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

Area of Science:

• * Agricultural Science
• * Plant Genetics
• * Crop Improvement

Background:

• * Groundnut (Arachis hypogaea) is a vital oilseed crop.
• * Lack of fresh seed dormancy (FSD) significantly reduces groundnut productivity and seed quality.
• * Identifying genetic control of FSD is crucial for developing improved cultivars.

Purpose of the Study:

• * To identify genetic donors for fresh seed dormancy (FSD) in groundnut.
• * To discover stable marker-trait associations (MTAs) linked to FSD using genomic and phenotypic data.
• * To develop molecular markers for marker-assisted selection of FSD in groundnut breeding.

Main Methods:

• * Phenotyping of 184 groundnut accessions for dormancy duration (days to 50% germination).
• * Whole genome re-sequencing and multi-season phenotypic evaluations.
• * Multi-locus genome-wide association study (ML-GWAS) to identify marker-trait associations (MTAs).
• * Development and validation of SNP-based Kompetitive Allele-Specific Polymerase chain reaction (KASP) markers.

Main Results:

• * Significant variation in dormancy duration observed, with days to 50% germination ranging from 1 to 30 days.
• * 27 MTAs identified in individual seasons and 12 MTAs in pooled data.
• * Candidate genes involved in Abscisic acid (ABA) and Gibberellic acid (GA) pathways identified.
• * Four SNP markers (snpAH00577, snpAH00580, snpAH00586, snpAH00588) proved useful for FSD selection.
• * Combination of favorable alleles from Ahfsd1, Ahfsd2, Ahfsd3, and Ahfsd4 confers stable 24-30 days of dormancy.

Conclusions:

• * Genetic basis of fresh seed dormancy (FSD) in groundnut elucidated.
• * Identified molecular markers and candidate genes can accelerate breeding for improved dormancy.
• * Selection of favorable alleles for Ahfsd1-4 can lead to groundnut cultivars with enhanced FSD (>2 weeks).