Domestication and selection footprints in Persian walnuts (Juglans regia)

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.

‘Sorrento’ and ‘Tulare’ Walnut Cultivars: Morphological Traits and Phytochemical Enhancement of Their Shell Waste

“…The local climate and environmental conditions in different cultivation areas have allowed for the diversification of different varieties adapt to specific agricultural ecosystems [ 38 , 39 , 40 ]. These genotypes, with particular bio-agronomic and organoleptic characteristics, constitute a significant reservoir of crop genetic diversity with good tolerance to abiotic and biotic stresses that can promote sustainable regional economic development [ 41 ]. Among these, the ‘Sorrento walnut’ is an indigenous Italian walnut originating from the Sorrento peninsula; today, it is cultivated throughout the Campania region (southern Italy), having become a mixture of heterogeneous genetic entities in terms of fruit size and yield, and marketed as ‘Sorrento walnut’ [ 42 ].…”

Genome‐wide diversity evaluation and core germplasm extraction in ex situ conservation: A case of golden Camellia tunghinensis

“…Many studies have demonstrated that genetic diversity in species is influenced by multiple factors, including gene flow (Feliciano et al, 2022;Su, Richardson, et al, 2017), selection (Luo et al, 2022;Niu et al, 2019), evolutionary history (Guerra-Garcia et al, 2022;Roy et al, 2017), and the level of inbreeding (Dicks et al, 2023). For example, Feliciano et al (2022) found low population genetic diversity associated with restricted gene flow in the endemic and endangered species Portulaca hatschbachii in Brazil.…”

Genome-Wide Identification of the CBF Gene Family and ICE Transcription Factors in Walnuts and Expression Profiles under Cold Conditions

“…Juglans regia (2n = 32, Persian walnut), being wind-pollinated and monoecious, is an important woody oil tree cultivated worldwide, naturally distributed in Eurasia and even southeastern Europe [ 20 , 21 , 22 ]. J. sigillata (iron walnut) is the most closely related to Persian walnut, which grows in the southwest of China [ 23 , 24 , 25 ].…”

“…J. sigillata (iron walnut) is the most closely related to Persian walnut, which grows in the southwest of China [ 23 , 24 , 25 ]. The kernels of Persian walnut and iron walnut are rich in nutrition and high in fatty acid content [ 20 , 21 , 22 , 23 , 24 , 25 ]. Persian walnut is the most important species in Juglans , which is distributed and cultivated widely across the world [ 21 , 22 ].…”

“…The kernels of Persian walnut and iron walnut are rich in nutrition and high in fatty acid content [ 20 , 21 , 22 , 23 , 24 , 25 ]. Persian walnut is the most important species in Juglans , which is distributed and cultivated widely across the world [ 21 , 22 ]. Persian walnuts and iron walnuts are also used as timber tree species for their high-quality wood [ 20 , 21 , 23 ].…”