Publications by authors named "Mahesh C Yadav"

8 Publications

  • Page 1 of 1

Genome-wide association mapping reveals key genomic regions for physiological and yield-related traits under salinity stress in wheat (Triticum aestivum L.).

Genomics 2021 Sep 19;113(5):3198-3215. Epub 2021 Jul 19.

ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India.

A genome-wide association study (GWAS) was conducted using six different multi-locus GWAS models and 35K SNP array to demarcate genomic regions underlying reproductive stage salinity tolerance. Marker-trait association analysis was performed for salt tolerance indices (STI) of 11 morpho-physiological traits, and the actual concentrations of Na and K, and the Na/K ratio in flag leaf. A total of 293 significantly associated quantitative trait nucleotides (QTNs) for 14 morpho-physiological traits were identified. Of these 293 QTNs, 12 major QTNs with R ≥ 10.0% were detected in three or more GWAS models. Novel major QTNs were identified for plant height, number of effective tillers, biomass, grain yield, thousand grain weight, Na and K content, and the Na/K ratio in flag leaf. Moreover, 48 candidate genes were identified from the associated genomic regions. The QTNs identified in this study could potentially be targeted for improving salinity tolerance in wheat.
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http://dx.doi.org/10.1016/j.ygeno.2021.07.014DOI Listing
September 2021

Genetic Dissection of Seedling Root System Architectural Traits in a Diverse Panel of Hexaploid Wheat through Multi-Locus Genome-Wide Association Mapping for Improving Drought Tolerance.

Int J Mol Sci 2021 Jul 2;22(13). Epub 2021 Jul 2.

Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA.

Cultivars with efficient root systems play a major role in enhancing resource use efficiency, particularly water absorption, and thus in drought tolerance. In this study, a diverse wheat association panel of 136 wheat accessions including mini core subset was genotyped using Axiom 35k Breeders' Array to identify genomic regions associated with seedling stage root architecture and shoot traits using multi-locus genome-wide association studies (ML-GWAS). The association panel revealed a wide variation of 1.5- to 50-fold and were grouped into six clusters based on 15 traits. Six different ML-GWAS models revealed 456 significant quantitative trait nucleotides (QTNs) for various traits with phenotypic variance in the range of 0.12-38.60%. Of these, 87 QTNs were repeatedly detected by two or more models and were considered reliable genomic regions for the respective traits. Among these QTNs, eleven were associated with average diameter and nine each for second order lateral root number (SOLRN), root volume (RV) and root length density (RLD). A total of eleven genomic regions were pleiotropic and each controlled two or three traits. Some important candidate genes such as Formin homology 1, Ubiquitin-like domain superfamily and ATP-dependent 6-phosphofructokinase were identified from the associated genomic regions. The genomic regions/genes identified in this study could potentially be targeted for improving root traits and drought tolerance in wheat.
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http://dx.doi.org/10.3390/ijms22137188DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8268147PMC
July 2021

Refinement of Draft Genome Assemblies of Pigeonpea ().

Front Genet 2020 15;11:607432. Epub 2020 Dec 15.

Indian Council for Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India.

Genome assembly of short reads from large plant genomes remains a challenge in computational biology despite major developments in next generation sequencing. Of late several draft assemblies have been reported in sequenced plant genomes. The reported draft genome assemblies of have different levels of genome completeness, a large number of repeats, gaps, and segmental duplications. Draft assemblies with portions of genome missing are shorter than the referenced original genome. These assemblies come with low map accuracy affecting further functional annotation and the prediction of gene components as desired by crop researchers. Genome coverage, i.e., the number of sequenced raw reads mapped onto a certain location of the genome is an important quality indicator of completeness and assembly quality in draft assemblies. The present work aimed to improve the coverage in reported sequenced draft genomes (GCA_000340665.1 and GCA_000230855.2) of pigeonpea, a legume widely cultivated in India. The two recently sequenced assemblies, A1 and A2 comprised 72% and 75% of the estimated coverage of the genome, respectively. We employed an assembly reconciliation approach to compare the draft assemblies and merge them, filling the gaps by employing an algorithm size sorting mate-pair library to generate a high quality and near complete assembly with enhanced contiguity. The majority of gaps present within scaffolds were filled with right-sized mate-pair reads. The improved assembly reduced the number of gaps than those reported in draft assemblies resulting in an improved genome coverage of 82.4%. Map accuracy of the improved assembly was evaluated using various quality metrics and for the presence of specific trait-related functional genes. Employed pair-end and mate-pair local libraries helped us to reduce gaps, repeats, and other sequence errors resulting in lengthier scaffolds compared to the two draft assemblies. We reported the prediction of putative host resistance genes against wilt disease by their performance and evaluated them both in wet laboratory and field phenotypic conditions.
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http://dx.doi.org/10.3389/fgene.2020.607432DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7770131PMC
December 2020

Identification and evolutionary analysis of polycistronic miRNA clusters in domesticated and wild wheat.

Genomics 2020 05 8;112(3):2334-2348. Epub 2020 Jan 8.

Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India.

MicroRNAs are ~22 nucleotide long non-coding RNAs that regulate gene expression at posttranscriptional level. Genome-wide analysis was performed to identify polycistronic miRNAs from wheat. Total 89 polycistronic miRNAs were identified in bread wheat which were distributed on three component sub-genomes (A = 26, B = 33 and D = 30). Except some, most of the identified polycistronic miRNAs were also present in other cultivated and wild wheat species. Expression of 11 identified polycistronic miRNAs could be validated using previously assembled transcriptomes, RNA-seq/s-RNA seq data of cultivated and wild wheats and RT-PCR. Polycistronic miRNAs orthologs were also localized on rice and Brachypodium genomes. As a case study, we also analyzed molecular evolution of miR395 family polycistrons in wheat. Both tandem and segmental duplications contributed to expansion of miR395 family polycistrons. Our findings provide a comprehensive view on wheat polycitronic miRNAs that will enable their in-depth functional analysis in the future.
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http://dx.doi.org/10.1016/j.ygeno.2020.01.005DOI Listing
May 2020

Comparative genomics in phytopathogenic prokaryotes reveals the higher relative abundance and density of long-SSRs in the smallest prokaryotic genome.

