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Wei W, Li S, Li P, Yu K, Fan G, Wang Y, Zhao F, Zhang X, Feng X, Shi G, Zhang W, Song G, Dan W, Wang F, Zhang Y, Li X, Wang D, Zhang W, Pei J, Wang X, Zhao Z. QTL analysis of important agronomic traits and metabolites in foxtail millet ( Setaria italica) by RIL population and widely targeted metabolome. FRONTIERS IN PLANT SCIENCE 2023; 13:1035906. [PMID: 36704173 PMCID: PMC9872001 DOI: 10.3389/fpls.2022.1035906] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
As a bridge between genome and phenotype, metabolome is closely related to plant growth and development. However, the research on the combination of genome, metabolome and multiple agronomic traits in foxtail millet (Setaria italica) is insufficient. Here, based on the linkage analysis of 3,452 metabolites via with high-quality genetic linkage maps, we detected a total of 1,049 metabolic quantitative trait loci (mQTLs) distributed in 11 hotspots, and 28 metabolite-related candidate genes were mined from 14 mQTLs. In addition, 136 single-environment phenotypic QTL (pQTLs) related to 63 phenotypes were identified by linkage analysis, and there were 12 hotspots on these pQTLs. We futher dissected 39 candidate genes related to agronomic traits through metabolite-phenotype correlation and gene function analysis, including Sd1 semidwarf gene, which can affect plant height by regulating GA synthesis. Combined correlation network and QTL analysis, we found that flavonoid-lignin pathway maybe closely related to plant architecture and yield in foxtail millet. For example, the correlation coefficient between apigenin 7-rutinoside and stem diameter reached 0.98, and they were co-located at 41.33-44.15 Mb of chromosome 5, further gene function analysis revealed that 5 flavonoid pathway genes, as well as Sd1, were located in this interval . Therefore, the correlation and co-localization between flavonoid-lignins and plant architecture may be due to the close linkage of their regulatory genes in millet. Besides, we also found that a combination of genomic and metabolomic for BLUP analysis can better predict plant agronomic traits than genomic or metabolomic data, independently. In conclusion, the combined analysis of mQTL and pQTL in millet have linked genetic, metabolic and agronomic traits, and is of great significance for metabolite-related molecular assisted breeding.
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Affiliation(s)
- Wei Wei
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Shuangdong Li
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Peiyu Li
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Kuohai Yu
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Guangyu Fan
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Yixiang Wang
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Fang Zhao
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Xiaolei Zhang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Xiaolei Feng
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Gaolei Shi
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Weiqin Zhang
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Guoliang Song
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Wenhan Dan
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Feng Wang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Yali Zhang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Xinru Li
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Dequan Wang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Wenying Zhang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Jingjing Pei
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Xiaoming Wang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Zhihai Zhao
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
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Liu W, Chen Z, Jiang S, Wang Y, Fang H, Zhang Z, Chen X, Wang N. Research Progress on Genetic Basis of Fruit Quality Traits in Apple ( Malus × domestica). FRONTIERS IN PLANT SCIENCE 2022; 13:918202. [PMID: 35909724 PMCID: PMC9330611 DOI: 10.3389/fpls.2022.918202] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/23/2022] [Indexed: 06/01/2023]
Abstract
Identifying the genetic variation characteristics of phenotypic traits is important for fruit tree breeding. During the long-term evolution of fruit trees, gene recombination and natural mutation have resulted in a high degree of heterozygosity. Apple (Malus × domestica Borkh.) shows strong ecological adaptability and is widely cultivated, and is among the most economically important fruit crops worldwide. However, the high level of heterozygosity and large genome of apple, in combination with its perennial life history and long juvenile phase, complicate investigation of the genetic basis of fruit quality traits. With continuing augmentation in the apple genomic resources available, in recent years important progress has been achieved in research on the genetic variation of fruit quality traits. This review focuses on summarizing recent genetic studies on apple fruit quality traits, including appearance, flavor, nutritional, ripening, and storage qualities. In addition, we discuss the mapping of quantitative trait loci, screening of molecular markers, and mining of major genes associated with fruit quality traits. The overall aim of this review is to provide valuable insights into the mechanisms of genetic variation and molecular breeding of important fruit quality traits in apple.
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Affiliation(s)
- Wenjun Liu
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Tai’an, China
| | - Zijing Chen
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Tai’an, China
| | - Shenghui Jiang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Yicheng Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Hongcheng Fang
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, College of Forestry, Shandong Agricultural University, Tai’an, China
| | - Zongying Zhang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Tai’an, China
| | - Xuesen Chen
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Tai’an, China
| | - Nan Wang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Tai’an, China
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Li J, Yan G, Duan X, Zhang K, Zhang X, Zhou Y, Wu C, Zhang X, Tan S, Hua X, Wang J. Research Progress and Trends in Metabolomics of Fruit Trees. FRONTIERS IN PLANT SCIENCE 2022; 13:881856. [PMID: 35574069 PMCID: PMC9106391 DOI: 10.3389/fpls.2022.881856] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/01/2022] [Indexed: 06/15/2023]
Abstract
Metabolomics is an indispensable part of modern systems biotechnology, applied in the diseases' diagnosis, pharmacological mechanism, and quality monitoring of crops, vegetables, fruits, etc. Metabolomics of fruit trees has developed rapidly in recent years, and many important research results have been achieved in combination with transcriptomics, genomics, proteomics, quantitative trait locus (QTL), and genome-wide association study (GWAS). These research results mainly focus on the mechanism of fruit quality formation, metabolite markers of special quality or physiological period, the mechanism of fruit tree's response to biotic/abiotic stress and environment, and the genetics mechanism of fruit trait. According to different experimental purposes, different metabolomic strategies could be selected, such as targeted metabolomics, non-targeted metabolomics, pseudo-targeted metabolomics, and widely targeted metabolomics. This article presents metabolomics strategies, key techniques in metabolomics, main applications in fruit trees, and prospects for the future. With the improvement of instruments, analysis platforms, and metabolite databases and decrease in the cost of the experiment, metabolomics will prompt the fruit tree research to achieve more breakthrough results.
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Affiliation(s)
- Jing Li
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin, China
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, China
| | - Guohua Yan
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, China
| | - Xuwei Duan
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, China
| | - Kaichun Zhang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, China
| | - Xiaoming Zhang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, China
| | - Yu Zhou
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, China
| | - Chuanbao Wu
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, China
| | - Xin Zhang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, China
| | - Shengnan Tan
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin, China
- Analysis and Test Center, Northeast Forestry University, Harbin, China
| | - Xin Hua
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Jing Wang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, China
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An Insight into Abiotic Stress and Influx Tolerance Mechanisms in Plants to Cope in Saline Environments. BIOLOGY 2022; 11:biology11040597. [PMID: 35453796 PMCID: PMC9028878 DOI: 10.3390/biology11040597] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/27/2022] [Accepted: 04/11/2022] [Indexed: 12/20/2022]
Abstract
Simple Summary This review focuses on plant growth and development harmed by abiotic stress, primarily salt stress. Salt stress raises the intracellular osmotic pressure, leading to hazardous sodium buildup. Plants react to salt stress signals by regulating ion homeostasis, activating the osmotic stress pathway, modulating plant hormone signaling, and altering cytoskeleton dynamics and cell wall composition. Understanding the processes underlying these physiological and biochemical responses to salt stress could lead to more effective agricultural crop yield measures. In this review, researchers outline recent advances in plant salt stress control. The study of plant salt tolerance processes is essential, both theoretically and practically, to improve agricultural output, produce novel salt-tolerant cultivars, and make full use of saline soil. Based on past research, this paper discusses the adverse effects of salt stress on plants, including photosynthesis suppression, ion homeostasis disturbance, and membrane peroxidation. The authors have also covered the physiological mechanisms of salt tolerance, such as the scavenging of reactive oxygen species and osmotic adjustment. This study further identifies specific salt stress-responsive mechanisms linked to physiological systems. Based on previous studies, this article reviews the current methodologies and techniques for improving plant salt tolerance. Overall, it is hoped that the above-mentioned points will impart helpful background information for future agricultural and crop plant production. Abstract Salinity is significant abiotic stress that affects the majority of agricultural, irrigated, and cultivated land. It is an issue of global importance, causing many socio-economic problems. Salt stress mainly occurs due to two factors: (1) soil type and (2) irrigation water. It is a major environmental constraint, limiting crop growth, plant productivity, and agricultural yield. Soil salinity is a major problem that considerably distorts ecological habitats in arid and semi-arid regions. Excess salts in the soil affect plant nutrient uptake and osmotic balance, leading to osmotic and ionic stress. Plant adaptation or tolerance to salinity stress involves complex physiological traits, metabolic pathways, the production of enzymes, compatible solutes, metabolites, and molecular or genetic networks. Different plant species have different salt overly sensitive pathways and high-affinity K+ channel transporters that maintain ion homeostasis. However, little progress has been made in developing salt-tolerant crop varieties using different breeding approaches. This review highlights the interlinking of plant morpho-physiological, molecular, biochemical, and genetic approaches to produce salt-tolerant plant species. Most of the research emphasizes the significance of plant growth-promoting rhizobacteria in protecting plants from biotic and abiotic stressors. Plant growth, survival, and yield can be stabilized by utilizing this knowledge using different breeding and agronomical techniques. This information marks existing research areas and future gaps that require more attention to reveal new salt tolerance determinants in plants—in the future, creating genetically modified plants could help increase crop growth and the toleration of saline environments.
