1
|
Liu Y, Zhou J, Yi C, Chen F, Liu Y, Liao Y, Zhang Z, Liu W, Lv J. Integrative analysis of non-targeted metabolome and transcriptome reveals the mechanism of volatile formation in pepper fruit. Front Genet 2023; 14:1290492. [PMID: 38028623 PMCID: PMC10667453 DOI: 10.3389/fgene.2023.1290492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction: Aroma is a key inherent quality attributes of pepper fruit, yet the underlying mechanisms of aroma compound biosynthesis remain unclear. Methods: In this study, the volatile profile of the QH (cultivated Capsicum chinense) and WH (cultivated Capsicum annuum) pepper varieties were putatively identified during fruit development using gas chromatography-mass spectrometry (GC-MS). Results and discussion: The results identified 203 volatiles in pepper, and most of the esters, terpenes, aldehydes and alcohols were significantly down-regulated with fruit ripening. The comparison of volatile components between varieties revealed that aldehydes and alcohols were highly expressed in the WH fruit, while esters and terpenes with fruity or floral aroma were generally highly accumulated in the QH fruit, providing QH with a fruity odor. Transcriptome analysis demonstrated the close relationship between the synthesis of volatiles and the fatty acid and terpene metabolic pathways, and the high expression of the ADH, AAT and TPS genes was key in determining the accumulation of volatiles in pepper fruit. Furthermore, integrative metabolome and transcriptome analysis revealed that 208 differentially expressed genes were highly correlated with 114 volatiles, and the transcription factors of bHLH, MYB, ARF and IAA were identified as fundamental for the regulation of volatile synthesis in pepper fruit. Our results extend the understanding of the synthesis and accumulation of volatiles in pepper fruit.
Collapse
Affiliation(s)
- Yuhua Liu
- College of Life Sciences, Hengyang Normal University, Hengyang, Hunan, China
- Hunan Key Laboratory for Conservation and Utilization of Biological Resources in the Nanyue Mountainous Region, Hengyang, Hunan, China
| | - Jiahao Zhou
- College of Life Sciences, Hengyang Normal University, Hengyang, Hunan, China
- Hunan Key Laboratory for Conservation and Utilization of Biological Resources in the Nanyue Mountainous Region, Hengyang, Hunan, China
| | - Cheng Yi
- College of Life Sciences, Hengyang Normal University, Hengyang, Hunan, China
- Hunan Key Laboratory for Conservation and Utilization of Biological Resources in the Nanyue Mountainous Region, Hengyang, Hunan, China
| | - Fengqingyang Chen
- College of Life Sciences, Hengyang Normal University, Hengyang, Hunan, China
| | - Yan Liu
- College of Life Sciences, Hengyang Normal University, Hengyang, Hunan, China
| | - Yi Liao
- College of Life Sciences, Hengyang Normal University, Hengyang, Hunan, China
| | - Zhuqing Zhang
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha, Hunan, China
| | - Wei Liu
- College of Medical Technology, Hunan Polytechnic of Environment and Biology, Hengyang, Hunan, China
| | - Junheng Lv
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, Yunnan, China
| |
Collapse
|
2
|
Koeda S, Noda T, Hachisu S, Kubo A, Tanaka Y, Yamamoto H, Ozaki S, Kinoshita M, Ohno K, Tanaka Y, Tomi K, Kamiyoshihara Y. Expression of alcohol acyltransferase is a potential determinant of fruit volatile ester variations in Capsicum. PLANT CELL REPORTS 2023; 42:1745-1756. [PMID: 37642676 DOI: 10.1007/s00299-023-03064-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 08/18/2023] [Indexed: 08/31/2023]
Abstract
KEY MESSAGE The transcript level of alcohol acyltransferase 1 (AAT1) may be the main factor influencing the variations in volatile esters that characterizing the fruity/exotic aroma of pepper fruit. Volatile esters are key components for characterizing the fruity/exotic aroma of pepper (Capsicum spp.) fruit. In general, the volatile ester content in the fruit is the consequence of a delicate balance between their synthesis by alcohol acyltransferases (AATs) and degradation by carboxylesterases (CXEs). However, the precise role of these families of enzymes with regard to volatile ester content remains unexplored in Capsicum. In this study, we found that the volatile ester content was relatively low in C. annuum and much higher