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3. A comprehensive genome variation map of melon identifies multiple domestication events and loci influencing agronomic traits

Author

Zhao, Guangwei, Lian, Qun, Zhang, Zhonghua, Fu, Qiushi, He, Yuhua, Ma, Shuangwu, Ruggieri, Valentino, Monforte, Antonio J., Wang, Pingyong, Julca, Irene, Wang, Huaisong, Liu, Junpu, Xu, Yong, Wang, Runze, Ji, Jiabing, Xu, Zhihong, Kong, Weihu, Zhong, Yang, Shang, Jianli, Pereira, Lara, Argyris, Jason, Zhang, Jian, Mayobre, Carlos, Pujol, Marta, Oren, Elad, Ou, Diandian, Wang, Jiming, Sun, Dexi, Zhao, Shengjie, Zhu, Yingchun, Li, Na, Katzir, Nurit, Gur, Amit, Dogimont, Catherine, Schaefer, Hanno, Fan, Wei, Bendahmane, Abdelhafid, Fei, Zhangjun, Pitrat, Michel, Gabaldón, Toni, Lin, Tao, Garcia-Mas, Jordi, Xu, Yongyang, and Huang, Sanwen

Published
2019
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4. The biosynthetic pathway of the nonsugar, high-intensity sweetener mogroside V from Siraitia grosvenorii

Author

Itkin, Maxim, Davidovich-Rikanati, Rachel, Cohen, Shahar, Portnoy, Vitaly, Doron-Faigenboim, Adi, Oren, Elad, Freilich, Shiri, Tzuri, Galil, Baranes, Nadine, Shen, Shmuel, Petreikov, Marina, Sertchook, Rotem, Ben-Dor, Shifra, Gottlieb, Hugo, Hernandez, Alvaro, Nelson, David R., Paris, Harry S., Tadmor, Yaakov, Burger, Yosef, Lewinsohn, Efraim, Katzir, Nurit, and Schaffer, Arthur

Published
2016

5. Pan‐genome and multi‐parental framework for high‐resolution trait dissection in melon ( Cucumis melo )

Author

Oren, Elad, primary, Dafna, Asaf, additional, Tzuri, Galil, additional, Halperin, Ilan, additional, Isaacson, Tal, additional, Elkabetz, Meital, additional, Meir, Ayala, additional, Saar, Uzi, additional, Ohali, Shachar, additional, La, Thuy, additional, Romay, Cinta, additional, Tadmor, Yaakov, additional, Schaffer, Arthur A., additional, Buckler, Edward S., additional, Cohen, Roni, additional, Burger, Joseph, additional, and Gur, Amit, additional

Published
2022
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6. Melon pan-genome and multi-parental framework for high-resolution trait dissection

Author

Oren, Elad, primary, Dafna, Asaf, additional, Tzuri, Galil, additional, Halperin, Ilan, additional, Isaacson, Tal, additional, Elkabetz, Meital, additional, Meir, Ayala, additional, Saar, Uzi, additional, Ohali, Shachar, additional, La, Thuy, additional, Romay, Cinta, additional, Tadmor, Yaakov, additional, Schaffer, Arthur A, additional, Buckler, Edward S, additional, Cohen, Roni, additional, Burger, Joseph, additional, and Gur, Amit, additional

Published
2022
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7. QTL mapping and genomic analyses of earliness and fruit ripening traits in a melon recombinant inbred lines population supported byde novoassembly of their parental genomes

Author

Oren, Elad, primary, Tzuri, Galil, additional, Dafna, Asaf, additional, Rees, Evan R, additional, Song, Baoxing, additional, Freilich, Shiri, additional, Elkind, Yonatan, additional, Isaacson, Tal, additional, Schaffer, Arthur A, additional, Tadmor, Yaakov, additional, Burger, Joseph, additional, Buckler, Edward S, additional, and Gur, Amit, additional

Published
2022
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8. Underground heterosis for yield improvement in melon

Author

Dafna, Asaf, primary, Halperin, Ilan, additional, Oren, Elad, additional, Isaacson, Tal, additional, Tzuri, Galil, additional, Meir, Ayala, additional, Schaffer, Arthur A, additional, Burger, Joseph, additional, Tadmor, Yaakov, additional, Buckler, Edward S, additional, and Gur, Amit, additional

Published
2021
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9. Underground Heterosis for Melons Yield

Author

Dafna, Asaf, primary, Halperin, Ilan, additional, Oren, Elad, additional, Isaacson, Tal, additional, Tzuri, Galil, additional, Meir, Ayala, additional, Schaffer, Arthur A, additional, Burger, Joseph, additional, Tadmor, Yaakov, additional, Buckler, Edward S., additional, and Gur, Amit, additional

Published
2021
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10. Comparative Metabolomics and Molecular Phylogenetics of Melon (Cucumis melo, Cucurbitaceae) Biodiversity