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James T, Johnson A, Schaller A, Vanderzande S, Luo F, Sandefur P, Ru S, Peace C. As It Stands: The Palouse Wild Cider Apple Breeding Program. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11040517. [PMID: 35214849 PMCID: PMC8877849 DOI: 10.3390/plants11040517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/09/2022] [Accepted: 02/11/2022] [Indexed: 05/10/2023]
Abstract
Providing hands-on education for the next generation of plant breeders would help maximize effectiveness of future breeding efforts. Such education should include training in introgression of crop wild relative alleles, which can increase genetic diversity while providing cultivar attributes that meet industry and consumer demands in a crop such as cider apple. Incorporation of DNA information in breeding decisions has become more common and is another skill future plant breeders need. The Palouse Wild Cider apple breeding program (PWCabp) was established at Washington State University in early 2014 as a student-run experiential learning opportunity. The objectives of this study were to describe the PWCabp's approaches, outcomes, and student involvement to date that has relied on a systematic operational structure, utilization of wild relatives, and incorporation of DNA information. Students chose the crop (cider apple) and initial target market and stakeholders (backyard growers and hobbyists of the Palouse region). Twelve target attributes were defined including high phenolics and red flesh. Phase one and two field trials were established. Two promising high-bitterness selections were identified and propagated. By running the PWCabp, more than 20 undergraduate and graduate students gained experience in the decisions and operations of a fruit breeding program. PWCabp activities have produced desirable new germplasm via utilization of highly diverse Malus germplasm and trained new plant breeding professionals via experiential learning.
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Affiliation(s)
- Tymon James
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (T.J.); (A.J.); (S.V.)
| | - Alexandra Johnson
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (T.J.); (A.J.); (S.V.)
| | - Alexander Schaller
- Department of Environmental Horticulture, University of Florida, Gainesville, FL 32611, USA;
| | - Stijn Vanderzande
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (T.J.); (A.J.); (S.V.)
| | - Feixiong Luo
- Department of Pomology, Hunan Agricultural University, Changsha 410128, China;
| | - Paul Sandefur
- Fall Creek Farm and Nursery, Inc., Lowell, OR 97452, USA;
| | - Sushan Ru
- Department of Horticulture, Auburn University, Auburn, AL 36849, USA;
| | - Cameron Peace
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (T.J.); (A.J.); (S.V.)
- Correspondence:
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Gong H, Rehman F, Ma Y, A B, Zeng S, Yang T, Huang J, Li Z, Wu D, Wang Y. Germplasm Resources and Strategy for Genetic Breeding of Lycium Species: A Review. FRONTIERS IN PLANT SCIENCE 2022; 13:802936. [PMID: 35222468 PMCID: PMC8874141 DOI: 10.3389/fpls.2022.802936] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/07/2022] [Indexed: 06/01/2023]
Abstract
Lycium species (goji), belonging to Solanaceae, are widely spread in the arid to semiarid environments of Eurasia, Africa, North and South America, among which most species have affinal drug and diet functions, resulting in their potential to be a superior healthy food. However, compared with other crop species, scientific research on breeding Lycium species lags behind. This review systematically introduces the present germplasm resources, cytological examination and molecular-assisted breeding progress in Lycium species. Introduction of the distribution of Lycium species around the world could facilitate germplasm collection for breeding. Karyotypes of different species could provide a feasibility analysis of fertility between species. The introduction of mapping technology has discussed strategies for quantitative trait locus (QTL) mapping in Lycium species according to different kinds of traits. Moreover, to extend the number of traits and standardize the protocols of trait detection, we also provide 1,145 potential traits (275 agronomic and 870 metabolic) in different organs based on different reference studies on Lycium, tomato and other Solanaceae species. Finally, perspectives on goji breeding research are discussed and concluded. This review will provide breeders with new insights into breeding Lycium species.
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Affiliation(s)
- Haiguang Gong
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Fazal Rehman
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yun Ma
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Biao A
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Shaohua Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Tianshun Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Jianguo Huang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Zhong Li
- Agricultural Comprehensive Development Center in Ningxia Hui Autonomous Region, Yinchuan, China
| | | | - Ying Wang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- School of Life Science, Gannan Normal University, Ganzhou, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing, China
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Bilbrey EA, Williamson K, Hatzakis E, Miller DD, Fresnedo-Ramírez J, Cooperstone JL. Integrating genomics and multiplatform metabolomics enables metabolite quantitative trait loci detection in breeding-relevant apple germplasm. THE NEW PHYTOLOGIST 2021; 232:1944-1958. [PMID: 34472097 DOI: 10.1111/nph.17693] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 08/10/2021] [Indexed: 05/12/2023]
Abstract
Apple (Malus × domestica) has commercial and nutritional value, but breeding constraints of tree crops limit varietal improvement. Marker-assisted selection minimises these drawbacks, but breeders lack applications for targeting fruit phytochemicals. To understand genotype-phytochemical associations in apples, we have developed a high-throughput integration strategy for genomic and multiplatform metabolomics data. Here, 124 apple genotypes, including members of three pedigree-connected breeding families alongside diverse cultivars and wild selections, were genotyped and phenotyped. Metabolite genome-wide association studies (mGWAS) were conducted with c. 10 000 single nucleotide polymorphisms and phenotypic data acquired via LC-MS and 1 H NMR untargeted metabolomics. Putative metabolite quantitative trait loci (mQTL) were then validated via pedigree-based analyses (PBA). Using our developed method, 519, 726 and 177 putative mQTL were detected in LC-MS positive and negative ionisation modes, and NMR, respectively. mQTL were indicated on each chromosome, with hotspots on linkage groups 16 and 17. A chlorogenic acid mQTL was discovered on chromosome 17 via mGWAS and validated with a two-step PBA, enabling discovery of novel candidate gene-metabolite relationships. Complementary data from three metabolomics approaches and dual genomics analyses increased confidence in validity of compound annotation and mQTL detection. Our platform demonstrates the utility of multiomic integration to advance data-driven, phytochemical-based plant breeding.
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Affiliation(s)
- Emma A Bilbrey
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, 43210, USA
| | - Kathryn Williamson
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, 43210, USA
| | - Emmanuel Hatzakis
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, 43210, USA
| | - Diane Doud Miller
- Department of Horticulture and Crop Science, The Ohio State University, Wooster, OH, 44691, USA
| | | | - Jessica L Cooperstone
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, 43210, USA
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, 43210, USA
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Chen Z, Yu L, Liu W, Zhang J, Wang N, Chen X. Research progress of fruit color development in apple (Malus domestica Borkh.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 162:267-279. [PMID: 33711720 DOI: 10.1016/j.plaphy.2021.02.033] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/17/2021] [Indexed: 06/12/2023]
Abstract
Apple (Malus domestica Borkh.) is one of the most widely produced and economically important fruits in temperate regions. Fruit color development in apple is a major focus for both breeders and researchers as consumers associate brightly colored red apples with ripeness and a good flavor. In recent years, great progress has been made in the research of apple fruit color development, but its development mechanism has not been systematic dissected from the aspects of genetics, transcription or environmental factors. Here, we summarize research on the coloration of apple fruit, including the development of important genomic databases to identify important genomic regions and genes, genetic and transcriptional factors that regulate pigment accumulation, environmental factors that affect anthocyanin synthesis, and the current breeding progress of red-skinned and red-fleshed apples. We describe key transcription factors, such as MYB, bHLH, and WD40, which are involved in the regulation of anthocyanin synthesis and fruit color development in apple. We also discuss the regulation of apple color by external environmental factors such as light, temperature, and water. The aim of this review is to provide insights into the molecular mechanisms underlying anthocyanin biosynthesis in apple. This information will provide significant guidance for the breeding of high-quality red-skinned and red-fleshed apple varieties.