in C. chinense, particularly in pungent varieties. Additionally, fruits collected from multiple non-pungent C. chinense varieties, which harbor loss-of-function mutations in capsaicinoid biosynthetic genes, acyltransferase (Pun1), putative aminotransferase (pAMT), or putative ketoacyl-ACP reductase (CaKR1) were analyzed. The volatile ester contents of non-pungent C. chinense varieties (pamt/pamt) were equivalent to those of pungent varieties, but their levels were significantly lower in non-pungent NMCA30036 (pun12/pun12) and C. chinense (Cakr1/Cakr1) varieties. Multiple AAT-like sequences were identified from the pepper genome sequences, whereas only one CXE-like sequence was identified. Among these, AAT1, AAT2, and CXE1 were isolated from fruits of C. chinense and C. annuum. Gene expression analysis revealed that the AAT1 transcript level is a potential determinant of fruit volatile ester variations in Capsicum. Furthermore, enzymatic assays demonstrated that AAT1 is responsible for the biosynthesis of volatile esters in pepper fruit. Identification of a key gene for aroma biosynthesis in pepper fruit will provide a theoretical basis for the development of molecular tools for flavor improvement.
Collapse
Affiliation(s)
- Sota Koeda
- Graduate School of Agriculture, Kindai University, Nara, 3327-204, Japan.
- Faculty of Agriculture, Kindai University, Nara, 3327-204, Japan.
| | - Tomona Noda
- Graduate School of Agriculture, Kindai University, Nara, 3327-204, Japan
| | - Shinkai Hachisu
- Graduate School of Agriculture, Kindai University, Nara, 3327-204, Japan
| | - Akiha Kubo
- Faculty of Agriculture, Kindai University, Nara, 3327-204, Japan
| | - Yasuto Tanaka
- Faculty of Agriculture, Kindai University, Nara, 3327-204, Japan
| | - Hiroto Yamamoto
- Graduate School of Agriculture, Kindai University, Nara, 3327-204, Japan
| | - Sayaka Ozaki
- Faculty of Agriculture, Kindai University, Nara, 3327-204, Japan
| | | | - Kouki Ohno
- Faculty of Agriculture, Kindai University, Nara, 3327-204, Japan
| | - Yoshiyuki Tanaka
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Kenichi Tomi
- Japan Society for Scientific Aromatherapy, Tokyo, 164-0003, Japan
| | - Yusuke Kamiyoshihara
- College of Bioresource Sciences, Nihon University, Kanagawa, 252-0880, Japan
- Graduate School of Bioresource Sciences, Nihon University, Kanagawa, 252-0880, Japan
| |
Collapse
|
3
|
Effect of biostimulants on the growth, yield and nutritional value of Capsicum annuum grown in an unheated plastic tunnel. Sci Rep 2021; 11:22335. [PMID: 34785738 PMCID: PMC8595353 DOI: 10.1038/s41598-021-01834-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/02/2021] [Indexed: 11/26/2022] Open
Abstract
Recent years have witnessed an increased interest in the cultivation and consumption of peppers. Therefore, new solutions are being sought to provide pepper plants with the most favorable conditions for growth and development. In view of the above, the aim of this study was to evaluate the effect of selected biostimulants on the biometric parameters, yield and nutritional value of Capsicum annuum fruit. The research hypothesis postulates that biostimulants can increase the yield and improve the nutritional quality of pepper fruit. The experiment was conducted in an unheated plastic tunnel. The experimental materials comprised three sweet (‘Solario F1’, ‘Turbine F1’ and ‘Whitney F1’) and two hot (‘Cyklon’ and ‘Palivec’) cultivars of C. annuum. It was found that the combined application of environmentally-friendly microbial-based biostimulants (BB Soil, BB Foliar, Multical, MK5 and Biocin F) did not clearly improve the morphological traits of pepper fruit, yield or the concentrations of sugars and organic acids in fruit, therefore their use is not economically justified. Hot peppers had a higher content of dry matter, total sugars and L-ascorbic acid than sweet peppers. The analyzed biostimulants increased nitrate (V) concentrations in the fruit of both hot and sweet peppers. ‘Turbine F1’ and ‘Solario F1’ were particularly prone to nitrate (V) accumulation in fruit, therefore the use of biostimulants should be limited in their cultivation. Pepper fruits with the largest horizontal diameter and the thickest skin should be preferred because these traits are associated with high sugar content.
