Identification and evaluation of low-pH-tolerant Cheongcheong/Nagdong-double haploid rice lines via QTL analysis

Low soil pH (acidic soil) is one of the most severe environmental constraints that severely inhibits crop production. Here, we screened 134 lines of the Cheongcheong/Nagdong Double Haploid (CNDH) rice population under low pH conditions to uncover candidate QTLs and identify low pH-resistant lines. A total of 17 QTLs against shoot length, root length and standard evaluation score in response to low pH were identified on 8 chromosomes (1, 2, 6, 7, 8, 9, 10, and 12). A QTL related to shoot length, qSL-6b, on chromosome 6 with an LOD of 5 and a QTL related to the standard evaluation score, qSES-9, on chromosome 6 with an LOD of 3 were further investigated for candidate genes. A total of 24 genes were predicted, i.e., 17 genes on qSL-6b and 7 genes on qSES-9 on the basis of closely related functional annotations via the NCBI and RiceXPro databases. Through qRT‒PCR of the resistant and susceptible lines, we identified four genes (Os06g0211200, Os09g0448200, Os09g0456200, and Os09g0472100) that were significantly expressed in the resistant lines but expressed at lower levels in the susceptible lines under low-pH soil stress. During early germination, ABA levels decreased in all the resistant lines but increased in all the susceptible lines. However, the ABA level at the seedling stage significantly increased in the resistant lines but decreased in all the susceptible lines. Our results suggest that the genes responsible for K⁺ ion homeostasis and ABA regulation play key roles in resistance to low pH in rice.