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Affiliation(s)
- Zijing Chen
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China; Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Tai'an, Shandong, 271000, China
| | - Lei Yu
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China; Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Tai'an, Shandong, 271000, China
| | - Wenjun Liu
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China; Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Tai'an, Shandong, 271000, China
| | - Jing Zhang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China; Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Tai'an, Shandong, 271000, China
| | - Nan Wang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China; Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Tai'an, Shandong, 271000, China.
| | - Xuesen Chen
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China; Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Tai'an, Shandong, 271000, China.
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Kumar R, Sharma V, Suresh S, Ramrao DP, Veershetty A, Kumar S, Priscilla K, Hangargi B, Narasanna R, Pandey MK, Naik GR, Thomas S, Kumar A. Understanding Omics Driven Plant Improvement and de novo Crop Domestication: Some Examples. Front Genet 2021; 12:637141. [PMID: 33889179 PMCID: PMC8055929 DOI: 10.3389/fgene.2021.637141] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/02/2021] [Indexed: 01/07/2023] Open
Abstract
In the current era, one of biggest challenges is to shorten the breeding cycle for rapid generation of a new crop variety having high yield capacity, disease resistance, high nutrient content, etc. Advances in the "-omics" technology have revolutionized the discovery of genes and bio-molecules with remarkable precision, resulting in significant development of plant-focused metabolic databases and resources. Metabolomics has been widely used in several model plants and crop species to examine metabolic drift and changes in metabolic composition during various developmental stages and in response to stimuli. Over the last few decades, these efforts have resulted in a significantly improved understanding of the metabolic pathways of plants through identification of several unknown intermediates. This has assisted in developing several new metabolically engineered important crops with desirable agronomic traits, and has facilitated the de novo domestication of new crops for sustainable agriculture and food security. In this review, we discuss how "omics" technologies, particularly metabolomics, has enhanced our understanding of important traits and allowed speedy domestication of novel crop plants.
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Affiliation(s)
- Rakesh Kumar
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | - Vinay Sharma
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Srinivas Suresh
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | | | - Akash Veershetty
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | - Sharan Kumar
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | - Kagolla Priscilla
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | | | - Rahul Narasanna
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | - Manish Kumar Pandey
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | | | - Sherinmol Thomas
- Department of Biosciences & Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Anirudh Kumar
- Department of Botany, Indira Gandhi National Tribal University, Amarkantak, India
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McClure KA, Gong Y, Song J, Vinqvist-Tymchuk M, Campbell Palmer L, Fan L, Burgher-MacLellan K, Zhang Z, Celton JM, Forney CF, Migicovsky Z, Myles S. Genome-wide association studies in apple reveal loci of large effect controlling apple polyphenols. HORTICULTURE RESEARCH 2019; 6:107. [PMID: 31645962 PMCID: PMC6804656 DOI: 10.1038/s41438-019-0190-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 07/19/2019] [Accepted: 07/24/2019] [Indexed: 05/03/2023]
Abstract
Apples are a nutritious food source with significant amounts of polyphenols that contribute to human health and wellbeing, primarily as dietary antioxidants. Although numerous pre- and post-harvest factors can affect the composition of polyphenols in apples, genetics is presumed to play a major role because polyphenol concentration varies dramatically among apple cultivars. Here we investigated the genetic architecture of apple polyphenols by combining high performance liquid chromatography (HPLC) data with ~100,000 single nucleotide polymorphisms (SNPs) from two diverse apple populations. We found that polyphenols can vary in concentration by up to two orders of magnitude across cultivars, and that this dramatic variation was often predictable using genetic markers and frequently controlled by a small number of large effect genetic loci. Using GWAS, we identified candidate genes for the production of quercitrin, epicatechin, catechin, chlorogenic acid, 4-O-caffeoylquinic acid and procyanidins B1, B2, and C1. Our observation that a relatively simple genetic architecture underlies the dramatic variation of key polyphenols in apples suggests that breeders may be able to improve the nutritional value of apples through marker-assisted breeding or gene editing.
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Affiliation(s)
- Kendra A. McClure
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3 Canada
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5 Canada
| | - YuiHui Gong
- College of Horticulture, South China Agriculture University, Guangzhou, 510642 China
| | - Jun Song
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5 Canada
| | - Melinda Vinqvist-Tymchuk
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5 Canada
| | - Leslie Campbell Palmer
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5 Canada
| | - Lihua Fan
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5 Canada
| | - Karen Burgher-MacLellan
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5 Canada
| | - ZhaoQi Zhang
- College of Horticulture, South China Agriculture University, Guangzhou, 510642 China
| | - Jean-Marc Celton
- IRHS, Agrocampus-Ouest, INRA, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Charles F. Forney
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5 Canada
| | - Zoë Migicovsky
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3 Canada
| | - Sean Myles
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3 Canada
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11
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Busatto N, Matsumoto D, Tadiello A, Vrhovsek U, Costa F. Multifaceted analyses disclose the role of fruit size and skin-russeting in the accumulation pattern of phenolic compounds in apple. PLoS One 2019; 14:e0219354. [PMID: 31306452 PMCID: PMC6629076 DOI: 10.1371/journal.pone.0219354] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 06/23/2019] [Indexed: 12/14/2022] Open
Abstract
Fruits are nowadays considered important suppliers of anti-oxidant molecules. Apples are particularly rich in phenolic compounds, non-nutritional phytochemicals that play active roles in controlling severe chronic diseases. In this work, 19 phenolic compounds were investigated in both skin and pulp tissues of seven apple accessions across the Malus genus collected at two stages: during fruit development and at harvest. The primary difference in phenolic concentration between wild and domesticated accessions, especially in the pulp, could be explained by the larger growth rate of the domesticated varieties. The proposed dilution effect was also confirmed through the observation of the increased content of procyanidin B2+B4 and phloridzin in russet-skinned apples, known to have higher concentrations of these compounds. The metabolite screening was also accompanied by the expression analysis of 16 polyphenolic genes showing, for nine elements, a higher expression at harvest than during fruit development. Finally, a polyphenolic comparison with red-fleshed apples was also carried out, underlying a larger amount of procyanidins and quercetin-3rhamnoside in the white-fleshed accessions. The results presented and discussed in this work suggest that specific white-fleshed apples, especially with russeted-skin, may play an important role in ameliorating the nutraceutical potential of apple fruit.
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Affiliation(s)
- Nicola Busatto
- Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | - Daiki Matsumoto
- Faculty of Agriculture, Department of Food, Life, and Environmental Sciences, Yamagata University, Tsuruoka, Japan
| | - Alice Tadiello
- Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
- Department of Biology, University of Padova, Padova, Italy
| | - Urska Vrhovsek
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | - Fabrizio Costa
- Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
- * E-mail:
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12
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van Treuren R, van Eekelen HDLM, Wehrens R, de Vos RCH. Metabolite variation in the lettuce gene pool: towards healthier crop varieties and food. Metabolomics 2018; 14:146. [PMID: 30830450 PMCID: PMC6208706 DOI: 10.1007/s11306-018-1443-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 10/20/2018] [Indexed: 12/01/2022]
Abstract
INTRODUCTION Lettuce (Lactuca sativa L.) is generally not specifically acknowledged for its taste and nutritional value, while its cultivation suffers from limited resistance against several pests and diseases. Such key traits are known to be largely dependent on the ability of varieties to produce specific phytochemicals. OBJECTIVES We aimed to identify promising genetic resources for the improvement of phytochemical composition of lettuce varieties. METHODS Phytochemical variation was investigated using 150 Lactuca genebank accessions, comprising a core set of the lettuce gene pool, and resulting data were related to available phenotypic information. RESULTS A hierarchical cluster analysis of the variation in relative abundance of 2026 phytochemicals, revealed by untargeted metabolic profiling, strongly resembled the known lettuce gene pool structure, indicating that the observed variation was to a large extent genetically determined. Many phytochemicals appeared species-specific, of which several are generally related to traits that are associated with plant health or nutritional value. For a large number of phytochemicals the relative abundance was either positively or negatively correlated with available phenotypic data on resistances against pests and diseases, indicating their potential role in plant resistance. Particularly the more primitive lettuces and the closely related wild relatives showed high levels of (poly)phenols and vitamin C, thus representing potential genetic resources for improving nutritional traits in modern crop types. CONCLUSION Our large-scale analysis of phytochemical variation is unprecedented in lettuce and demonstrated the ample availability of suitable genetic resources for the development of improved lettuce varieties with higher nutritional quality and more sustainable production.
