Biology subjects

Deshpande, S. P.

Publications and source records attributed to Deshpande, S. P..

4 recordsLinked to original sources

bioRxiv2022

DeepVariant calling provides insights into race diversity and its implication for sorghum breeding

Due to evolutionary divergence, sorghum race populations exhibit vast genetic and morphological variations. A k-mer-based sorghum race sequence comparison identified the conserved k-mers of all sorghum race accessions and the race-specific genetic signatures identified the gene variability in 10,321 genes (PAVs). To understand the sorghum race structure, diversity and domestication, deep learning-based variant calling approach was employed in a set of genotypic data derived from a diverse panel of 272 sorghum accessions. The data resulted in 1.7 million high-quality genome-wide SNPs and identified selective signature (both positive and negative) regions through a genome-wide scan with different (iHS and XP-EHH) statistical methods. We discovered 2,370 genes associated with selection signatures including 179 selective sweep regions distributed over 10 chromosomes. Localization of these regions undergoing selective pressure with previously reported QTLs and genes revealed that the signatures of selection could be related to the domestication of important agronomic traits such as biomass and plant height. The developed k-mer signatures will be useful in the future to identify the sorghum race and SNP markers assist in plant breeding programs.

plant biology↗

bioRxiv2022

Genetics of Fertility Restoration in A1 Cytoplasmic Genetic Male Sterility (CGMS) Systems in Sorghum (Sorghum bicolor L. Moench)

The cause of Cytoplasmic Genetic Male Sterility (CGMS) is specific nuclear and mitochondrial interactions. Almost all commercial sorghum hybrids were developed using the A1 cytoplasmic genetic male sterility system. Understanding the inheritance of fertility restoration in sorghum for A1 cytoplasm, for example, can improve the selection efficiency of restorer lines for increased seed production. In a cross of male sterile line 296A with A1 cytoplasm and restorer lines comprised of a set of Recombinant Inbred Lines (RILs), the inheritance pattern of fertility restoration of sorghum was studied. The F1 hybrid was completely fertile, revealing the dominant nature of fertility restoration, which is controlled by one or two major genes with modifiers. In this study, the genetics of fertility restoration of the A1 cytoplasmic nuclear male sterility system (CGMS) in sorghum were investigated in segregating F2 and BC1 populations of A1 cytoplasm crosses. Fertility restoration was governed by a monogenic inheritance (3F:1S) mechanism represented by a single dominant gene responsible for fertility restoration in all of the crosses studied.

genetics↗

bioRxiv2022

Standardization of cytological behavior of pollens in sorghum by Image analysis

The development of iso-nuclear male sterile (A) and maintainer (B) line along with male fertile (R) lines, referred to as fertility restorers, helped in cost-effective seed production and deployment of hybrids. The pollen viability/fertility for maintenance (B-line) and restoration (R-line) remains a significant phenotyping hurdle in developing new lines. We carried out the present investigation to evaluate the pollen fertility status of Cytoplasmic Genetic Male Sterility (CGMS) based hybrids in sorghum. The experimental material consisted of 238 CGMS based hybrids developed from the crossing of individuals of (296B xIS 188551) - based Recombinant Inbred Line (RIL) population (F7:F8) with male-sterile line (296A). The experiment was conducted in the rainy and post-rainy seasons during 2016 to evaluate pollen fertility. The authors illustrated the pollen fertility status by counting pollen counts using two methods: viz., visual counting by the naked eye, and image analysis using ImageJ (NIH, USA) software. We compared results between counts recorded visually and ImageJ reads for randomly selected 50 individuals each during the rainy and post-rainy seasons. The pollen counts from ImageJ were 95% efficient in detecting sterile vs. fertile counts. These results provide a better, efficient, and quick tool for characterizing the pollen behavior and also add value to the genetics studies by accounting for the quantitative variation encoded by multiple loci.

genetics↗

bioRxiv2019

A sorghum Practical Haplotype Graph facilitates genome-wide imputation and cost-effective genomic prediction

Successful management and utilization of increasingly large genomic datasets is essential for breeding programs to increase genetic gain and accelerate cultivar development. To help with data management and storage, we developed a sorghum Practical Haplotype Graph (PHG) pangenome database that stores all identified haplotypes and variant information for a given set of individuals. We developed two PHGs in sorghum, one with 24 individuals and another with 398 individuals, that reflect the diversity across genic regions of the sorghum genome. 24 founders of the Chibas sorghum breeding program were sequenced at low coverage (0.01x) and processed through the PHG to identify genome-wide variants. The PHG called SNPs with only 5.9% error at 0.01x coverage - only 3% lower than its accuracy when calling SNPs from 8x coverage sequence. Additionally, 207 progeny from the Chibas genomic selection (GS) training population were sequenced and processed through the PHG. Missing genotypes in the progeny were imputed from the parental haplotypes available in the PHG and used for genomic prediction. Mean prediction accuracies with PHG SNP calls range from 0.57-0.73 for different traits, and are similar to prediction accuracies obtained with genotyping-by-sequencing (GBS) or markers from sequencing targeted amplicons (rhAmpSeq). This study provides a proof of concept for using a sorghum PHG to call and impute SNPs from low-coverage sequence data and also shows that the PHG can unify genotype calls from different sequencing platforms. By reducing the amount of input sequence needed, the PHG has the potential to decrease the cost of genotyping for genomic selection, making GS more feasible and facilitating larger breeding populations that can capture maximum recombination. Our results demonstrate that the PHG is a useful research and breeding tool that can maintain variant information from a diverse group of taxa, store sequence data in a condensed but readily accessible format, unify genotypes from different genotyping methods, and provide a cost-effective option for genomic selection for any species.

genomics↗