Association mapping for root system architecture under varying levels of phosphorus application in Brassica juncea L. Czern & Coss.

Background: Low phosphate (Pi) availability causes severe decline in crop productivity worldwide. Root system architecture (RSAr) plays a crucial role in Pi uptake from soil and thereby improving phosphorus use efficiency (PUE) of plants. Studying the genetic variability of RSAr traits across various Pi levels offers insights for enhancing crop resilience to Pi deficiency. In the present study, we estimated the response of 280 mustard (Brassica juncea L. Czern and Coss.) genotypes for several root architectural traits (root length-RL, root surface area-RSA, root volume-RV, root average diameter-RAD, root fresh weight-RFW, shoot fresh weight-SFW and root shoot ratio-R/S) at the seedling stage in a hydroponic system at three Pi doses (low-LP, normal-NP and high-HP). Besides, LD-based genome wide association study was also conducted to identify genetic determinants governing RSAr traits at three Pi levels.

Results: Significant genetic variation was observed for the estimated root traits at all Pi levels. A marked increase in mean RL, RSA, RV, RAD, RFW and R/S and decrease in SFW were observed upon Pi starvation. Among 280 genotypes, six genotypes viz., KDM-49-1, DRMRIJ-17-39, RNN-505, NPJ-161, DRMRIJ-17-46, RH-749 were found promising which showed high efficiency at LP and improved responsive behaviour under HP. Genome wide association study allowed the identification of 30 genomic regions involving 140 unique SNPs significantly associated with five traits (RL, RSA, RV, RAD and RFW) on all excluding chromosome A07 of B. juncea. Identification of all Pi dose specific loci except one indicated high interactions between associated loci and Pi applications. Functional annotation of peak SNPs helped to predict 30 putative candidate genes for RSAr at varying Pi applications. Of these, 21 genes were found to be differently expressed in response to LP in high Pi efficient genotype as revealed from RNA seq analysis. Notable among these were genes LPR2 (triggering Pi starvation signaling pathway), PAH2 (Apase encoding gene) and hormone responsive genes (G6PD5, PLGG, LAX3, TIR1, LOG1 and LOG7).

Conclusions: These findings shed light on the genetic mechanisms underlying root architectural traits in response to varying Pi levels, with potential implications for crop improvement strategies aimed at enhancing phosphorus use efficiency in Brassica juncea.