Association of Apolipoprotein E Polymorphism With Risk of Metabolic Syndrome: A Case-Control Study And Meta‐Analysis

Background: This study aimed to assess the genetic association between Apolipoprotein E (APOE) polymorphisms and susceptibility to metabolic syndrome (MetS) among the Tehran cardiometabolic genetic study (TCGS) participants. The results were then compared with similar studies in other populations using meta-analysis. Methods: the metabolic syndrome was defined according to the Joint Interim Statement (JIS) criteria. A total of 12282 subjects (5696 cases with metabolic syndrome and 6586 healthy controls) were genotyped using Human OmniExpress-24-v1-0 BeadChip. Subsequently, PubMed, Scopus, and Google Scholar databases were searched using relevant Medical Subject Headings (MeSH) terms to collect all studies that examined the association between polymorphisms of the APOE gene and risk of MetS. Results: the presence of the APOE-ε4 allele could not significantly increase the risk of MetS in the carriers of this allele compared to individuals lacking the risk allele in the TCGS population (OR = 1.11, 95% CI: 0.92 to 1.32). The meta-analysis results also indicated no significant association between the APOE-ε 4 allele and the risk of MetS. Conclusion: the frequency of the ε4 allele was almost same in the cases and the controls. Therefore, this allele cannot be considered as biomarker to predict the MetS susceptibility in the TCGS population or other populations with different genetic pools.

Species Delimitation and Conservation in Taxonomically Challenging Lineages: The Case of Two Clades of Capurodendron (Sapotaceae) in Madagascar

Capurodendron is the largest endemic genus of plants from Madagascar, with around 76% of its species threatened by deforestation and illegal logging. However, some species are not well circumscribed and many of them remain undescribed, impeding a confident evaluation of their conservation status. Here we focus on taxa delimitation and conservation of two species complexes within Capurodendron: the Arid and Western complexes, each containing undescribed morphologies as well as intermediate specimens alongside well-delimited taxa. To solve these taxonomic issues, we studied 381 specimens morphologically and selected 85 of them to obtain intergenic, intronic, and exonic protein-coding sequences of 794 nuclear genes and 227 microsatellite loci. These data were used to test species limits and putative hybrid patterns using different approaches such as phylogenies, PCA, structure analyses, heterozygosity level, FST, and ABBA-BABA tests. The potential distributions were furthermore estimated for each inferred species. The results show that the Capurodendron Western Complex contains three well-delimited species, C. oblongifolium, C. perrieri, and C. pervillei, the first two hybridizing sporadically with the last and producing morphologies similar to, but genetically distinct from C. pervillei. The Arid Complex shows a more intricate situation, as it contains three species morphologically well-delimited but genetically intermixed. Capurodendron mikeorum nom. prov. is shown to be an undescribed species with a restricted distribution, while C. androyense and C. mandrarense have wider and mostly sympatric distributions. Each of the latter two species contains two major genetic pools, one showing interspecific admixture in areas where both taxa coexist, and the other being less admixed and comprising allopatric populations having fewer contacts with the other species. Only two specimens out of 172 showed clear genetic and morphological signals of recent hybridization, while all the others were morphologically well-delimited, independent of their degree of genetic admixture. Hybridization between Capurodendron androyense and C. microphyllum, the sister species of the Arid Complex, was additionally detected in areas where both species coexist, producing intermediate morphologies. Among the two complexes, species are well-defined morphologically with the exception of seven specimens (1.8%) displaying intermediate patterns and genetic signals compatible with a F1 hybridization. A provisional conservation assessment for each species is provided.

