Journal of Genetics最新文献

Volunteer wheat is a kind of wheat with weed characteristics, distributed widely in the main wheat-producing areas of China. It seriously damages the yield and quality of cultivated wheat. To study the genetic diversity and population structure within and between volunteer wheat and cultivated wheat (Triticum aestivum L.), 195 volunteer wheat seeds and 29 cultivated wheat seeds were analysed based on 16 pairs of highly-polymorphic microsatellite simple sequence repeats (SSR) primers and a microchip capillary electrophoresis (MCE) detection system. A total of 110 polymorphic alleles were detected by MCE with each pair of primers identifying 2–15 alleles with an average of 6.875 alleles. The polymorphic information content (PIC) ranged from 0.1089 to 0.7843, with an average of 0.5613. Genetic diversity arguments from 224 samples showed that the volunteer wheat was more varied than cultivated wheat. Based on the SSR information, the 224 samples were classified into seven groups, which corresponded to the volunteer wheats and cultivated wheats through principal coordinates analysis (PCA). We propose that the volunteer wheat and cultivated wheat have rather distant phylogenetic relationships. Hence, it is important for wheat breeding to study the genetic relationship between volunteer wheat and cultivated wheat.

Olf413 gene annotated as CG12673 in the genome of Drosophila melanogaster has been predicted to code for a protein with putative function in octopamine biosynthesis. The expression pattern and the biological function of the gene awaits investigation. The present study is the first report where we describe its expression in the late pupal brain as depicted by enhancer-driven green fluorescent protein (GFP) expression. With experiments using loss of function olf413 mutant flies, we have demonstrated that olf413 function is essential for motor activity, gravity sensing and spatial balancing of the body against gravity during climbing.

Geography shapes the structure and function of human gut microbiomes. In this study, we have explored the available human gut microbiome 16S rRNA sequence datasets of cohorts representing large geographical gradients. The 16S rRNA sequences representing V3-V4 as well as V4 regions generated using Illumina sequencing chemistry in the MiSeq platform encompassing the United States of America, Chile, South Africa, Kuwait, and Malaysia were subjected to in-depth computational biology analyses. Firmicutes and Bacteroidetes were the most dominant phyla present in all studied cohorts but Actinobacteria was exclusively present in high abundance in cohorts from Malaysia (15.99%). The relative abundance of five families, namely Bacteroidaceae, Ruminococcaceae, Prevotellaceae, Clostridiaceae, and Eubacteriaceae were highest representing the studied cohorts. The permutational multivariate analysis of variance (PERMANOVA) showed that the dissimilarity in the gut microbiome structure of cohorts representing studied countries was significant (R² = 0.28, P < 0.001). The calculated Firmicutes to Bacteroidetes (F : B) ratio was found to be lowest in cohorts from South Africa (1.11) and Chile (0.95). The cohorts from South Africa exhibited the highest alpha diversity based on Hill numbers at q=0, whereas at q=1 and 2, cohorts from Malaysia had the highest alpha diversity. The beta diversity analysis revealed that cohorts from Chile formed a distinct cluster among all the studied geographical locations. For the first time, the study also showed that cohorts from Malaysia representing short geographical distances exhibited distinct intrapopulation differences in the gut microbiome and may not be influenced by cultural and genetic factors.

Differences in the distribution of RBC antigens defining the blood group types among different populations have been well established. Fewer studies exist that have explored the blood group profiles of indigenous populations worldwide. With the availability of population-scale genomic datasets, we have explored the blood group profiles of theOrang Aslis, who are the indigenous population in Peninsular Malaysia and provide a systematic comparison of the same with major global population datasets. Variant call files fromwhole genome sequence data (hg19) of 114 Orang Asli were retrieved from The Orang Asli Genome Project. Systematic variant annotations were performed using ANNOVAR and only those variants mapping back to genes associated with 43 blood group systems and transcription factors KLF1 and GATA1 were filtered. Blood group-associated allele and phenotype frequencies were determined and were duly compared with other datasets including Singapore SequencingMalay Project, aboriginal western desert Australians and global population datasets including The 1000 Genomes Project and gnomAD. This study reports four alleles (rs12075, rs7683365, rs586178 and rs2298720) of DUFFY, MNS, RH and KIDD blood group systems which were significantly distinct between indigenous Orang Asli and cosmopolitanMalaysians. Eighteen alleles that belong to 14 blood group systems were found statistically distinct in comparison to global population datasets. Although not much significant differences were observed in phenotypes of most blood group systems, major insights were observed when comparing Orang Asli with aboriginal Australians and cosmopolitanMalaysians.This study serves as the first of its kind to utilize genomic data to interpret blood group antigen profiles of the OrangAsli population. In addition, a systematic comparison of blood group profiles with related populations was also analysed and documented.

Pterocarpus santalinus L.f. (red sanders) is an endemic, endangered and economically important tree species distributed in the Eastern Ghats of Andhra Pradesh, India. This tree is well known for its blood-red coloured timber which has a high value in the international market. Due to its high timber demand, illegally logging of red sanders has resulted in fragmentation and depletion of its natural populations. Assessing the genetic diversity is a prerequisite for the identification of distinct populations of red sanders in the natural habitat for prioritizing conservation efforts. The present study has focussed on genome sequencing, identification and validation of microsatellite markers of P. santalinus. A total of 282,918 simple sequence repeat (SSR) loci were identified using whole genome sequence from P. santalinus leaf tissue. A total of 28 SSRs were selected for polymorphism analysis across the 52 individuals belonging to three populations of P. santalinus and identified a sum of 502 alleles with polymorphic information content of 0.83; observed heteozygosity (Ho) 0.42 and expected heterozygosity (He) 0.69. Genetic differentiation coefficient (F_ST) of 0.19 (F_ST˂0.25) which is indicating moderate genetic differentiation among the populations. Six SSRs from P. indicus Willd. and P. erinaceus Poir. were successfully amplified in P. santalinus and produced 131 alleles. These newly identified SSRs are useful in detecting genetic diversity and further developing conservation strategies for P. santalinus.

Diabetic nephropathy (DN), a common cause of chronic renal failure and end-stage renal disease, leads to a high mortality. However, the role of TTN-AS1 in extracellular matrix (ECM) accumulation during DN remains unclear. In our study, TTN-AS1 exhibited high expression in high glucose-treated mesangial cells, and TTN-AS1 silencing alleviated high glucose-induced ECM accumulation in mesangial cells. Additionally, animal study revealed that TTN-AS1 was upregulated in renal tissues of DN rats, and TTN-AS1 knockdown mitigated renal injury of DN rats. Mechanistically, TTN-AS1 was validated to bind to miR-493-3p, and miR-493-3p targeted forkhead box P2 (FOXP2) 3'untranslated region in mesangial cells. TTN-AS1 interacted with miR-493-3p to upregulate FOXP2 in vitro and in vivo. Moreover, FOXP2 overexpression counteracted the effects of TTN-AS1 silencing on the ECM accumulation. In conclusion, TTN-AS1 exacerbated ECM accumulation via the miR-493-3p/FOXP2 axis during DN development. This research may provide a potential new direction for DN treatment.