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Domestication and selection footprints in Persian walnuts (Juglans regia)

Walnut (Juglans) species are economically important hardwood trees cultivated worldwide for both edible nuts and high-quality wood. Broad-scale assessments of species diversity, evolutionary history, and domestication are needed to improve walnut breeding. In this study, we sequenced 309 walnut acce...

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Autores principales: Luo, Xiang, Zhou, Huijuan, Cao, Da, Yan, Feng, Chen, Pengpeng, Wang, Jiangtao, Woeste, Keith, Chen, Xin, Fei, Zhangjun, An, Hong, Malvolti, Maria, Ma, Kai, Liu, Chaobin, Ebrahimi, Aziz, Qiao, Chengkui, Ye, Hang, Li, Mengdi, Lu, Zhenhua, Xu, Jiabao, Cao, Shangying, Zhao, Peng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9728896/
https://www.ncbi.nlm.nih.gov/pubmed/36477175
http://dx.doi.org/10.1371/journal.pgen.1010513
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author Luo, Xiang
Zhou, Huijuan
Cao, Da
Yan, Feng
Chen, Pengpeng
Wang, Jiangtao
Woeste, Keith
Chen, Xin
Fei, Zhangjun
An, Hong
Malvolti, Maria
Ma, Kai
Liu, Chaobin
Ebrahimi, Aziz
Qiao, Chengkui
Ye, Hang
Li, Mengdi
Lu, Zhenhua
Xu, Jiabao
Cao, Shangying
Zhao, Peng
author_facet Luo, Xiang
Zhou, Huijuan
Cao, Da
Yan, Feng
Chen, Pengpeng
Wang, Jiangtao
Woeste, Keith
Chen, Xin
Fei, Zhangjun
An, Hong
Malvolti, Maria
Ma, Kai
Liu, Chaobin
Ebrahimi, Aziz
Qiao, Chengkui
Ye, Hang
Li, Mengdi
Lu, Zhenhua
Xu, Jiabao
Cao, Shangying
Zhao, Peng
author_sort Luo, Xiang
collection PubMed
description Walnut (Juglans) species are economically important hardwood trees cultivated worldwide for both edible nuts and high-quality wood. Broad-scale assessments of species diversity, evolutionary history, and domestication are needed to improve walnut breeding. In this study, we sequenced 309 walnut accessions from around the world, including 55 Juglans relatives, 98 wild Persian walnuts (J. regia), 70 J. regia landraces, and 86 J. regia cultivars. The phylogenetic tree indicated that J. regia samples (section Dioscaryon) were monophyletic within Juglans. The core areas of genetic diversity of J. regia germplasm were southwestern China and southern Asia near the Qinghai-Tibet Plateau and the Himalayas, and the uplift of the Himalayas was speculated to be the main factor leading to the current population dynamics of Persian walnut. The pattern of genomic variation in terms of nucleotide diversity, linkage disequilibrium, single nucleotide polymorphisms, and insertions/deletions revealed the domestication and selection footprints in Persian walnut. Selective sweep analysis, GWAS, and expression analysis further identified two transcription factors, JrbHLH and JrMYB6, that influence the thickness of the nut diaphragm as loci under selection during domestication. Our results elucidate the domestication and selection footprints in Persian walnuts and provide a valuable resource for the genomics-assisted breeding of this important crop.
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spelling pubmed-97288962022-12-08 Domestication and selection footprints in Persian walnuts (Juglans regia) Luo, Xiang Zhou, Huijuan Cao, Da Yan, Feng Chen, Pengpeng Wang, Jiangtao Woeste, Keith Chen, Xin Fei, Zhangjun An, Hong Malvolti, Maria Ma, Kai Liu, Chaobin Ebrahimi, Aziz Qiao, Chengkui Ye, Hang Li, Mengdi Lu, Zhenhua Xu, Jiabao Cao, Shangying Zhao, Peng PLoS Genet Research Article Walnut (Juglans) species are economically important hardwood trees cultivated worldwide for both edible nuts and high-quality wood. Broad-scale assessments of species diversity, evolutionary history, and domestication are needed to improve walnut breeding. In this study, we sequenced 309 walnut accessions from around the world, including 55 Juglans relatives, 98 wild Persian walnuts (J. regia), 70 J. regia landraces, and 86 J. regia cultivars. The phylogenetic tree indicated that J. regia samples (section Dioscaryon) were monophyletic within Juglans. The core areas of genetic diversity of J. regia germplasm were southwestern China and southern Asia near the Qinghai-Tibet Plateau and the Himalayas, and the uplift of the Himalayas was speculated to be the main factor leading to the current population dynamics of Persian walnut. The pattern of genomic variation in terms of nucleotide diversity, linkage disequilibrium, single nucleotide polymorphisms, and insertions/deletions revealed the domestication and selection footprints in Persian walnut. Selective sweep analysis, GWAS, and expression analysis further identified two transcription factors, JrbHLH and JrMYB6, that influence the thickness of the nut diaphragm as loci under selection during domestication. Our results elucidate the domestication and selection footprints in Persian walnuts and provide a valuable resource for the genomics-assisted breeding of this important crop. Public Library of Science 2022-12-07 /pmc/articles/PMC9728896/ /pubmed/36477175 http://dx.doi.org/10.1371/journal.pgen.1010513 Text en © 2022 Luo et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Luo, Xiang
Zhou, Huijuan
Cao, Da
Yan, Feng
Chen, Pengpeng
Wang, Jiangtao
Woeste, Keith
Chen, Xin
Fei, Zhangjun
An, Hong
Malvolti, Maria
Ma, Kai
Liu, Chaobin
Ebrahimi, Aziz
Qiao, Chengkui
Ye, Hang
Li, Mengdi
Lu, Zhenhua
Xu, Jiabao
Cao, Shangying
Zhao, Peng
Domestication and selection footprints in Persian walnuts (Juglans regia)
title Domestication and selection footprints in Persian walnuts (Juglans regia)
title_full Domestication and selection footprints in Persian walnuts (Juglans regia)
title_fullStr Domestication and selection footprints in Persian walnuts (Juglans regia)
title_full_unstemmed Domestication and selection footprints in Persian walnuts (Juglans regia)
title_short Domestication and selection footprints in Persian walnuts (Juglans regia)
title_sort domestication and selection footprints in persian walnuts (juglans regia)
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9728896/
https://www.ncbi.nlm.nih.gov/pubmed/36477175
http://dx.doi.org/10.1371/journal.pgen.1010513
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