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Oh H, Mengist MF, Ma G, Giongo L, Pottorff M, Spencer JA, Perkins-Veazie P, Iorizzo M. Unraveling the genetic architecture of blueberry fruit quality traits: major loci control organic acid content while more complex genetic mechanisms control texture and sugar content. BMC PLANT BIOLOGY 2025; 25:36. [PMID: 39789463 PMCID: PMC11721283 DOI: 10.1186/s12870-025-06061-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2024] [Accepted: 01/06/2025] [Indexed: 01/12/2025]
Abstract
BACKGROUND Fruit quality traits, including taste, flavor, texture, and shelf-life, have emerged as important breeding priorities in blueberry (Vaccinium corymbosum). Organic acids and sugars play crucial roles in the perception of blueberry taste/flavor, where low and high consumer liking are correlated with high organic acids and high sugars, respectively. Blueberry texture and appearance are also critical for shelf-life quality and consumers' willingness-to-pay. As the genetic mechanisms that determine these fruit quality traits remain largely unknown, in this study, an F1 mapping population was used to perform quantitative trait loci (QTL) mapping for pH, titratable acidity (TA), organic acids, total soluble solids (TSS), sugars, fruit size, and texture at harvest and/or post-storage and weight loss. RESULTS Twenty-eight QTLs were detected for acidity-related parameters (pH, TA, and organic acid content). Six QTLs for pH, TA, and citric acid, two for quinic acid, and two for shikimic acid with major effects were consistently detected across two years on the same genomic regions on chromosomes 3, 4, and 5, respectively. Putative candidate genes for these QTLs were also identified using comparative transcriptomic analysis. No QTL was detected for malic acid content, TSS, or individual sugar content. A total of 146 QTLs with minor effects were identified for texture- and size-related parameters. With a few exceptions, these QTLs were generally inconsistent over years and post-storage, indicating a highly quantitative nature. CONCLUSIONS Our findings enhance the understanding of the genetic basis underlying fruit quality traits in blueberry and guide future work to exploit DNA-informed selection strategies in blueberry breeding programs. The major-effect QTLs identified for acidity-related fruit characteristics could be potential targets to develop DNA markers for marker-assisted selection (MAS). On the other hand, genomic selection may be a more suitable approach than MAS when targeting fruit texture, sugars, or size.
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Affiliation(s)
- Heeduk Oh
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, 28081, USA
- Department of Horticulture, North Carolina State University, Raleigh, NC, 27607, USA
| | - Molla F Mengist
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, 28081, USA
- Agricultural Research Station, Virginia State University, Petersburg, VA, 23806, USA
| | - Guoying Ma
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, 28081, USA
| | - Lara Giongo
- Fondazione Edmund Mach, Research and Innovation Centre, San Michele a/A, Trento, Italy
| | - Marti Pottorff
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, 28081, USA
| | - Jessica A Spencer
- Department of Horticulture, North Carolina State University, Raleigh, NC, 27607, USA
| | - Penelope Perkins-Veazie
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, 28081, USA.
- Department of Horticulture, North Carolina State University, Raleigh, NC, 27607, USA.
| | - Massimo Iorizzo
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, 28081, USA.
- Department of Horticulture, North Carolina State University, Raleigh, NC, 27607, USA.
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Nonaka S, Ezura H. Possibility of genome editing for melon breeding. BREEDING SCIENCE 2024; 74:47-58. [PMID: 39246433 PMCID: PMC11375426 DOI: 10.1270/jsbbs.23074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 03/07/2024] [Indexed: 09/10/2024]
Abstract
Genome editing technologies are promising for conventional mutagenesis breeding, which takes a long time to remove unnecessary mutations through backcrossing and create new lines because they directly modify the target genes of elite strains. In particular, this technology has advantages for traits caused by the loss of function. Many efforts have been made to utilize this technique to introduce valuable features into crops, including maize, soybeans, and tomatoes. Several genome-edited crops have already been commercialized in the US and Japan. Melons are an important vegetable crop worldwide, produced and used in various areas. Therefore, many breeding efforts have been made to improve its fruit quality, resistance to plant diseases, and stress tolerance. Quantitative trait loci (QTL) analysis was performed, and various genes related to important traits were identified. Recently, several studies have shown that the CRISPR/Cas9 system can be applied to melons, resulting in its possible utilization as a breeding technique. Focusing on two productivity-related traits, disease resistance, and fruit quality, this review introduces the progress in genetics, examples of melon breeding through genome editing, improvements required for breeding applications, and the possibilities of genome editing in melon breeding.
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Affiliation(s)
- Satoko Nonaka
- Laboratory of Vegetable and Ornamental Horticulture, Institute of Life and Environmental Sciences and Tsukuba-Plant Innovation Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Hiroshi Ezura
- Laboratory of Vegetable and Ornamental Horticulture, Institute of Life and Environmental Sciences and Tsukuba-Plant Innovation Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
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3
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Shahwar D, Khan Z, Park Y. Molecular Marker-Assisted Mapping, Candidate Gene Identification, and Breeding in Melon ( Cucumis melo L.): A Review. Int J Mol Sci 2023; 24:15490. [PMID: 37895169 PMCID: PMC10607903 DOI: 10.3390/ijms242015490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
Melon (Cucumis melo L.) is an important crop that is cultivated worldwide for its fleshy fruit. Understanding the genetic basis of a plant's qualitative and quantitative traits is essential for developing consumer-favored varieties. This review presents genetic and molecular advances related to qualitative and quantitative phenotypic traits and biochemical compounds in melons. This information guides trait incorporation and the production of novel varieties with desirable horticultural and economic characteristics and yield performance. This review summarizes the quantitative trait loci, candidate genes, and development of molecular markers related to plant architecture, branching patterns, floral attributes (sex expression and male sterility), fruit attributes (shape, rind and flesh color, yield, biochemical compounds, sugar content, and netting), and seed attributes (seed coat color and size). The findings discussed in this review will enhance demand-driven breeding to produce cultivars that benefit consumers and melon breeders.
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Affiliation(s)
- Durre Shahwar
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, Republic of Korea;
| | - Zeba Khan
- Center for Agricultural Education, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh 202002, India;
| | - Younghoon Park
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, Republic of Korea;
- Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea
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4
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Song Z, Zhu X, Lai X, Chen H, Wang L, Yao Y, Chen W, Li X. MaBEL1 regulates banana fruit ripening by activating cell wall and starch degradation-related genes. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2036-2055. [PMID: 37177912 DOI: 10.1111/jipb.13506] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/12/2023] [Indexed: 05/15/2023]
Abstract
Banana is a typical subtropical fruit, sensitive to chilling injuries and prone to softening disorder. However, the underlying regulatory mechanisms of the softening disorder caused by cold stress remain obscure. Herein, we found that BEL1-LIKE HOMEODOMAIN transcription factor 1 (MaBEL1) and its associated proteins regulate the fruit softening and ripening process. The transcript and protein levels of MaBEL1 were up-regulated with fruit ripening but severely repressed by the chilling stress. Moreover, the MaBEL1 protein interacted directly with the promoters of the cell wall and starch degradation-related genes, such as MaAMY3, MaXYL32, and MaEXP-A8. The transient overexpression of MaBEL1 alleviated fruit chilling injury and ripening disorder caused by cold stress and promoted fruit softening and ripening of "Fenjiao" banana by inducing ethylene production and starch and cell wall degradation. The accelerated ripening was also validated by the ectopic overexpression in tomatoes. Conversely, MaBEL1-silencing aggravated the chilling injury and ripening disorder and repressed fruit softening and ripening by inhibiting ethylene production and starch and cell wall degradation. MaABI5-like and MaEBF1, the two positive regulators of the fruit softening process, interacted with MaBEL1 to enhance the promoter activity of the starch and cell wall degradation-related genes. Moreover, the F-box protein MaEBF1 does not modulate the degradation of MaBEL1, which regulates the transcription of MaABI5-like protein. Overall, we report a novel MaBEL1-MaEBF1-MaABI5-like complex system that mediates the fruit softening and ripening disorder in "Fenjiao" bananas caused by cold stress.
