# Understanding the genetics of root system architecture in pigeonpea [Cajanus cajan (L.) Millsp.]

## TL;DR

This study explores the genetic basis of root system architecture in pigeonpea to improve drought and stress tolerance through marker-assisted breeding.

## Contribution

The study identifies genomic regions and candidate genes associated with root system architecture traits in pigeonpea using GWAS.

## Key findings

- Significant genetic variance was found for most RSA traits except root angle from second lateral roots.
- 45 marker-trait associations were identified, with some explaining up to 18.73% of phenotypic variation for tap root length.
- Candidate genes like BAG family regulator and Protein MAIN were linked to root growth under stress conditions.

## Abstract

Field-based phenotyping of root system architectural (RSA) traits in a diversity panel (PI-GAP) of pigeonpea was conducted across three diverse pigeonpea growing environments along with identification of genomic regions associated with these traits through GWAS analysis.

Root system architecture (RSA) plays a crucial role in plant stress tolerance mechanisms serving as the main route for water and nutrient acquisition, while also mediating plant-rhizosphere signalling. In the current study, an attempt was made to understand the genetic variability and genomic regions associated with RSA traits, as a relatively unexplored area of research in pigeonpea. The field-based “Shovelomics” approach was utilized to phenotype eight RSA traits: tap root length (TRL), lateral root length (LRL), number of lateral roots (NRL), stem diameter (SD), root diameter (RD), root angle from first and second lateral roots (RA1 and RA2) and root fresh weight (RFW) at physiological maturity. The pigeonpea international genome-wide association panel (PI-GAP) comprising of 185 genotypes from the reference set and 15 elite genotypes were used in the study. The combined ANOVA revealed significant genetic variance for all RSA traits except for RA2. Genome-wide association study was conducted using the Axiom Cajanus 56 K SNP array, leading to identification of 45 marker trait associations (MTAs) associated with RSA traits in pigeonpea. Multi-locus GWAS models detected six MTAs accounting for 4.84% to 18.73% of the phenotypic variation estimated (PVE) for TRL, 12 MTAs for LRL (4.73–13.92% PVE) and 11 MTAs for NLR (3.03–14.03% PVE value), respectively. Candidate gene analysis revealed genes associated with these traits, including BAG (Bcl-2-Associated athanogene) family molecular chaperone regulator 6 (CcLG01_17476096 and CcLG01_17476721), root cap (CcLG04_5972718) and Protein MAINTENANCE OF MERISTEMS (MAIN) (CcLG06_8242342). These genes were found to have key roles in growth and establishment of roots under stress-related conditions in model crops. Further validation of identified MTAs would provide an opportunity to develop trait-specific markers paving the way for marker-assisted breeding in pigeonpea. Based on RSA traits, pigeonpea genotypes were categorized into deep, spreading and dimorphic root system. These classifications facilitate the phenotypic selection of genotypes for breeding against drought, heat, waterlogging and salinity adaptation. Improved cultivars with an ideal root architecture designed for efficient resource uptake and high yield under diverse environments could help address food security challenges in semi-arid tropics.

The online version contains supplementary material available at 10.1007/s00122-025-05136-y.