multiple environments. Transcriptome analysis identified 5458 differentially expressed genes (DEGs) including 2243 positive DEGs and 3215 negative DEGs involved in oil synthesis process. Genome-wide association study identified 48 significant insertion/deletion (InDel) markers associated with seed oil content across five environments. A comparative genomics and transcriptomics analysis detected a total of 147 common gene clusters located in 17 chromosomes. Interestingly, an InDel cluster associated with seed oil content on A03 chromosome was detected in three different environments. Candidate genes identified on A03 form a haplotype, in which variable alleles were found to be different in oil content in an independent population. This locus is important for understanding the genetic control of peanut oil content and may be useful for marker-assisted selection in peanut breeding programs.
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Affiliation(s)
- Xiaohua Wang
- Key Laboratory for Peanut Biology, Genetics and Breeding, Ministry of Agriculture, Shandong Peanut Research Institute, Qingdao, 266100 China
| | - Ping Xu
- Key Laboratory for Peanut Biology, Genetics and Breeding, Ministry of Agriculture, Shandong Peanut Research Institute, Qingdao, 266100 China
| | - Liang Yin
- Key Laboratory for Peanut Biology, Genetics and Breeding, Ministry of Agriculture, Shandong Peanut Research Institute, Qingdao, 266100 China
| | - Yan Ren
- Key Laboratory for Peanut Biology, Genetics and Breeding, Ministry of Agriculture, Shandong Peanut Research Institute, Qingdao, 266100 China
| | - Shuangling Li
- Key Laboratory for Peanut Biology, Genetics and Breeding, Ministry of Agriculture, Shandong Peanut Research Institute, Qingdao, 266100 China
| | - Yanmao Shi
- Key Laboratory for Peanut Biology, Genetics and Breeding, Ministry of Agriculture, Shandong Peanut Research Institute, Qingdao, 266100 China
| | - Thomas D. Alcock
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - Qing Xiong
- College of Computer and Information Science, Southwest University, Chongqing, 400715 China
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Xiaoyuan Chi
- Key Laboratory for Peanut Biology, Genetics and Breeding, Ministry of Agriculture, Shandong Peanut Research Institute, Qingdao, 266100 China
| | - Manish K. Pandey
- International Crops Research Institute for Semi-Arid Tropics (ICRISAT), Hyderabad, 502324 India
| | - Rajeev K. Varshney
- International Crops Research Institute for Semi-Arid Tropics (ICRISAT), Hyderabad, 502324 India
| | - Mei Yuan
- Key Laboratory for Peanut Biology, Genetics and Breeding, Ministry of Agriculture, Shandong Peanut Research Institute, Qingdao, 266100 China
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