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Affiliation(s)
- Zunyang Song
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
- Key Laboratory of Food Processing Technology and Quality Control in Shandong Province, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China
| | - Xiaoyang Zhu
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Xiuhua Lai
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Hangcong Chen
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Lihua Wang
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Yulin Yao
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Weixin Chen
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Xueping Li
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
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5
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Yan H, Wang K, Wang M, Feng L, Zhang H, Wei X. QTL Mapping and Genome-Wide Association Study Reveal Genetic Loci and Candidate Genes Related to Soluble Solids Content in Melon. Curr Issues Mol Biol 2023; 45:7110-7129. [PMID: 37754234 PMCID: PMC10530127 DOI: 10.3390/cimb45090450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/21/2023] [Accepted: 08/25/2023] [Indexed: 09/28/2023] Open
Abstract
Melon (Cucumis melo L.) is an economically important Cucurbitaceae crop grown around the globe. The sweetness of melon is a significant factor in fruit quality and consumer appeal, and the soluble solids content (SSC) is a key index of melon sweetness. In this study, 146 recombinant inbred lines (RILs) derived from two oriental melon materials with different levels of sweetness containing 1427 bin markers, and 213 melon accessions containing 1,681,775 single nucleotide polymorphism (SNP) markers were used to identify genomic regions influencing SSC. Linkage mapping detected 10 quantitative trait loci (QTLs) distributed on six chromosomes, seven of which were overlapped with the reported QTLs. A total of 211 significant SNPs were identified by genome-wide association study (GWAS), 138 of which overlapped with the reported QTLs. Two new stable, co-localized regions on chromosome 3 were identified by QTL mapping and GWAS across multiple environments, which explained large phenotypic variance. Five candidate genes related to SSC were identified by QTL mapping, GWAS, and qRT-PCR, two of which were involved in hydrolysis of raffinose and sucrose located in the new stable loci. The other three candidate genes were involved in raffinose synthesis, sugar transport, and production of substrate for sugar synthesis. The genomic regions and candidate genes will be helpful for molecular breeding programs and elucidating the mechanisms of sugar accumulation.
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Campos M, Gonzalo MJ, Díaz A, Picó B, Gómez-Guillamón ML, Monforte AJ, Esteras C. A Novel Introgression Line Library Derived from a Wild Melon Gives Insights into the Genetics of Melon Domestication, Uncovering New Genetic Variability Useful for Breeding. Int J Mol Sci 2023; 24:10099. [PMID: 37373247 DOI: 10.3390/ijms241210099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/06/2023] [Accepted: 06/10/2023] [Indexed: 06/29/2023] Open
Abstract
A collection of 30 melon introgression lines (ILs) was developed from the wild accession Ames 24297 (TRI) into 'Piel de Sapo' (PS) genetic background. Each IL carried an average of 1.4 introgressions from TRI, and the introgressions represented 91.4% of the TRI genome. Twenty-two ILs, representing 75% of the TRI genome, were evaluated in greenhouse (Algarrobo and Meliana) and field (Alcàsser) trials, mainly to study traits related to domestication syndrome such as fruit weight (FW) and flesh content (FFP), as well as other fruit quality traits as fruit shape (FS), flesh firmness (FF), soluble solid concentration (SSC), rind color and abscission layer. The IL collection showed an impressive variation in size-related traits, with FW ranging from 800 to 4100 g, reflecting the strong effect of the wild genome on these traits. Most of the ILs produced smaller fruits compared with PS; however, unexpectedly, the IL TRI05-2 produced bigger fruits, likely due to new epistatic interacions with the PS genetic background. In contrast, the genotypic effect for FS was smaller, and few QTLs with notable effects were detected. Interestingly, variability was also observed for FFP, FF and SSC, rind color and abscission layer formation. Genes in these introgressions are candidates for having been involved in melon domestication and diversification as well. These results confirm that the TRI IL collection is a very powerful tool for mapping traits of agronomic interest in melon, allowing the confirmation of previously reported QTLs and the identification of new ones to better understand the domestication process of this crop.
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Affiliation(s)
- Manuel Campos
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
| | - Maria José Gonzalo
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
| | - Aurora Díaz
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
- Departamento de Ciencia Vegetal, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Avda, Montañana 930, 50059 Zaragoza, Spain
- Instituto Agroalimentario de Aragón-IA2, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Universidad de Zaragoza, 50013 Zaragoza, Spain
| | - Belén Picó
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV-UPV), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Maria Luisa Gómez-Guillamón
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora' (IHSM, CSIC-UMA), Algarrobo-Costa, 29750 Málaga, Spain
| | - Antonio José Monforte
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
| | - Cristina Esteras
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV-UPV), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
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7
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Gao G, Yang F, Wang C, Duan X, Li M, Ma Y, Wang F, Qi H. The transcription factor CmERFI-2 represses CmMYB44 expression to increase sucrose levels in oriental melon fruit. PLANT PHYSIOLOGY 2023; 192:1378-1395. [PMID: 36938625 PMCID: PMC10231561 DOI: 10.1093/plphys/kiad155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 11/29/2022] [Accepted: 11/29/2022] [Indexed: 06/01/2023]
Abstract
Soluble sugar accumulation in fruit ripening determines fleshy fruit quality. However, the molecular mechanism for this process is not yet understood. Here, we showed a transcriptional repressor, CmMYB44 regulates sucrose accumulation and ethylene synthesis in oriental melon (Cucumis. melo var. makuwa Makino) fruit. Overexpressing CmMYB44 suppressed sucrose accumulation and ethylene production. Furthermore, CmMYB44 repressed the transcriptional activation of CmSPS1 (sucrose phosphate synthase 1) and CmACO1 (ACC oxidase 1), two key genes in sucrose and ethylene accumulation, respectively. During the later stages of fruit ripening, the repressive effect of CmMYB44 on CmSPS1 and CmACO1 could be released by overexpressing CmERFI-2 (ethylene response factor I-2) and exogenous ethylene in "HS" fruit (high sucrose accumulation fruit). CmERFI-2 acted upstream of CmMYB44 as a repressor by directly binding the CmMYB44 promoter region, indirectly stimulating the expression level of CmSPS1 and CmACO1. Taken together, we provided a molecular regulatory pathway mediated by CmMYB44, which determines the degree of sucrose and ethylene accumulation in oriental melon fruit and sheds light on transcriptional responses triggered by ethylene sensing that enable the process of fruit ripening.