Collapse
|
4
|
Barbey CR, Hogshead MH, Harrison B, Schwartz AE, Verma S, Oh Y, Lee S, Folta KM, Whitaker VM. Genetic Analysis of Methyl Anthranilate, Mesifurane, Linalool, and Other Flavor Compounds in Cultivated Strawberry ( Fragaria × ananassa). FRONTIERS IN PLANT SCIENCE 2021; 12:615749. [PMID: 34093602 PMCID: PMC8170412 DOI: 10.3389/fpls.2021.615749] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 03/30/2021] [Indexed: 05/27/2023]
Abstract
The cultivated strawberry (Fragaria × ananassa) is an economically important fruit crop that is intensively bred for improved sensory qualities. The diversity of fruit flavors and aromas in strawberry results mainly from the interactions of sugars, acids, and volatile organic compounds (VOCs) that are derived from diverse biochemical pathways influenced by the expression of many genes. This study integrates multiomic analyses to identify QTL and candidate genes for multiple aroma compounds in a complex strawberry breeding population. Novel fruit volatile QTL was discovered for methyl anthranilate, methyl 2-hexenoate, methyl 2-methylbutyrate, mesifurane, and a shared QTL on Chr 3 was found for nine monoterpene and sesquiterpene compounds, including linalool, 3-carene, β-phellandrene, α-limonene, linalool oxide, nerolidol, α-caryophellene, α-farnesene, and β-farnesene. Fruit transcriptomes from a subset of 64 individuals were used to support candidate gene identification. For methyl esters including the grape-like methyl anthranilate, a novel ANTHANILIC ACID METHYL TRANSFERASE-like gene was identified. Two mesifurane QTL correspond with the known biosynthesis gene O-METHYL TRANSFERASE 1 and a novel FURANEOL GLUCOSYLTRANSFERASE. The shared terpene QTL contains multiple fruit-expressed terpenoid pathway-related genes including NEROLIDOL SYNTHASE 1 (FanNES1). The abundance of linalool and other monoterpenes is partially governed by a co-segregating expression-QTL (eQTL) for FanNES1 transcript variation, and there is additional evidence for quantitative effects from other terpenoid-pathway genes in this narrow genomic region. These QTLs present new opportunities in breeding for improved flavor in commercial strawberry.