Author

Moing, Annick, Allwood, J. William, Aharoni, Asaph, Baker, John, Beale, Michael H., Ben-Dor, Shifra, Biais, Benoit, Brigante, Federico, Burger, Yosef, Deborde, Catherine, Erban, Alexander, Faigenboim, Adi, Gur, Amit, Goodacre, Royston, Hansen, Thomas H., Jacob, Daniel, Katzir, Nurit, Kopka, Joachim, Lewinsohn, Efraim, Maucourt, Mickael, Meir, Sagit, Miller, Sonia, Mumm, Roland, Oren, Elad, Paris, Harry S., Rogachev, Ilana, Rolin, Dominique, Saar, Uzi, Schjoerring, Jan K., Tadmor, Yaakov, Tzuri, Galil, de Vos, Ric C. H., Ward, Jane L., Yeselson, Elena, Hall, Robert D., Schaffer, Arthur A., Moing, Annick, Allwood, J. William, Aharoni, Asaph, Baker, John, Beale, Michael H., Ben-Dor, Shifra, Biais, Benoit, Brigante, Federico, Burger, Yosef, Deborde, Catherine, Erban, Alexander, Faigenboim, Adi, Gur, Amit, Goodacre, Royston, Hansen, Thomas H., Jacob, Daniel, Katzir, Nurit, Kopka, Joachim, Lewinsohn, Efraim, Maucourt, Mickael, Meir, Sagit, Miller, Sonia, Mumm, Roland, Oren, Elad, Paris, Harry S., Rogachev, Ilana, Rolin, Dominique, Saar, Uzi, Schjoerring, Jan K., Tadmor, Yaakov, Tzuri, Galil, de Vos, Ric C. H., Ward, Jane L., Yeselson, Elena, Hall, Robert D., and Schaffer, Arthur A.

Abstract

The broad variability of Cucumis melo (melon, Cucurbitaceae) presents a challenge to conventional classification and organization within the species. To shed further light on the infraspecific relationships within C. melo, we compared genotypic and metabolomic similarities among 44 accessions representative of most of the cultivar-groups. Genotyping-by-sequencing (GBS) provided over 20,000 single-nucleotide polymorphisms (SNPs). Metabolomics data of the mature fruit flesh and rind provided over 80,000 metabolomic and elemental features via an orchestra of six complementary metabolomic platforms. These technologies probed polar, semi-polar, and non-polar metabolite fractions as well as a set of mineral elements and included both flavor- and taste-relevant volatile and non-volatile metabolites. Together these results enabled an estimate of "metabolomic/elemental distance" and its correlation with the genetic GBS distance of melon accessions. This study indicates that extensive and non-targeted metabolomics/elemental characterization produced classifications that strongly, but not completely, reflect the current and extensive genetic classification. Certain melon Groups, such as Inodorous, clustered in parallel with the genetic classifications while other genome to metabolome/element associations proved less clear. We suggest that the combined genomic, metabolic, and element data reflect the extensive sexual compatibility among melon accessions and the breeding history that has, for example, targeted metabolic quality traits, such as taste and flavor.

Published
2020

11. Comparative Metabolomics and Molecular Phylogenetics of Melon (Cucumis melo, Cucurbitaceae) Biodiversity

Author

Moing, Annick, primary, Allwood, J. William, additional, Aharoni, Asaph, additional, Baker, John, additional, Beale, Michael H., additional, Ben-Dor, Shifra, additional, Biais, Benoît, additional, Brigante, Federico, additional, Burger, Yosef, additional, Deborde, Catherine, additional, Erban, Alexander, additional, Faigenboim, Adi, additional, Gur, Amit, additional, Goodacre, Royston, additional, Hansen, Thomas H., additional, Jacob, Daniel, additional, Katzir, Nurit, additional, Kopka, Joachim, additional, Lewinsohn, Efraim, additional, Maucourt, Mickael, additional, Meir, Sagit, additional, Miller, Sonia, additional, Mumm, Roland, additional, Oren, Elad, additional, Paris, Harry S., additional, Rogachev, Ilana, additional, Rolin, Dominique, additional, Saar, Uzi, additional, Schjoerring, Jan K., additional, Tadmor, Yaakov, additional, Tzuri, Galil, additional, de Vos, Ric C.H., additional, Ward, Jane L., additional, Yeselson, Elena, additional, Hall, Robert D., additional, and Schaffer, Arthur A., additional

Published
2020
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12. A comprehensive genome variation map of melon identifies multiple domestication events and loci influencing agronomic traits