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Affiliation(s)
- Ge Gao
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Protected Horticulture of Education of Ministry and Liaoning Province/National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology, Shenyang 110866, China
| | - Fan Yang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Protected Horticulture of Education of Ministry and Liaoning Province/National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology, Shenyang 110866, China
| | - Cheng Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Protected Horticulture of Education of Ministry and Liaoning Province/National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology, Shenyang 110866, China
| | - Xiaoyu Duan
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Protected Horticulture of Education of Ministry and Liaoning Province/National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology, Shenyang 110866, China
| | - Meng Li
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Protected Horticulture of Education of Ministry and Liaoning Province/National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology, Shenyang 110866, China
| | - Yue Ma
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Feng Wang
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Hongyan Qi
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Protected Horticulture of Education of Ministry and Liaoning Province/National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology, Shenyang 110866, China
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8
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Zhao H, Zhang T, Meng X, Song J, Zhang C, Gao P. Genetic Mapping and QTL Analysis of Fruit Traits in Melon ( Cucumis melo L.). Curr Issues Mol Biol 2023; 45:3419-3433. [PMID: 37185748 PMCID: PMC10137213 DOI: 10.3390/cimb45040224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 05/17/2023] Open
Abstract
Melon (Cucumis melo L.) is an important horticultural cash crop and its quality traits directly affect consumer choice and market price. These traits are controlled by genetic as well as environmental factors. In this study, a quantitative trait locus (QTL) mapping strategy was used to identify the potential genetic loci controlling quality traits of melons (i.e., exocarp and pericarp firmness and soluble solid content) based on newly derived whole-genome single nucleotide polymorphism-based cleaved amplified polymorphic sequence (SNP-CAPS) markers. Specifically, SNPs of two melon varieties, M4-5 and M1-15, as revealed by whole-genome sequencing, were converted to the CAPS markers, which were used to construct a genetic linkage map comprising 12 chromosomes with a total length of 1414.88 cM, in the F2 population of M4-5 and M1-15. The six identified QTLs included: SSC6.1 and SSC11.1 related to soluble solid content; EF12.1 associated with exocarp firmness; and EPF3.1, EPF3.2 and EPF7.1 related to edible pericarp firmness. These genes were located on five chromosomes (3, 6, 7, 11, and 12) in the flanking regions of the CAPS markers. Moreover, the newly developed CAPS markers will be useful in guiding genetic engineering and molecular breeding in melon.
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Affiliation(s)
- Haiyong Zhao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600, Changjiang Road, Harbin 150030, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Taifeng Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600, Changjiang Road, Harbin 150030, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Xiaobing Meng
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600, Changjiang Road, Harbin 150030, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Jiayan Song
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600, Changjiang Road, Harbin 150030, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Chen Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600, Changjiang Road, Harbin 150030, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Peng Gao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600, Changjiang Road, Harbin 150030, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
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9
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Hussain A, Farooq M, Naqvi RZ, Aslam MQ, Siddiqui HA, Amin I, Liu C, Liu X, Scheffler J, Asif M, Mansoor S. Whole-Genome Resequencing Deciphers New Insight Into Genetic Diversity and Signatures of Resistance in Cultivated Cotton Gossypium hirsutum. Mol Biotechnol 2023; 65:34-51. [PMID: 35778659 DOI: 10.1007/s12033-022-00527-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 06/07/2022] [Indexed: 01/11/2023]
Abstract
Cotton is an important crop that produces fiber and cottonseed oil for the textile and oil industry. However, cotton leaf curl virus disease (CLCuD) stress is limiting its yield in several Asian countries. In this study, we have sequenced Mac7 accession, a Gossypium hirsutum resistance source against several biotic stresses. By aligning with the Gossypium hirsutum (AD1) 'TM-1' genome, a total of 4.7 and 1.2 million SNPs and InDels were identified in the Mac7 genome. The gene ontology and metabolic pathway enrichment indicated SNPs and InDels role in nucleotide bindings, secondary metabolite synthesis, and plant-pathogen interaction pathways. Furthermore, the RNA-seq data in different tissues and qPCR expression profiling under CLCuD provided individual gene roles in resistant and susceptible accessions. Interestingly, the differential NLR genes demonstrated higher expression in resistant plants rather than in susceptible plants expression. The current resequencing results may provide primary data to identify DNA resistance markers which will be helpful in marker-assisted breeding for development of Mac7-derived resistance lines.
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Affiliation(s)
- Athar Hussain
- National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Muhammad Farooq
- National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan.,Bioinformatics Group, Wageningen University & Research (WUR), Wageningen, Netherlands
| | - Rubab Zahra Naqvi
- National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Muhammad Qasim Aslam
- National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Hamid Anees Siddiqui
- National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Imran Amin
- National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | | | - Xin Liu
- Beijing Genomics Institute (BGI), Shenzhen, China
| | - Jodi Scheffler
- Genomics and Bioinformatics Research Unit, United States Department of Agriculture-Agricultural Research Service, USDA-ARS), 141 Experimental Station Road, Stoneville, MS, USA
| | - Muhammad Asif
- National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan.
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10
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Oren E, Dafna A, Tzuri G, Halperin I, Isaacson T, Elkabetz M, Meir A, Saar U, Ohali S, La T, Romay C, Tadmor Y, Schaffer AA, Buckler ES, Cohen R, Burger J, Gur A. Pan-genome and multi-parental framework for high-resolution trait dissection in melon (Cucumis melo). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1525-1542. [PMID: 36353749 PMCID: PMC10100132 DOI: 10.1111/tpj.16021] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/27/2022] [Accepted: 10/29/2022] [Indexed: 06/16/2023]
Abstract
Linking genotype with phenotype is a fundamental goal in biology and requires robust data for both. Recent advances in plant-genome sequencing have expedited comparisons among multiple-related individuals. The abundance of structural genomic within-species variation that has been discovered indicates that a single reference genome cannot represent the complete sequence diversity of a species, leading to the expansion of the pan-genome concept. For high-resolution forward genetics, this unprecedented access to genomic variation should be paralleled and integrated with phenotypic characterization of genetic diversity. We developed a multi-parental framework for trait dissection in melon (Cucumis melo), leveraging a novel pan-genome constructed for this highly variable cucurbit crop. A core subset of 25 diverse founders (MelonCore25), consisting of 24 accessions from the two widely cultivated subspecies of C. melo, encompassing 12 horticultural groups, and 1 feral accession was sequenced using a combination of short- and long-read technologies, and their genomes were assembled de novo. The construction of this melon pan-genome exposed substantial variation in genome size and structure, including detection of ~300 000 structural variants and ~9 million SNPs. A half-diallel derived set of 300 F2 populations, representing all possible MelonCore25 parental combinations, was constructed as a framework for trait dissection through integration with the pan-genome. We demonstrate the potential of this unified framework for genetic analysis of various melon traits, including rind color intensity and pattern, fruit sugar content, and resistance to fungal diseases. We anticipate that utilization of this integrated resource will enhance genetic dissection of important traits and accelerate melon breeding.
