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Domestication and selection footprints in Persian walnuts (Juglans regia)

Xiang Luo, Huijuan Zhou, Da Cao (UGent) , Feng Yan, Pengpeng Chen, Jiangtao Wang, Keith Woeste, Xin Chen, Zhangjun Fei, Hong An, et al.
(2022) PLOS GENETICS. 18(12).
Author
Organization
Abstract
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.
Keywords
GENETIC DIVERSITY, PHYLOGENETIC ANALYSIS, GENOME ASSOCIATION, HISTORY, JUGLANDACEAE, BIOSYNTHESIS, ADAPTATION, EVOLUTION, ADMIXTURE, SOFTWARE

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MLA
Luo, Xiang, et al. “Domestication and Selection Footprints in Persian Walnuts (Juglans Regia).” PLOS GENETICS, vol. 18, no. 12, 2022, doi:10.1371/journal.pgen.1010513.
APA
Luo, X., Zhou, H., Cao, D., Yan, F., Chen, P., Wang, J., … Zhao, P. (2022). Domestication and selection footprints in Persian walnuts (Juglans regia). PLOS GENETICS, 18(12). https://doi.org/10.1371/journal.pgen.1010513
Chicago author-date
Luo, Xiang, Huijuan Zhou, Da Cao, Feng Yan, Pengpeng Chen, Jiangtao Wang, Keith Woeste, et al. 2022. “Domestication and Selection Footprints in Persian Walnuts (Juglans Regia).” PLOS GENETICS 18 (12). https://doi.org/10.1371/journal.pgen.1010513.
Chicago author-date (all authors)
Luo, Xiang, Huijuan Zhou, Da Cao, Feng Yan, Pengpeng Chen, Jiangtao Wang, Keith Woeste, Xin Chen, Zhangjun Fei, Hong An, Maria Malvolti, Kai Ma, Chaobin Liu, Aziz Ebrahimi, Chengkui Qiao, Hang Ye, Mengdi Li, Zhenhua Lu, Jiabao Xu, Shangying Cao, and Peng Zhao. 2022. “Domestication and Selection Footprints in Persian Walnuts (Juglans Regia).” PLOS GENETICS 18 (12). doi:10.1371/journal.pgen.1010513.
Vancouver
1.
Luo X, Zhou H, Cao D, Yan F, Chen P, Wang J, et al. Domestication and selection footprints in Persian walnuts (Juglans regia). PLOS GENETICS. 2022;18(12).
IEEE
[1]
X. Luo et al., “Domestication and selection footprints in Persian walnuts (Juglans regia),” PLOS GENETICS, vol. 18, no. 12, 2022.
@article{01H9Q88ZG7WS13G8CMTGHRHJE9,
  abstract     = {{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.}},
  articleno    = {{e1010513}},
  author       = {{Luo, Xiang and  Zhou, Huijuan and Cao, Da and  Yan, Feng and  Chen, Pengpeng and  Wang, Jiangtao and  Woeste, Keith and  Chen, Xin and  Fei, Zhangjun and  An, Hong and  Malvolti, Maria and  Ma, Kai and  Liu, Chaobin and  Ebrahimi, Aziz and  Qiao, Chengkui and  Ye, Hang and  Li, Mengdi and  Lu, Zhenhua and  Xu, Jiabao and  Cao, Shangying and  Zhao, Peng}},
  issn         = {{1553-7404}},
  journal      = {{PLOS GENETICS}},
  keywords     = {{GENETIC DIVERSITY,PHYLOGENETIC ANALYSIS,GENOME ASSOCIATION,HISTORY,JUGLANDACEAE,BIOSYNTHESIS,ADAPTATION,EVOLUTION,ADMIXTURE,SOFTWARE}},
  language     = {{eng}},
  number       = {{12}},
  pages        = {{19}},
  title        = {{Domestication and selection footprints in Persian walnuts (Juglans regia)}},
  url          = {{http://doi.org/10.1371/journal.pgen.1010513}},
  volume       = {{18}},
  year         = {{2022}},
}
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