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Affiliation(s)
- Rob van Treuren
- Centre for Genetic Resources, the Netherlands, Wageningen Plant Research, P.O. Box 16, 6700 AA, Wageningen, The Netherlands.
| | | | - Ron Wehrens
- Bioscience, Wageningen Plant Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- Biometris, Wageningen Plant Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Ric C H de Vos
- Bioscience, Wageningen Plant Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
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13
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Manganaris GA, Goulas V, Mellidou I, Drogoudi P. Antioxidant Phytochemicals in Fresh Produce: Exploitation of Genotype Variation and Advancements in Analytical Protocols. Front Chem 2018; 5:95. [PMID: 29468146 PMCID: PMC5807909 DOI: 10.3389/fchem.2017.00095] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/24/2017] [Indexed: 01/27/2023] Open
Abstract
Horticultural commodities (fruit and vegetables) are the major dietary source of several bioactive compounds of high nutraceutical value for humans, including polyphenols, carotenoids and vitamins. The aim of the current review was dual. Firstly, toward the eventual enhancement of horticultural crops with bio-functional compounds, the natural genetic variation in antioxidants found in different species and cultivars/genotypes is underlined. Notably, some landraces and/or traditional cultivars have been characterized by substantially higher phytochemical content, i.e., small tomato of Santorini island (cv. "Tomataki Santorinis") possesses appreciably high amounts of ascorbic acid (AsA). The systematic screening of key bioactive compounds in a wide range of germplasm for the identification of promising genotypes and the restoration of key gene fractions from wild species and landraces may help in reducing the loss of agro-biodiversity, creating a healthier "gene pool" as the basis of future adaptation. Toward this direction, large scale comparative studies in different cultivars/genotypes of a given species provide useful insights about the ones of higher nutritional value. Secondly, the advancements in the employment of analytical techniques to determine the antioxidant potential through a convenient, easy and fast way are outlined. Such analytical techniques include electron paramagnetic resonance (EPR) and infrared (IR) spectroscopy, electrochemical, and chemometric methods, flow injection analysis (FIA), optical sensors, and high resolution screening (HRS). Taking into consideration that fruits and vegetables are complex mixtures of water- and lipid-soluble antioxidants, the exploitation of chemometrics to develop "omics" platforms (i.e., metabolomics, foodomics) is a promising tool for researchers to decode and/or predict antioxidant activity of fresh produce. For industry, the use of optical sensors and IR spectroscopy is recommended to estimate the antioxidant activity rapidly and at low cost, although legislation does not allow its correlation with health claims.
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Affiliation(s)
- George A. Manganaris
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Lemesos, Cyprus
| | - Vlasios Goulas
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Lemesos, Cyprus
| | - Ifigeneia Mellidou
- Hellenic Agricultural Organization ‘Demeter’, Institute of Plant Breeding and Genetic Resources, Thessaloniki, Greece
| | - Pavlina Drogoudi
- Hellenic Agricultural Organization ‘Demeter’, Department of Deciduous Fruit Trees, Institute of Plant Breeding and Genetic Resources, Naoussa, Greece
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14
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Sweet taste in apple: the role of sorbitol, individual sugars, organic acids and volatile compounds. Sci Rep 2017; 7:44950. [PMID: 28322320 PMCID: PMC5359574 DOI: 10.1038/srep44950] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 02/16/2017] [Indexed: 11/08/2022] Open
Abstract
Sweetness is one of the main drivers of consumer preference, and thus is given high priority in apple breeding programmes. Due to the complexity of sweetness evaluation, soluble solid content (SSC) is commonly used as an estimation of this trait. Nevertheless, it has been demonstrated that SSC and sweet taste are poorly correlated. Though individual sugar content may vary greatly between and within apple cultivars, no previous study has tried to investigate the relationship between the amount of individual sugars, or ratios of these, and apple sweetness. In this work, we quantified the major sugars (sucrose, glucose, fructose, xylose) and sorbitol and explored their influence on perceived sweetness in apple; we also related this to malic acid content, SSC and volatile compounds. Our data confirmed that the correlation between sweetness and SSC is weak. We found that sorbitol content correlates (similarly to SSC) with perceived sweetness better than any other single sugar or total sugar content. The single sugars show no differentiable importance in determining apple sweetness. Our predictive model based on partial least squares regression shows that after sorbitol and SSC, the most important contribution to apple sweetness is provided by several volatile compounds, mainly esters and farnesene.
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15
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Comparative and parallel genome-wide association studies for metabolic and agronomic traits in cereals. Nat Commun 2016; 7:12767. [PMID: 27698483 PMCID: PMC5059443 DOI: 10.1038/ncomms12767] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 07/29/2016] [Indexed: 01/19/2023] Open
Abstract
The plant metabolome is characterized by extensive diversity and is often regarded as a bridge between genome and phenome. Here we report metabolic and phenotypic genome-wide studies (mGWAS and pGWAS) in rice grain that, in addition to previous metabolic GWAS in rice leaf and maize kernel, show both distinct and overlapping aspects of genetic control of metabolism within and between species. We identify new candidate genes potentially influencing important metabolic and/or morphological traits. We show that the differential genetic architecture of rice metabolism between different tissues is in part determined by tissue specific expression. Using parallel mGWAS and pGWAS we identify new candidate genes potentially responsible for variation in traits such as grain colour and size, and provide evidence of metabotype-phenotype linkage. Our study demonstrates a powerful strategy for interactive functional genomics and metabolomics in plants, especially the cloning of minor QTLs for complex phenotypic traits.
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16
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Tenenboim H, Brotman Y. Omic Relief for the Biotically Stressed: Metabolomics of Plant Biotic Interactions. TRENDS IN PLANT SCIENCE 2016; 21:781-791. [PMID: 27185334 DOI: 10.1016/j.tplants.2016.04.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 03/08/2016] [Accepted: 04/19/2016] [Indexed: 05/19/2023]
Abstract
Many aspects of the way plants protect themselves against pathogen attack, or react upon such an attack, are realized by metabolites. The ambitious aim of metabolomics, namely the identification and annotation of the entire cellular metabolome, still poses a considerable challenge due to the high diversity of the metabolites in the cell. Recent advances in analytical methods and data analysis have resulted in improved sensitivity, accuracy, and capacity, allowing the analysis of several hundreds or even thousands of compounds within one sample. Investigators have only recently begun to acknowledge and harness the power of metabolomics to elucidate key questions in the study of plant biotic interactions; we review trends and developments in the field.
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Affiliation(s)
- Hezi Tenenboim
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam, Germany
| | - Yariv Brotman
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel.
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17
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Scossa F, Brotman Y, de Abreu E Lima F, Willmitzer L, Nikoloski Z, Tohge T, Fernie AR. Genomics-based strategies for the use of natural variation in the improvement of crop metabolism. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:47-64. [PMID: 26566824 DOI: 10.1016/j.plantsci.2015.05.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 05/29/2015] [Accepted: 05/31/2015] [Indexed: 05/08/2023]
Abstract
Next-generation genomics holds great potential in the study of plant phenotypic variation. With several crop reference genomes now available, the affordable costs of de novo genome assembly or target resequencing offer the opportunity to mine the enormous amount of genetic diversity hidden in crop wild relatives. Wide introgressions from these wild ancestors species or land races represent a possible strategy to improve cultivated varieties. In this review, we discuss the mechanisms underlying metabolic diversity within plant species and the possible strategies (and barriers) to introgress novel metabolic traits into cultivated varieties. We show how deep genomic surveys uncover various types of structural variants from extended gene pools of major crops and highlight how this variation may be used for the improvement of crop metabolism.
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Affiliation(s)
- Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany; Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per la Frutticoltura, Via di Fioranello 52, 00134 Rome, Italy.
| | - Yariv Brotman
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | | | - Lothar Willmitzer
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Zoran Nikoloski
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Takayuki Tohge
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
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18
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Igarashi M, Hatsuyama Y, Harada T, Fukasawa-Akada T. Biotechnology and apple breeding in Japan. BREEDING SCIENCE 2016; 66:18-33. [PMID: 27069388 PMCID: PMC4780799 DOI: 10.1270/jsbbs.66.18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 12/23/2015] [Indexed: 05/11/2023]
Abstract
Apple is a fruit crop of significant economic importance, and breeders world wide continue to develop novel cultivars with improved characteristics. The lengthy juvenile period and the large field space required to grow apple populations have imposed major limitations on breeding. Various molecular biological techniques have been employed to make apple breeding easier. Transgenic technology has facilitated the development of apples with resistance to fungal or bacterial diseases, improved fruit quality, or root stocks with better rooting or dwarfing ability. DNA markers for disease resistance (scab, powdery mildew, fire-blight, Alternaria blotch) and fruit skin color have also been developed, and marker-assisted selection (MAS) has been employed in breeding programs. In the last decade, genomic sequences and chromosome maps of various cultivars have become available, allowing the development of large SNP arrays, enabling efficient QTL mapping and genomic selection (GS). In recent years, new technologies for genetic improvement, such as trans-grafting, virus vectors, and genome-editing, have emerged. Using these techniques, no foreign genes are present in the final product, and some of them show considerable promise for application to apple breeding.