Corrigenda: Cytogenetic markers as a tool for characterization of hybrids of Astyanax Baird & Girard, 1854 and Hyphessobrycon Eigenmann, 1907. Comparative Cytogenetics 14(2): 231–242. https://doi.org/10.3897/CompCytogen.v14i2.49513

Astyanax Baird et Girard, 1854, is one of the largest genera in the family Characidae and comprises 177 valid species. This genus has been the focus of cytogenetic studies primarily owing to the presence of B chromosomes and high karyotypic diversity among different populations. The intense genetic variability in Astyanax is one of the factors responsible for the occurrence of species complexes, which are groups (1) with certain difficulties in establishing common genetic pools or (2) belonging to different cryptic species. To evaluate cytogenetic marker inheritance and the possibility of the identification of these hybrids, this study aimed to describe cytogenetic hybrids from three strains of species of the genera Astyanax and Hyphessobrycon Eigenmann, 1908. A. lacustris Lütken, 1875, A. schubarti Britski, 1964, A. fasciatus Cuvier, 1819, and H. anisitsi Eigenmann, 1907 were used to generate three hybrid lineages. The diploid number, heterochromatin sites, and ribosomal genes (18S and 5S rDNA) of the parental strains and the hybrids were analyzed. The results indicated that the three hybrid lineages had cytogenetic markers of both parents, presenting Mendelian inheritance. However, differences in distribution of heterochromatic blocks were observed between the hybrids and the parent strains. Our results allowed the identification of the hybrid strains based on the cytogenetic markers applied, reinforcing the efficiency of cytogenetic markers as tools for identification and indicating that such events may increase the karyotypic diversity in the genera Astyanax and Hyphessobrycon.

Magnaporthe oryzae populations in Sub-Saharan Africa are diverse and show signs of local adaptation

Rice blast caused by Magnaporthe oryzae is one of the most economically damaging diseases of rice worldwide. The disease originated in Asia but was detected for the first time in Sub-Saharan Africa (SSA) around 100 years ago. Despite its importance, the evolutionary processes involved in shaping the population structure of M. oryzae in SSA remain unclear. In this study, we investigate the population history of M. oryzae using a combined dataset of 180 genomes. Our results show that SSA populations are more diverse than earlier perceived, and harbor all genetic groups previously reported in Asia. While M. oryzae populations in SSA and Asia draw from the same genetic pools, both are experiencing different evolutionary trajectories resulting from unknown selection pressures or demographic processes. The distribution of rare alleles, measured as Tajima’s D values, show significant differences at the substructure level. Genome-wide analysis indicates potential events of population contraction strongly affecting M. oryzae in SSA. In addition, the distribution and haplotype diversity of effectors might suggest a process of local adaptation to SSA conditions. These findings provide additional clues about the evolutionary history of M. oryzae outside the center of origin and help to build customized disease management strategies.

Detection of polymorphic simple-sequence repeat markers that show linkage to a novel sugarcane brown rust disease resistance gene in resistant and susceptible genetic pools

Sugarcane brown rust, caused by Puccinia melanocephala, is one of the main diseases of sugarcane in China. The identification and discovery of new resistance genes have important theoretical and practical significance for preventing outbreaks of brown rust and ensuring the sustainable production of sugarcane. To screen for polymorphic simple-sequence repeat (SSR) molecular markers for localization of brown rust resistance genes, we used two populations that are suitable for genetic linkage map construction and mapping of new resistance genes to construct resistant and susceptible genetic pools. We then screened 449 pairs of primers to identify polymorphic SSR markers in the parental lines and the resistant/susceptible genetic pools. The results showed that 25 pairs of primers directed amplification of polymorphic DNA fragments between the parents of the cross combination ‘Yuetang 03-393’ × ‘ROC 24’, and 16 pairs of primers amplified polymorphic fragments between the parents of the cross combination ‘Liucheng 03-1137’ × ‘Dezhe 93-88’. Four pairs of primers (SMC236CG, SCESSR0928, SCESSR0636 and SCESSR2551) amplified polymorphic DNA fragments between the parental lines and the resistant/susceptible genetic pools in ‘Yuetang 03-393’ × ‘ROC 24’. The results of this study will establish a solid foundation for the mapping of new brown rust resistance genes, genetic linkage map construction and the development of closely-associated molecular markers in sugarcane.