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Affiliation(s)
- Elad Oren
- Cucurbits Section, Department of Vegetable SciencesAgricultural Research Organization, Newe Ya‘ar Research CenterP.O. Box 1021Ramat Yishay3009500Israel
| | - Asaf Dafna
- Cucurbits Section, Department of Vegetable SciencesAgricultural Research Organization, Newe Ya‘ar Research CenterP.O. Box 1021Ramat Yishay3009500Israel
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of AgricultureThe Hebrew University of JerusalemRehovotIsrael
| | - Galil Tzuri
- Cucurbits Section, Department of Vegetable SciencesAgricultural Research Organization, Newe Ya‘ar Research CenterP.O. Box 1021Ramat Yishay3009500Israel
| | - Ilan Halperin
- Cucurbits Section, Department of Vegetable SciencesAgricultural Research Organization, Newe Ya‘ar Research CenterP.O. Box 1021Ramat Yishay3009500Israel
| | - Tal Isaacson
- Cucurbits Section, Department of Vegetable SciencesAgricultural Research Organization, Newe Ya‘ar Research CenterP.O. Box 1021Ramat Yishay3009500Israel
| | - Meital Elkabetz
- Cucurbits Section, Department of Vegetable SciencesAgricultural Research Organization, Newe Ya‘ar Research CenterP.O. Box 1021Ramat Yishay3009500Israel
| | - Ayala Meir
- Cucurbits Section, Department of Vegetable SciencesAgricultural Research Organization, Newe Ya‘ar Research CenterP.O. Box 1021Ramat Yishay3009500Israel
| | - Uzi Saar
- Cucurbits Section, Department of Vegetable SciencesAgricultural Research Organization, Newe Ya‘ar Research CenterP.O. Box 1021Ramat Yishay3009500Israel
| | - Shachar Ohali
- Cucurbits Section, Department of Vegetable SciencesAgricultural Research Organization, Newe Ya‘ar Research CenterP.O. Box 1021Ramat Yishay3009500Israel
| | - Thuy La
- Institute for Genomic Diversity, Cornell UniversityIthacaNew York14853USA
| | - Cinta Romay
- Institute for Genomic Diversity, Cornell UniversityIthacaNew York14853USA
| | - Yaakov Tadmor
- Cucurbits Section, Department of Vegetable SciencesAgricultural Research Organization, Newe Ya‘ar Research CenterP.O. Box 1021Ramat Yishay3009500Israel
| | - Arthur A. Schaffer
- Department of Vegetable SciencesInstitute of Plant Sciences, Agricultural Research Organization, The Volcani CenterP.O. Box 15159Rishon LeZiyyon7507101Israel
| | - Edward S. Buckler
- Institute for Genomic Diversity, Cornell UniversityIthacaNew York14853USA
- United States Department of Agriculture‐Agricultural Research ServiceRobert W. Holley Center for Agriculture and HealthIthacaNew York14853USA
| | - Roni Cohen
- Cucurbits Section, Department of Vegetable SciencesAgricultural Research Organization, Newe Ya‘ar Research CenterP.O. Box 1021Ramat Yishay3009500Israel
| | - Joseph Burger
- Cucurbits Section, Department of Vegetable SciencesAgricultural Research Organization, Newe Ya‘ar Research CenterP.O. Box 1021Ramat Yishay3009500Israel
| | - Amit Gur
- Cucurbits Section, Department of Vegetable SciencesAgricultural Research Organization, Newe Ya‘ar Research CenterP.O. Box 1021Ramat Yishay3009500Israel
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11
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Santo Domingo M, Mayobre C, Pereira L, Argyris J, Valverde L, Martín-Hernández AM, Garcia-Mas J, Pujol M. Fruit Morphology and Ripening-Related QTLs in a Newly Developed Introgression Line Collection of the Elite Varieties 'Védrantais' and 'Piel de Sapo'. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11223120. [PMID: 36432848 PMCID: PMC9694011 DOI: 10.3390/plants11223120] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/21/2022] [Accepted: 11/10/2022] [Indexed: 05/28/2023]
Abstract
Melon is an economically important crop with widely diverse fruit morphology and ripening characteristics. Its diploid sequenced genome and multiple genomic tools make this species suitable to study the genetic architecture of fruit traits. With the development of this introgression line population of the elite varieties 'Piel de Sapo' and 'Védrantais', we present a powerful tool to study fruit morphology and ripening traits that can also facilitate characterization or pyramidation of QTLs in inodorous melon types. The population consists of 36 lines covering almost 98% of the melon genome, with an average of three introgressions per chromosome and segregating for multiple fruit traits: morphology, ripening and quality. High variability in fruit morphology was found within the population, with 24 QTLs affecting six different traits, confirming previously reported QTLs and two newly detected QTLs, FLQW5.1 and FWQW7.1. We detected 20 QTLs affecting fruit ripening traits, six of them reported for the first time, two affecting the timing of yellowing of the rind (EYELLQW1.1 and EYELLQW8.1) and four at the end of chromosome 8 affecting aroma, abscission and harvest date (EAROQW8.3, EALFQW8.3, ABSQW8.3 and HARQW8.3). We also confirmed the location of several QTLs, such as fruit-quality-related QTLs affecting rind and flesh appearance and flesh firmness.
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Affiliation(s)
- Miguel Santo Domingo
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Barcelona, Spain
| | - Carlos Mayobre
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Barcelona, Spain
| | - Lara Pereira
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Barcelona, Spain
| | - Jason Argyris
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), 08193 Barcelona, Spain
| | - Laura Valverde
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Barcelona, Spain
| | - Ana Montserrat Martín-Hernández
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), 08193 Barcelona, Spain
| | - Jordi Garcia-Mas
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), 08193 Barcelona, Spain
| | - Marta Pujol
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), 08193 Barcelona, Spain
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12
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Fine Mapping and Functional Analysis of Major Regulatory Genes of Soluble Solids Content in Wax Gourd (Benincasa hispida). Int J Mol Sci 2022; 23:ijms23136999. [PMID: 35806004 PMCID: PMC9266771 DOI: 10.3390/ijms23136999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 11/17/2022] Open
Abstract
Soluble solids content (SSC) is an important quality trait of wax gourd, but reports about its regulatory genes are scarce. In this study, the SSC regulatory gene BhSSC2.1 in wax gourd was mined via quantitative trait locus (QTL) mapping based on high-density genetic mapping containing 12 linkage groups (LG) and bulked segregant analysis (BSA)-seq. QTL mapping and BSA-seq revealed for the first time that the SSC QTL (107.658–108.176 cM) of wax gourd was on Chr2 (LG2). The interpretable phenotypic variation rate and maximum LOD were 16.033% and 6.454, respectively. The QTL interval contained 13 genes. Real-time fluorescence quantitative expression analysis, functional annotation, and sequence analysis suggested that Bch02G016960, named BhSSC2.1, was a candidate regulatory gene of the SSC in wax gourd. Functional annotation of this gene showed that it codes for a NADP-dependent malic enzyme. According to BhSSC2.1 sequence variation, an InDel marker was developed for molecular marker-assisted breeding of wax gourd. This study will lay the foundation for future studies regarding breeding and understanding genetic mechanisms of wax gourd.
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13
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Wang Z, Ma B, Yang N, Jin L, Wang L, Ma S, Ruan YL, Ma F, Li M. Variation in the promoter of the sorbitol dehydrogenase gene MdSDH2 affects binding of the transcription factor MdABI3 and alters fructose content in apple fruit. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1183-1198. [PMID: 34888978 DOI: 10.1111/tpj.15624] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/14/2021] [Accepted: 12/06/2021] [Indexed: 06/13/2023]
Abstract
Fructose (Fru) content is a key determinant of fruit sweetness and quality. An F1 hybrid population of the apple cultivars 'Honeycrisp' × 'Qinguan' was used to investigate the quantitative trait locus (QTL) regions and genes controlling Fru content in fruit. A stable QTL on linkage group (LG) 01 in 'Honeycrisp' was detected on the single nucleotide polymorphism (SNP) genetic linkage maps. In this region, a sorbitol dehydrogenase (SDH) gene, MdSDH2, was detected and showed promoter variations and differential expression patterns between 'Honeycrisp' and 'Qinguan' fruits as well as their hybrids. A SNP variant (A/G) in the MdSDH2 promoter region (SDH2p-491) affected the binding ability of the transcription factor MdABI3, which can affect the expression of MdSDH2. Promoter sequences with an A nucleotide at SDH2p-491 had stronger binding affinity for MdABI3 than those with a G. Among 27 domesticated apple cultivars and wild relatives, this SNP (A/G) was associated with Fru content. Our results indicate that MdSDH2 can alter Fru content as the major regulatory gene and that ABA signaling might be involved in Fru content accumulation in apple fruit.
