Chronic renal insufficiency among Asian Indians with type 2 diabetes: I. Role of RAAS gene polymorphisms

BACKGROUND: Renal failure in diabetes is mediated by multiple pathways. Experimental and clinical evidences suggest that renin-angiotensin-aldosterone system (RAAS) has a crucial role in diabetic kidney disease. A relationship between the RAAS genotypes and chronic renal insufficiency (CRI) among type 2 diabetes subjects has therefore been speculated. We investigated the contribution of selected RAAS gene polymorphisms to CRI among type 2 diabetic Asian Indian subjects. METHODS: Twelve single nucleotide polymorphisms (SNPs) from six genes namely-renin (REN), angiotensinogen (ATG), angiotensin converting enzyme I (ACE), angiotensin II type 1 receptor (AT1) and aldosterone synthase (CYP11B2) gene from the RAAS pathway and one from chymase pathway were genotyped using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method and tested for their association with diabetic CRI using a case-control approach. Successive cases presenting to study centres with type 2 diabetes of ≥2 years duration and moderate CRI diagnosed by serum creatinine ≥3 mg/dl after exclusion of non-diabetic causes of CRI (n = 196) were compared with diabetes subjects with no evidence of renal disease (n = 225). Logistic regression analysis was carried out to correlate various clinical parameters with genotypes, and to study pair wise interactions between SNPs of different genes. RESULTS: Of the 12 SNPs genotyped, Glu53Stop in AGT and A>T (-777) in AT1 genes, were monomorphic and not included for further analysis. We observed a highly significant association of Met235Thr SNP in angiotensinogen gene with CRI (O.R. 2.68, 95%CI: 2.01–3.57 for Thr allele, O.R. 2.94, 95%CI: 1.88–4.59 for Thr/Thr genotype and O.R. 2.68, 95%CI: 1.97–3.64 for ACC haplotype). A significant allelic and genotypic association of T>C (-344) SNP in aldosterone synthase gene (O.R. 1.57, 95%CI: 1.16–2.14 and O.R. 1.81, 95%CI: 1.21–2.71 respectively), and genotypic association of GA genotype of G>A (-1903) in chymase gene (O.R. 2.06, 95%CI: 1.34–3.17) were also observed. CONCLUSION: SNPs Met235Thr in angiotensinogen, T>C (-344) in aldosterone synthase, and G>A (-1903) in chymase genes are significantly associated with diabetic chronic renal insufficiency in Indian patients and warrant replication in larger sample sets. Use of such markers for prediction of susceptibility to diabetes specific renal disease in the ethnically Indian population appears promising

Mapping QTLs for Salt Tolerance in Rice (<i>Oryza sativa</i> L.) by Bulked Segregant Analysis of Recombinant Inbred Lines Using 50K SNP Chip

<div><p>Soil salinity is a major constraint to rice production in large inland and coastal areas around the world. Modern high yielding rice varieties are particularly sensitive to high salt stress. There are salt tolerant landraces and traditional varieties of rice but with limited information on genomic regions (QTLs) and genes responsible for their tolerance. Here we describe a method for rapid identification of QTLs for reproductive stage salt tolerance in rice using bulked segregant analysis (BSA) of bi-parental recombinant inbred lines (RIL). The number of RILs required for the creation of two bulks with extreme phenotypes was optimized to be thirty each. The parents and bulks were genotyped using a 50K SNP chip to identify genomic regions showing homogeneity for contrasting alleles of polymorphic SNPs in the two bulks. The method was applied to ‘CSR11/MI48’ RILs segregating for reproductive stage salt tolerance. Genotyping of the parents and RIL bulks, made on the basis of salt sensitivity index for grain yield, revealed 6,068 polymorphic SNPs and 21 QTL regions showing homogeneity of contrasting alleles in the two bulks. The method was validated further with ‘CSR27/MI48’ RILs used earlier for mapping salt tolerance QTLs using low-density SSR markers. BSA with 50K SNP chip revealed 5,021 polymorphic loci and 34 QTL regions. This not only confirmed the location of previously mapped QTLs but also identified several new QTLs, and provided a rapid way to scan the whole genome for mapping QTLs for complex agronomic traits in rice.</p></div

Correlation coefficients of yield and yield component traits with SSI for grain yield under normal, moderate and high sodicity regimes in CSR11/MI48 RILs.

<p>Correlation coefficients of yield and yield component traits with SSI for grain yield under normal, moderate and high sodicity regimes in CSR11/MI48 RILs.</p

Physical map positions of QTLs identified by BSA of CSR11/MI48 RIL population using 50K SNP chip.

<p>QTLs shown in green color have salt tolerant allele coming from the tolerant parent CSR11 and those in red color have tolerant allele contributed by the sensitive parent MI48.</p

QTL positions identified in CSR27/MI48 population by BSA using 50k SNP chip.

<p>Physical map position of QTLs with green color showing tolerant allele coming from tolerant parent CSR27 (11 loci), red color showing tolerant allele coming from sensitive parent MI48 (23 loci). Blue and violet bars represent earlier identified QTLs by Ammar <i>et al</i>. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0153610#pone.0153610.ref042" target="_blank">42</a>] and Pandit <i>et al</i>. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0153610#pone.0153610.ref008" target="_blank">8</a>], respectively.</p

Variation for yield and yield contributing traits among 216 RILs derived from CSR11/MI48 over 3 seasons under control (N), moderate sodic (MS) and high sodic (HS) conditions.

<p>Variation for yield and yield contributing traits among 216 RILs derived from CSR11/MI48 over 3 seasons under control (N), moderate sodic (MS) and high sodic (HS) conditions.</p