Regional Heritability Mapping provides insights into Dry matter (DM) Content in African white and yellow cassava populations

Open Access ArticleThe HarvestPlus program for cassava (Manihot esculenta Crantz) fortifies cassava with beta-carotene by breeding for carotene-rich tubers (yellow cassava). However, a negative correlation between yellowness and dry matter (DM) content has been identified. Here, we investigated the genetic control of DM in white and yellow cassava subpopulations. We used regional heritability mapping (RHM) to associate DM to genomic segments in both subpopulations. Significant segments were subjected to candidate gene analysis and we attempted to validate candidates using prediction accuracies. The RHM procedure was validated using a simulation approach. The RHM revealed significant hits for white cassava on chromosomes 1, 4, 5, 10, 17 and 18 while hits for the yellow were on chromosome 1. Candidate gene analysis revealed genes in the carbohydrate biosynthesis pathway including the plant serine-threonine protein kinases (SnRKs), UDP-glycosyltransferases, UDP-sugar transporters, invertases, pectinases, and regulons. Validation using 1252 unique identifiers from the SnRK gene family genome-wide recovered 50% of the predictive accuracy of whole genome SNPs for DM while validation using 53 likely (extracted from literature) genes from significant segments recovered 32%. Genes including an acid invertase, a neutral/alkaline invertase and a glucose-6-phosphate isomerase were validated based on an a priori list for the cassava starch pathway and also a fructose-biphosphate aldolase from the calvin cycle pathway. The power of the RHM procedure was estimated at 47 percent when the causal QTL generated 10% of the phenotypic variance with sample size of 451. Cassava DM genetics is complex. RHM may be useful for complex traits

Design, synthesis and biological activity of selective hCAs inhibitors based on 2-(benzylsulfinyl)benzoic acid scaffold

A large library of derivatives based on the scaffold of 2-(benzylsulfinyl)benzoic acid were synthesised and tested as atypical inhibitors against four different isoforms of human carbonic anhydrase (hCA I, II, IX and XII, EC 4.2.1.1). The exploration of the chemical space around the main functional groups led to the discovery of selective hCA IX inhibitors in the micromolar/nanomolar range, thus establishing robust structure-activity relationships within this versatile scaffold. HPLC separation of some selected chiral compounds and biological evaluation of the corresponding enantiomers was performed along with molecular modelling studies on the most active derivatives

Ostracods as ecological and isotopic indicators of lake water salinity changes: the Lake Van example

Ostracods are common lacustrine calcitic microfossils. Their faunal assemblage and morphological characteristics are important ecological proxies, and their valves are archives of geochemical information related to palaeoclimatic and palaeohydrological changes. In an attempt to assess ostracod ecology (taxonomic diversity and valve morphology) combined with valve geochemistry (δ18O and δ13C) as palaeosalinity indicators, we analysed sedimentary material from the International Continental Scientific Drilling Program (ICDP) Ahlat Ridge site from a terminal and alkaline lake, Lake Van (Turkey), covering the last 150&thinsp;kyr. Despite a low species diversity, the ostracod faunal assemblage reacted sensitively to changes in the concentration of total dissolved salts in their aquatic environment. Limnocythere inopinata is present throughout the studied interval, while Limnocythere sp. A is restricted to the Last Glacial period and related to increased lake water salinity and alkalinity. The presence of species belonging to the genus Candona is limited to periods of lower salinity. Valves of Limnocytherinae species (incl. L. inopinata) display nodes (hollow protrusions) during intervals of increased salinity. Both the number of noded valves and the number of nodes per valve appear to increase with rising salinity, suggesting that node formation is related to hydrological changes (salinity and/or alkalinity). In contrast to Lake Van's bulk δ18O record, the δ18O values of ostracod valves do record relative changes of the lake volume, with lower values during high lake level periods. The δ13C values of different species reflect ostracod habitat preferences (i.e. infaunal vs. epifaunal) but are less sensitive to hydrological changes. However, combined with other proxies, decreasing Holocene δ13C values may indicate a freshening of the lake water compared to the low lake level during the Last Glacial period. The Lake Van example underscores the significance and value of coupling ostracod ecology and valve geochemistry in palaeoenvironmental studies of endorheic lake basins.</p

Accuracies of univariate and multivariate genomic prediction models in African cassava

Open Access Journal; Published online:15 March 2017Background: Genomic selection (GS) promises to accelerate genetic gain in plant breeding programs especially for crop species such as cassava that have long breeding cycles. Practically, to implement GS in cassava breeding, it is necessary to evaluate different GS models and to develop suitable models for an optimized breeding pipeline. In this paper, we compared (1) prediction accuracies from a single-trait (uT) and a multi-trait (MT) mixed model for a singleenvironment genetic evaluation (Scenario 1), and (2) accuracies from a compound symmetric multi-environment model (uE) parameterized as a univariate multi-kernel model to a multivariate (ME) multi-environment mixed model that accounts for genotype-by-environment interaction for multi-environment genetic evaluation (Scenario 2). For these analyses, we used 16 years of public cassava breeding data for six target cassava traits and a fivefold cross-validation scheme with 10-repeat cycles to assess model prediction accuracies. Results: In Scenario 1, the MT models had higher prediction accuracies than the uT models for all traits and locations analyzed, which amounted to on average a 40% improved prediction accuracy. For Scenario 2, we observed that the ME model had on average (across all locations and traits) a 12% improved prediction accuracy compared to the uE model. Conclusions: We recommend the use of multivariate mixed models (MT and ME) for cassava genetic evaluation. These models may be useful for other plant species

