Woody perennial angiosperms (i.e., hardwood trees) are polyphyletic in origin and occur in most angiosperm orders. Despite their independent origins, hardwoods have shared physiological, anatomical, and life history traits distinct from their herbaceous relatives. New high-throughput DNA sequencing platforms have provided access to numerous woody plant genomes beyond the early reference genomes of Populus and Eucalyptus, references that now include willow and oak, with pecan and chestnut soon to follow. Genomic studies within these diverse and undomesticated species have successfully linked genes to ecological, physiological, and developmental traits directly. Moreover, comparative genomic approaches are providing insights into speciation events while large-scale DNA resequencing of native collections is identifying population-level genetic diversity responsible for variation in key woody plant biology across and within species. Current research is focused on developing genomic prediction models for breeding, defining speciation and local adaptation, detecting and characterizing somatic mutations, revealing the mechanisms of gender determination and flowering, and application of systems biology approaches to model complex regulatory networks underlying quantitative traits. Emerging technologies such as single-molecule, long-read sequencing is being employed as additional woody plant species, and genotypes within species, are sequenced, thus enabling a comparative ("evo-devo") approach to understanding the unique biology of large woody plants. Resource availability, current genomic and genetic applications, new discoveries and predicted future developments are illustrated and discussed for poplar, eucalyptus, willow, oak, chestnut, and pecan.

/pdf/hardwood-tree-genomics-unlocking-woody-plant-biology-2usbzurrgn.pdf

Hardwood Tree Genomics: Unlocking Woody Plant Biology

The chestnuts and chinquapins are a group of about seven species of trees and shrubs in the genus Castanea. They are of considerable importance ecologically in all the areas of their natural occurrence, and the chestnuts especially are of great economic value for their lumber and for their nut crop wherever they are cultivated. Two catastrophic diseases, chestnut blight caused by the ascomycete fungus Cryphonectria parasitica (Murr.) Barr and Phytophthora root rot (ink disease) caused primarily by the soil-borne oomycetes Phytophthora cinnamomi Rands and P. cambivora (Petri) Buisman, have severely impacted chestnut in Europe and North America. Therefore, much of the breeding work continues to focus on breeding for resistance to these two diseases. The most serious insect pest of Castanea is the Asian chestnut gall wasp, Dryocosmus kuriphilus Yasumatsu. Variation in host tolerance to D. kuriphilus has led to development of new gall-resistant chestnut cultivars. Interspecific hybridization offers great opportunity to combine the most favorable traits found in the ample genetic diversity of the genus through introgression into locally-adapted populations. Chestnut breeders in eastern Asia have made great strides towards improvement of chestnut fruit quality and crop yields, and researchers in all chestnut growing regions have made gains in disease resistance by using molecular markers and other genomic tools to assist selection. Biotechnologies that include transmissible hypovirulence as a biocontrol for chestnut blight, tissue culture and other micropropagation techniques, and genetic engineering and transformation technologies are complementary to classical plant breeding programs.

Chestnut (Castanea spp. Miller) Breeding

Objectives Spata19 was one of genes involved in neurogenesis, which mutated in some psychiatric disorders. In the current study, using Spata19 knockout mice, we showed the effect of this gene inactivation on some behaviors of mice. Methods Twenty-four wild-type (WT) and global Spata19 knockout (KO) mice were divided into four groups (Male: WT, n = 9 (6) | Male: KO, n = 5| Female: WT, n = 6| Female: KO, n = 4 (3)). Four of them died during the study. The behavior of these mice was compared with Open Field, Novel Object Recognition, Social Interaction Test and Forced Swimming Test. In these tests, respectively, time spent in centers and locomotor activity, number of smells, fighting and number of stops were evaluated. Results Spata19 gene inactivation had not any effect on the behavior of the female mice but in male mice showed greater locomotor activity and time spent in center of arena in the open field test, different coping behavior in Forced Swimming Test, aggressive behavior in Social Interaction Test and cognitive impairment in Novel Object Recognition. This behavioral difference in male KO vs. other mice was significant with a p-value less than 0.05. Conclusions The results showed that gene inactivation was involved in the development of behavioral disorders in males.

