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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 (N_A = 3.839, H_O = 0.558, U_HE = 0.580), and eight populations had positive inbreeding coefficient (F_IS) values. Low among-population differentiation was indicated by AMOVA, pairwise F_ST and D_C. 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.

SUBMITTER: Magige EA

PROVIDER: S-EPMC9269025 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BACKGROUND:Unravelling the genetic architecture of agronomic traits in walnut such as budbreak date and bearing habit, is crucial for climate change adaptation and yield improvement. A Genome-Wide Association Study (GWAS) using multi-locus models was conducted in a panel of 170 walnut accessions genotyped using the Axiom™ J. regia 700?K SNP array, with phenological data from 2018, 2019 and legacy data. These accessions come from the INRAE walnut germplasm collection which is the result of important prospecting work performed in many countries around the world. In parallel, an F1 progeny of 78 individuals segregating for phenology-related traits, was genotyped with the same array and phenotyped for the same traits, to construct linkage maps and perform Quantitative Trait Loci (QTLs) detection. RESULTS:Using GWAS, we found strong associations of SNPs located at the beginning of chromosome 1 with both budbreak and female flowering dates. These findings were supported by QTLs detected in the same genomic region. Highly significant associated SNPs were also detected using GWAS for heterodichogamy and lateral bearing habit, both on chromosome 11. We developed a Kompetitive Allele Specific PCR (KASP) marker for budbreak date in walnut, and validated it using plant material from the Walnut Improvement Program of the University of California, Davis, demonstrating its effectiveness for marker-assisted selection in Persian walnut. We found several candidate genes involved in flowering events in walnut, including a gene related to heterodichogamy encoding a sugar catabolism enzyme and a cell division related gene linked to female flowering date. CONCLUSIONS:This study enhances knowledge of the genetic architecture of important agronomic traits related to male and female flowering processes and lateral bearing in walnut. The new marker available for budbreak date, one of the most important traits for good fruiting, will facilitate the selection and development of new walnut cultivars suitable for specific climates.

Project description:The distribution and survival of trees during the last glacial maximum (LGM) has been of interest to paleoecologists, biogeographers, and geneticists. Ecological niche models that associate species occurrence and abundance with climatic variables are widely used to gain ecological and evolutionary insights and to predict species distributions over space and time. The present study deals with the glacial history of walnut to address questions related to past distributions through genetic analysis and ecological modeling of the present, LGM and Last Interglacial (LIG) periods. A maximum entropy method was used to project the current walnut distribution model on to the LGM (21-18 kyr BP) and LIG (130-116 kyr BP) climatic conditions. Model tuning identified the walnut data set filtered at 10 km spatial resolution as the best for modeling the current distribution and to hindcast past (LGM and LIG) distributions of walnut. The current distribution model predicted southern Caucasus, parts of West and Central Asia extending into South Asia encompassing northern Afghanistan, Pakistan, northwestern Himalayan region, and southwestern Tibet, as the favorable climatic niche matching the modern distribution of walnut. The hindcast of distributions suggested the occurrence of walnut during LGM was somewhat limited to southern latitudes from southern Caucasus, Central and South Asian regions extending into southwestern Tibet, northeastern India, Himalayan region of Sikkim and Bhutan, and southeastern China. Both CCSM and MIROC projections overlapped, except that MIROC projected a significant presence of walnut in the Balkan Peninsula during the LGM. In contrast, genetic analysis of the current walnut distribution suggested a much narrower area in northern Pakistan and the surrounding areas of Afghanistan, northwestern India, and southern Tajikistan as a plausible hotspot of diversity where walnut may have survived glaciations. Overall, the findings suggest that walnut perhaps survived the last glaciations in several refugia across a wide geographic area between 30° and 45° North latitude. However, humans probably played a significant role in the recent history and modern distribution of walnut.

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

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