Biology subjects

Senthil, R.

Publications and source records attributed to Senthil, R..

3 recordsLinked to original sources

bioRxiv2025

Genomic analysis uncovers unique haplotype signatures from subspecies and agronomic types associated with blanchability in groundnut

Blanchability, defined as the ease of seed coat removal after roasting, is a vital trait for enhancing processing efficiency and product quality in groundnut (Arachis hypogaea L.). To enable a comprehensive haplotype-level genetic dissection of this trait, SNPs derived from whole-genome resequencing (WGRS) were used to perform genome-wide association study (GWAS) using multi-locus models (BLINK and FarmCPU) on a diverse groundnut mini-core collection phenotyped across two crop seasons. A total of 26 significant SNP-trait associations (STAs) were identified across multiple chromosomes, with major loci on chromosomes Ah05, Ah06, and Ah17, some of which were further validated using KASP (Kompetitive Allele-Specific PCR) markers. Candidate genes, such as those involved in cell wall biosynthesis (e.g., galactoside 2-alpha-L-fucosyltransferase-like protein, protein kinase superfamily members, and glycerophosphoryl diester phosphodiesterase 3), were found to be within linkage disequilibrium (LD) of the identified STAs, suggesting their plausible association with blanchability. Haplo-pheno analyses identified superior high-blanchability haplotypes; Ah05HapBL3, Ah06HapBL5, Ah06HapBL10, and Ah17HapBL6, which were predominantly found in the fastigiata subspecies (including Valencia and Spanish bunch agronomic types) from South Asia and South America, while the low-blanchability haplotypes were from hypogaea subspecies (including Virginia runner and Virginia bunch agronomic types) from Africa. Overall, this study provides valuable insights for customizing blanchability through haplotype-based breeding of processing-grade cultivars thereby improving groundnut value chains to meet diverse industrial demands.

genomics↗

bioRxiv2025

Genomic analysis reveals the interplay between ABA-GA in determining dormancy duration in groundnut

Groundnut is an important leguminous crop however; its productivity and seed quality are frequently reduced due to lack of fresh seed dormancy (FSD). To address this challenge, a mini-core collection of 184 accessions was phenotyped to identify donors in each agronomic type, in addition to analysing data on whole genome re-sequencing and multi-season phenotypic evaluations to identify stable marker-trait associations (MTAs) associated with FSD. Phenotypic analysis revealed substantial variability in dormancy durations, with days to 50% germination (DFG) ranging from 1 to 30 days. Multi-locus genome-wide association studies (ML-GWAS) identified 27 MTAs in individual seasons and 12 MTAs in pooled seasons data, respectively. Key candidate genes identified included Cytochrome P450 superfamily proteins, protein kinase superfamily proteins, and MYB transcription factors involved in the Abscisic acid (ABA) pathway, as well as F-box interaction domain proteins, ATP-binding ABC transporters, associated with the Gibberellic acid (GA) pathway. SNP-based KASP (Kompetitive Allele-Specific Polymerase chain reaction) markers for 12 SNPs were developed and validated, of these 6 markers (snpAH00577, snpAH00580, snpAH00582, snpAH00585, snpAH00586 and snpAH00588) showed polymorphism between dormant and non-dormant lines. Incorporating favourable dormant alleles into breeding strategies could enable the development of high-yielding cultivars with a dormancy period of 2-3 weeks.

genomics↗

bioRxiv2025

Identification of High Blanchability Donors, Candidate genes and Markers in Groundnut

Blanchability in groundnut, the ability of seeds to shed their seed coat (testa), is a trait of economic importance in the food processing industry, yet remains underexplored in breeding programs. This study aimed to assess blanchability in 184 accessions from the ICRISAT minicore collection and identify associated genomic regions, candidate genes, and molecular markers. Significant variability was observed over two seasons, with blanchability ranging from 3.98% to 70.08%. Ten genotypes, including ICG10890, ICG9507, ICG13982, and ICG297, exhibited good blanchability, with ICG297 emerging as a promising donor based on cluster analysis of blanchability and agronomic traits. Genome-wide association studies (GWAS) using the 58K Axiom_Arachis SNP array revealed 58 significant SNP-trait associations and important candidate genes such as isocitrate dehydrogenase and ubiquitin ligase, which influence seed coat structure and cell wall integrity. Nine SNPs were validated via allele mining, with four markers--on chromosomes A01 (snpAH00551), A06 (snpAH00554), B04 (snpAH00558), and B07 (snpAH00559), effectively distinguishing between high and low blanchability genotypes. These validated SNPs present valuable tools for genomics-assisted breeding. Overall, the findings is the first study contributing to a better understanding of the genomics and genetic basis of blanchability and offer resources for improving processing traits in groundnut.

genomics↗