Additional file 1: of Differentiation of Mycobacterium tuberculosis complex from non-tubercular mycobacteria by nested multiplex PCR targeting IS6110, MTP40 and 32kD alpha antigen encoding gene fragments

Comparison of conventional procedures with single-step & nested multiplex PCR for detection of M. tuberculosis complex in different groups of patients. (DOCX 15 kb

Band patterns obtained through Geno Type MTBDR<i>plus</i> assay.

<p>Band patterns obtained through Geno Type MTBDR<i>plus</i> assay.</p

Concordance between Geno Type MTBDR<i>plus</i> assay and phenotypic DST.

<p>Concordance between Geno Type MTBDR<i>plus</i> assay and phenotypic DST.</p

Performance of Geno Type MTBDR<i>plus</i> assay as compared to 1% proportion method in detecting resistance to rifampicin, isoniazid, and MDR-EPTB in 51 extra pulmonary clinical isolates.

<p>Performance of Geno Type MTBDR<i>plus</i> assay as compared to 1% proportion method in detecting resistance to rifampicin, isoniazid, and MDR-EPTB in 51 extra pulmonary clinical isolates.</p

Band patterns of Geno Type MTBDR<i>plus</i> assay.

<p><b>Lane 1 and lane 2:</b> Susceptible to rifampicin (RIF) and isoniazid (INH), <b>Lane 3 and lane 4:</b> MDR- TB (<i>rpoB</i> S531L mutation and <i>katG</i> S315T1 mutation), <b>Lane 5:</b> isoniazid monoresistant (<i>katG</i> S315T1 mutation), <b>Lane 6:</b> Absence of TUB band (invalid result), <b>Lane 7:</b> DNA negative control, <b>Lane 8:</b> Master mix negative control, <b>Lane 9:</b> Positive control (susceptible to rifampicin and isoniazid)</p

Validation of selected housekeeping genes under drought stress conditions.

<p>Expression profiling of candidate gene responsible for universal stress protein A-like (<i>uspA</i>) protein in drought imposed tissues (root, stem and leaves). The expression value of candidate gene was normalized with stable, combination of stable and least stable genes namely (i) <i>IF4α</i> (ii) <i>TUB6</i> (iii) <i>HSP90</i> (iv) <i>IF4α + TUB6</i> (v) <i>IF4α + HSP90</i> (vi) <i>IF4α + TUB6+HSP90</i> (vii) <i>ACT1</i> and (viii) <i>18SrRNA</i>. The relative quantitative values of selected drought responsive candidate gene were obtained after scaling to control samples. EDR: vegetative root stressed; LDR: reproductive root stressed; EDS: vegetative stem stressed; LDS: reproductive stem stressed; EDL: vegetative leaves stressed; LDL: reproductive leaves stressed.</p

Details of primers used for qRT-PCR analysis.

<p>Details of primers used for qRT-PCR analysis.</p

Ct variation and expression stability analysis of each candidate reference gene among different tissue samples using NormFinder.

<p>(a) Boxplot depicting absolute Ct values, which was calculated using GenEx program. Lower and upper boxes indicate the 25th and 75th percentile, respectively. The median is depicted by the line and all outliers are indicated by dots. (b) Gene expression stability graph using NormFinder algorithm based on stability values. Lower the stability value indicates higher stability of the housekeeping gene. The direction of the arrow indicates the most and least stable housekeeping genes.</p

DataSheet_1_Superior haplotypes towards the development of blast and bacterial blight-resistant rice.docx

Rice blast and bacterial leaf blight, are major disease, significantly threatens rice yield in all rice growing regions under favorable conditions and identification of resistance genes and their superior haplotypes is a potential strategy for effectively managing and controlling this devastating disease. In this study, we conducted a genome-wide association study (GWAS) using a diverse set of 147 rice accessions for blast and bacterial blight diseases in replications. Results revealed 23 (9 for blast and 14 for BLB) significant marker-trait associations (MTAs) that corresponded to 107 and 210 candidate genes for blast and BLB, respectively. The haplo-pheno analysis of the candidate genes led to the identification of eight superior haplotypes for blast, with an average SES score ranging from 0.00 to 1.33, and five superior haplotypes for BLB, with scores ranging from 1.52cm to 4.86cm superior haplotypes. Among these, superior haplotypes LOC_OS12G39700-H4 and LOC_Os06g30440-H33 were identified with the lowest average blast scores of 0.00-0.67, and superior haplotype LOC_Os02g12660-H39 exhibited the lowest average lesion length (1.88 - 2.06cm) for BLB. A total of ten accessions for blast and eight accessions for BLB were identified carrying superior haplotypes were identified. These haplotypes belong to aus and indx subpopulations of five countries (Bangladesh, Brazil, India, Myanmar, and Pakistan). For BLB resistance, eight accessions from six countries (Bangladesh, China, India, Myanmar, Pakistan, and Sri Lanka) and four subpopulations (aus, ind1A, ind2, and ind3) were identified carrying superior haplotypes. Interestingly, four candidate genes, LOC_Os06g21040, LOC_Os04g23960, LOC_Os12g39700, and LOC_Os01g24640 encoding transposon and retrotransposon proteins were among those with superior haplotypes known to play a crucial role in plant defense responses. These identified superior haplotypes have the potential to be combined into a single genetic background through haplotype-based breeding for a broader resistance spectrum against blast and bacterial blight diseases.</p

Table_1_Superior haplotypes towards the development of blast and bacterial blight-resistant rice.xlsx

Rice blast and bacterial leaf blight, are major disease, significantly threatens rice yield in all rice growing regions under favorable conditions and identification of resistance genes and their superior haplotypes is a potential strategy for effectively managing and controlling this devastating disease. In this study, we conducted a genome-wide association study (GWAS) using a diverse set of 147 rice accessions for blast and bacterial blight diseases in replications. Results revealed 23 (9 for blast and 14 for BLB) significant marker-trait associations (MTAs) that corresponded to 107 and 210 candidate genes for blast and BLB, respectively. The haplo-pheno analysis of the candidate genes led to the identification of eight superior haplotypes for blast, with an average SES score ranging from 0.00 to 1.33, and five superior haplotypes for BLB, with scores ranging from 1.52cm to 4.86cm superior haplotypes. Among these, superior haplotypes LOC_OS12G39700-H4 and LOC_Os06g30440-H33 were identified with the lowest average blast scores of 0.00-0.67, and superior haplotype LOC_Os02g12660-H39 exhibited the lowest average lesion length (1.88 - 2.06cm) for BLB. A total of ten accessions for blast and eight accessions for BLB were identified carrying superior haplotypes were identified. These haplotypes belong to aus and indx subpopulations of five countries (Bangladesh, Brazil, India, Myanmar, and Pakistan). For BLB resistance, eight accessions from six countries (Bangladesh, China, India, Myanmar, Pakistan, and Sri Lanka) and four subpopulations (aus, ind1A, ind2, and ind3) were identified carrying superior haplotypes. Interestingly, four candidate genes, LOC_Os06g21040, LOC_Os04g23960, LOC_Os12g39700, and LOC_Os01g24640 encoding transposon and retrotransposon proteins were among those with superior haplotypes known to play a crucial role in plant defense responses. These identified superior haplotypes have the potential to be combined into a single genetic background through haplotype-based breeding for a broader resistance spectrum against blast and bacterial blight diseases.</p