Collapse
Affiliation(s)
- Christopher R. Barbey
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Maxwell H. Hogshead
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Benjamin Harrison
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Anne E. Schwartz
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Sujeet Verma
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Youngjae Oh
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Seonghee Lee
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Kevin M. Folta
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Vance M. Whitaker
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| |
Collapse
|
5
|
Barbey CR, Hogshead MH, Harrison B, Schwartz AE, Verma S, Oh Y, Lee S, Folta KM, Whitaker VM. Genetic Analysis of Methyl Anthranilate, Mesifurane, Linalool, and Other Flavor Compounds in Cultivated Strawberry ( Fragaria × ananassa). FRONTIERS IN PLANT SCIENCE 2021; 12:615749. [PMID: 34093602 DOI: 10.1101/2020.10.07.330001v1.full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 03/30/2021] [Indexed: 05/27/2023]
Abstract
The cultivated strawberry (Fragaria × ananassa) is an economically important fruit crop that is intensively bred for improved sensory qualities. The diversity of fruit flavors and aromas in strawberry results mainly from the interactions of sugars, acids, and volatile organic compounds (VOCs) that are derived from diverse biochemical pathways influenced by the expression of many genes. This study integrates multiomic analyses to identify QTL and candidate genes for multiple aroma compounds in a complex strawberry breeding population. Novel fruit volatile QTL was discovered for methyl anthranilate, methyl 2-hexenoate, methyl 2-methylbutyrate, mesifurane, and a shared QTL on Chr 3 was found for nine monoterpene and sesquiterpene compounds, including linalool, 3-carene, β-phellandrene, α-limonene, linalool oxide, nerolidol, α-caryophellene, α-farnesene, and β-farnesene. Fruit transcriptomes from a subset of 64 individuals were used to support candidate gene identification. For methyl esters including the grape-like methyl anthranilate, a novel ANTHANILIC ACID METHYL TRANSFERASE-like gene was identified. Two mesifurane QTL correspond with the known biosynthesis gene O-METHYL TRANSFERASE 1 and a novel FURANEOL GLUCOSYLTRANSFERASE. The shared terpene QTL contains multiple fruit-expressed terpenoid pathway-related genes including NEROLIDOL SYNTHASE 1 (FanNES1). The abundance of linalool and other monoterpenes is partially governed by a co-segregating expression-QTL (eQTL) for FanNES1 transcript variation, and there is additional evidence for quantitative effects from other terpenoid-pathway genes in this narrow genomic region. These QTLs present new opportunities in breeding for improved flavor in commercial strawberry.
Collapse
Affiliation(s)
- Christopher R Barbey
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Maxwell H Hogshead
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Benjamin Harrison
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Anne E Schwartz
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Sujeet Verma
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Youngjae Oh
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Seonghee Lee
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Kevin M Folta
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Vance M Whitaker
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| |
Collapse
|
6
|
Parry C, Wang YW, Lin SW, Barchenger DW. Reproductive compatibility in Capsicum is not necessarily reflected in genetic or phenotypic similarity between species complexes. PLoS One 2021; 16:e0243689. [PMID: 33760824 PMCID: PMC8508556 DOI: 10.1371/journal.pone.0243689] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/17/2021] [Indexed: 11/18/2022] Open
Abstract
Wild relatives of domesticated Capsicum represent substantial
genetic diversity and thus sources of traits of potential interest. Furthermore,
the hybridization compatibility between members of Capsicum
species complexes remains unresolved. Improving our understanding of the
relationship between Capsicum species relatedness and their
ability to form hybrids is a highly pertinent issue. Through the development of
novel interspecific hybrids in this study, we demonstrate interspecies
compatibility is not necessarily reflected in relatedness according to
established Capsicum genepool complexes. Based on a phylogeny
constructed by genotyping using simple sequence repeat (SSR) markers and with a
portion of the waxy locus, and through principal component
analysis (PCA) of phenotypic data, we clarify the relationships among wild and
domesticated Capsicum species. Together, the phylogeny and
hybridization studies provide evidence for the misidentification of a number of
species from the World Vegetable Center genebank included in this study. The
World Vegetable Center holds the largest collection of Capsicum
genetic material globally, therefore this may reflect a wider issue in the
misidentification of Capsicum wild relatives. The findings
presented here provide insight into an apparent disconnect between compatibility
and relatedness in the Capsicum genus, which will be valuable
in identifying candidates for future breeding programs.
