beloved and consummate University citizen who contributed to the well being of the institution and his fellow faculty in innumerable ways. He spearheaded the creation of Hitchhiker, led its compilation and subsequent annual updates, and edited the first three editions. He will be missed. This guide was prepared by members of the Penn Association of Senior and Emeritus Faculty as a summary of issues that faculty members should review as they begin to consider retirement. It is not intended to be a detailed description of available benefits, nor is it intended to replace any of the official documents published by the University of Pennsylvania. The guide was not prepared by and is not published by the University of Pennsylvania, its Division of Human Resources, or any University benefits administrators. The University therefore makes no representations or assurances regarding its accuracy or completeness. Faculty are strongly encouraged to review in detail any summary plan description of benefits they consider to be important, as well as to speak to representatives from the Division of Human Resources before making any decision regarding retirement or benefits. The University offers many benefits to active and retired faculty, the terms of which are set forth in various plans and summary plan descriptions, which may be subject to change.

https://www.jstor.org/stable/10.1641/0006-3568(2005)055%5B1024:AHGT%5D2.0.CO;2

A Hitchhiker's Guide to…

The walnut (Juglans spp.) is an appreciated nut that belongs to the Juglandaceae family. The fruit includes four main parts: the kernel, the skin, the shell, and the green husk. It is widely cultivated due to its edible kernel. In walnut production centers, high amounts of the husk as an agro-forest waste product are produced and discarded away. Recently, it has been demonstrated that the walnut green husk could be valued as a source of different natural bioactive compounds with excellent antioxidant and antimicrobial properties. Regarding this respect, in this contribution, the current scientific knowledge on the antioxidant and antiradical activities, various identified and isolated individual chemical constituents, as well as the functional applications of the walnut husk with more emphasis on the Persian walnut (Juglans regia L.) are reviewed.

https://www.mdpi.com/1422-0067/20/16/3920/pdf

A Comprehensive Review on the Chemical Constituents and Functional Uses of Walnut ( Juglans spp.) Husk

Author(s): Marrano, Annarita; Britton, Monica; Zaini, Paulo A; Zimin, Aleksey V; Workman, Rachael E; Puiu, Daniela; Bianco, Luca; Pierro, Erica Adele Di; Allen, Brian J; Chakraborty, Sandeep; Troggio, Michela; Leslie, Charles A; Timp, Winston; Dandekar, Abhaya; Salzberg, Steven L; Neale, David B | Abstract: BackgroundThe release of the first reference genome of walnut (Juglans regia L.) enabled many achievements in the characterization of walnut genetic and functional variation. However, it is highly fragmented, preventing the integration of genetic, transcriptomic, and proteomic information to fully elucidate walnut biological processes.FindingsHere, we report the new chromosome-scale assembly of the walnut reference genome (Chandler v2.0) obtained by combining Oxford Nanopore long-read sequencing with chromosome conformation capture (Hi-C) technology. Relative to the previous reference genome, the new assembly features an 84.4-fold increase in N50 size, with the 16 chromosomal pseudomolecules assembled and representing 95% of its total length. Using full-length transcripts from single-molecule real-time sequencing, we predicted 37,554 gene models, with a mean gene length higher than the previous gene annotations. Most of the new protein-coding genes (90%) present both start and stop codons, which represents a significant improvement compared with Chandler v1.0 (only 48%). We then tested the potential impact of the new chromosome-level genome on different areas of walnut research. By studying the proteome changes occurring during male flower development, we observed that the virtual proteome obtained from Chandler v2.0 presents fewer artifacts than the previous reference genome, enabling the identification of a new potential pollen allergen in walnut. Also, the new chromosome-scale genome facilitates in-depth studies of intraspecies genetic diversity by revealing previously undetected autozygous regions in Chandler, likely resulting from inbreeding, and 195 genomic regions highly differentiated between Western and Eastern walnut cultivars.ConclusionOverall, Chandler v2.0 will serve as a valuable resource to better understand and explore walnut biology.

/pdf/high-quality-chromosome-scale-assembly-of-the-walnut-juglans-4kqcq6lybr.pdf

High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome.

Over the last 20 years, global production of Persian walnut (Juglans regia L.) has grown enormously, likely reflecting increased consumption due to its numerous benefits to human health. However, advances in genome-wide association (GWA) studies and genomic selection (GS) for agronomically important traits in walnut remain limited due to the lack of powerful genomic tools. Here, we present the development and validation of a high-density 700K single nucleotide polymorphism (SNP) array in Persian walnut. Over 609K high-quality SNPs have been thoroughly selected from a set of 9.6 m genome-wide variants, previously identified from the high-depth re-sequencing of 27 founders of the Walnut Improvement Program (WIP) of University of California, Davis. To validate the effectiveness of the array, we genotyped a collection of 1284 walnut trees, including 1167 progeny of 48 WIP families and 26 walnut cultivars. More than half of the SNPs (55.7%) fell in the highest quality class of 'Poly High Resolution' (PHR) polymorphisms, which were used to assess the WIP pedigree integrity. We identified 151 new parent-offspring relationships, all confirmed with the Mendelian inheritance test. In addition, we explored the genetic variability among cultivars of different origin, revealing how the varieties from Europe and California were differentiated from Asian accessions. Both the reconstruction of the WIP pedigree and population structure analysis confirmed the effectiveness of the Applied Biosystems™ Axiom™ J. regia 700K SNP array, which initiates a novel genomic and advanced phase in walnut genetics and breeding.