Author

Agriculture Research System of China, Guandong Academy Of Agricultural Sciences, National Natural Science Foundation of China, National Key Research and Development Program (China), National Institute of Food and Agriculture (US), European Research Council, Ministerio de Economía y Competitividad (España), Generalitat de Catalunya, German Research Foundation, Zhao, Guangwei, Lian, Qun, Zhang, Zhonghua, Fu, Qiushi, He, Yuhua, Ma, Shuangwu, Ruggieri, Valentino, Monforte, Antonio J., Wang, Pingyong, Julca, Irene, Wang, Huaisong, Liu, Junpu, Xu, Yong, Wang, Runze, Ji, Jiabing, Xu, Zhihong, Kong, Weihu, Zhong, Yang, Shang, Jianli, Pereira, Lara, Argyris, Jason, Zhang, Jian, Mayobre, Carlos, Pujol, Marta, Oren, Elad, Ou, Diandian, Wang, Jiming, Sun, Dexi, Zhao, Shengjie, Zhu, Yingchun, Li, Na, Katzir, Nurit, Gur, Amit, Dogimont, Catherine, Schaefer, Hanno, Fan, Wei, Bendahmane, Abdelhafid, Fei, Zhangjun, Pitrat, Michel, Gabaldón, Toni, Lin, Tao, García-Mas, Jordi, Xu, Yongyang, Huang, Sanwen, Agriculture Research System of China, Guandong Academy Of Agricultural Sciences, National Natural Science Foundation of China, National Key Research and Development Program (China), National Institute of Food and Agriculture (US), European Research Council, Ministerio de Economía y Competitividad (España), Generalitat de Catalunya, German Research Foundation, Zhao, Guangwei, Lian, Qun, Zhang, Zhonghua, Fu, Qiushi, He, Yuhua, Ma, Shuangwu, Ruggieri, Valentino, Monforte, Antonio J., Wang, Pingyong, Julca, Irene, Wang, Huaisong, Liu, Junpu, Xu, Yong, Wang, Runze, Ji, Jiabing, Xu, Zhihong, Kong, Weihu, Zhong, Yang, Shang, Jianli, Pereira, Lara, Argyris, Jason, Zhang, Jian, Mayobre, Carlos, Pujol, Marta, Oren, Elad, Ou, Diandian, Wang, Jiming, Sun, Dexi, Zhao, Shengjie, Zhu, Yingchun, Li, Na, Katzir, Nurit, Gur, Amit, Dogimont, Catherine, Schaefer, Hanno, Fan, Wei, Bendahmane, Abdelhafid, Fei, Zhangjun, Pitrat, Michel, Gabaldón, Toni, Lin, Tao, García-Mas, Jordi, Xu, Yongyang, and Huang, Sanwen

Abstract

Melon is an economically important fruit crop that has been cultivated for thousands of years; however, the genetic basis and history of its domestication still remain largely unknown. Here we report a comprehensive map of the genomic variation in melon derived from the resequencing of 1,175 accessions, which represent the global diversity of the species. Our results suggest that three independent domestication events occurred in melon, two in India and one in Africa. We detected two independent sets of domestication sweeps, resulting in diverse characteristics of the two subspecies melo and agrestis during melon breeding. Genome-wide association studies for 16 agronomic traits identified 208 loci significantly associated with fruit mass, quality and morphological characters. This study sheds light on the domestication history of melon and provides a valuable resource for genomics-assisted breeding of this important crop.

Published
2019

13. Alkaloid chemodiversity in Mandragora spp. is associated with loss-of-functionality of MoH6H, a hyoscyamine 6β-hydroxylase gene

Author

Schlesinger, Daniel, primary, Davidovich Rikanati, Rachel, additional, Volis, Sergei, additional, Faigenboim, Adi, additional, Vendramin, Vera, additional, Cattonaro, Federica, additional, Hooper, Matthew, additional, Oren, Elad, additional, Taylor, Mark, additional, Sitrit, Yaron, additional, Inbar, Moshe, additional, and Lewinsohn, Efraim, additional

Published
2019
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14. The multi-allelic APRR2 gene is associated with fruit pigment accumulation in melon and watermelon

Author

Oren, Elad, primary, Tzuri, Galil, additional, Vexler, Lea, additional, Dafna, Asaf, additional, Meir, Ayala, additional, Faigenboim, Adi, additional, Kenigswald, Merav, additional, Portnoy, Vitaly, additional, Schaffer, Arthur A, additional, Levi, Amnon, additional, Buckler, Edward S, additional, Katzir, Nurit, additional, Burger, Joseph, additional, Tadmor, Yaakov, additional, and Gur, Amit, additional

Published
2019
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15. Multi-allelic APRR2 Gene is Associated with Fruit Pigment Accumulation in Melon and Watermelon

Author

Oren, Elad, primary, Tzuri, Galil, additional, Vexler, Lea, additional, Dafna, Asaf, additional, Meir, Ayala, additional, Saar, Uzi, additional, Faigenboim, Adi, additional, Kenigswald, Merav, additional, Portnoy, Vitaly, additional, Schaffer, Arthur A, additional, Levi, Amnon, additional, Buckler, Edward S., additional, Katzir, Nurit, additional, Burger, Joseph, additional, Tadmor, Yaakov, additional, and Gur, Amit, additional

