PubMed Health⌕ Search

Biomedical subjects

Kuldeep Singh

Publications and source records attributed to Kuldeep Singh.

8 recordsLinked to original sources
PubMed2026

Pan-genome-based resequencing of 2,320 accessions reveals structural variations and accelerates breeding advances in cultivated peanut.

The cultivated peanut is a crucial global legume crop that is essential for food security and nutrition, particularly in developing regions. However, its limited genetic variation hampers breeding progress and yield improvement. Here we constructed a graph-based pan-genome for peanut, incorporating 14 genomes that represent all 6 peanut varieties. Using this pan-genome, we genotyped 2,320 accessions, covering 88.03% of ICRISAT and 59.21% of USDA core germplasm, enriching valuable resources for genomic studies and breeding. We cataloged genomic structural variations and investigated the role of homoeologous exchanges in population divergence. Through our pan-genome approach, we overcame the challenges of genotyping posed by homoeologous exchanges and identified key genes associated with flowering and dwarfism in peanut. By integrating superior haplotypes and germplasm resources guided by the pan-genome, we further developed high-yield dwarf lines. This work provides essential genomic resources to accelerate functional gene discovery and modern peanut breeding.

Journal Article↗
PubMed2025

Development and validation of a high-density 'Amahysnp' genotyping array in grain amaranth (Amaranthus hypochondriacus).

BACKGROUND: Grain amaranth has recently gained global attention as a promising crop alternative to traditional cereals due to its nutritional value and adaptability to various growing conditions. Although gene banks conserve extensive collections of amaranth germplasm, the genomic and phenotypic characterization of these resources is limited, which hinders their full utilization in breeding programs. A major challenge is the lack of high-throughput genotyping assays essential for comprehensive genomic characterization and trait mapping. High-density SNP arrays have become standard tools for genome-wide analysis across multiple loci, enabling molecular breeding across a range of crop species. RESULTS: In this study, we developed a 64 K high-throughput SNP genotyping array named "AmahySNP", using Affymetrix® Axiom® technology. The array contains 64,069 high-density SNPs distributed across both genic (55.17%) and non-genic (44.83%) regions of the Amaranthus hypochondriacus genome. The genic region includes 8,879 genes, which consist of 4,830 single-copy genes and 4,049 multi-copy genes distributed across 16 scaffolds. These genes cover various functional regions, including exons (10.5%), introns (40.1%), 5'UTRs (1.6%), and 3'UTRs (2.9%), respectively. The AmahySNP array was effectively utilized for population structure analysis, genetic diversity studies, core development, and genome wide association studies (GWAS) in amaranth germplasm. A representative core set of 112 accessions was identified, which includes two released varieties (Annapurna and Suvarna) and 100 diverse accessions from 12 different regions, representing 12% of the total 917 accessions evaluated. Phylogenetic analysis revealed three major genetic clusters, independent of their geographical origins. GWAS conducted using 22,763 polymorphic SNPs from 540 genotypes identified 13 novel loci associated days to flowering (DTF) trait, seven of which were located within annotated genes. CONCLUSIONS: The AmahySNP 64 K SNP chip a valuable genomic tool for amaranth research and breeding with a strong potential to accelerate its genetic improvement. It enables high-throughput genotyping for a wide range of applications, including GWAS and other genomic studies, and will significantly advance the exploration of natural genetic variations. Ultimately, this resource will empower amaranth breeders to develop improved amaranth cultivars with enhanced crop yield, resilience, and nutritional quality, contributing to global food security and sustainable agriculture.

Amaranthus↗
PubMed2006

Spontaneous subcutaneous myxosarcoma in a captive European hedgehog (Erinsceus europaeus).

A surgically excised biopsy representing a subcutaneous mass on the left side of the neck from a 3-year-old female European hedgehog (Erinsceus europaeus) was presented. Spontaneous myxosarcoma was diagnosed based on histological, immunohistochemical, and ultrastructural characteristics. The neoplasm grossly consisted of a firm, pale, multilobulated mass with a characteristic clear gelatinous fluid. Histologically, the neoplasm was nonencapsulated and composed of pleomorphic stellate or spindle-shaped vimentin and periodic acid-Schiff-positive cells arranged in loose sheets and occasionally whorls. The neoplastic cells were suspended in Alcian blue-positive stroma and contained infrequent mitotic figures. Evidence of a viral etiology was not detected using electron microscopy and polymerase chain reaction. This is the first case report of a myxosarcoma in a captive European hedgehog.