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Affiliation(s)
- Zhengyang Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Baiquan Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Nanxiang Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ling Jin
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lan Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Songya Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yong-Ling Ruan
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Mingjun Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
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14
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Wang X, Ando K, Wu S, Reddy UK, Tamang P, Bao K, Hammar SA, Grumet R, McCreight JD, Fei Z. Genetic characterization of melon accessions in the U.S. National Plant Germplasm System and construction of a melon core collection. MOLECULAR HORTICULTURE 2021; 1:11. [PMID: 37789496 PMCID: PMC10515074 DOI: 10.1186/s43897-021-00014-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/25/2021] [Indexed: 09/28/2023]
Abstract
Melon (C. melo L.) is an economically important vegetable crop cultivated worldwide. The melon collection in the U.S. National Plant Germplasm System (NPGS) is a valuable resource to conserve natural genetic diversity and provide novel traits for melon breeding. Here we use the genotyping-by-sequencing (GBS) technology to characterize 2083 melon accessions in the NPGS collected from major melon production areas as well as regions where primitive melons exist. Population structure and genetic diversity analyses suggested that C. melo ssp. melo was firstly introduced from the centers of origin, Indian and Pakistan, to Central and West Asia, and then brought to Europe and Americas. C. melo ssp. melo from East Asia was likely derived from C. melo ssp. agrestis in India and Pakistan and displayed a distinct genetic background compared to the rest of ssp. melo accessions from other geographic regions. We developed a core collection of 383 accessions capturing more than 98% of genetic variation in the germplasm, providing a publicly accessible collection for future research and genomics-assisted breeding of melon. Thirty-five morphological characters investigated in the core collection indicated high variability of these characters across accessions in the collection. Genome-wide association studies using the core collection panel identified potentially associated genome regions related to fruit quality and other horticultural traits. This study provides insights into melon origin and domestication, and the constructed core collection and identified genome loci potentially associated with important traits provide valuable resources for future melon research and breeding.
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Affiliation(s)
- Xin Wang
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Kaori Ando
- U.S. Department of Agriculture-Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA, 93905, USA
- Nunhems USA, Inc, Acampo, CA, 95220, USA
| | - Shan Wu
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Umesh K Reddy
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, 25112, USA
| | - Prabin Tamang
- U.S. Department of Agriculture-Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA, 93905, USA
- U.S. Department of Agriculture-Agricultural Research Service, Natural Products Utilization Research Unit, Thad Cochran Research Center, P.O. Box 1848, Oxford, MS, 38677, USA
| | - Kan Bao
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Sue A Hammar
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Rebecca Grumet
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - James D McCreight
- U.S. Department of Agriculture-Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA, 93905, USA.
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA.
- U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA.
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15
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Hyun DY, Sebastin R, Lee GA, Lee KJ, Kim SH, Yoo E, Lee S, Kang MJ, Lee SB, Jang I, Ro NY, Cho GT. Genome-Wide SNP Markers for Genotypic and Phenotypic Differentiation of Melon ( Cucumis melo L.) Varieties Using Genotyping-by-Sequencing. Int J Mol Sci 2021; 22:ijms22136722. [PMID: 34201603 PMCID: PMC8268568 DOI: 10.3390/ijms22136722] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/16/2021] [Accepted: 06/16/2021] [Indexed: 12/29/2022] Open
Abstract
Melon (Cucumis melo L.) is an economically important horticultural crop with abundant morphological and genetic variability. Complex genetic variations exist even among melon varieties and remain unclear to date. Therefore, unraveling the genetic variability among the three different melon varieties, muskmelon (C. melo subsp. melo), makuwa (C. melo L. var. makuwa), and cantaloupes (C. melo subsp. melo var. cantalupensis), could provide a basis for evolutionary research. In this study, we attempted a systematic approach with genotyping-by-sequencing (GBS)-derived single nucleotide polymorphisms (SNPs) to reveal the genetic structure and diversity, haplotype differences, and marker-based varieties differentiation. A total of 6406 GBS-derived SNPs were selected for the diversity analysis, in which the muskmelon varieties showed higher heterozygote SNPs. Linkage disequilibrium (LD) decay varied significantly among the three melon varieties, in which more rapid LD decay was observed in muskmelon (r2 = 0.25) varieties. The Bayesian phylogenetic tree provided the intraspecific relationships among the three melon varieties that formed, as expected, individual clusters exhibiting the greatest genetic distance based on the posterior probability. The haplotype analysis also supported the phylogeny result by generating three major networks for 48 haplotypes. Further investigation for varieties discrimination allowed us to detect a total of 52 SNP markers that discriminated muskmelon from makuwa varieties, of which two SNPs were converted into cleaved amplified polymorphic sequence markers for practical use. In addition to these markers, the genome-wide association study identified two SNPs located in the genes on chromosome 6, which were significantly associated with the phenotypic traits of melon seed. This study demonstrated that a systematic approach using GBS-derived SNPs could serve to efficiently classify and manage the melon varieties in the genebank.
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Affiliation(s)
- Do Yoon Hyun
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Jeonju 54874, Korea; (R.S.); (G.-A.L.); (K.J.L.); (S.-H.K.); (E.Y.); (S.L.); (M.-J.K.); (S.B.L.); (I.J.); (N.-Y.R.); (G.-T.C.)
- Correspondence:
| | - Raveendar Sebastin
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Jeonju 54874, Korea; (R.S.); (G.-A.L.); (K.J.L.); (S.-H.K.); (E.Y.); (S.L.); (M.-J.K.); (S.B.L.); (I.J.); (N.-Y.R.); (G.-T.C.)
| | - Gi-An Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Jeonju 54874, Korea; (R.S.); (G.-A.L.); (K.J.L.); (S.-H.K.); (E.Y.); (S.L.); (M.-J.K.); (S.B.L.); (I.J.); (N.-Y.R.); (G.-T.C.)
| | - Kyung Jun Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Jeonju 54874, Korea; (R.S.); (G.-A.L.); (K.J.L.); (S.-H.K.); (E.Y.); (S.L.); (M.-J.K.); (S.B.L.); (I.J.); (N.-Y.R.); (G.-T.C.)
- Honam National Institute of Biological Resources, Mokpo-si 58762, Korea
| | - Seong-Hoon Kim
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Jeonju 54874, Korea; (R.S.); (G.-A.L.); (K.J.L.); (S.-H.K.); (E.Y.); (S.L.); (M.-J.K.); (S.B.L.); (I.J.); (N.-Y.R.); (G.-T.C.)
| | - Eunae Yoo
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Jeonju 54874, Korea; (R.S.); (G.-A.L.); (K.J.L.); (S.-H.K.); (E.Y.); (S.L.); (M.-J.K.); (S.B.L.); (I.J.); (N.-Y.R.); (G.-T.C.)
| | - Sookyeong Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Jeonju 54874, Korea; (R.S.); (G.-A.L.); (K.J.L.); (S.-H.K.); (E.Y.); (S.L.); (M.-J.K.); (S.B.L.); (I.J.); (N.-Y.R.); (G.-T.C.)
| | - Man-Jung Kang
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Jeonju 54874, Korea; (R.S.); (G.-A.L.); (K.J.L.); (S.-H.K.); (E.Y.); (S.L.); (M.-J.K.); (S.B.L.); (I.J.); (N.-Y.R.); (G.-T.C.)
| | - Seung Bum Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Jeonju 54874, Korea; (R.S.); (G.-A.L.); (K.J.L.); (S.-H.K.); (E.Y.); (S.L.); (M.-J.K.); (S.B.L.); (I.J.); (N.-Y.R.); (G.-T.C.)
| | - Ik Jang
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Jeonju 54874, Korea; (R.S.); (G.-A.L.); (K.J.L.); (S.-H.K.); (E.Y.); (S.L.); (M.-J.K.); (S.B.L.); (I.J.); (N.-Y.R.); (G.-T.C.)
| | - Na-Young Ro
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Jeonju 54874, Korea; (R.S.); (G.-A.L.); (K.J.L.); (S.-H.K.); (E.Y.); (S.L.); (M.-J.K.); (S.B.L.); (I.J.); (N.-Y.R.); (G.-T.C.)
| | - Gyu-Taek Cho
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Jeonju 54874, Korea; (R.S.); (G.-A.L.); (K.J.L.); (S.-H.K.); (E.Y.); (S.L.); (M.-J.K.); (S.B.L.); (I.J.); (N.-Y.R.); (G.-T.C.)