https://onlinelibrary.wiley.com/doi/epdf/10.1111/pbi.13034

A new genomic tool for walnut (Juglans regia L.): development and validation of the high-density Axiom™ J. regia 700K SNP genotyping array.

Persian or English walnut (Juglans regia L.), the walnut species cultivated for nut production, is one of the oldest food sources known and is grown worldwide in temperate areas. France is the 7th leading producer as of 2016 with 39 kt. Deciphering walnut genetic diversity and structure is important for efficient management and use of genetic resources. In this work, 253 worldwide accessions from the INRA walnut germplasm collection, containing English walnut and several related species, were genotyped using 13 SSR (Single Sequence Repeat) markers selected from the literature to assess diversity and structure. Genetic diversity parameters showed a deficiency of heterozygotes and, for several SSRs, allele-specificities among the accessions tested. Principal Coordinate Analysis (PCoA) showed the 253 accessions clustered in largely in agreement with the existing botanical classification of the genus. Among the 217 J. regia accessions, two main clusters, accessions from Eastern Europe and Asia, and accessions from Western Europe and America, were identified using STRUCTURE software. This was confirmed by Principal Coordinate Analysis and supported by Neighbor-Joining tree construction using DARwin software. Moreover, a substructure was found within the two clusters, mainly according to geographical origin. A core collection containing 50 accessions was selected using the maximum length sub-tree method and prior knowledge about their phenotype. The present study constitutes a preliminary population genetics overview of INRA walnut genetic resources collection using SSR markers. The resulting estimations of genetic diversity and structure are useful for germplasm management and for future walnut breeding programs.

/pdf/analysis-of-genetic-diversity-and-structure-in-a-worldwide-3erdbf353z.pdf

Analysis of genetic diversity and structure in a worldwide walnut (Juglans regia L.) germplasm using SSR markers.

Persian or English walnut (Juglans regia L.), the walnut species cultivated for nut production, is one of the oldest food sources known. Persian walnuts, native to the mountain valleys of Central Asia, are grown worldwide in temperate areas. World production exceeds three million tons since 2012, mostly provided by China, the USA, and Iran. Despite very ancient culture of walnut species (Juglans spp.), breeding actually started in the twentieth century. Using a range of methodologies, from morphological markers to the most recent advances in genome analysis, many genetic studies of walnut have been conducted during the past 30 years, including examination of diversity, determination of relationships within or among germplasm collections and populations, phylogenetic and origin elucidation, genetic map construction, and biotic or abiotic stress investigations. The genetic improvement of walnut has undergone great evolution. The producing countries of the Middle East have widely studied morphological characteristics of walnut. The USA and France, for example, are behind important cultivar releases such as “Chandler” and “Franquette.” Finally, genomics represents a major breakthrough in walnut improvement, in particular by recent sequencing of both chloroplast and nuclear genomes. This review summarizes worldwide molecular and “omics” studies and gives an overview of the main walnut breeding programs.

/pdf/walnut-past-and-future-of-genetic-improvement-2tr7ofgwb2.pdf

Walnut: past and future of genetic improvement

Persian walnut (Juglans regia L.), the walnut species cultivated for nut production, is grown worldwide in temperate areas. In this work, chronological phenotypic data have been collected regarding a part of the walnut genetic resources of the French National Institute for Agricultural Research (INRA) of Bordeaux. Using a well described ontology, these data have been collected in order to assess the phenotypic variations among the accessions, and to better manage the germplasm collection. These data can also be helpful for any breeding program as they provide a clear phenotypic characterization of the main cultivars. This paper introduces a dataset collected for 150 J. regia accessions for a period from 1965 to 2016, and for 3 observation sites, released as comma separated value spreadsheet. It includes observations about phenological traits (e.g. flowering dates), traits related to in-shell walnut (e.g. weight and size), and traits related to kernel (e.g. color). It can be used by other researchers particularly for multi-site phenological studies in the context of climate change since climate data files are also available. In addition, a complete walnut ontology was deposited in this repository and can assist to standardize the management of any walnut germplasm collection.

/pdf/the-walnut-genetic-resources-of-inra-chronological-4zdutusg98.pdf

Anthony Bernard

Papers

Walnut: past and future of genetic improvement

Analysis of genetic diversity and structure in a worldwide walnut (Juglans regia L.) germplasm using SSR markers.

The walnut genetic resources of INRA: chronological phenotypic data and ontology.