Published
2019
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17. Systems approach for exploring the intricate associations between sweetness, color and aroma in melon fruits

Author

Freilich, Shiri, primary, Lev, Shery, additional, Gonda, Itay, additional, Reuveni, Eli, additional, Portnoy, Vitaly, additional, Oren, Elad, additional, Lohse, Marc, additional, Galpaz, Navot, additional, Bar, Einat, additional, Tzuri, Galil, additional, Wissotsky, Guy, additional, Meir, Ayala, additional, Burger, Joseph, additional, Tadmor, Yaakov, additional, Schaffer, Arthur, additional, Fei, Zhangjun, additional, Giovannoni, James, additional, Lewinsohn, Efraim, additional, and Katzir, Nurit, additional

Published
2015
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18. QTL mapping and genomic analyses of earliness and fruit ripening traits in a melon recombinant inbred lines population supported by de novoassembly of their parental genomes

Author

Oren, Elad, Tzuri, Galil, Dafna, Asaf, Rees, Evan R, Song, Baoxing, Freilich, Shiri, Elkind, Yonatan, Isaacson, Tal, Schaffer, Arthur A, Tadmor, Yaakov, Burger, Joseph, Buckler, Edward S, and Gur, Amit

Abstract

Earliness and ripening behavior are important attributes of fruits on and off the vine, and affect quality and preference of both growers and consumers. Fruit ripening is a complex physiological process that involves metabolic shifts affecting fruit color, firmness, and aroma production. Melon is a promising model crop for the study of fruit ripening, as the full spectrum of climacteric behavior is represented across the natural variation. Using Recombinant Inbred Lines (RILs) population derived from the parental lines “Dulce” (reticulatus, climacteric) and “Tam Dew” (inodorus, non-climacteric) that vary in earliness and ripening traits, we mapped QTLs for ethylene emission, fruit firmness and days to flowering and maturity. To further annotate the main QTL intervals and identify candidate genes, we used Oxford Nanopore long-read sequencing in combination with Illumina short-read resequencing, to assemble the parental genomes de-novo. In addition to 2.5 million genome-wide SNPs and short InDels detected between the parents, we also highlight here the structural variation between these lines and the reference melon genome. Through systematic multi-layered prioritization process, we identified 18 potential polymorphisms in candidate genes within multi-trait QTLs. The associations of selected SNPs with earliness and ripening traits were further validated across a panel of 177 diverse melon accessions and across a diallel population of 190 F1 hybrids derived from a core subset of 20 diverse parents. The combination of advanced genomic tools with diverse germplasm and targeted mapping populations is demonstrated as a way to leverage forward genetics strategies to dissect complex horticulturally important traits.

Published
2022
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19. QTL mapping and genomic analyses of earliness and fruit ripening traits in a melon Recombinant Inbred Lines population supported by de novo assembly of their parental genomes.

Author

Oren E, Tzuri G, Dafna A, Rees ER, Song B, Freilich S, Elkind Y, Isaacson T, Schaffer AA, Tadmor Y, Burger J, Buckler ES, and Gur A

Abstract

Earliness and ripening behavior are important attributes of fruits on and off the vine, and affect quality and preference of both growers and consumers. Fruit ripening is a complex physiological process that involves metabolic shifts affecting fruit color, firmness, and aroma production. Melon is a promising model crop for the study of fruit ripening, as the full spectrum of climacteric behavior is represented across the natural variation. Using Recombinant Inbred Lines (RILs) population derived from the parental lines "Dulce" (reticulatus, climacteric) and "Tam Dew" (inodorus, non-climacteric) that vary in earliness and ripening traits, we mapped QTLs for ethylene emission, fruit firmness and days to flowering and maturity. To further annotate the main QTL intervals and identify candidate genes, we used Oxford Nanopore long-read sequencing in combination with Illumina short-read resequencing, to assemble the parental genomes de-novo. In addition to 2.5 million genome-wide SNPs and short InDels detected between the parents, we also highlight here the structural variation between these lines and the reference melon genome. Through systematic multi-layered prioritization process, we identified 18 potential polymorphisms in candidate genes within multi-trait QTLs. The associations of selected SNPs with earliness and ripening traits were further validated across a panel of 177 diverse melon accessions and across a diallel population of 190 F1 hybrids derived from a core subset of 20 diverse parents. The combination of advanced genomic tools with diverse germplasm and targeted mapping populations is demonstrated as a way to leverage forward genetics strategies to dissect complex horticulturally important traits., (© The Author(s) 2022. Published by Oxford University Press. All rights reserved.)

Published
2022
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