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Affiliation(s)
- Megumi Igarashi
- Hirosaki Industrial Research Institute, Aomori Prefectural Industrial Technology Research Center,
Ogimachi 1-1-8, Hirosaki, Aomori 036-8104,
Japan
| | - Yoshimichi Hatsuyama
- Apple Research Institute, Aomori Prefectural Industrial Technology Research Center,
Fukutami 24, Botandaira, Kuroishi, Aomori 036-0332,
Japan
| | - Takeo Harada
- Department of Agriculture and Life Science, Hirosaki University,
Bunkyouchou 3, Hirosaki, Aomori 036-8563,
Japan
| | - Tomoko Fukasawa-Akada
- Hirosaki Industrial Research Institute, Aomori Prefectural Industrial Technology Research Center,
Ogimachi 1-1-8, Hirosaki, Aomori 036-8104,
Japan
- Corresponding author (e-mail: )
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19
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Ma B, Liao L, Zheng H, Chen J, Wu B, Ogutu C, Li S, Korban SS, Han Y. Genes Encoding Aluminum-Activated Malate Transporter II and their Association with Fruit Acidity in Apple. THE PLANT GENOME 2015; 8:eplantgenome2015.03.0016. [PMID: 33228269 DOI: 10.3835/plantgenome2015.03.0016] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 05/27/2015] [Indexed: 05/25/2023]
Abstract
A gene encoding aluminum-activated malate transporter (ALMT) was previously reported as a candidate for the Ma locus controlling acidity in apple (Malus × domestica Borkh.). In this study, we found that apple ALMT genes can be divided into three families and the Ma1 gene belongs to the ALMTII family. Duplication of ALMTII genes in apple is related to the polyploid origin of the apple genome. Divergence in expression has occurred between the Ma1 gene and its homologs in the ALMTII family and only the Ma1 gene is significantly associated with malic acid content. The Ma locus consists of two alleles, Ma1 and ma1. Ma1 resides in the tonoplast and its ectopic expression in yeast was found to increase the influx of malic acid into yeast cells significantly, suggesting it may function as a vacuolar malate channel. In contrast, ma1 encodes a truncated protein because of a single nucleotide substitution of G with A in the last exon. As this truncated protein resides within the cell membrane, it is deemed to be nonfunctional as a vacuolar malate channel. The frequency of the Ma1Ma1 genotype is very low in apple cultivars but is high in wild relatives, which suggests that apple domestication may be accompanied by selection for the Ma1 gene. In addition, variations in the malic acid content of mature fruits were also observed between accessions with the same genotype in the Ma locus. This suggests that the Ma gene is not the only genetic determinant of fruit acidity in apple.
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Affiliation(s)
- Baiquan Ma
- Key Lab. of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, P.R. China
- Graduate Univ. of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, P.R. China
| | - Liao Liao
- Key Lab. of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, P.R. China
| | - Hongyu Zheng
- Key Lab. of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, P.R. China
- Graduate Univ. of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, P.R. China
| | - Jie Chen
- Beijing Key Lab. of Grape Sciences and Enology, and Key Lab. of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- Graduate Univ. of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, P.R. China
| | - Benhong Wu
- Beijing Key Lab. of Grape Sciences and Enology, and Key Lab. of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Collins Ogutu
- Key Lab. of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, P.R. China
- Graduate Univ. of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, P.R. China
| | - Shaohua Li
- Key Lab. of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, P.R. China
| | - Schuyler S Korban
- Dep. of Biology, Univ. of Massachusetts-Boston, Boston, MA, 02184, USA
| | - Yuepeng Han
- Key Lab. of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, P.R. China
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20
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Leforestier D, Ravon E, Muranty H, Cornille A, Lemaire C, Giraud T, Durel CE, Branca A. Genomic basis of the differences between cider and dessert apple varieties. Evol Appl 2015; 8:650-61. [PMID: 26240603 PMCID: PMC4516418 DOI: 10.1111/eva.12270] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 04/15/2015] [Indexed: 12/26/2022] Open
Abstract
Unraveling the genomic processes at play during variety diversification is of fundamental interest for understanding evolution, but also of applied interest in crop science. It can indeed provide knowledge on the genetic bases of traits for crop improvement and germplasm diversity management. Apple is one of the most important fruit crops in temperate regions, having both great economic and cultural values. Sweet dessert apples are used for direct consumption, while bitter cider apples are used to produce cider. Several important traits are known to differentiate the two variety types, in particular fruit size, biennial versus annual fruit bearing, and bitterness, caused by a higher content in polyphenols. Here, we used an Illumina 8k SNP chip on two core collections, of 48 dessert and 48 cider apples, respectively, for identifying genomic regions responsible for the differences between cider and dessert apples. The genome-wide level of genetic differentiation between cider and dessert apples was low, although 17 candidate regions showed signatures of divergent selection, displaying either outlier FST values or significant association with phenotypic traits (bitter versus sweet fruits). These candidate regions encompassed 420 genes involved in a variety of functions and metabolic pathways, including several colocalizations with QTLs for polyphenol compounds.
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Affiliation(s)
- Diane Leforestier
- UMR 1345 Institut de Recherche en Horticulture et Semences, Université d'Angers Angers, France
| | - Elisa Ravon
- UMR 1345 Institut de Recherche en Horticulture et Semences, INRA Beaucouzé, France
| | - Hélène Muranty
- UMR 1345 Institut de Recherche en Horticulture et Semences, INRA Beaucouzé, France
| | - Amandine Cornille
- Ecologie, Systématique et Evolution, Université Paris-Sud Orsay, France ; Ecologie, Systématique et Evolution, CNRS Orsay, France
| | - Christophe Lemaire
- UMR 1345 Institut de Recherche en Horticulture et Semences, Université d'Angers Angers, France
| | - Tatiana Giraud
- Ecologie, Systématique et Evolution, Université Paris-Sud Orsay, France ; Ecologie, Systématique et Evolution, CNRS Orsay, France
| | - Charles-Eric Durel
- UMR 1345 Institut de Recherche en Horticulture et Semences, INRA Beaucouzé, France
| | - Antoine Branca
- Ecologie, Systématique et Evolution, Université Paris-Sud Orsay, France ; Ecologie, Systématique et Evolution, CNRS Orsay, France
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Alseekh S, Tohge T, Wendenberg R, Scossa F, Omranian N, Li J, Kleessen S, Giavalisco P, Pleban T, Mueller-Roeber B, Zamir D, Nikoloski Z, Fernie AR. Identification and mode of inheritance of quantitative trait loci for secondary metabolite abundance in tomato. THE PLANT CELL 2015; 27:485-512. [PMID: 25770107 PMCID: PMC4558650 DOI: 10.1105/tpc.114.132266] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 01/27/2015] [Accepted: 02/16/2015] [Indexed: 05/18/2023]
Abstract
A large-scale metabolic quantitative trait loci (mQTL) analysis was performed on the well-characterized Solanum pennellii introgression lines to investigate the genomic regions associated with secondary metabolism in tomato fruit pericarp. In total, 679 mQTLs were detected across the 76 introgression lines. Heritability analyses revealed that mQTLs of secondary metabolism were less affected by environment than mQTLs of primary metabolism. Network analysis allowed us to assess the interconnectivity of primary and secondary metabolism as well as to compare and contrast their respective associations with morphological traits. Additionally, we applied a recently established real-time quantitative PCR platform to gain insight into transcriptional control mechanisms of a subset of the mQTLs, including those for hydroxycinnamates, acyl-sugar, naringenin chalcone, and a range of glycoalkaloids. Intriguingly, many of these compounds displayed a dominant-negative mode of inheritance, which is contrary to the conventional wisdom that secondary metabolite contents decreased on domestication. We additionally performed an exemplary evaluation of two candidate genes for glycolalkaloid mQTLs via the use of virus-induced gene silencing. The combined data of this study were compared with previous results on primary metabolism obtained from the same material and to other studies of natural variance of secondary metabolism.