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16
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Pereira L, Santo Domingo M, Argyris J, Mayobre C, Valverde L, Martín-Hernández AM, Pujol M, Garcia-Mas J. A novel introgression line collection to unravel the genetics of climacteric ripening and fruit quality in melon. Sci Rep 2021; 11:11364. [PMID: 34059766 PMCID: PMC8166866 DOI: 10.1038/s41598-021-90783-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 05/18/2021] [Indexed: 11/09/2022] Open
Abstract
Introgression lines are valuable germplasm for scientists and breeders, since they ease genetic studies such as QTL interactions and positional cloning as well as the introduction of favorable alleles into elite varieties. We developed a novel introgression line collection in melon using two commercial European varieties with different ripening behavior, the climacteric cantalupensis 'Védrantais' as recurrent parent and the non-climacteric inodorus 'Piel de Sapo' as donor parent. The collection contains 34 introgression lines, covering 99% of the donor genome. The mean introgression size is 18.16 Mb and ~ 3 lines were obtained per chromosome, on average. The high segregation of these lines for multiple fruit quality traits allowed us to identify 27 QTLs that modified sugar content, altered fruit morphology or were involved in climacteric ripening. In addition, we confirmed the genomic location of five major genes previously described, which control mainly fruit appearance, such as mottled rind and external color. Most of the QTLs had been reported before in other populations sharing parental lines, while three QTLs (EAROQP11.3, ECDQP11.2 and FIRQP4.1) were newly detected in our work. These introgression lines would be useful to perform additional genetic studies, as fine mapping and gene pyramiding, especially for important complex traits such as fruit weight and climacteric ripening.
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Affiliation(s)
- Lara Pereira
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193, Bellaterra, Barcelona, Spain
| | - Miguel Santo Domingo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193, Bellaterra, Barcelona, Spain
| | - Jason Argyris
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193, Bellaterra, Barcelona, Spain.,Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, 08193, Bellaterra, Barcelona, Spain
| | - Carlos Mayobre
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193, Bellaterra, Barcelona, Spain
| | - Laura Valverde
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193, Bellaterra, Barcelona, Spain
| | - Ana Montserrat Martín-Hernández
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193, Bellaterra, Barcelona, Spain.,Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, 08193, Bellaterra, Barcelona, Spain
| | - Marta Pujol
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193, Bellaterra, Barcelona, Spain. .,Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, 08193, Bellaterra, Barcelona, Spain.
| | - Jordi Garcia-Mas
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193, Bellaterra, Barcelona, Spain. .,Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, 08193, Bellaterra, Barcelona, Spain.
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Discovery of SNPs and InDels in papaya genotypes and its potential for marker assisted selection of fruit quality traits. Sci Rep 2021; 11:292. [PMID: 33431939 PMCID: PMC7801719 DOI: 10.1038/s41598-020-79401-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/08/2020] [Indexed: 01/29/2023] Open
Abstract
Papaya is a tropical and climacteric fruit that is recognized for its nutritional benefits and medicinal applications. Its fruits ripen quickly and show a drastic fruit softening, leading to great post-harvest losses. To overcome this scenario, breeding programs of papaya must invest in exploring the available genetic variation to continue developing superior cultivars with improved fruit quality traits. The objective of this study was to perform a whole-genome genotyping (WGG) of papaya, predict the effects of the identified variants, and develop a list of ripening-related genes (RRGs) with linked variants. The Formosa elite lines of papaya Sekati and JS-12 were submitted to WGG with an Illumina Miseq platform. The effects of variants were predicted using the snpEff program. A total of 28,451 SNPs having Ts/Tv (Transition/Transversion) ratio of 2.45 and 1,982 small insertions/deletions (InDels) were identified. Most variant effects were predicted in non-coding regions, with only 2,104 and 138 effects placed in exons and splice site regions, respectively. A total of 106 RRGs were found to be associated with 460 variants, which may be converted into PCR markers to facilitate genetic mapping and diversity studies and to apply marker-assisted selection (MAS) for specific traits in papaya breeding programs.
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Liu S, Gao P, Zhu Q, Zhu Z, Liu H, Wang X, Weng Y, Gao M, Luan F. Resequencing of 297 melon accessions reveals the genomic history of improvement and loci related to fruit traits in melon. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:2545-2558. [PMID: 32559013 PMCID: PMC7680547 DOI: 10.1111/pbi.13434] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 06/01/2020] [Accepted: 06/04/2020] [Indexed: 05/21/2023]
Abstract
Domestication and improvement are two important stages in crop evolution. Melon (Cucumis melo L.) is an important vegetable crop with wide phenotypic diversity in many horticultural traits, especially fruit size, flesh thickness and aroma, which are likely the results of long-term extensive selection during its evolution. However, selective signals in domestication and improvement stages for these remarkable variations remain unclear. We resequenced 297 wild, landrace and improved melon accessions and obtained 2 045 412 high-quality SNPs. Population structure and genetic diversity analyses revealed independent and two-step selections in two subspecies of melon: ssp. melo and ssp. agrestis during melon breeding. We detected 233 (~18.35 Mbp) and 159 (~17.71 Mbp) novel potential selective signals during the improvement stage in ssp. agrestis and spp. melo, respectively. Two alcohol acyltransferase genes (CmAATs) unique to the melon genome compared with other cucurbit crops may have undergone stronger selection in ssp. agrestis for the characteristic aroma as compared with other cucurbits. Genome-wide association analysis identified eight fruit size and seven flesh thickness signals overlapping with selective sweeps. Compared with thin-skinned ssp. agrestis, thick-skinned ssp. melo has undergone a stronger selection for thicker flesh. In most melon accessions, CmCLV3 has pleiotropic effects on carpel number and fruit shape. Findings from this study provide novel insights into melon crop evolution, and new tools to advance melon breeding.
