A genome sequence for the threatened whitebark pine.

Whitebark pine (WBP, Pinus albicaulis) is a white pine of subalpine regions in the Western contiguous United States and Canada. WBP has become critically threatened throughout a significant part of its natural range due to mortality from the introduced fungal pathogen white pine blister rust (WPBR, Cronartium ribicola) and additional threats from mountain pine beetle (Dendroctonus ponderosae), wildfire, and maladaptation due to changing climate. Vast acreages of WBP have suffered nearly complete mortality.

Comparative analysis of differential gene expression indicates divergence in ontogenetic strategies of leaves in two conifer genera.

In land plants, heteroblasty broadly refers to a drastic change in morphology during growth through ontogeny. and are conifers of independent lineages known to exhibit leaf heteroblasty between the juvenile and adult life stage of development. Juvenile leaves of develop spirally on the main stem and appear decurrent, flattened, and needle-like; whereas adult photosynthetic leaves are triangular or semi-circular needle-like, and grow in whorls on secondary or tertiary compact dwarf shoots.

Assembled and annotated 26.5 Gbp coast redwood genome: a resource for estimating evolutionary adaptive potential and investigating hexaploid origin.

Sequencing, assembly, and annotation of the 26.5 Gbp hexaploid genome of coast redwood (Sequoia sempervirens) was completed leading toward discovery of genes related to climate adaptation and investigation of the origin of the hexaploid genome. Deep-coverage short-read Illumina sequencing data from haploid tissue from a single seed were combined with long-read Oxford Nanopore Technologies sequencing data from diploid needle tissue to create an initial assembly, which was then scaffolded using proximity ligation data to produce a highly contiguous final assembly, SESE 2.

Selective Sweeps and Polygenic Adaptation Drive Local Adaptation along Moisture and Temperature Gradients in Natural Populations of Coast Redwood and Giant Sequoia.

Dissecting the genomic basis of local adaptation is a major goal in evolutionary biology and conservation science. Rapid changes in the climate pose significant challenges to the survival of natural populations, and the genomic basis of long-generation plant species is still poorly understood. Here, we investigated genome-wide climate adaptation in giant sequoia and coast redwood, two iconic and ecologically important tree species.

Dissecting the Polygenic Basis of Cold Adaptation Using Genome-Wide Association of Traits and Environmental Data in Douglas-fir.

Understanding the genomic and environmental basis of cold adaptation is key to understand how plants survive and adapt to different environmental conditions across their natural range. Univariate and multivariate genome-wide association (GWAS) and genotype-environment association (GEA) analyses were used to test associations among genome-wide SNPs obtained from whole-genome resequencing, measures of growth, phenology, emergence, cold hardiness, and range-wide environmental variation in coastal Douglas-fir (). Results suggest a complex genomic architecture of cold adaptation, in which traits are either highly polygenic or controlled by both large and small effect genes.

Pet Macaques in Vietnam: An NGO's Perspective.

In this article, we attempt to characterize the widespread trade in pet macaques in Vietnam. Data on confiscations as well as surrenders, releases, and individuals housed at rescue centers across Vietnam for 2015-2019 were opportunistically recorded. Data comparisons between Education for Nature Vietnam and three government-run wildlife rescue centers show that at least 1254 cases of macaque keeping occurred during the study period, including a minimum of 32 Assamese macaques (), 158 long-tailed macaques (), 291 Northern pig-tailed macaques (), 65 rhesus macaques (), and 110 stump-tailed macaques ().

Genetic Analysis of Walnut ( L.) Pellicle Pigment Variation Through a Novel, High-Throughput Phenotyping Platform.

Walnut pellicle color is a key quality attribute that drives consumer preference and walnut sales. For the first time a high-throughput, computer vision-based phenotyping platform using a custom algorithm to quantitatively score each walnut pellicle in L* a* b* color space was deployed at large-scale. This was compared to traditional qualitative scoring by eye and was used to dissect the genetics of pellicle pigmentation.

A Reference Genome Sequence for Giant Sequoia.

The giant sequoia () of California are massive, long-lived trees that grow along the U.S. Sierra Nevada mountains.

Reconstruction of the Largest Pedigree Network for Pear Cultivars and Evaluation of the Genetic Diversity of the USDA-ARS National Collection.

The USDA-ARS National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon, maintains one of the world's largest and most diverse living collection. A thorough genetic characterization of this germplasm will provide relevant information to optimize the conservation strategy of pear biodiversity, support the use of this germplasm in breeding, and increase our knowledge of taxonomy, evolution, and domestication. In the last two decades simple sequence repeat (SSR) markers have been used at the NCGR for cultivar identification and small population structure analysis.

