Uncovering Genomic Regions Associated With 36 Agro-Morphological Traits in Indian Spring Wheat Using GWAS

Wheat genetic improvement by integration of advanced genomic technologies is one way of improving productivity. To facilitate the breeding of economically important traits in wheat, SNP loci and underlying candidate genes associated with the 36 agro-morphological traits were studied in a diverse panel of 404 genotypes. By using Breeders’ 35K Axiom array in a comprehensive genome-wide association study covering 4364.79 cM of the wheat genome and applying a compressed mixed linear model, a total of 146 SNPs (-log10P ≥ 4) were found associated with 23 traits out of 36 traits studied explaining 3.7–47.0% of phenotypic variance. To reveal this a subset of 260 genotypes was characterized phenotypically for six quantitative traits [days to heading (DTH), days to maturity (DTM), plant height (PH), spike length (SL), awn length (Awn_L), and leaf length (Leaf_L)] under five environments. Gene annotations mined ∼38 putative candidate genes which were confirmed using tissue and stage specific gene expression data from RNA Seq. We observed strong co-localized loci for four traits (glume pubescence, SL, PH, and awn color) on chromosome 1B (24.64 cM) annotated five putative candidate genes. This study led to the discovery of hitherto unreported loci for some less explored traits (such as leaf sheath wax, awn attitude, and glume pubescence) besides the refined chromosomal regions of known loci associated with the traits. This study provides valuable information of the genetic loci and their potential genes underlying the traits such as awn characters which are being considered as important contributors toward yield enhancement

Do environmentally induced DNA variations mediate adaptation in Aspergillus flavus exposed to chromium stress in tannery sludge?

Abstract Background Environmental stress induced genetic polymorphisms have been suggested to arbitrate functional modifications influencing adaptations in microbes. The relationship between the genetic processes and concomitant functional adaptation can now be investigated at a genomic scale with the help of next generation sequencing (NGS) technologies. Using a NGS approach we identified genetic variations putatively underlying chromium tolerance in a strain of Aspergillus flavus isolated from a tannery sludge. Correlation of nsSNPs in the candidate genes (n = 493) were investigated for their influence on protein structure and possible function. Whole genome sequencing of chromium tolerant A. flavus strain (TERIBR1) was done (Illumina HiSeq2000). The alignment of quality trimmed data of TERIBR1 with reference NRRL3357 (accession number EQ963472) strain was performed using Bowtie2 version 2.2.8. SNP with a minimum read depth of 5 and not in vicinity (10 bp) of INDEL were filtered. Candidate genes conferring chromium resistance were selected and SNPs were identified. Protein structure modeling and interpretation for protein-ligand (CrO4 − 2) docking for selected proteins harbouring non-synonymous substitutions were done using Phyre2 and PatchDock programs. Results High rate of nsSNPs (approximately 11/kb) occurred in selected candidate genes for chromium tolerance. Of the 16 candidate genes selected for studying effect of nsSNPs on protein structure and protein-ligand interaction, four proteins belonging to the Major Facilitator Superfamily (MFS) and recG protein families showed significant interaction with chromium ion only in the chromium tolerant A. flavus strain TERIBR1. Conclusions Presence of nsSNPs and subsequent amino-acid alterations evidently influenced the 3D structures of the candidate proteins, which could have led to improved interaction with (CrO4 − 2) ion. Such structural modifications might have enhanced chromium efflux efficiency of A. flavus (TERIBR1) and thereby offered the adaptation benefits in counteracting chromate stress. Our findings are of fundamental importance to the field of heavy-metal bio-remediation

Data from: Phylogenetic analyses reveal molecular signatures associated with functional divergence among Subtilisin like Serine Proteases are linked to lifestyle transitions in Hypocreales

