Genetic Analysis of Hexaploid Wheat (Triticum aestivum L.) Using the Complete Sequencing of Chloroplast DNA and Haplotype Analysis of the Wknox1 Gene

The aim of the presented study is a genetic characterization of the hexaploid wheat Triticum aestivum L. Two approaches were used for the genealogical study of hexaploid wheats—the complete sequencing of chloroplast DNA and PCR-based haplotype analysis of the fourth intron of Wknox1d and of the fifth-to-sixth-exon region of Wknox1b. The complete chloroplast DNA sequences of 13 hexaploid wheat samples were determined: Free-threshing—T. aestivum subsp. aestivum, one sample; T. aestivum subsp. compactum, two samples; T. aestivum subsp. sphaerococcum, one sample; T. aestivum subsp. carthlicoides, four samples. Hulled—T. aestivum subsp. spelta, three samples; T. aestivum subsp. vavilovii jakubz., two samples. The comparative analysis of complete cpDNA sequences of 20 hexaploid wheat samples (13 samples in this article plus 7 samples sequenced in this laboratory in 2018) was carried out. PCR-based haplotype analysis of the fourth intron of Wknox1d and of the fifth-to-sixth exon region of Wknox1b of all 20 hexaploid wheat samples was carried out. The 20 hexaploid wheat samples (13 samples in this article plus 7 samples in 2018) can be divided into two groups—T. aestivum subsp. spelta, three samples and T. aestivum subsp. vavilovii collected in Armenia, and the remaining 16 samples, including T. aestivum subsp. vavilovii collected in Europe (Sweden). If we take the cpDNA of Chinese Spring as a reference, 25 SNPs can be identified. Furthermore, 13–14 SNPs can be identified in T. aestivum subsp. spelta and subsp. vavilovii (Vav1). In the other samples up to 11 SNPs were detected. 22 SNPs are found in the intergenic regions, 2 found in introns, and 10 SNPs were found in the genes, of which seven are synonymous. PCR-based haplotype analysis of the fourth intron of Wknox1d and the fifth-to-sixth-exon region of Wknox1b provides an opportunity to make an assumption that hexaploid wheats T. aestivum subsp. macha var. palaeocolchicum and var. letshckumicum differ from other macha samples by the absence of a 42 bp insertion in the fourth intron of Wknox1d. One possible explanation for this observation would be that two Aegilops tauschii Coss. (A) and (B) participated in the formation of hexaploids through the D genome: Ae. tauschii (A)—macha (1–5, 7, 8, 10–12), and Ae. tauschii (B)—macha M6, M9, T. aestivum subsp. aestivum cv. ‘Chinese Spring’ and cv. ‘Red Doly’.

Intramolecular G-quadruplex-hairpin loop structure competition of a GC-rich exon region in the TMPRSS2 gene

We identified cytosine-rich regions adjacent to guanine-rich regions in protease genes. A typical GC-rich sequence derived from the TMPRSS2 gene showed structural competition between a G-quadruplex and a hairpin loop,...

Prevalence of inherited changes of uric acid levels in kidney dysfunction including stage 5 D and T: a systematic review

Background/aims Familial juvenile hereditary nephropathy (FJHN) is characterized by hyperuricemia due to severely impaired urinary excretion of urate. Hereditary renal hypouricemia is an inborn error of membrane transport. Because studies of inherited tubulopathy is rare, prevalence and diagnosis of these inherited tubulopathy increase with genetic testing.The aim of this study is to investigate prevalence of clinical features, biochemical profiles, and genetic analysis of patients with changes in serum uric acid levels in inherited tubulopathy. Main body The paper has written based on searching PubMed and Google Scholar to identify potentially relevant articles or abstracts. In this retrospective study, a total 65 patients with changes of serum uric acid levels and kidney dysfunction were investigated. Clinical features, laboratory data at initial presentation, management, and outcomes were collected. Forty studies (65 participants) included in this review. The mean ± SD of age of study patients in inherited tubulointerstitial kidney disease was 25.29 ± 14.69 years. Mean ± SD age of patients at time of diagnosis in inherited renal hypouricemia was 18.83 ± 10.59 years. Correlation between exon region in mutated UMOD, SLC22A12, and SLC2A9 genes and serum uric acid levels were assessed and revealed significant statistical correlation between exon region of SLC2A9 mutation and serum uric acid levels. Prevalence of progression to end-stage kidney disease in patients with inherited tubulointerstitial kidney disease and inherited renal hypouricemia were assessed 20% and 2.5%, respectively. There was nephrolithiasis in two patients (2/25, 8%) with inherited renal hypouricemia. Conclusions This study shows that UMOD and SLC22A12 gene mutations were responsible for majority of autosomal-dominant tubulointerstitial kidney disease and inherited renal hypouricemia, respectively.