Collapse
Affiliation(s)
- Catherine Parry
- Department of Biology and Biochemistry, University of Bath, Claverton
Down, Bath, United Kingdom
| | - Yen-Wei Wang
- World Vegetable Center, Shanhua, Tainan, 74151, Taiwan
| | - Shih-wen Lin
- World Vegetable Center, Shanhua, Tainan, 74151, Taiwan
| | | |
Collapse
|
7
|
Ji L, Li P, Su Z, Li M, Guo S. Cold-tolerant introgression line construction and low-temperature stress response analysis for bell pepper. PLANT SIGNALING & BEHAVIOR 2020; 15:1773097. [PMID: 32522139 PMCID: PMC8570733 DOI: 10.1080/15592324.2020.1773097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/24/2020] [Accepted: 04/26/2020] [Indexed: 06/11/2023]
Abstract
We aimed to screen cold-tolerant introgression lines (ILs) of bell pepper and investigate stress responses of these bell peppers under low temperature. Seedlings of cold-resistant wild-type bell pepper CA157, cultivated bell pepper CA52, and their ILs were evaluated for their tolerance to low temperature. Electrical conductivity measurement was performed on ILs and two parents. Then, contents of physiological and biochemical indexes including malondialdehyde (MDA), proline, and soluble sugar content were examined. Moreover, the superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), and peroxidase (POD) activities were further investigated. Finally, the chlorophyll fluorescence (PSII) parameters in all pant leaves were examined. A total of 22 IL plants showed better resistance than their recurrent parent CA52. CL122 was one of the most outstanding plants in ILs that had similar performance with wild bell pepper CA157. Cold resistance analysis based on physiological and biochemical indexes showed that factors such as electrical conductivity, MDA, and PSII were closely related to cold resistance among CA157, CA52, and CL122 under low-temperature stress. In conclusion, ILs constructed in the current study might be used for cold resistance gene introgression between wild and cultured species. Moreover, CL122 might be a novel bridge material for understanding low-temperature response in bell pepper. Furthermore, electrical conductivity, MDA, and PSII might be used to identify the low-temperature resistance of bell pepper plants in a period of obvious differentiation.
Collapse
Affiliation(s)
- Lusha Ji
- College of Pharmacy, Liaocheng University, Liaocheng, China
| | - Pan Li
- College of Pharmacy, Liaocheng University, Liaocheng, China
| | - Zhenhua Su
- College of Life Science, Liaocheng University, Liaocheng, China
| | - Meifang Li
- College of Life Science, Liaocheng University, Liaocheng, China
| | - Shangjing Guo
- College of Agriculture, Liaocheng University, Liaocheng, China
| |
Collapse
|
8
|
Arjun K, Dhaliwal MS, Jindal SK, Fakrudin B. Mapping of fruit length related QTLs in interspecific cross ( Capsicum annuum L. × Capsicum galapagoense Hunz.) of chilli. BREEDING SCIENCE 2018; 68:219-226. [PMID: 29875605 PMCID: PMC5982179 DOI: 10.1270/jsbbs.17073] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 11/24/2017] [Indexed: 06/08/2023]
Abstract
Fruit length in chilli is quantitatively inherited trait and selection based on phenotypic performance is tedious and time consuming. To detect QTLs determining fruit length in Capsicum spp., an interspecific F2 mapping population was developed from the cross of C. annuum L. cv. 'FL 201' with C. galapagoense Hunz. accession 'TC 07245'. Fruit length in this cross showed a quantitative inheritance with the population depicting a symmetric distribution in histogram. To map quantitative trait loci (QTLs) for fruit length 400 SSR markers were surveyed on the parental genotypes but only 28 markers were observed to be polymorphic indicating less genetic diversity between the two Capsicum species. Polymorphic markers were then analyzed in F2 population consisting of 210 plants and 24 of these markers were mapped on to three linkage groups (LGs): LG 1, LG 2 and LG 3. Two fruit length determining QTLs designated as paufl2.1 and paufl2.2 were identified and both the QTLs were mapped on to LG 2. The two QTLs together explained 21.78 per cent of the phenotypic variation. Apart from the two QTLs, positive alleles were detected in the small fruited parent 'TC 07245' which might be of potential use in chilli breeding programs.