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Affiliation(s)
- Saleh Alseekh
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Takayuki Tohge
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Regina Wendenberg
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Federico Scossa
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per la Frutticoltura, 00134 Rome, Italy
| | - Nooshin Omranian
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany Institute of Biochemistry and Biology, University of Potsdam, D-14476 Potsdam-Golm, Germany
| | - Jie Li
- Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Sabrina Kleessen
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Patrick Giavalisco
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Tzili Pleban
- Institute of Plant Sciences and Genetics and Otto Warburg Centre for Biotechnology, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Bernd Mueller-Roeber
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany Institute of Biochemistry and Biology, University of Potsdam, D-14476 Potsdam-Golm, Germany
| | - Dani Zamir
- Institute of Plant Sciences and Genetics and Otto Warburg Centre for Biotechnology, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Zoran Nikoloski
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
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Liao L, Vimolmangkang S, Wei G, Zhou H, Korban SS, Han Y. Molecular characterization of genes encoding leucoanthocyanidin reductase involved in proanthocyanidin biosynthesis in apple. FRONTIERS IN PLANT SCIENCE 2015; 6:243. [PMID: 25914714 PMCID: PMC4392590 DOI: 10.3389/fpls.2015.00243] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 03/26/2015] [Indexed: 05/03/2023]
Abstract
Proanthocyanidins (PAs) are the major component of phenolics in apple, but mechanisms involved in PA biosynthesis remain unclear. Here, the relationship between the PA biosynthesis and the expression of genes encoding leucoanthocyanidin reductase (LAR) and anthocyanidin reductase (ANR) was investigated in fruit skin of one apple cultivar and three crabapples. Transcript levels of LAR1 and ANR2 genes were significantly correlated with the contents of catechin and epicatechin, respectively, which suggests their active roles in PA synthesis. Surprisingly, transcript levels for both LAR1 and LAR2 genes were almost undetectable in two crabapples that accumulated both flavan-3-ols and PAs. This contradicts the previous finding that LAR1 gene is a strong candidate regulating the accumulation of metabolites such as epicatechin and PAs in apple. Ectopic expression of apple MdLAR1 gene in tobacco suppresses expression of the late genes in anthocyanin biosynthetic pathway, resulting in loss of anthocyanin in flowers. Interestingly, a decrease in PA biosynthesis was also observed in flowers of transgenic tobacco plants overexpressing the MdLAR1 gene, which could be attributed to decreased expression of both the NtANR1 and NtANR2 genes. Our study not only confirms the in vivo function of apple LAR1 gene, but it is also helpful for understanding the mechanism of PA biosynthesis.
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Affiliation(s)
- Liao Liao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of SciencesWuhan, China
| | - Sornkanok Vimolmangkang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of SciencesWuhan, China
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn UniversityBangkok, Thailand
| | - Guochao Wei
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of SciencesWuhan, China
- Graduate University of Chinese Academy of SciencesBeijing, China
| | - Hui Zhou
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of SciencesWuhan, China
- Graduate University of Chinese Academy of SciencesBeijing, China
| | - Schuyler S. Korban
- Department of Biology, University of Massachusetts BostonBoston, MA, USA
| | - Yuepeng Han
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of SciencesWuhan, China
- *Correspondence: Yuepeng Han, Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Lumo Road No. 1, 430074 Wuhan, China
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23
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Verdu CF, Guyot S, Childebrand N, Bahut M, Celton JM, Gaillard S, Lasserre-Zuber P, Troggio M, Guilet D, Laurens F. QTL analysis and candidate gene mapping for the polyphenol content in cider apple. PLoS One 2014; 9:e107103. [PMID: 25271925 PMCID: PMC4182701 DOI: 10.1371/journal.pone.0107103] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 08/12/2014] [Indexed: 11/25/2022] Open
Abstract
Polyphenols have favorable antioxidant potential on human health suggesting that their high content is responsible for the beneficial effects of apple consumption. They control the quality of ciders as they predominantly account for astringency, bitterness, color and aroma. In this study, we identified QTLs controlling phenolic compound concentrations and the average polymerization degree of flavanols in a cider apple progeny. Thirty-two compounds belonging to five groups of phenolic compounds were identified and quantified by reversed phase liquid chromatography on both fruit extract and juice, over three years. The average polymerization degree of flavanols was estimated in fruit by phloroglucinolysis coupled to HPLC. Parental maps were built using SSR and SNP markers and used for the QTL analysis. Sixty-nine and 72 QTLs were detected on 14 and 11 linkage groups of the female and male maps, respectively. A majority of the QTLs identified in this study are specific to this population, while others are consistent with previous studies. This study presents for the first time in apple, QTLs for the mean polymerization degree of procyanidins, for which the mechanisms involved remains unknown to this day. Identification of candidate genes underlying major QTLs was then performed in silico and permitted the identification of 18 enzymes of the polyphenol pathway and six transcription factors involved in the apple anthocyanin regulation. New markers were designed from sequences of the most interesting candidate genes in order to confirm their co-localization with underlying QTLs by genetic mapping. Finally, the potential use of these QTLs in breeding programs is discussed.
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Affiliation(s)
- Cindy F. Verdu
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L'UNAM, Angers, France
- AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
- Université d'Angers, EA921 Laboratoire de Substances d'Origine Naturelle et Analogues Structuraux, SFR 4207 Quasav, PRES L'UNAM, Angers, France
| | - Sylvain Guyot
- INRA, UR1268 Biopolymères, Interactions & Assemblages, Equipe « Polyphénols, Réactivité & Procédés », Le Rheu, France
| | - Nicolas Childebrand
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L'UNAM, Angers, France
- AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
| | - Muriel Bahut
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L'UNAM, Angers, France
- AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
| | - Jean-Marc Celton
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L'UNAM, Angers, France
- AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
| | - Sylvain Gaillard
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L'UNAM, Angers, France
- AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
| | - Pauline Lasserre-Zuber
- INRA-UBP, UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Clermont-Ferrand, France
| | - Michela Troggio
- Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige, TN, Italy
| | - David Guilet
- Université d'Angers, EA921 Laboratoire de Substances d'Origine Naturelle et Analogues Structuraux, SFR 4207 Quasav, PRES L'UNAM, Angers, France
| | - François Laurens
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L'UNAM, Angers, France
- AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
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24
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Verdu CF, Childebrand N, Marnet N, Lebail G, Dupuis F, Laurens F, Guilet D, Guyot S. Polyphenol variability in the fruits and juices of a cider apple progeny. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2014; 94:1305-1314. [PMID: 24115016 DOI: 10.1002/jsfa.6411] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 05/30/2013] [Accepted: 10/01/2013] [Indexed: 06/02/2023]
Abstract
BACKGROUND Polyphenols have a favourable antioxidant potential on human health, suggesting that their high content in apple is responsible for the beneficial effects of apple consumption. They are also linked to the quality of apple juices and ciders since they are predominantly responsible for astringency, bitterness and colour. Major phenolic compounds were quantified by liquid chromatography in fruits and juices from a cider apple progeny harvested for 3 years. The total content of procyanidins and their average degree of polymerisation (DPn) were also determined in fruits by phloroglucinolysis. Variability and extraction yield of these compounds were determined. RESULTS The variability observed in the progeny was representative of the variability observed in many cider apple varieties. Hydroxycinnamic acids were the most extractable group, with an average extraction yield of 67%, whereas flavonols and anthocyanins were the least. CONCLUSION This study is the first to introduce variability and extraction yields of the main phenolic compounds in both fruits and juices of a cider apple progeny. This dataset will be used for an upcoming QTL mapping study, an original approach that has never been undertaken for cider apple.