Identification of a Natural Hybrid between Castanopsis sclerophylla and Castanopsis tibetana (Fagaceae) Based on Chloroplast and Nuclear DNA Sequences

Castanopsis × kuchugouzhui Huang et Y. T. Chang was recorded in Flora Reipublicae Popularis Sinicae (FRPS) as a hybrid species on Yuelushan mountain, but it is treated as a hybrid between Castanopsis sclerophylla (Lindl.) Schott. and Castanopsis tibetana Hance in Flora of China. After a thorough investigation on Yuelushan mountain, we found a population of C. sclerophylla and one individual of C. × kuchugouzhui, but no living individual of C. tibetana. We collected C. × kuchugouzhui, and we sampled 42 individuals of C. sclerophylla from Yuelushan and Xiushui and 43 individuals of C. tibetana from Liangyeshan and Xiushui. We used chloroplast DNA sequences and 29 nuclear microsatellite markers to investigate if C. × kuchugouzhui is a natural hybrid between C. sclerophylla and C. tibetana. The chloroplast haplotype analysis showed that C. × kuchugouzhui shared haplotype H2 with C. sclerophylla on Yuelushan. The STRUCTURE analysis identified two distinct genetic pools that corresponded well to C. sclerophylla and C. tibetana, revealing the genetic admixture of C. × kuchugouzhui. Furthermore, the NewHybrids analysis suggested that C. × kuchugouzhui is an F2 hybrid between C. sclerophylla and C. tibetana. Our results confirm that C. × kuchugouzhui recorded in FRPS is a rare hybrid between C. sclerophylla and C. tibetana.

P0065DOUBLE MUTATION INHERITANCE IN PATIENTS WITH FOCAL SEGMENTAL GLOMERULOSCLEROSIS AND ALPORT SUNDROME

Background and Aims Focal segmental glomerulosclerosis (FSGS) and Alport syndrome (AS) are the leading causes of ESRD globally. FSGS and AS are clinically heterogeneous nephropathies and mainly genetic causes are the mutations in genes expressed in podocytes and glomerular basement membrane (GBM) respectively. A simple Mendelian model fail to explain the genetic control of both nephropathies completely because of the heterogeneous nature and presence of incomplete penetrance. Therefore, here we investigated the possible digenic control of FSGS and AS. Method To detect the double mutational (mono- or di-genic) cause of FSGS and AS, we conducted whole exome sequencing (WES) and panel sequencing in 67 kidney patients during the period of four years (2015 to June 2019). Inclusion criteria was the proband's clinical symptoms confirming the FSGS or AS based on clinical symptoms and renal biopsy. Clinical and genetic analyses were implemented to correlate the phenotypes with genotypes. Results Genetic analysis discovered that 35 out of 67 (52.23%) had genetic cause of selected nephropathies and 24 out of 35 (68.57%) had mutations in COL4A (3,4 & 5) genes and 11 (31.42%) in other genes. Interestingly, we found 7 out of 35 patients (20%) with double mutations (mono- or di-genic) in COL4A3/COL4A4 genes. After the mentioned period, during routine genetic screening, we also found another patient having double mutations in COL4A3 gene. Subsequently, Sanger sequencing confirmed that the identified mutations were co-segregating with the disease(s) in an incomplete penetrance fashion within the family. Lastly, we found 16 mutations in 8 patients having either monogenic or digeneic double mutations in COL4A3 and/or COL4A4 genes. In sum, we found 12 (75%) mutations in COL4A3 and 4 in COL4A4 (25%), and5 probands (62.5%) had compound heterozygous mutations in COL4A3, 1 proband (12.5%) had in COL4A4 and 2 probands (25%) had digenic (COL4A3/COL4A4) mutations. Last of all, among all the mutations, 10 were novel and 6 have been described previously. Conclusion This genetic analysis provides the first evidence for digenic inheritance of FSGS. The nephrologists and clinical geneticists should keep this possibility in mind for the accuracy in diagnosis, disease management and genetic counseling in future. Additionally, we are also adding 10 novel mutations in COL4A3 and COL4A4 genetic pools.

