Upadhyay Priyanka, Gupta Mehak, Sra Simarjeet Kaur, Cheema Gurdeep, Sardana Virender K, Sharda Rakesh, Sandhu Nitika, Akhatar Javed, Kaur Gurpreet
Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India.
Department of Soil & Water Engineering, Punjab Agricultural University, Ludhiana, Punjab, 141004, India.
BMC Genomics. 2025 Aug 11;26(1):740. doi: 10.1186/s12864-025-11840-2.
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.
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).
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.
全球范围内，低磷有效性导致作物生产力严重下降。根系结构在植物从土壤中吸收磷并进而提高磷利用效率方面起着关键作用。研究不同磷水平下根系结构性状的遗传变异性，可为增强作物对磷缺乏的耐受性提供见解。在本研究中，我们评估了280个芥菜（Brassica juncea L. Czern and Coss.）基因型在水培系统中幼苗期对三种磷剂量（低磷-LP、正常磷-NP和高磷-HP）下几种根系结构性状（根长-RL、根表面积-RSA、根体积-RV、根平均直径-RAD、根鲜重-RFW、地上部鲜重-SFW和根冠比-R/S）的响应。此外，还进行了基于连锁不平衡的全基因组关联研究，以鉴定在三种磷水平下控制根系结构性状的遗传决定因素。
在所有磷水平下，所评估的根系性状均观察到显著的遗传变异。磷饥饿时，平均根长、根表面积、根体积、根平均直径、根鲜重和根冠比显著增加，地上部鲜重降低。在280个基因型中，发现KDM-49-1、DRMRIJ-17-39、RNN-505、NPJ-161、DRMRIJ-17-46、RH-749这六个基因型很有前景，它们在低磷水平下表现出高效率，在高磷水平下具有改善的响应行为。全基因组关联研究在除芥菜A07染色体外的所有染色体上鉴定出30个基因组区域，涉及140个与五个性状（根长、根表面积、根体积、根平均直径和根鲜重）显著相关的独特单核苷酸多态性（SNP）。除一个位点外，所有磷剂量特异性位点的鉴定表明相关位点与磷施用之间存在高度相互作用。峰值SNP的功能注释有助于预测在不同磷施用条件下根系结构的30个假定候选基因。其中，21个基因在高磷效率基因型中对低磷的响应表现出不同表达，这从RNA测序分析中可以看出。其中值得注意的是LPR2基因（触发磷饥饿信号通路）、PAH2基因（酸性磷酸酶编码基因）和激素响应基因（G6PD5、PLGG、LAX3、TIR1、LOG1和LOG7）。
这些发现揭示了根系结构性状响应不同磷水平的遗传机制，对旨在提高芥菜磷利用效率的作物改良策略具有潜在意义。
