Breeding for Heat Tolerant Aromatic Rice Varieties and Identification of Novel QTL Regions Associated with Heat Tolerance During Reproductive Phase by QTL-Seq

Extremely high temperatures under climate change have become a major challenge for increasing rice production. Therefore, our objective was to develop aromatic heat-tolerant rice varieties using the pedigree method, focusing on selecting for seed-setting ability under extremely high temperatures together with the use of single nucleotide polymorphism/insert and delete (SNP/InDels) markers to improve aromatic properties and grain quality. Furthermore, the QTL-seq approach was utilized to identify QTLs for seed-setting rate in an F 2 population subjected to heat stress. The candidate QTL regions were then aligned to confirm SNPs/InDels in synonymous F 7 candidate heat tolerance lines. The results revealed that four promising lines, namely 84-7-1-9, 84-7-1-10, 159-3-3-1, and 159-3-3-10, were classified as heat-tolerant with low amylose content. In addition, lines 84-7-1-9 and 84-7-1-10 were identified as aromatic rice encompassing the aroma gene ( badh2 ). Regarding the QTL-seq results, the qSF2.1 region ranged from 311 051 to 3 929 422 bp on chromosome 2, was identified based on the highest contrasting SNP index between the heat-susceptible and tolerant bulks. The candidate genes within this region include two genes related to heat shock proteins, three genes associated with pollen fertility, and four genes involved in heat stress and other abiotic stress responses. These genes are proposed as potential candidates for heat tolerance and could be targets in rice breeding programs aimed at enhancing heat tolerance.