Cytogenetic markers as a tool for characterization of hybrids of Astyanax Baird & Girard, 1854 and Hyphessobrycon Eigenmann, 1907

Astyanax Baird et Girard, 1854, is one of the largest genera in the family Characidae and comprises 177 valid species. This genus has been the focus of cytogenetic studies primarily owing to the presence of B chromosomes and high karyotypic diversity among different populations. The intense genetic variability in Astyanax is one of the factors responsible for the occurrence of species complexes, which are groups (1) with certain difficulties in establishing common genetic pools or (2) belonging to different cryptic species. To evaluate cytogenetic marker inheritance and the possibility of the identification of these hybrids, this study aimed to describe cytogenetic hybrids from three strains of species of the genera Astyanax and Hyphessobrycon Eigenmann, 1908. A. lacustris Lütken, 1875, A. schubarti Britski, 1964, A. fasciatus Cuvier, 1819, and H. anisitsi Eigenmann, 1907 were used to generate three hybrid lineages. The diploid number, heterochromatin sites, and ribosomal genes (18S and 5S rDNA) of the parental strains and the hybrids were analyzed. The results indicated that the three hybrid lineages had cytogenetic markers of both parents, presenting Mendelian inheritance. However, differences in distribution of heterochromatic blocks were observed between the hybrids and the parent strains. Our results allowed the identification of the hybrid strains based on the cytogenetic markers applied, reinforcing the efficiency of cytogenetic markers as tools for identification and indicating that such events may increase the karyotypic diversity in the genera Astyanax and Hyphessobrycon.

Contemporary evolution of maize landraces and their wild relatives influenced by gene flow with modern maize varieties

Mexico is recognized as the center of origin and domestication of maize. Introduction of modern maize varieties (MVs) into Mexico raised concerns regarding the possible effects of gene flow from MVs into maize landraces (LRs) and their wild relatives (WRs), teosintes. However, after more than 60 y from the release of the first MVs, the impact of the sympatry with LRs and their WRs has not been explored with genetic data. In this work, we assessed changes in the genomes of 7 maize LRs and 2 WR subspecies from collections spanning over 70 y. We compared the genotypes obtained by genotyping by sequencing (GBS) for LRs and WRs before and after the adoption of MVs, and observed introgression from sympatric MVs into LRs and into the WR Zea mays ssp. mexicana sampled after the year 2000. We also found a decrease in the paired divergence index (FST) between MV-LR and MV-WR over the same time frame. Moreover, we determined that LR genetic diversity increased after 2000, probably as a result of gene flow from MVs introduced in the 1990s. Our findings allowed us to identify ongoing changes in the domesticated and wild maize genetic pools, and concur with previous works that have evaluated short-term gene flow from MVs into LRs in other crops. Our approach represents a useful tool for tracking evolutionary change in wild and domesticated genetic resources, as well as for developing strategies for their conservation.

Morphological and Agronomic Characterization of Spanish Landraces of Phaseolus vulgaris L.

Beans (Phaseolus vulgaris L.) originated on the American continent, specifically in the Mesoamerican zone, and their domestication took place independently in the Mesoamerican area and the Andean zone, giving rise to two well-differentiated genetic pools. It was also noted that the Andean wild populations originated from only a few thousand individuals from the Mesoamerican wild populations, which produced a great bottleneck in the formation of the Andean population. During centuries of cultivation in the Iberian Peninsula after its introduction in the 16th century, beans adapted to new environments, evolving numerous local landraces. Twenty-four local landraces of P. vulgaris from Spain were analyzed in the greenhouse during two consecutive seasons. From each genotype, five plants were grown and characterized for 17 quantitative and 15 qualitative traits using the International Board for Plant Genetic Resources (IBPGR) descriptors. Data were analyzed statistically by analysis of variance (ANOVA), principal component analysis (PCA), and cluster analysis. The results obtained indicate a high variability for most traits, especially those related to the yield and its components. The PCA and cluster analysis separated the landraces according to the color of the seed, the yield, and the pod and seed traits related to yield. Numerous traits exhibited interactions between the genotype and the environment. Most accessions reached higher yields in spring, in which solar radiation favors photosynthesis and, consequently, photoassimilation. The different response to the changing environment of the set of accessions studied in the present work is of great interest, and it can be exploited in breeding cultivars adapted to a broader range of environmental conditions.