Background: Subtilisin-like serine proteases or Subtilases in fungi are important for penetration and colonization of host. In Hypocreales, these proteins share several properties with other fungal, bacterial, plant and mammalian homologs. However, adoption of specific roles in entomopathogenesis may be governed by attainment of unique biochemical and structural features during the evolutionary course. Due to such functional shifts Subtilases coded by different family members of Hypocreales acquire distinct features according to respective hosts and lifestyle. We conducted phylogenetic and DIVERGE analyses and identified important protein residues that putatively assign functional specificity to Subtilases in fungal families/species under the order Hypocreales. Results: A total of 161 Subtilases coded by 10 species from five different families under the fungal order Hypocreales was included in the analysis. Based on the presence of conserved domains, the Subtilase genes were divided into three subfamilies, Subtilisin (S08.005), Proteinase K (S08.054) and Serine-carboxyl peptidases (S53.001). These subfamilies were investigated for phylogenetic associations, protein residues under positive selection and functional divergence among paralogous clades. The observations were co-related with the life-styles of the fungal families/species. Phylogenetic and Divergence analyses of Subtilisin (S08.005) and Proteinase K (S08.054) families of proteins revealed that the paralogous clades were clear-cut representation of familial origin of the protein sequences. We observed divergence between the paralogous clades of plant-pathogenic fungi (Nectriaceae), insect-pathogenic fungi (Cordycipitaceae/Clavicipitaceae) and nematophagous fungi (Ophiocordycipitaceae). In addition, Subtilase genes from the nematode-parasitic fungus Purpureocillium lilacinum made a unique cluster which putatively indicated that the fungus might have developed distinctive mechanisms for nematode-pathogenesis. Our evolutionary genetics analysis revealed evidence of positive selection on the Subtilisin (S08.005) and Proteinase K (S08.054) protein sequences of the entomopathogenic and nematophagous species belonging to Cordycipitaceae, Clavicipitaceae and Ophiocordycipitaceae families of Hypocreales. Conclusions: Our study provided new insights into the evolution of Subtilisin like serine proteases in Hypocreales, a fungal order largely consisting of biological control species. Subtilisin (S08.005) and Proteinase K (S08.054) proteins seemed to play important roles during life style modifications among different families and species of Hypocreales. Protein residues found significant in functional divergence analysis in the present study may provide support for protein engineering in future

Protein Sequence of Serine Proteases of Purpureocillium_lilacinum_TERI_BC1

A total of 44 serine protease sequences present in Purpureocillium lilacinum genome are provided here

Additional file 8: Figure S6. of Phylogenetic analyses reveal molecular signatures associated with functional divergence among Subtilisin like Serine Proteases are linked to lifestyle transitions in Hypocreales

Functional divergence in Subtilisin (S08.005) protein sequences among clades Nectriaceae and Cordycipitaceae/Clavicipitaceae. (a) The RVS (Rate Variation among Sites) amino acids sites are identified by DIVERGE 3.0 mapped on the Subtilisin structure (Cyan colour) of a member (fx|XP5977|Fusarium oxysporum) of the Nectriaceae clade. The identified RVS sites are shown in stick (Magenta). (b) The highlighted (encircled) RVS sites are also observed in TYPE II divergence (Nectriaceae vs. Cordycipitaceae/Clavicipitaceae). Figure S7. Functional divergence type II and RVS sites on 3D structure of Subtilisin (S08.005) protein sequences among clades Nectriaceae and Cordycipitaceae/Clavicipitaceae. (a) The RVS (Rate Variation among Sites) amino acids sites are identified by DIVERGE 3.0 mapped on Subtilisin structure (Red colour) of a member (bb|XP2612|Beauveria bassiana) of the Cordycipitaceae/Clavicipitaceae clade. The identified RVS sites are shown in stick (Green). (b) The highlighted RVS sites are also observed in TYPE II divergence (Nectriaceae vs. Cordycipitaceae/Clavicipitaceae). The catalytic triad is shown in yellow colour. Figure S8. Functional divergence in Subtilisin (S08.005) when Nectriaceae and Ophiocordycipitaceae clades are compared. (a) The RVS (Rate Variation among Sites) amino acids sites are identified by DIVERGE 3.0 mapped on Subtilisin structure (Blue colour) of a member (pl|XP5939|Purpureocillium lilacinum) of the Ophiocordycipitaceae clade. The identified RVS sites are shown in stick (Yellow). (b) The highlighted (encircled) RVS sites are also observed in TYPE II divergence (Nectriaceae vs. Ophiocordycipitaceae). The putative catalytic triad and substrate binding pocket are shown in blue colour on the 3 D structure of the protein. (DOCX 844 kb