3 Biotech 2019 Sep 22;9(9):340. Epub 2019 Aug 22.

4Department of Wildlife Science, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002 India.

Frequency and distribution of long-SSRs were studied in 18 phytopathogenic prokaryotes. Higher relative abundance of the long-SSRs was observed in phytopathogenic prokaryotes when compared to non-pathogenic control. The frequency of these SSRs was positively correlated with size and GC content of the genomes of phytopathogenic prokaryotes. Interestingly, phytopathogens with higher GC content in the genome were found to posses longer repeat motifs of SSRs, whereas those having lesser GC content were harbouring shorter repeat motifs. Higher abundance of tri- and hexa-nucleotide repeat motifs were the characteristic of actinomycetes, where as higher abundance of mono- and tetra-nucleotide repeats were the characteristic of the mollicutes. The maximum relative abundance and relative density of SSR were found in the smallest genome of host-adapted pathogen Aster yellow, however, length of microsatellite repeat units was the least. On the basis of presence of SSRs in the housekeeping genes, a phylogenetic relationship between these phytopathogenic prokaryotes was deduced and compared with the phylogeny developed based on 16S ribosomal RNA gene.
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http://dx.doi.org/10.1007/s13205-019-1872-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6706511PMC
September 2019

Identification, analysis and development of salt responsive candidate gene based SSR markers in wheat.

BMC Plant Biol 2018 Oct 20;18(1):249. Epub 2018 Oct 20.

Division of Germplasm Conservation, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012, India.

Background: Salinity severely limits wheat production in many parts of the world. Development of salt tolerant varieties represents the most practical option for enhancing wheat production from these areas. Application of marker assisted selection may assist in fast tracking development of salt tolerant wheat varieties. However, SSR markers available in the public domain are not specifically targeted to functional regions of wheat genome, therefore large numbers of these need to be analysed for identification of markers associated with traits of interest. With the availability of a fully annotated wheat genome assembly, it is possible to develop SSR markers specifically targeted to genic regions. We performed extensive analysis to identify candidate gene based SSRs and assessed their utility in characterizing molecular diversity in a panel of wheat genotypes.

Results: Our analysis revealed, 161 SSR motifs in 94 salt tolerance candidate genes of wheat. These SSR motifs were nearly equally distributed on the three wheat sub-genomes; 29.8% in A, 35.7% in B and 34.4% in D sub-genome. The maximum number of SSR motifs was present in exons (31.1%) followed by promoters (29.8%), 5'UTRs (21.1%), introns (14.3%) and 3'UTRs (3.7%). Out of the 65 candidate gene based SSR markers selected for validation, 30 were found polymorphic based on initial screening and employed for characterizing genetic diversity in a panel of wheat genotypes including salt tolerant and susceptible lines. These markers generated an average of 2.83 alleles/locus. Phylogenetic analysis revealed four clusters. Salt susceptible genotypes were mainly represented in clusters I and III, whereas high and moderate salt tolerant genotypes were distributed in the remaining two clusters. Population structure analysis revealed two sub-populations, sub-population 1 contained the majority of salt tolerant whereas sub-population 2 contained majority of susceptible genotypes. Moreover, we observed reasonably higher transferability of SSR markers to related wheat species.

Conclusion: We have developed salt responsive gene based SSRs in wheat for the first time. These were highly useful in unravelling functional diversity among wheat genotypes with varying responses to salt stress. The identified gene based SSR markers will be valuable genomic resources for genetic/association mapping of salinity tolerance in wheat.
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http://dx.doi.org/10.1186/s12870-018-1476-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6195990PMC
October 2018

Microsatellite repeat dynamics in mitochondrial genomes of phytopathogenic fungi: frequency and distribution in the genic and intergenic regions.

Bioinformation 2012 23;8(23):1171-5. Epub 2012 Nov 23.

Department of Biotechnology and Bioinformatics, Barkatullah University, Bhopal 462 026, Madhya Pradesh, India.

The frequency and distribution of microsatellites were analyzed in the 19 mitogenomes of phytopathogenic fungi covering five phyla. Our analysis revealed that in all the mitogenomes studied, the frequency and relative abundance varied, and it was neither influenced by genome size nor by GC content. SSRs were found to be differential distributed in genic and intergenic regions. An average of 5.14 (23.6%) SSRs were present in genic sequences and 21.7 (76.4%) SSRs were located in the intergenic sequences. Relative abundance of SSRs in mitogenomes was the highest in Aspergillus tubigensis, whereas, it was the least in Phaeosphaeria nodurum, the average being 0.45. Trinucleotide repeats were the most abundant motifs in the genic and intergenic regions of the mitogenomes of the phytopathogenic fungi. Among the genes, cox1 harbors the maximum SSRs, whereas cox3 and nad 7 contain the least. Based on the presence of SSRs in a particular gene, genetic relationships among individual organisms were also established.
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http://dx.doi.org/10.6026/97320630081171DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530887PMC
January 2013

Monosomic analysis reveals duplicated chromosomal segments in maize genome.

J Genet 2009 Dec;88(3):331-5

Division of Genetics, Indian Agricultural Research Institute, New Delhi 110 012, India.

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http://dx.doi.org/10.1007/s12041-009-0048-4DOI Listing
December 2009
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