Population-genomic analyses reveal bottlenecks and asymmetric introgression from Persian into iron walnut during domestication

Abstract

Background Persian walnut, Juglans regia, occurs naturally from Greece to western China, while its closest relative, the iron walnut, Juglans sigillata, is endemic in southwest China; both species are cultivated for their nuts and wood. Here, we infer their demographic histories and the time and direction of possible hybridization and introgression between them. Results We use whole-genome resequencing data, different population-genetic approaches (PSMC and GONE), and isolation-with-migration models (IMa3) on individuals from Europe, Iran, Kazakhstan, Pakistan, and China. IMa3 analyses indicate that the two species diverged from each other by 0.85 million years ago, with unidirectional gene flow from eastern J. regia and its ancestor into J. sigillata, including the shell-thickness gene. Within J. regia, a western group, located from Europe to Iran, and an eastern group with individuals from northern China, experienced dramatically declining population sizes about 80 generations ago (roughly 2400 to 4000 years), followed by an expansion at about 40 generations, while J. sigillata had a constant population size from about 100 to 20 generations ago, followed by a rapid decline. Conclusions Both J. regia and J. sigillata appear to have suffered sudden population declines during their domestication, suggesting that the bottleneck scenario of plant domestication may well apply in at least some perennial crop species. Introgression from introduced J. regia appears to have played a role in the domestication of J. sigillata.

Unravelling the genetic diversity and population structure of common walnut in the Iranian Plateau

“…Common walnut is one of the most essential fruit trees cultivated primarily for edible nuts since ancient times. It is highly supported that walnut originated from the Iranian Plateau [ 13 - 15 ]; previous findings proposed that the walnut’s domestication first occurred in the plateau, including parts of Iran, the southern Caucasus, Turkmenistan, and afterward expanded east to China and west to Europe by human movement via the Persian Royal Road and Silk Road [ 14 , 16 - 18 ].…”

Domestication and selection footprints in Persian walnuts (Juglans regia)

“…J. regia is considered as food used by humans back to Persia (7,000 BCE) [7,9,12,16], however, as an important annual crop, both rice and soybean ancient human domestication started from ~8,000 BCE [19][20][37][38][39]. Moreover, the walnut population had declined by the bottleneck scenario [40], which limited the expansion of genetic diversity. Third, intensive breeding may not be necessary where landraces already expressed desirable commercial traits to a considerable degree.…”

Unravelling the genetic diversity and population structure of Persian walnut in the Iranian Plateau

“…Common walnut is one of the most important fruit trees cultivated primarily for edible nuts since ancient times. It is highly supported that walnut originated in the Iranian Plateau (13)(14)(15); previous ndings proposed that the walnut's domestication rst occurred in the plateau, including parts of Iran, the southern Caucasus, Turkmenistan, and afterward expanded east to China and west to Europe by human movement via the Persian Royal Road and Silk Road (14,(16)(17)(18).…”