Collapse
Affiliation(s)
- Konana Arjun
- Department of Vegetable Science, Punjab Agricultural University,
Ludhiana 141004,
India
| | - Major S Dhaliwal
- Directorate of Research, Punjab Agricultural University,
Ludhiana 141004,
India
| | - Salesh K Jindal
- Department of Vegetable Science, Punjab Agricultural University,
Ludhiana 141004,
India
| | - Bashasab Fakrudin
- Department of Biotechnology & Crop Improvement, University of Horticultural Sciences,
Bagalkot 587104,
India
| |
Collapse
|
9
|
Liu Z, Zhang Y, Ou L, Kang L, Liu Y, Lv J, Wei G, Yang B, Yang S, Chen W, Dai X, Li X, Zhou S, Zhang Z, Ma Y, Zou X. Identification and characterization of novel microRNAs for fruit development and quality in hot pepper (Capsicum annuum L.). Gene 2017; 608:66-72. [PMID: 28122266 DOI: 10.1016/j.gene.2017.01.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 01/16/2017] [Accepted: 01/20/2017] [Indexed: 10/20/2022]
Abstract
MicroRNAs (miRNAs) are non-coding small RNAs which play an important regulatory role in various biological processes. Previous studies have reported that miRNAs are involved in fruit development in model plants. However, the miRNAs related to fruit development and quality in hot pepper (Capsicum annuum L.) remains unknown. In this study, small RNA populations from different fruit ripening stages and different varieties were compared using next-generation sequencing technology. Totally, 59 known miRNAs and 310 novel miRNAs were identified from four libraries using miRDeep2 software. For these novel miRNAs, 656 targets were predicted and 402 of them were annotated. GO analysis and KEGG pathways suggested that some of the predicted miRNAs targeted genes involved in starch sucrose metabolism and amino sugar as well as nucleotide sugar metabolism. Quantitative RT-PCR validated the contrasting expression patterns between several miRNAs and their target genes. These results will provide an important foundation for future studies on the regulation of miRNAs involved in fruit development and quality.
Collapse
Affiliation(s)
- Zhoubin Liu
- Longping Branch, Graduate School of Hunan university, Changsha 410125, China; Hunan Vegetable Research Institute, Changsha 410125, China
| | - Yuping Zhang
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China
| | - Lijun Ou
- Hunan Vegetable Research Institute, Changsha 410125, China
| | - Linyu Kang
- Longping Branch, Graduate School of Hunan university, Changsha 410125, China; Hunan Vegetable Research Institute, Changsha 410125, China
| | - Yuhua Liu
- Longping Branch, Graduate School of Hunan university, Changsha 410125, China; Hunan Vegetable Research Institute, Changsha 410125, China
| | - Junheng Lv
- Longping Branch, Graduate School of Hunan university, Changsha 410125, China; Hunan Vegetable Research Institute, Changsha 410125, China
| | - Ge Wei
- Hunan Vegetable Research Institute, Changsha 410125, China
| | - Bozhi Yang
- Hunan Vegetable Research Institute, Changsha 410125, China
| | - Sha Yang
- Hunan Vegetable Research Institute, Changsha 410125, China
| | - Wenchao Chen
- Hunan Vegetable Research Institute, Changsha 410125, China
| | - Xiongze Dai
- Hunan Vegetable Research Institute, Changsha 410125, China
| | - Xuefeng Li
- Hunan Vegetable Research Institute, Changsha 410125, China
| | - Shudong Zhou
- Hunan Vegetable Research Institute, Changsha 410125, China
| | - Zhuqing Zhang
- Hunan Vegetable Research Institute, Changsha 410125, China.
| | - Yanqing Ma
- Hunan Vegetable Research Institute, Changsha 410125, China.
| | - Xuexiao Zou
- Longping Branch, Graduate School of Hunan university, Changsha 410125, China; Hunan Vegetable Research Institute, Changsha 410125, China.
| |
Collapse
|
10
|
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.