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Affiliation(s)
- Cindy F Verdu
- Université d'Angers, EA 921, Laboratoire de Substances d'Origine Naturelle et Analogues Structuraux, SFR 4207 QUASAV, PRES L'UNAM, 49045, Angers, France; Université d'Angers, UMR1345, Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L'UNAM, 49045, Angers, France; AgroCampus-Ouest, UMR1345, Institut de Recherche en Horticulture et Semences, 49045, Angers, France; INRA, UMR1345, Institut de Recherche en Horticulture et Semences, 49071, Beaucouzé, France
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25
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Ikeda S, Abe T, Nakamura Y, Kibinge N, Hirai Morita A, Nakatani A, Ono N, Ikemura T, Nakamura K, Altaf-Ul-Amin M, Kanaya S. Systematization of the protein sequence diversity in enzymes related to secondary metabolic pathways in plants, in the context of big data biology inspired by the KNApSAcK motorcycle database. PLANT & CELL PHYSIOLOGY 2013; 54:711-727. [PMID: 23509110 DOI: 10.1093/pcp/pct041] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Biology is increasingly becoming a data-intensive science with the recent progress of the omics fields, e.g. genomics, transcriptomics, proteomics and metabolomics. The species-metabolite relationship database, KNApSAcK Core, has been widely utilized and cited in metabolomics research, and chronological analysis of that research work has helped to reveal recent trends in metabolomics research. To meet the needs of these trends, the KNApSAcK database has been extended by incorporating a secondary metabolic pathway database called Motorcycle DB. We examined the enzyme sequence diversity related to secondary metabolism by means of batch-learning self-organizing maps (BL-SOMs). Initially, we constructed a map by using a big data matrix consisting of the frequencies of all possible dipeptides in the protein sequence segments of plants and bacteria. The enzyme sequence diversity of the secondary metabolic pathways was examined by identifying clusters of segments associated with certain enzyme groups in the resulting map. The extent of diversity of 15 secondary metabolic enzyme groups is discussed. Data-intensive approaches such as BL-SOM applied to big data matrices are needed for systematizing protein sequences. Handling big data has become an inevitable part of biology.
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Affiliation(s)
- Shun Ikeda
- Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma-shi, Nara, 630-0192 Japan
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26
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Afendi FM, Ono N, Nakamura Y, Nakamura K, Darusman LK, Kibinge N, Morita AH, Tanaka K, Horai H, Altaf-Ul-Amin M, Kanaya S. Data Mining Methods for Omics and Knowledge of Crude Medicinal Plants toward Big Data Biology. Comput Struct Biotechnol J 2013; 4:e201301010. [PMID: 24688691 PMCID: PMC3962233 DOI: 10.5936/csbj.201301010] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Revised: 03/09/2013] [Accepted: 03/09/2013] [Indexed: 01/01/2023] Open
Abstract
Molecular biological data has rapidly increased with the recent progress of the Omics fields, e.g., genomics, transcriptomics, proteomics and metabolomics that necessitates the development of databases and methods for efficient storage, retrieval, integration and analysis of massive data. The present study reviews the usage of KNApSAcK Family DB in metabolomics and related area, discusses several statistical methods for handling multivariate data and shows their application on Indonesian blended herbal medicines (Jamu) as a case study. Exploration using Biplot reveals many plants are rarely utilized while some plants are highly utilized toward specific efficacy. Furthermore, the ingredients of Jamu formulas are modeled using Partial Least Squares Discriminant Analysis (PLS-DA) in order to predict their efficacy. The plants used in each Jamu medicine served as the predictors, whereas the efficacy of each Jamu provided the responses. This model produces 71.6% correct classification in predicting efficacy. Permutation test then is used to determine plants that serve as main ingredients in Jamu formula by evaluating the significance of the PLS-DA coefficients. Next, in order to explain the role of plants that serve as main ingredients in Jamu medicines, information of pharmacological activity of the plants is added to the predictor block. Then N-PLS-DA model, multiway version of PLS-DA, is utilized to handle the three-dimensional array of the predictor block. The resulting N-PLS-DA model reveals that the effects of some pharmacological activities are specific for certain efficacy and the other activities are diverse toward many efficacies. Mathematical modeling introduced in the present study can be utilized in global analysis of big data targeting to reveal the underlying biology.
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Affiliation(s)
- Farit M Afendi
- Graduate School of Information Science, Nara Institute of Science and Technology, Nara 630-0101, Ikoma, Japan ; Department of Statistics, Bogor Agricultural University, Jln. Meranti, Kampus IPB Darmaga, Bogor 16680, Indonesia
| | - Naoaki Ono
- Graduate School of Information Science, Nara Institute of Science and Technology, Nara 630-0101, Ikoma, Japan
| | - Yukiko Nakamura
- Graduate School of Information Science, Nara Institute of Science and Technology, Nara 630-0101, Ikoma, Japan
| | - Kensuke Nakamura
- Maebashi Institute of technology, 450-1 Kamisadori, Maebashi-shi, Gunma, 371-0816 Japan
| | - Latifah K Darusman
- Biopharmaca Research Center, Bogor Agricultural University, Kampas IPB Taman Kencana, Jln. Taman Kencana No. 3 Bogor 16151, Indonesia
| | - Nelson Kibinge
- Graduate School of Information Science, Nara Institute of Science and Technology, Nara 630-0101, Ikoma, Japan
| | - Aki Hirai Morita
- Graduate School of Information Science, Nara Institute of Science and Technology, Nara 630-0101, Ikoma, Japan
| | - Ken Tanaka
- Department of Medicinal Resources, Institute of Natural Medicine, University of Toyama, 2630 Toyama, 930-0194, Japan
| | - Hisayuki Horai
- Department of Electronic and Computer Engineering, Ibaraki National College of Technology, 866 Nakane, Hitachinaka, Ibaraki 312-8508, Japan
| | - Md Altaf-Ul-Amin
- Graduate School of Information Science, Nara Institute of Science and Technology, Nara 630-0101, Ikoma, Japan
| | - Shigehiko Kanaya
- Graduate School of Information Science, Nara Institute of Science and Technology, Nara 630-0101, Ikoma, Japan
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Zardo DM, Silva KM, Guyot S, Nogueira A. Phenolic profile and antioxidant capacity of the principal apples produced in Brazil. Int J Food Sci Nutr 2013; 64:611-20. [PMID: 23360097 DOI: 10.3109/09637486.2013.763909] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
This study evaluated the phenols of the Gala, Fuji and Golden Delicious varieties, which make up 95% of Brazilian production. The phenolic profiles (whole fruit) were determined by high pressure liquid chromatography, total phenols were determined using the Folin-Ciocalteau method and antioxidant capacity by the FRAP method (whole fruit, skin, pulp and centre). The Golden Delicious had the highest phenol content (408 mg/fruit) compared to Fuji (194 mg/fruit) and Gala (162 mg/fruit), and the antioxidant capacity of the Golden Delicious was 2.5 and 3.6 times higher than that found in the Fuji and Gala, respectively. The phenolic profile for the three varieties showed 5-caffeoylquinic acid, ( - )-epicatechin, procyanidin B2 and phloridzin as major components with procyanidins as the predominant class and quercetin as the minority. The consumption of apple pulp may provide 48-78% of the antioxidant capacity; however, if the peel is ingested, it may increase to 79-89%. The type of apple variety and the parts ingested are factors that must be taken into consideration in consumption.
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Affiliation(s)
- Danianni Marinho Zardo
- Department of Pharmaceutical Sciences, State University of Ponta Grossa (UEPG), Ponta Grossa, PR, Brazil
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28
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Khan SA, Schaart JG, Beekwilder J, Allan AC, Tikunov YM, Jacobsen E, Schouten HJ. The mQTL hotspot on linkage group 16 for phenolic compounds in apple fruits is probably the result of a leucoanthocyanidin reductase gene at that locus. BMC Res Notes 2012; 5:618. [PMID: 23121691 PMCID: PMC3599437 DOI: 10.1186/1756-0500-5-618] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2012] [Accepted: 10/29/2012] [Indexed: 11/16/2022] Open
Abstract
Background Our previous study on ripe apples from a progeny of a cross between the apple cultivars ‘Prima’ and ‘Fiesta’ showed a hotspot of mQTLs for phenolic compounds at the top of LG16, both in peel and in flesh tissues. In order to find the underlying gene(s) of this mQTL hotspot, we investigated the expression profiles of structural and putative transcription factor genes of the phenylpropanoid and flavonoid pathways during different stages of fruit development in progeny genotypes. Results Only the structural gene leucoanthocyanidin reductase (MdLAR1) showed a significant correlation between transcript abundance and content of metabolites that mapped on the mQTL hotspot. This gene is located on LG16 in the mQTL hotspot. Progeny that had inherited one or two copies of the dominant MdLAR1 alleles (Mm, MM) showed a 4.4- and 11.8-fold higher expression level of MdLAR1 respectively, compared to the progeny that had inherited the recessive alleles (mm). This higher expression was associated with a four-fold increase of procyanidin dimer II as one representative metabolite that mapped in the mQTL hotspot. Although expression level of several structural genes were correlated with expression of other structural genes and with some MYB and bHLH transcription factor genes, only expression of MdLAR1 was correlated with metabolites that mapped at the mQTL hotspot. MdLAR1 is the only candidate gene that can explain the mQTL for procyanidins and flavan-3-ols. However, mQTLs for other phenylpropanoids such as phenolic esters, dihydrochalcones and flavonols, that appear to map at the same locus, have so far not been considered to be dependent on LAR, as their biosynthesis does not involve LAR activity. An explanation for this phenomenon is discussed. Conclusions Transcript abundances and genomic positions indicate that the mQTL hotspot for phenolic compounds at the top of LG16 is controlled by the MdLAR1 gene. The dominant allele of the MdLAR1 gene, causing increased content of metabolites that are potentially health beneficial, could be used in marker assisted selection of current apple breeding programs and for cisgenesis.
