Population Structure, Genetic Diversity, and Gene Introgression of Two Closely Related Walnuts (Juglans regia and J. sigillata) in Southwestern China Revealed by EST-SSR Markers

Abstract

The common walnut (Juglans regia L.) and iron walnut (J. sigillata Dode) are well-known economically important species cultivated for their edible nuts, high-quality wood, and medicinal properties and display a sympatric distribution in southwestern China. However, detailed research on the genetic diversity and introgression of these two closely related walnut species, especially in southwestern China, are lacking. In this study, we analyzed a total of 506 individuals from 28 populations of J. regia and J. sigillata using 25 EST-SSR markers to determine if their gene introgression was related to sympatric distribution. In addition, we compared the genetic diversity estimates between them. Our results indicated that all J. regia populations possess slightly higher genetic diversity than J. sigillata populations. The Geostatistical IDW technique (HO, PPL, NA and PrA) revealed that northern Yunnan and Guizhou provinces had high genetic diversity for J. regia while the northwestern Yunnan province had high genetic diversity for J. sigillata. AMOVA analysis revealed that significant genetic variation was mainly distributed within population as 73% in J. regia and 76% in J. sigillata. The genetic differentiation (FST) was 0.307 between the two walnut species (p < 0.0001), which was higher than FST values within populations (J. regia FST = 0.265 and J. sigillata FST = 0.236). However, the STRUCTURE analysis of the J. regia and J. sigillata populations revealed two genetic clusters in which gene introgression exists, therefore, the boundary of separation between these two walnut species is not clear. Moreover, these results were validated by NJ and UPGMA analysis with additional conformation from the PCoA. Based on the SSR data, our results indicate that J. sigillata is an ecotype of J. regia. Taken together, these results reveal novel information on population genetics and provide specific geographical regions containing high genetic diversity of the Juglans species sampled, which will assist in future conservation management.

SNP discovery for genetic diversity and population structure analysis coupled with restriction-associated DNA (RAD) sequencing in walnut cultivars of Sichuan Province, China

“…The migration from ES to SS was significantly greater than that in the reverse direction. Consistent with this result, a high asymmetric historical gene flow was detected among these two species, which occurred predominantly from J. regia into J. sigillata [52]. Based on the above results, we suggest that the walnuts in Sichuan province were likely derived from the North China population.…”

“…The walnut perhaps survived the last glaciations in some refugia, and all the modern distribution probably was affected by humans [51]. Some previous studies also suggested that J. regia and J. sigillata should be considered as a single species, and J. sigillata might be an ecotype of J. regia [42,52]. So further research could uncover more information about the phylogenetic relationships among them.…”

Phylogenomics Reveals an Ancient Hybrid Origin of the Persian Walnut

“…The genomic mosaicism of both the Persian walnut (incl. J. sigillata) and the American butternut J. cinerea provides evidence for the importance of hybridization throughout the evolution of walnuts, matching (Bai et al 2016;Yuan et al 2018;Zhao et al 2018). However, our results from the entire genus, which today is most species-rich in North and South America while Europe has a single species (supplementary fig.…”

Genetic Diversity and Population Genetic Structure of Cinnamomum camphora in South China Revealed by EST-SSR Markers

“…EST-SSR markers have been extensively used in the study of genetic diversity and population structure because of several advantages over studies of noncoding nuclear genomes, such as increased transferability to related species [37], increased accuracy when accessing differences in adaptation among populations [38], increased amplification success, conserved primer sites and a simplified analysis [39]. However, even though whole-genome sequencing has been completed [1], only a few EST-SSR markers have been developed in earlier studies [9,16,20], and a number of polymorphic and informative EST-SSR markers in particular are still lacking.…”