Male Spata19 knockout mice have behavioral disorders

Karyotypy-phenotype-genotype correlation in a 4p;12q rearrangement

Karyotype-phenotype-genotype correlation in a 4p;12q rearrangement

Jacobsen syndrome (JBS) is a contiguous gene deletion syndrome involving terminal chromosome 11q. The haploinsufficiency of multiple genes contributes to the overall clinical phenotype, which can include the variant Paris-Trousseau syndrome, a transient thrombocytopenia related to FLI1 hemizygous deletion. We investigated a boy with features of JBS using classic cytogenetic methods, FISH and high-resolution array CGH. The proband was found to have a mosaic ring chromosome 11 resulting in a hemizygous 11q terminal deletion of 8.6 Mb, leading to a copy number loss of 52 genes. The patient had a hemizygous deletion in the FLI1 gene region without apparent thrombocytopenia, and he developed diabetes mellitus type I, which has not previously been described in the spectrum of disorders associated with JBS. The relationship of some of the genes within the context of the phenotype caused by a partial deletion of 11q has provided insights concerning the developmental anomalies presented in this patient with atypical features of JBS.

/pdf/complex-mosaic-ring-chromosome-11-associated-with-hemizygous-17rszt9kjk.pdf

Complex Mosaic Ring Chromosome 11 Associated with Hemizygous Loss of 8.6 Mb of 11q24.2qter in Atypical Jacobsen Syndrome

Duplication of the short arm of chromosome 12 is a rare chromosomal abnormality that may arise de novo or result from malsegregation of a balanced parental translocation. This study comprises the clinical description, cytogenetic and cytogenomic analyses and genotype-phenotype correlation in a patient with facial dysmorphism, developmental delay and intellectual impairment caused by non-mosaic partial duplication and a paracentric inversion 12p. The patient's GTG-banded karyotype was 46,XX,invdup(12)(pter → p13.32::p11.1 → p13.31::p13.31 → qter). A genetic gain of approximately 28 Mb was detected in the chromosomal region arr[GRCh37]12p13.31-p11.1(6914072_34756209)x3. The chromosomal alteration seen in our patient is described as "pure" partial duplication 12p. In most cases, duplication 12p phenotype is characterized by dysmorphic features, multiple congenital anomalies and intellectual disability. A small number of cases in literature have described genes associated with neurodevelopmental disease, such as ING4, CHD4, MFAP5, GRIN2B, SOX5, SCN8A and PIANP. In our patient the duplication 12p was de novo. This study should contribute to the genotype-phenotype correlation in partial duplication 12p cases.

/pdf/non-mosaic-partial-duplication-12p-in-a-patient-with-4yb1fmtdj8.pdf

Non-mosaic partial duplication 12p in a patient with dysmorphic characteristics and developmental delay

22q11.2 microdeletion is the most common microdeletion syndrome in humans and occurs with a frequency of 1 in 2,000-6,000 live births. Its main clinical features are associated with a failure to form derivatives of the third and fourth branchial arches during embryonic development. The phenotype includes heart outflow tract defects, craniofacial dysmorphisms (prominent and bulbous tip, external ears malformations, and posterior cleft palate) and endocrinological and immune system dysfunctions, as well as neurological and psychiatric disorders. Patients with this syndrome received different names, such as DiGeorge syndrome and velocardiofacial syndrome, since the recognition was based on the phenotype. Recently, molecular and genomic techniques have shown that this syndrome has great phenotypic heterogeneity. Two children with quite distinct phenotypes from this microdeletion syndrome are described in order to review the most common clinical manifestations and highlight that the great clinical heterogeneity can complicate its recognition by pediatricians.

T. M. Joaquim

Papers

Karyotypy-phenotype-genotype correlation in a 4p;12q rearrangement

Karyotype-phenotype-genotype correlation in a 4p;12q rearrangement

Complex Mosaic Ring Chromosome 11 Associated with Hemizygous Loss of 8.6 Mb of 11q24.2qter in Atypical Jacobsen Syndrome

Non-mosaic partial duplication 12p in a patient with dysmorphic characteristics and developmental delay

Multiple terms for a complex phenotype: contribution of two clinical cases for the recognition of 22q11.2 deletion syndrome