Collapse
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.
| |
Collapse
|
11
|
Nimmakayala P, Abburi VL, Saminathan T, Almeida A, Davenport B, Davidson J, Reddy CVCM, Hankins G, Ebert A, Choi D, Stommel J, Reddy UK. Genome-Wide Divergence and Linkage Disequilibrium Analyses for Capsicum baccatum Revealed by Genome-Anchored Single Nucleotide Polymorphisms. FRONTIERS IN PLANT SCIENCE 2016; 7:1646. [PMID: 27857720 PMCID: PMC5093146 DOI: 10.3389/fpls.2016.01646] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 10/18/2016] [Indexed: 05/03/2023]
Abstract
Principal component analysis (PCA) with 36,621 polymorphic genome-anchored single nucleotide polymorphisms (SNPs) identified collectively for Capsicum annuum and Capsicum baccatum was used to characterize population structure and species domestication of these two important incompatible cultivated pepper species. Estimated mean nucleotide diversity (π) and Tajima's D across various chromosomes revealed biased distribution toward negative values on all chromosomes (except for chromosome 4) in cultivated C. baccatum, indicating a population bottleneck during domestication of C. baccatum. In contrast, C. annuum chromosomes showed positive π and Tajima's D on all chromosomes except chromosome 8, which may be because of domestication at multiple sites contributing to wider genetic diversity. For C. baccatum, 13,129 SNPs were available, with minor allele frequency (MAF) ≥0.05; PCA of the SNPs revealed 283 C. baccatum accessions grouped into 3 distinct clusters, for strong population structure. The fixation index (FST ) between domesticated C. annuum and C. baccatum was 0.78, which indicates genome-wide divergence. We conducted extensive linkage disequilibrium (LD) analysis of C. baccatum var. pendulum cultivars on all adjacent SNP pairs within a chromosome to identify regions of high and low LD interspersed with a genome-wide average LD block size of 99.1 kb. We characterized 1742 haplotypes containing 4420 SNPs (range 9-2 SNPs per haplotype). Genome-wide association study (GWAS) of peduncle length, a trait that differentiates wild and domesticated C. baccatum types, revealed 36 significantly associated genome-wide SNPs. Population structure, identity by state (IBS) and LD patterns across the genome will be of potential use for future GWAS of economically important traits in C. baccatum peppers.
Collapse
Affiliation(s)
- Padma Nimmakayala
- Department of Biology, Gus R. Douglass Institute, West Virginia State UniversityInstitute, WV, USA
| | - Venkata L. Abburi
- Department of Biology, Gus R. Douglass Institute, West Virginia State UniversityInstitute, WV, USA
| | - Thangasamy Saminathan
- Department of Biology, Gus R. Douglass Institute, West Virginia State UniversityInstitute, WV, USA
| | - Aldo Almeida
- Department of Biology, Gus R. Douglass Institute, West Virginia State UniversityInstitute, WV, USA
| | - Brittany Davenport
- Department of Biology, Gus R. Douglass Institute, West Virginia State UniversityInstitute, WV, USA
| | - Joshua Davidson
- Department of Biology, Gus R. Douglass Institute, West Virginia State UniversityInstitute, WV, USA
| | | | - Gerald Hankins
- Department of Biology, Gus R. Douglass Institute, West Virginia State UniversityInstitute, WV, USA
| | - Andreas Ebert
- Genetic Resources and Seed Unit, Asian Vegetable Research and Development Center-The World Vegetable CenterTainan, Taiwan
| | - Doil Choi
- Department of Plant Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National UniversitySeoul, South Korea
| | - John Stommel
- Genetic Improvement of Fruits and Vegetables Laboratory (United States Department of Agriculture, Agricultural Research Service)Beltsville, MD, USA
| | - Umesh K. Reddy
- Department of Biology, Gus R. Douglass Institute, West Virginia State UniversityInstitute, WV, USA
- *Correspondence: Umesh K. Reddy
| |
Collapse
|
12
|
Manzur JP, Fita A, Prohens J, Rodríguez-Burruezo A. Successful Wide Hybridization and Introgression Breeding in a Diverse Set of Common Peppers (Capsicum annuum) Using Different Cultivated Ají (C. baccatum) Accessions as Donor Parents. PLoS One 2015; 10:e0144142. [PMID: 26642059 PMCID: PMC4671682 DOI: 10.1371/journal.pone.0144142] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 10/13/2015] [Indexed: 11/19/2022] Open
Abstract