Additional file 6: Figure S5. of Phylogenetic analyses reveal molecular signatures associated with functional divergence among Subtilisin like Serine Proteases are linked to lifestyle transitions in Hypocreales

Conserved Motifs identified by MEME in Proteinase K (S08.054). (DOCX 36 kb

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Not AvailableGenetic diversity is crucial for successful adaptation and sustained improvement in crops. India is bestowed with diverse agro-climatic conditions which makes it rich in wheat germplasm adapted to various niches. Germplasm repository consists of local landraces, trait specific genetic stocks including introgressions from wild relatives, exotic collections, released varieties, and improved germplasm. Characterization of genetic diversity is done using morpho-physiological characters as well as by analyzing variations at DNA level. However, there are not many reports on array based high throughput SNP markers having characteristics of genome wide coverage employed in Indian spring wheat germplasm. Amongst wheat SNP arrays, 35K Axiom Wheat Breeder’s Array has the highest SNP polymorphism efficiency suitable for genetic mapping and genetic diversity characterization. Therefore, genotyping was done using 35K in 483 wheat genotypes resulting in 14,650 quality filtered SNPs, that were distributed across the B (~ 50%), A (~ 39%), and D (~ 10%) genomes. The total genetic distance coverage was 4477.85 cM with 3.27 SNP/cM and 0.49 cM/SNP as average marker density and average inter-marker distance, respectively. The PIC ranged from 0.09 to 0.38 with an average of 0.29 across genomes. Population structure and Principal Coordinate Analysis resulted in two subpopulations (SP1 and SP2). The analysis of molecular variance revealed the genetic variation of 2% among and 98% within subpopulations indicating high gene flow between SP1 and SP2. The subpopulation SP2 showed high level of genetic diversity based on genetic diversity indices viz. Shannon’s information index (I) = 0.648, expected heterozygosity (He) = 0.456 and unbiased expected heterozygosity (uHe) = 0.456. To the best of our knowledge, this study is the first to include the largest set of Indian wheat genotypes studied exclusively for genetic diversity. These findings may serve as a potential source for the identification of uncharacterized QTL/gene using genome wide association studies and marker assisted selection in wheat breeding programs.Not Availabl

Not Available

Not AvailableWheat genetic improvement by integration of advanced genomic technologies is one way of improving productivity. To facilitate the breeding of economically important traits in wheat, SNP loci and underlying candidate genes associated with the 36 agro-morphological traits were studied in a diverse panel of 404 genotypes. By using Breeders’ 35K Axiom array in a comprehensive genome-wide association study covering 4364.79 cM of the wheat genome and applying a compressed mixed linear model, a total of 146 SNPs (−log10 P ≥ 4) were found associated with 23 traits out of 36 traits studied explaining 3.7–47.0% of phenotypic variance. To reveal this a subset of 260 genotypes was characterized phenotypically for six quantitative traits [days to heading (DTH), days to maturity (DTM), plant height (PH), spike length (SL), awn length (Awn_L), and leaf length (Leaf_L)] under five environments. Gene annotations mined ∼38 putative candidate genes which were confirmed using tissue and stage specific gene expression data from RNA Seq. We observed strong co-localized loci for four traits (glume pubescence, SL, PH, and awn color) on chromosome 1B (24.64 cM) annotated five putative candidate genes. This study led to the discovery of hitherto unreported loci for some less explored traits (such as leaf sheath wax, awn attitude, and glume pubescence) besides the refined chromosomal regions of known loci associated with the traits. This study provides valuable information of the genetic loci and their potential genes underlying the traits such as awn characters which are being considered as important contributors toward yield enhancement.Not Availabl