Rice homolog of Arabidopsis Xylem NAC domain 1 (OsXND1), a NAC transcription factor regulates drought stress responsive root system architecture in indica rice

Rice yield is greatly constrained by drought stress. In Arabidopsis, XYLEM NAC DOMAIN 1 (XND1) gene regulates the xylem formation, efficiency of water transport, and the delicate equilibrium between drought tolerance and resistance to pathogens. However, diversity and the role of rice homologs of OsXND1 is not reported so far. This study hypothesized that the rice homolog of OsXND1 also regulates drought stress tolerance through modulation of root architecture. Initially, phylogenetic analysis identified two OsXND1 homologs (Os02g0555300 and Os04g0437000) in rice. Further, 14 haplotypes were identified in the OsXND1 of which Hap1 and Hap3 were major haplotypes. The association analysis of OsXND1 with 16 different traits, including 10 root traits, showed three SNPs (Chr02:20972728-Promoter variant; Chr02:20972791-5 ' UTR variant, and Chr02:20973745-3 ' UTR variant) were significantly associated with root area, root surface area, total root length, and convex hull area only under drought stress in indica rice. Besides, the superior haplotype of OsXND1 increased the root area, root surface area, total root length, and convex hull area by 46%, 40%, 38%, and 42%, respectively, under drought stress conditions. Therefore, the identified superior haplotype of OsXND1 can be utilized in haplotype breeding programs for the improvement of drought tolerance in rice.