Capsicum baccatum, commonly known as ají, has been reported as a source of variation for many different traits to improve common pepper (C. annuum), one of the most important vegetables in the world. However, strong interspecific hybridization barriers exist between them. A comparative study of two wide hybridization approaches for introgressing C. baccatum genes into C. annuum was performed: i) genetic bridge (GB) using C. chinense and C. frutescens as bridge species; and, ii) direct cross between C. annuum and C. baccatum combined with in vitro embryo rescue (ER). A diverse and representative collection of 18 accessions from four cultivated species of Capsicum was used, including C. annuum (12), C. baccatum (3), C. chinense (2), and C. frutescens (1). More than 5000 crosses were made and over 1000 embryos were rescued in the present study. C. chinense performed as a good bridge species between C. annuum and C. baccatum, with the best results being obtained with the cross combination [C. baccatum (♀) × C. chinense (♂)] (♀) × C. annuum (♂), while C. frutescens gave poor results as bridge species due to strong prezygotic and postzygotic barriers. Virus-like-syndrome or dwarfism was observed in F1 hybrids when both C. chinense and C. frutescens were used as female parents. Regarding the ER strategy, the best response was found in C. annuum (♀) × C. baccatum (♂) crosses. First backcrosses to C. annuum (BC1s) were obtained according to the crossing scheme [C. annuum (♀) × C. baccatum (♂)] (♀) × C. annuum (♂) using ER. Advantages and disadvantages of each strategy are discussed in relation to their application to breeding programmes. These results provide breeders with useful practical information for the regular utilization of the C. baccatum gene pool in C. annuum breeding.
Collapse
Affiliation(s)
- Juan Pablo Manzur
- Instituto de Investigaciones Agropecuarias CRI La Platina, Santiago, Chile
| | - Ana Fita
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Adrián Rodríguez-Burruezo
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| |
Collapse
|
13
|
Screening Genetic Resources of Capsicum Peppers in Their Primary Center of Diversity in Bolivia and Peru. PLoS One 2015; 10:e0134663. [PMID: 26402618 PMCID: PMC4581705 DOI: 10.1371/journal.pone.0134663] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 09/03/2015] [Indexed: 11/19/2022] Open
Abstract
For most crops, like Capsicum, their diversity remains under-researched for traits of interest for food, nutrition and other purposes. A small investment in screening this diversity for a wide range of traits is likely to reveal many traditional varieties with distinguished values. One objective of this study was to demonstrate, with Capsicum as model crop, the application of indicators of phenotypic and geographic diversity as effective criteria for selecting promising genebank accessions for multiple uses from crop centers of diversity. A second objective was to evaluate the expression of biochemical and agromorphological properties of the selected Capsicum accessions in different conditions. Four steps were involved: 1) Develop the necessary diversity by expanding genebank collections in Bolivia and Peru; 2) Establish representative subsets of ~100 accessions for biochemical screening of Capsicum fruits; 3) Select promising accessions for different uses after screening; and 4) Examine how these promising accessions express biochemical and agromorphological properties when grown in different environmental conditions. The Peruvian Capsicum collection now contains 712 accessions encompassing all five domesticated species (C. annuum, C. chinense, C. frutescens, C. baccatum, and C. pubescens). The collection in Bolivia now contains 487 accessions, representing all five domesticates plus four wild taxa (C. baccatum var. baccatum, C. caballeroi, C. cardenasii, and C. eximium). Following the biochemical screening, 44 Bolivian and 39 Peruvian accessions were selected as promising, representing wide variation in levels of antioxidant capacity, capsaicinoids, fat, flavonoids, polyphenols, quercetins, tocopherols, and color. In Peru, 23 promising accessions performed well in different environments, while each of the promising Bolivian accessions only performed well in a certain environment. Differences in Capsicum diversity and local contexts led to distinct outcomes in each country. In Peru, mild landraces with high values in health-related attributes were of interest to entrepreneurs. In Bolivia, wild Capsicum have high commercial demand.
Collapse
|