Genomic basis of white pine blister rust quantitative disease resistance and its relationship with qualitative resistance.

The genomic architecture and molecular mechanisms controlling variation in quantitative disease resistance loci are not well understood in plant species and have been barely studied in long-generation trees. Quantitative trait loci mapping and genome-wide association studies were combined to test a large single nucleotide polymorphism (SNP) set for association with quantitative and qualitative white pine blister rust resistance in sugar pine. In the absence of a chromosome-scale reference genome, a high-density consensus linkage map was generated to obtain locations for associated SNPs.

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

Background: The 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.

Quantitative phenotyping of shell suture strength in walnut (Juglans regia L.) enhances precision for detection of QTL and genome-wide association mapping.

Walnut shell suture strength directly impacts the ability to maintain shell integrity during harvest and processing, susceptibility to insect damage and other contamination, and the proportion of kernel halves recovered during cracking. Suture strength is therefore an important breeding objective. Here, two methods of phenotyping this trait were investigated: 1) traditional, qualitative and rather subjective scoring on an interval scale by human observers, and; 2) quantitative and continuous measurements captured by a texturometer.

Association and linkage mapping to unravel genetic architecture of phenological traits and lateral bearing in Persian walnut (Juglans regia L.).

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.

Comparative genomics of six Juglans species reveals disease-associated gene family contractions.

Juglans (walnuts), the most speciose genus in the walnut family (Juglandaceae), represents most of the family's commercially valuable fruit and wood-producing trees. It includes several species used as rootstock for their resistance to various abiotic and biotic stressors. We present the full structural and functional genome annotations of six Juglans species and one outgroup within Juglandaceae (Juglans regia, J.

Pseudo-chromosome-length genome assembly of a double haploid "Bartlett" pear (Pyrus communis L.).

Background: We report an improved assembly and scaffolding of the European pear (Pyrus communis L.) genome (referred to as BartlettDHv2.0), obtained using a combination of Pacific Biosciences RSII long-read sequencing, Bionano optical mapping, chromatin interaction capture (Hi-C), and genetic mapping.

Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa.

Background: Populus trichocarpa is an important forest tree species for the generation of lignocellulosic ethanol. Understanding the genomic basis of biomass production and chemical composition of wood is fundamental in supporting genetic improvement programs. Considerable variation has been observed in this species for complex traits related to growth, phenology, ecophysiology and wood chemistry.

Combining phenotype, genotype, and environment to uncover genetic components underlying water use efficiency in Persian walnut.

Walnut production is challenged by climate change and abiotic stresses. Elucidating the genomic basis of adaptation to climate is essential to breeding drought-tolerant cultivars for enhanced productivity in arid and semi-arid regions. Here, we aimed to identify loci potentially involved in water use efficiency (WUE) and adaptation to drought in Persian walnut using a diverse panel of 95 walnut families (950 seedlings) from Iran, which show contrasting levels of water availability in their native habitats.

Deciphering of the Genetic Control of Phenology, Yield, and Pellicle Color in Persian Walnut ( L.).

Yield, nut quality, and ability to adapt to specific climate conditions, are all important factors to consider in the development and selection of new Persian walnut ( L.) varieties. The genetic control of these traits is still unknown in walnut, limiting the accuracy and rapidity of releasing new cultivars for commercial use.

Environmental Genome-Wide Association Reveals Climate Adaptation Is Shaped by Subtle to Moderate Allele Frequency Shifts in Loblolly Pine.

Understanding the genomic basis of local adaptation is crucial to determine the potential of long-lived woody species to withstand changes in their natural environment. In the past, efforts to dissect the genomic architecture in gymnosperms species have been limited due to the absence of reference genomes. Recently, the genomes of some commercially important conifers, such as loblolly pine, have become available, allowing whole-genome studies of these species.

A Reference Genome Sequence for the European Silver Fir ( Mill.): A Community-Generated Genomic Resource.

Silver fir ( Mill.) is a keystone conifer of European montane forest ecosystems that has experienced large fluctuations in population size during during the Quaternary and, more recently, due to land-use change. To forecast the species' future distribution and survival, it is important to investigate the genetic basis of adaptation to environmental change, notably to extreme events.

Development of a highly efficient Axiom™ 70 K SNP array for Pyrus and evaluation for high-density mapping and germplasm characterization.

Background: Both a source of diversity and the development of genomic tools, such as reference genomes and molecular markers, are equally important to enable faster progress in plant breeding. Pear (Pyrus spp.) lags far behind other fruit and nut crops in terms of employment of available genetic resources for new cultivar development.