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Affiliation(s)
- Shi Liu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region)Ministry of Agriculture and Rural AffairsNortheast Agricultural UniversityHarbin CityHeilongjiang ProvinceChina
- College of Horticulture and Landscape ArchitectureNortheast Agricultural UniversityHarbin CityHeilongjiang ProvinceChina
| | - Peng Gao
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region)Ministry of Agriculture and Rural AffairsNortheast Agricultural UniversityHarbin CityHeilongjiang ProvinceChina
- College of Horticulture and Landscape ArchitectureNortheast Agricultural UniversityHarbin CityHeilongjiang ProvinceChina
| | - Qianglong Zhu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region)Ministry of Agriculture and Rural AffairsNortheast Agricultural UniversityHarbin CityHeilongjiang ProvinceChina
- College of Horticulture and Landscape ArchitectureNortheast Agricultural UniversityHarbin CityHeilongjiang ProvinceChina
| | - Zicheng Zhu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region)Ministry of Agriculture and Rural AffairsNortheast Agricultural UniversityHarbin CityHeilongjiang ProvinceChina
- College of Horticulture and Landscape ArchitectureNortheast Agricultural UniversityHarbin CityHeilongjiang ProvinceChina
| | - Hongyu Liu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region)Ministry of Agriculture and Rural AffairsNortheast Agricultural UniversityHarbin CityHeilongjiang ProvinceChina
- College of Horticulture and Landscape ArchitectureNortheast Agricultural UniversityHarbin CityHeilongjiang ProvinceChina
| | - Xuezheng Wang
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region)Ministry of Agriculture and Rural AffairsNortheast Agricultural UniversityHarbin CityHeilongjiang ProvinceChina
- College of Horticulture and Landscape ArchitectureNortheast Agricultural UniversityHarbin CityHeilongjiang ProvinceChina
| | - Yiqun Weng
- USDA‐ARSVegetable Crops Research UnitHorticulture DepartmentUniversity of WisconsinMadison CityWIUSA
| | - Meiling Gao
- College of Life Sciences, Agriculture and ForestryQiqihar UniversityQiqihar CityHeilongjiang ProvinceChina
| | - Feishi Luan
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region)Ministry of Agriculture and Rural AffairsNortheast Agricultural UniversityHarbin CityHeilongjiang ProvinceChina
- College of Horticulture and Landscape ArchitectureNortheast Agricultural UniversityHarbin CityHeilongjiang ProvinceChina
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19
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Seed protein content and its relationships with agronomic traits in pigeonpea is controlled by both main and epistatic effects QTLs. Sci Rep 2020; 10:214. [PMID: 31937848 PMCID: PMC6959250 DOI: 10.1038/s41598-019-56903-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/10/2019] [Indexed: 11/08/2022] Open
Abstract
The genetic architecture of seed protein content (SPC) and its relationships to agronomic traits in pigeonpea is poorly understood. Accordingly, five F2 populations segregating for SPC and four agronomic traits (seed weight (SW), seed yield (SY), growth habit (GH) and days to first flowering (DFF)) were phenotyped and genotyped using genotyping-by-sequencing approach. Five high-density population-specific genetic maps were constructed with an average inter-marker distance of 1.6 to 3.5 cM, and subsequently, integrated into a consensus map with average marker spacing of 1.6 cM. Based on analysis of phenotyping data and genotyping data, 192 main effect QTLs (M-QTLs) with phenotypic variation explained (PVE) of 0.7 to 91.3% were detected for the five traits across the five populations. Major effect (PVE ≥ 10%) M-QTLs included 14 M-QTLs for SPC, 16 M-QTLs for SW, 17 M-QTLs for SY, 19 M-QTLs for GH and 24 M-QTLs for DFF. Also, 573 epistatic QTLs (E-QTLs) were detected with PVE ranging from 6.3 to 99.4% across traits and populations. Colocalization of M-QTLs and E-QTLs explained the genetic basis of the significant (P < 0.05) correlations of SPC with SW, SY, DFF and GH. The nature of genetic architecture of SPC and its relationship with agronomic traits suggest that genomics-assisted breeding targeting genome-wide variations would be effective for the simultaneous improvement of SPC and other important traits.
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Zhang H, Li X, Yu H, Zhang Y, Li M, Wang H, Wang D, Wang H, Fu Q, Liu M, Ji C, Ma L, Tang J, Li S, Miao J, Zheng H, Yi H. A High-Quality Melon Genome Assembly Provides Insights into Genetic Basis of Fruit Trait Improvement. iScience 2019; 22:16-27. [PMID: 31739171 PMCID: PMC6864349 DOI: 10.1016/j.isci.2019.10.049] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/23/2019] [Accepted: 10/24/2019] [Indexed: 01/28/2023] Open
Abstract
Accurate reference genomes have become indispensable tools for characterization of genetic and functional variations. Here we generated a high-quality assembly of the melon Payzawat using a combination of short-read sequencing, single-molecule real-time sequencing, Hi-C, and a high-density genetic map. The final 12 chromosome-level scaffolds cover ∼94.13% of the estimated genome (398.57 Mb). Compared with the published DHL92 genome, our assembly exhibits a 157-fold increase in contig length and remarkable improvements in the assembly of centromeres and telomeres. Six genes within STHQF12.4 on pseudochromosome 12, identified from whole-genome comparison between Payzawat and DHL92, may explain a considerable proportion of the skin thickness. In addition, our population study showed that melon domesticated at multiple times from whole-genome perspective and melons in China are introduced from different routes. Selective sweeps underlying the genes related to desirable traits, haplotypes of alleles associated with agronomic traits, and the variants from resequencing data enable efficient breeding. Provides a high-quality assembly for melon genome Explains a considerable proportion of epidermis thickness Melons in China are introduced from different routes Haplotypes of alleles associated with agronomic traits enable efficient breeding
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Affiliation(s)
- Hong Zhang
- Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang 830091, China
| | - Xuming Li
- Biomarker Technologies Corporation, Beijing 101200, China
| | - Haiyan Yu
- Biomarker Technologies Corporation, Beijing 101200, China
| | - Yongbing Zhang
- Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang 830091, China
| | - Meihua Li
- Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang 830091, China
| | - Haojie Wang
- Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang 830091, China
| | - Dengming Wang
- Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang 830091, China
| | - Huaisong Wang
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qiushi Fu
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Min Liu
- Biomarker Technologies Corporation, Beijing 101200, China
| | - Changmian Ji
- Biomarker Technologies Corporation, Beijing 101200, China
| | - Liming Ma
- Biomarker Technologies Corporation, Beijing 101200, China
| | - Juan Tang
- Biomarker Technologies Corporation, Beijing 101200, China
| | - Song Li
- Biomarker Technologies Corporation, Beijing 101200, China
| | - Jianshun Miao
- Biomarker Technologies Corporation, Beijing 101200, China
| | - Hongkun Zheng
- Biomarker Technologies Corporation, Beijing 101200, China.
| | - Hongping Yi
- Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang 830091, China.
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21
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Can H, Kal U, Ozyigit II, Paksoy M, Turkmen O. Construction, characteristics and high throughput molecular screening methodologies in some special breeding populations: a horticultural perspective. J Genet 2019; 98:86. [PMID: 31544799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Advanced marker technologies are widely used for evaluation of genetic diversity in cultivated crops, wild ancestors, landraces or any special plant genotypes. Developing agricultural cultivars requires the following steps: (i) determining desired characteristics to be improved, (ii) screening genetic resources to help find a superior cultivar, (iii) intercrossing selected individuals, (iv) generating genetically hybrid populations and screening them for agro-morphological or molecular traits, (v) evaluating the superior cultivar candidates, (vi) testing field performance at different locations, and (vii) certifying. In the cultivar development process valuable genes can be identified by creating special biparental or multiparental populations and analysing their association using suitable markers in given populations. These special populations and advanced marker technologies give us a deeper knowledge about the inherited agronomic characteristics. Unaffected by the changing environmental conditions, these provide a higher understanding of genome dynamics in plants. The last decade witnessed new applications for advanced molecular techniques in the area of breeding,with low costs per sample. These, especially, include next-generation sequencing technologies like reduced representation genome sequencing (genotyping by sequencing, restriction site-associated DNA). These enabled researchers to develop new markers, such as simple sequence repeat and single- nucleotide polymorphism, for expanding the qualitative and quantitative information onpopulation dynamics. Thus, the knowledge acquired from novel technologies is a valuable asset for the breeding process and to better understand the population dynamics, their properties, and analysis methods.
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Affiliation(s)
- Hasan Can
- Faculty of Agriculture, Department of Field Crops and Horticulture, Kyrgyz-Turkish Manas University, Bishkek 720038, Kyrgyzstan.
