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Evidence of an additional center of apple domestication in Iran, with contributions from the Caucasian crab apple Malus orientalis

Bina Hamid, Yousefzadeh Hamed, Venon Anthony, Remoué Carine, Rousselet Agnès, Falque Matthieu, Shadab Faramarzi, Xilong Chen, Jarkyn Samanchina, David Gill, Akylai Kabaeva, Giraud Tatiana, Hossainpour Batool, Abdollahi Hamid, Gabrielyan Ivan, Nersesyan Anush, View ORCID ProfileCornille Amandine
doi: https://doi.org/10.1101/2021.03.28.437401
Bina Hamid
1Department of Forestry, Tarbiat Modares University, Noor, Iran
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Yousefzadeh Hamed
2Department of Environmental science, Biodiversity Branch, Natural resources faculty, Tarbiat Modares University, Noor, Iran
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  • For correspondence: amandine.cornille@universite-paris-saclay.fr hamed.yousefzadeh@modares.ir
Venon Anthony
3Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France
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Remoué Carine
3Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France
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Rousselet Agnès
3Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France
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Falque Matthieu
3Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France
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Shadab Faramarzi
4Department of Plant Production and Genetics, Faculty of Agriculture, Razi University, Kermanshah, Iran
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Xilong Chen
3Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France
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Jarkyn Samanchina
5Fauna & Flora International, Cambridge, UK
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David Gill
5Fauna & Flora International, Cambridge, UK
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Akylai Kabaeva
5Fauna & Flora International, Cambridge, UK
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Giraud Tatiana
6Ecologie Systematique Evolution, Universite Paris-Saclay, CNRS, AgroParisTech, Orsay, France
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Hossainpour Batool
7Iranian Research Organization for Science and Technology (IROST), Institute of Agriculture, Department of Agriculture, Tehran, Iran
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Abdollahi Hamid
8Temperate Fruits Research Center, Horticultural Sciences Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
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Gabrielyan Ivan
9Department of Conservation of Genetic Resources of Armenian Flora, A. Takhtajyan Institute of Botany, Armenian National Academy of Sciences, Acharyan Str.1, 0040 Yerevan, Armenia
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Nersesyan Anush
10Department of Palaeobotany, A. Takhtajyan Institute of Botany, Armenian National Academy of Sciences, Acharyan Str.1, 0040 Yerevan, Armenia
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Cornille Amandine
3Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France
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  • ORCID record for Cornille Amandine
  • For correspondence: amandine.cornille@universite-paris-saclay.fr hamed.yousefzadeh@modares.ir
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Abstract

Anthropogenic and natural divergence processes in crop-wild fruit tree complexes are less studied than in annual crops, especially in the Caucasus, a pivotal region for plant domestication. We investigated anthropogenic and natural divergence processes in apples in the Caucasus using 26 microsatellite markers amplified in 550 wild and cultivated samples. We found two distinct cultivated populations in Iran, that were both genetically differentiated from Malus domestica, the standard cultivated apple worldwide. Coalescent-based inferences using approximate Bayesian computation showed that these two cultivated populations originated from specific domestication events in Iran. One of the Iranian clusters encompassed both cultivated and forest trees, suggesting that either farmers use of local wild apple for cultivation or that some forest trees represent feral cultivars. We found evidence of substantial wild-to-crop, crop-crop and crop-to-wild gene flow in the Caucasus, as has been previously described in apple in Europe and in fruit trees in general. In the Caucasus, we identified seven genetically differentiated populations of wild apple (Malus orientalis). Niche modeling combined with genetic diversity estimates indicated that these populations likely resulted from range changes during the last glaciation. This study identifies Iran as a key region in the evolution and domestication of apple and further demonstrates the role of wild-to-crop gene flow during fruit tree domestication. Our results support the view that domestication of fruit trees was likely a geographically diffuse and protracted process, involving multiple, geographically disparate, origins of domestication. We also highlight the impact of climate change on the natural divergence of a wild fruit tree and provides a base for apple conservation and breeding programs in the Caucasus.

Competing Interest Statement

The authors have declared no competing interest.

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Posted August 31, 2021.
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Evidence of an additional center of apple domestication in Iran, with contributions from the Caucasian crab apple Malus orientalis
Bina Hamid, Yousefzadeh Hamed, Venon Anthony, Remoué Carine, Rousselet Agnès, Falque Matthieu, Shadab Faramarzi, Xilong Chen, Jarkyn Samanchina, David Gill, Akylai Kabaeva, Giraud Tatiana, Hossainpour Batool, Abdollahi Hamid, Gabrielyan Ivan, Nersesyan Anush, Cornille Amandine
bioRxiv 2021.03.28.437401; doi: https://doi.org/10.1101/2021.03.28.437401
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Evidence of an additional center of apple domestication in Iran, with contributions from the Caucasian crab apple Malus orientalis
Bina Hamid, Yousefzadeh Hamed, Venon Anthony, Remoué Carine, Rousselet Agnès, Falque Matthieu, Shadab Faramarzi, Xilong Chen, Jarkyn Samanchina, David Gill, Akylai Kabaeva, Giraud Tatiana, Hossainpour Batool, Abdollahi Hamid, Gabrielyan Ivan, Nersesyan Anush, Cornille Amandine
bioRxiv 2021.03.28.437401; doi: https://doi.org/10.1101/2021.03.28.437401

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