Genetic correlation, genome-wide association and genomic prediction of portable NIRS predicted carotenoids in cassava roots

Open Access Journal; Published online: 04 Dec 2019Random forests (RF) was used to correlate spectral responses to known wet chemistry carotenoid concentrations including total carotenoid content (TCC), all-trans β-carotene (ATBC), violaxanthin (VIO), lutein (LUT), 15-cis beta-carotene (15CBC), 13-cis beta-carotene (13CBC), alpha-carotene (AC), 9-cis beta-carotene (9CBC), and phytoene (PHY) from laboratory analysis of 173 cassava root samples in Columbia. The cross-validated correlations between the actual and estimated carotenoid values using RF ranged from 0.62 in PHY to 0.97 in ATBC. The developed models were used to evaluate the carotenoids of 594 cassava clones with spectral information collected across three locations in a national breeding program (NRCRI, Umudike), Nigeria. Both populations contained cassava clones characterized as white and yellow. The NRCRI evaluated phenotypes were used to assess the genetic correlations, conduct genome-wide association studies (GWAS), and genomic predictions. Estimates of genetic correlation showed various levels of the relationship among the carotenoids. The associations between TCC and the individual carotenoids were all significant (P 0.75, except in LUT and PHY where r < 0.3). The GWAS revealed significant genomic regions on chromosomes 1, 2, 4, 13, 14, and 15 associated with variation in at least one of the carotenoids. One of the identified candidate genes, phytoene synthase (PSY) has been widely reported for variation in TCC in cassava. On average, genomic prediction accuracies from the single-trait genomic best linear unbiased prediction (GBLUP) and RF as well as from a multiple-trait GBLUP model ranged from ∼0.2 in LUT and PHY to 0.52 in TCC. The multiple-trait GBLUP model gave slightly higher accuracies than the single trait GBLUP and RF models. This study is one of the initial attempts in understanding the genetic basis of individual carotenoids and demonstrates the usefulness of NIRS in cassava improvement

Biallelic variants in ADAMTS15 cause a novel form of distal arthrogryposis

Purpose We aimed to identify the underlying genetic cause for a novel form of distal arthrogryposis. Methods Rare variant family-based genomics, exome sequencing, and disease-specific panel sequencing were used to detect ADAMTS15 variants in affected individuals. Adamts15 expression was analyzed at the single-cell level during murine embryogenesis. Expression patterns were characterized using in situ hybridization and RNAscope. Results We identified homozygous rare variant alleles of ADAMTS15 in 5 affected individuals from 4 unrelated consanguineous families presenting with congenital flexion contractures of the interphalangeal joints and hypoplastic or absent palmar creases. Radiographic investigations showed physiological interphalangeal joint morphology. Additional features included knee, Achilles tendon, and toe contractures, spinal stiffness, scoliosis, and orthodontic abnormalities. Analysis of mouse whole-embryo single-cell sequencing data revealed a tightly regulated Adamts15 expression in the limb mesenchyme between embryonic stages E11.5 and E15.0. A perimuscular and peritendinous expression was evident in in situ hybridization in the developing mouse limb. In accordance, RNAscope analysis detected a significant coexpression with Osr1, but not with markers for skeletal muscle or joint formation. Conclusion In aggregate, our findings provide evidence that rare biallelic recessive trait variants in ADAMTS15 cause a novel autosomal recessive connective tissue disorder, resulting in a distal arthrogryposis syndrome

Extraforaminal ligament attachments of the thoracic spinal nerves in humans

An anatomical study of the extraforaminal attachments of the thoracic spinal nerves was performed using human spinal columns. The objectives of the study are to identify and describe the existence of ligamentous structures at each thoracic level that attach spinal nerves to structures at the extraforaminal region. During the last 120 years, several mechanisms have been described to protect the spinal nerve against traction. All the described structures were located inside the spinal canal proximal to the intervertebral foramen. Ligaments with a comparable function just outside the intervertebral foramen are mentioned ephemerally. No studies are available about ligamentous attachments of thoracic spinal nerves to the spine. Five embalmed human thoracic spines (Th2–Th11) were dissected. Bilaterally, the extraforaminal region was dissected to describe and measure anatomical structures and their relationships with the thoracic spinal nerves. Histology was done at the sites of attachment of the ligaments to the nerves and along the ligaments. The thoracic spinal nerves are attached to the transverse process of the vertebrae cranial and caudal to the intervertebral foramen. The ligaments consist mainly of collagenous fibers. In conclusion, at the thoracic level, direct ligamentous connections exist between extraforaminal thoracic spinal nerves and nearby structures. They may serve as a protective mechanism against traction and compression of the nerves by positioning the nerve in the intervertebral foramen

Left atrial giant thrombus infected by Escherichia Coli. Case report

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