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22
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Can H, Kal U, Ozyigit II, Paksoy M, Turkmen O. Construction, characteristics and high throughput molecular screening methodologies in some special breeding populations: a horticultural perspective. J Genet 2019. [DOI: 10.1007/s12041-019-1129-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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23
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Vallarino JG, Pott DM, Cruz-Rus E, Miranda L, Medina-Minguez JJ, Valpuesta V, Fernie AR, Sánchez-Sevilla JF, Osorio S, Amaya I. Identification of quantitative trait loci and candidate genes for primary metabolite content in strawberry fruit. HORTICULTURE RESEARCH 2019; 6:4. [PMID: 30603090 PMCID: PMC6312544 DOI: 10.1038/s41438-018-0077-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 07/23/2018] [Accepted: 07/31/2018] [Indexed: 05/09/2023]
Abstract
Improvement of nutritional and organoleptic quality of fruits is a key goal in current strawberry breeding programs. The ratio of sugars to acids is a determinant factor contributing to fruit liking, although different sugars and acids contribute in varying degrees to this complex trait. A segregating F1 population of 95 individuals, previously characterized for several fruit quality characters, was used to map during 2 years quantitative trait loci (QTL) for 50 primary metabolites, l-ascorbic acid (L-AA) and other related traits such as soluble solid content (SSC), titratable acidity (TA), and pH. A total of 133 mQTL were detected above the established thresholds for 44 traits. Only 12.9% of QTL were detected in the 2 years, suggesting a large environmental influence on primary metabolite content. An objective of this study was the identification of key metabolites that were associated to the overall variation in SSC and acidity. As it was observed in previous studies, a number of QTL controlling several metabolites and traits were co-located in homoeology group V (HG V). mQTL controlling a large variance in raffinose, sucrose, succinic acid, and L-AA were detected in approximate the same chromosomal regions of different homoeologous linkage groups belonging to HG V. Candidate genes for selected mQTL are proposed based on their co-localization, on the predicted function, and their differential gene expression among contrasting F1 progeny lines. RNA-seq analysis from progeny lines contrasting in L-AA content detected 826 differentially expressed genes and identified Mannose-6-phosphate isomerase, FaM6PI1, as a candidate gene contributing to natural variation in ascorbic acid in strawberry fruit.
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Affiliation(s)
- José G. Vallarino
- Department of Molecular Biology and Biochemistry, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, University of Málaga – Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus de Teatinos, 29071 Málaga, Spain
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Delphine M. Pott
- Department of Molecular Biology and Biochemistry, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, University of Málaga – Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus de Teatinos, 29071 Málaga, Spain
| | - Eduardo Cruz-Rus
- Genómica y Biotecnología, Centro de Málaga, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA), 29140 Málaga, Spain
| | - Luis Miranda
- Ingeniería y Tecnología Agroalimentaria, Centro Las Torres-Tomejil, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA) Alcalá del Río, Sevilla, Spain
| | - Juan J. Medina-Minguez
- Ingeniería y Tecnología Agroalimentaria, Centro de Huelva, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA), Huelva, Spain
| | - Victoriano Valpuesta
- Department of Molecular Biology and Biochemistry, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, University of Málaga – Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus de Teatinos, 29071 Málaga, Spain
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - José F. Sánchez-Sevilla
- Genómica y Biotecnología, Centro de Málaga, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA), 29140 Málaga, Spain
| | - Sonia Osorio
- Department of Molecular Biology and Biochemistry, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, University of Málaga – Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus de Teatinos, 29071 Málaga, Spain
| | - Iraida Amaya
- Genómica y Biotecnología, Centro de Málaga, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA), 29140 Málaga, Spain
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Pereira L, Ruggieri V, Pérez S, Alexiou KG, Fernández M, Jahrmann T, Pujol M, Garcia-Mas J. QTL mapping of melon fruit quality traits using a high-density GBS-based genetic map. BMC PLANT BIOLOGY 2018; 18:324. [PMID: 30509167 PMCID: PMC6278158 DOI: 10.1186/s12870-018-1537-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 11/19/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND Melon shows a broad diversity in fruit morphology and quality, which is still underexploited in breeding programs. The knowledge of the genetic basis of fruit quality traits is important for identifying new alleles that may be introduced in elite material by highly efficient molecular breeding tools. RESULTS In order to identify QTLs controlling fruit quality, a recombinant inbred line population was developed using two commercial cultivars as parental lines: "Védrantais", from the cantalupensis group, and "Piel de Sapo", from the inodorus group. Both have desirable quality traits for the market, but their fruits differ in traits such as rind and flesh color, sugar content, ripening behavior, size and shape. We used a genotyping-by-sequencing strategy to construct a dense genetic map, which included around five thousand variants distributed in 824 bins. The RIL population was phenotyped for quality and morphology traits, and we mapped 33 stable QTLs involved in sugar and carotenoid content, fruit and seed morphology and major loci controlling external color of immature fruit and mottled rind. The median confidence interval of the QTLs was 942 kb, suggesting that the high density of the genetic map helped in increasing the mapping resolution. Some of these intervals contained less than a hundred annotated genes, and an integrative strategy combining gene expression and resequencing data enabled identification of candidate genes for some of these traits. CONCLUSION Several QTLs controlling fruit quality traits in melon were identified and delimited to narrow genomic intervals, using a RIL population and a GBS-based genetic map.
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Affiliation(s)
- L. Pereira
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Cerdanyola, Barcelona, Spain
| | - V. Ruggieri
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Cerdanyola, Barcelona, Spain
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Campus UAB, 08193 Cerdanyola, Barcelona, Spain
| | - S. Pérez
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Cerdanyola, Barcelona, Spain
| | - K. G. Alexiou
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Cerdanyola, Barcelona, Spain
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Campus UAB, 08193 Cerdanyola, Barcelona, Spain
| | - M. Fernández
- Semillas Fitó S.A., 08348 Cabrera de Mar, Barcelona, Spain
| | - T. Jahrmann
- Semillas Fitó S.A., 08348 Cabrera de Mar, Barcelona, Spain
| | - M. Pujol
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Cerdanyola, Barcelona, Spain
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Campus UAB, 08193 Cerdanyola, Barcelona, Spain
| | - J. Garcia-Mas
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Cerdanyola, Barcelona, Spain
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Campus UAB, 08193 Cerdanyola, Barcelona, Spain
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Beauvoit B, Belouah I, Bertin N, Cakpo CB, Colombié S, Dai Z, Gautier H, Génard M, Moing A, Roch L, Vercambre G, Gibon Y. Putting primary metabolism into perspective to obtain better fruits. ANNALS OF BOTANY 2018; 122:1-21. [PMID: 29718072 PMCID: PMC6025238 DOI: 10.1093/aob/mcy057] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 03/29/2017] [Indexed: 05/18/2023]
Abstract
Background One of the key goals of fruit biology is to understand the factors that influence fruit growth and quality, ultimately with a view to manipulating them for improvement of fruit traits. Scope Primary metabolism, which is not only essential for growth but is also a major component of fruit quality, is an obvious target for improvement. However, metabolism is a moving target that undergoes marked changes throughout fruit growth and ripening. Conclusions Agricultural practice and breeding have successfully improved fruit metabolic traits, but both face the complexity of the interplay between development, metabolism and the environment. Thus, more fundamental knowledge is needed to identify further strategies for the manipulation of fruit metabolism. Nearly two decades of post-genomics approaches involving transcriptomics, proteomics and/or metabolomics have generated a lot of information about the behaviour of fruit metabolic networks. Today, the emergence of modelling tools is providing the opportunity to turn this information into a mechanistic understanding of fruits, and ultimately to design better fruits. Since high-quality data are a key requirement in modelling, a range of must-have parameters and variables is proposed.
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Affiliation(s)
| | - Isma Belouah
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
| | | | | | - Sophie Colombié
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
| | - Zhanwu Dai
- UMR 1287 EGFV, INRA, Univ. Bordeaux, Bordeaux Sci Agro, F-Villenave d’Ornon, France
| | | | | | - Annick Moing
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
| | - Léa Roch
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
| | | | - Yves Gibon
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
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