Genetic Diversity and Structure of Persian Walnut (Juglans regia L.) in Pakistan: Implications for Conservation

Abstract

Persian (Common) walnut (Juglans regia L.) is a famous fruit tree species valued for its nutritious nuts and high-quality wood. Although walnut is widely distributed and plays an important role in the economy and culture of Pakistan, the genetic diversity and structure of its populations in the country remains poorly understood. Therefore, using 31 nuclear microsatellites, we assessed the genetic diversity and population structure of 12 walnut populations sampled across Pakistan. We also implemented the geostatistical IDW technique in ArcGIS to reveal “hotspots” of genetic diversity. Generally, the studied populations registered relatively low indices of genetic diversity (NA = 3.839, HO = 0.558, UHE = 0.580), and eight populations had positive inbreeding coefficient (FIS) values. Low among-population differentiation was indicated by AMOVA, pairwise FST and DC. STRUCTURE, PCoA and neighbor joining (NJ) analysis revealed a general lack of clear clustering in the populations except that one population in Upper Dir was clearly genetically distinct from the rest. Furthermore, the Mantel test showed no correlation between the geographic and genetic distance (r = 0.14, p = 0.22), while barrier analysis suggested three statistically significant genetic barriers. Finally, the spatial interpolation results indicated that populations in Ziarat, Kashmir, Dir, Swat, Chitral, and upper Dir had high intrapopulation genetic diversity, suggesting the need to conserve populations in those areas. The results from this study will be important for future breeding improvement and conservation of walnuts in Pakistan.

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

“…Our findings indicate that populations of J. regia from the Iranian Plateau possess moderate genetic diversity. The average H O and H E , and N E in the current study were lower than in the previous studies [ 9 , 42 - 46 ] (Table 4 ). The lowest genetic diversity was observed in the populations from Iraq and Georgia.…”

“…DNA concentration and quality were measured on 1% TAE agarose gels and using a NanoDrop®ND-1000 spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA); subsequently, all samples were diluted to 30–50 ng/mL for PCR reactions. Previous studies [ 46 , 61 ] described a multiplex of 31 pairs was used for genotyping the 508 walnut trees (Tables 1 , S 2 ). PCR amplification and cycling conditions were performed according to Magige et al [ 46 ].…”

“…Previous studies [ 46 , 61 ] described a multiplex of 31 pairs was used for genotyping the 508 walnut trees (Tables 1 , S 2 ). PCR amplification and cycling conditions were performed according to Magige et al [ 46 ]. Briefly, pre-denaturation at 98 °C for 2 min, 35 cycles of denaturation at 98 °C for 10 s, primer annealing at 53–61 °C for 15 s, extension at 72 °C for 10 s, and a final extension at 72 °C for 5 min, with a holding temperature of 4 °C.…”

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

“…DNA concentration and quality were measured on 1% TAE agarose gels and using a NanoDrop®ND-1000 spectrophotometer (Thermo Fisher Scienti c, Wilmington, DE, USA), subsequently, all samples were diluted to 30-50 ng/mL for PCR reactions. Previous studies (34,40,59) described a multiplex of 31 pairs was used for genotyping the 508 walnut trees (Table 1). PCR amplification and cycling conditions were performed according to Magige et al (40).…”

“…Previous studies (34,40,59) described a multiplex of 31 pairs was used for genotyping the 508 walnut trees (Table 1). PCR amplification and cycling conditions were performed according to Magige et al (40). Brie y, pre-denaturation at 98°C for 2 min, 35 cycles of denaturation at 98°C for 10 s, primer annealing at 53-61°C for 15 s, extension at 72°C for 10 s, and a nal extension at 72°C for 5 min, with a holding temperature of 4°C.…”