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Affiliation(s)
- Sabaz Ali Khan
- Wageningen UR Plant Breeding, P,O, Box 16, Wageningen, 6700 AA, The Netherlands
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Mellidou I, Chagné D, Laing WA, Keulemans J, Davey MW. Allelic variation in paralogs of GDP-L-galactose phosphorylase is a major determinant of vitamin C concentrations in apple fruit. PLANT PHYSIOLOGY 2012; 160:1613-29. [PMID: 23001142 PMCID: PMC3490610 DOI: 10.1104/pp.112.203786] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 09/19/2012] [Indexed: 05/18/2023]
Abstract
To identify the genetic factors underlying the regulation of fruit vitamin C (L-ascorbic acid [AsA]) concentrations, quantitative trait loci (QTL) studies were carried out in an F1 progeny derived from a cross between the apple (Malus × domestica) cultivars Telamon and Braeburn over three years. QTL were identified for AsA, glutathione, total antioxidant activity in both flesh and skin tissues, and various quality traits, including flesh browning. Four regions on chromosomes 10, 11, 16, and 17 contained stable fruit AsA-QTL clusters. Mapping of AsA metabolic genes identified colocations between orthologs of GDP-L-galactose phosphorylase (GGP), dehydroascorbate reductase (DHAR), and nucleobase-ascorbate transporter within these QTL clusters. Of particular interest are the three paralogs of MdGGP, which all colocated within AsA-QTL clusters. Allelic variants of MdGGP1 and MdGGP3 derived from the cultivar Braeburn parent were also consistently associated with higher fruit total AsA concentrations both within the mapping population (up to 10-fold) and across a range of commercial apple germplasm (up to 6-fold). Striking differences in the expression of the cv Braeburn MdGGP1 allele between fruit from high- and low-AsA genotypes clearly indicate a key role for MdGGP1 in the regulation of fruit AsA concentrations, and this MdGGP allele-specific single-nucleotide polymorphism marker represents an excellent candidate for directed breeding for enhanced fruit AsA concentrations. Interestingly, colocations were also found between MdDHAR3-3 and a stable QTL for browning in the cv Telamon parent, highlighting links between the redox status of the AsA pool and susceptibility to flesh browning.
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Affiliation(s)
- Ifigeneia Mellidou
- Laboratory for Fruit Breeding and Biotechnology, Department Biosystems, Faculty of Bioscience Engineering, Katholieke Universiteit Leuven, B–3001 Heverlee, Belgium (I.M., J.K., M.W.D.); New Zealand Institute for Plant and Food Research Limited, Palmerston North Research Centre, Palmerston North 4442, New Zealand (D.C.); and New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, Auckland 1142, New Zealand (W.A.L.)
| | - David Chagné
- Laboratory for Fruit Breeding and Biotechnology, Department Biosystems, Faculty of Bioscience Engineering, Katholieke Universiteit Leuven, B–3001 Heverlee, Belgium (I.M., J.K., M.W.D.); New Zealand Institute for Plant and Food Research Limited, Palmerston North Research Centre, Palmerston North 4442, New Zealand (D.C.); and New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, Auckland 1142, New Zealand (W.A.L.)
| | - William A. Laing
- Laboratory for Fruit Breeding and Biotechnology, Department Biosystems, Faculty of Bioscience Engineering, Katholieke Universiteit Leuven, B–3001 Heverlee, Belgium (I.M., J.K., M.W.D.); New Zealand Institute for Plant and Food Research Limited, Palmerston North Research Centre, Palmerston North 4442, New Zealand (D.C.); and New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, Auckland 1142, New Zealand (W.A.L.)
| | - Johan Keulemans
- Laboratory for Fruit Breeding and Biotechnology, Department Biosystems, Faculty of Bioscience Engineering, Katholieke Universiteit Leuven, B–3001 Heverlee, Belgium (I.M., J.K., M.W.D.); New Zealand Institute for Plant and Food Research Limited, Palmerston North Research Centre, Palmerston North 4442, New Zealand (D.C.); and New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, Auckland 1142, New Zealand (W.A.L.)
| | - Mark W. Davey
- Laboratory for Fruit Breeding and Biotechnology, Department Biosystems, Faculty of Bioscience Engineering, Katholieke Universiteit Leuven, B–3001 Heverlee, Belgium (I.M., J.K., M.W.D.); New Zealand Institute for Plant and Food Research Limited, Palmerston North Research Centre, Palmerston North 4442, New Zealand (D.C.); and New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, Auckland 1142, New Zealand (W.A.L.)
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30
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Mubarak A, Swinny EE, Ching SYL, Jacob SR, Lacey K, Hodgson JM, Croft KD, Considine MJ. Polyphenol composition of plum selections in relation to total antioxidant capacity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2012; 60:10256-10262. [PMID: 22971250 DOI: 10.1021/jf302903k] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Dietary polyphenols are associated with protection against chronic diseases such as cardiovascular disease. Pharmacological studies show a range of bioactivities and efficacy attributable to specific polyphenols. While many fruits are rich in polyphenols, wide cultivar variation of polyphenol composition is common. Our objective was to determine the composition of major bioactive polyphenols in 29 prevarietal selections of Western Australian plums, and Black Amber as an evaluation in developing breeding tools to develop fruit that may have enhanced health-promoting capacities. Total phenolics were quantified colorimetrically; selected polyphenols were quantified by HPLC; and the total antioxidant capacity (TAC) was measured by the antioxidant inhibition of oxygen radicals (AIOR) assay. Total phenolic concentration was significantly correlated with TAC (R = 0.95, P < 0.01). Neo-chlorogenic acid and quercetin glycosides were found to be the predominant polyphenols (mean 29.9 mg·kg(-1) and 50.7 mg·kg(-1), respectively). No significant correlations were found between the composition of predominant polyphenols in plums and the TAC. We argue that the value of in vitro TAC assays to breeding programs may be limited, and future research should focus on the heritability of known bioactive polyphenols.
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Affiliation(s)
- Aidilla Mubarak
- School of Plant Biology and the Institute of Agriculture, University of Western Australia, Crawley, Western Australia 6009, Australia
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31
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Cuthbertson D, Andrews PK, Reganold JP, Davies NM, Lange BM. Utility of metabolomics toward assessing the metabolic basis of quality traits in apple fruit with an emphasis on antioxidants. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2012; 60:8552-60. [PMID: 22881116 PMCID: PMC3551554 DOI: 10.1021/jf3031088] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
A gas chromatography-mass spectrometry approach was employed to evaluate the use of metabolite patterns to differentiate fruit from six commercially grown apple cultivars harvested in 2008. Principal component analysis (PCA) of apple fruit peel and flesh data indicated that individual cultivar replicates clustered together and were separated from all other cultivar samples. An independent metabolomics investigation with fruit harvested in 2003 confirmed the separate clustering of fruit from different cultivars. Further evidence for cultivar separation was obtained using a hierarchical clustering analysis. An evaluation of PCA component loadings revealed specific metabolite classes that contributed the most to each principal component, whereas a correlation analysis demonstrated that specific metabolites correlate directly with quality traits such as antioxidant activity, total phenolics, and total anthocyanins, which are important parameters in the selection of breeding germplasm. These data sets lay the foundation for elucidating the metabolic basis of commercially important fruit quality traits.
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Affiliation(s)
- Daniel Cuthbertson
- Institute of Biological Chemistry and M. J. Murdock Metabolomics Laboratory, Washington State University, P.O. Box 646340, Pullman, Washington 99164-6340, United States
| | - Preston K. Andrews
- Department of Horticulture and Landscape Architecture, Washington State University, P.O. Box 646414, Pullman, Washington 99164-6414, United States
| | - John P. Reganold
- Department of Crop and Soil Sciences, Washington State University, P.O. Box 646420, Pullman, Washington 99164-6420, United States
| | - Neal M. Davies
- Department of Pharmaceutical Sciences, College of Pharmacy, Washington State University, P.O. Box 646510, Pullman, Washington 99164-6534, United States
| | - B. Markus Lange
- Institute of Biological Chemistry and M. J. Murdock Metabolomics Laboratory, Washington State University, P.O. Box 646340, Pullman, Washington 99164-6340, United States
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