Animals↗
PubMed2004

Phosphohippolin expression in the rat central nervous system.

The FXYD family is a small single-span membrane protein family; recently, we have identified a novel member of this family from the cDNA library of the rat hippocampus and named phosphohippolin (Php) (Mol. Br. Res. vol. 86, 2001). The deduced amino acid sequence of this novel Php comprises 93 residues with a core motif of FXYD and a single transmembrane domain. This indicates that Php belongs to FXYD6 subfamily of the seven FXYD subfamilies (FXYD1-7). Php shows a 48.1% homology with rat phospholemman (FXYD1), a transmembrane family protein. In this study, polyclonal antibodies against the carboxyl-terminal sequence of rat Php were raised and purified. The spatial expression of the Php protein was in the neuronal fibers of the medial part of lateral habenula nucleus, thalamus, hypothalamus, stria terminalis, zona incerta, amygdaloid body and cingulum, olfactory bulb, hippocampus, cerebral cortex and cerebellum. A unique Php distribution was identified in the cerebellum, with a predominant expression pattern in the granule layer of lobules VI-IX of the posterior lobe. Developmental studies demonstrated that the highest level of Php expression was seen in the postnatal (PN) 3-week-old rat brain, and a significant amount of Php still existed in the adult brain. These findings suggest that Php may play an important role in the excitability of neurons in the central nervous system during postnatal development, as well as those in the adult brain.

Aging↗
PubMed2004

Uterine secretion of ISP1 & 2 tryptases is regulated by progesterone and estrogen during pregnancy and the endometrial cycle.

We have described two novel implantation serine proteinase (ISP) genes that are expressed during the implantation period. The ISP1 gene may encode the embryo-derived enzyme strypsin, which is necessary for blastocyst hatching in vitro and the initiation of invasion. The ISP2 gene, which encodes a related tryptase, is expressed in endometrial glands and is regulated by progesterone during the peri-implantation period. Based on similarities between ISP2 gene expression and that of a progesterone-regulated lumenal serine proteinase activity associated with lysis of the zona pellucida, we have suggested that the strypsin related protein, ISP2, may encode a zona lysin proteinase. Recently strypsin has also been found within uterine fluid, suggesting a second potential role in hatching. Consistently, we have discovered that ISP1 is also expressed in the uterine secretory gland at the time of hatching. In this study we demonstrate that both ISP1 and ISP2 are secreted together into the uterine lumen at peri-implantation, and that the appearance of ISP protein is regulated positively at the transcriptional level by progesterone and negatively at the posttranscriptional level by estrogen. This negative regulation by estrogen may be overridden in pregnancy as ISP protein expression is restored during oil-induced decidualization. ISP1 and ISP2 proteins are also expressed in proestrous suggesting additional roles in the endometrial cycle.

Animals↗
PubMed2004

Histochemical accumulation of oxidative damage products is associated with Alzheimer-like pathology in the canine.

An important lesion in Alzheimer's disease (AD) patient brains is the neurofibrillary tangle (NFT). Hyperphosphorylated tau is its major component. In a former paper we described some NFT in the canine brain. During aging, moreover, advanced glycation end products (AGE) might accumulate. Glycated tau induces lipid peroxidation in vivo and tau and AGE antigens have been mentioned to co-localize in NFT. This indicates that AGE may play an important role in Alzheimer disease (AD) by oxidation of tau. The aim of the present study was to investigate amyloid, neurofibrillary tangles, Abeta precursor protein, Abeta, tau, ubiquitin, advanced glycation end products, 4-hyroxynonenal protein and lipofuscin in a series of dogs of varying ages. The results showed a significant positive correlation between age and amyloid quantity (Congo red staining), HNE staining and lipofuscin (LF), and between amyloid quantity and HNE staining and LF. Staining for AbetaPP seemed to have a tendency to increase with age, whereas staining for tau, ubiquitin and AGE each only gave limited positive results in a proportion of the older dogs. Preliminary studies including loss of cognitive capabilities in the older dogs and chemical measurement of lipofuscin-like pigment (LFP) accumulation in brain extracts revealed an increase with old age and dementia. The Congo red, HNE and LF results suggest that deposition of amyloid with aging might be associated with formation of end products of lipid peroxidation. The finding of the limited positive signals for tau, ubiquitin and AGE in some old cases might indicate that the spontaneous brain pathology of the aged dog reveals similarities to early stages observed in AD in humans especially those with Down syndrome.

Aging↗