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Heading date is an important agronomic trait in rice (Oryza sativa L.). We previously fine‐mapped two complementary genes, Late Heading Date 1 and Late Heading Date 2 (LH2), that control the late heading trait in rice. Here, we cloned and analyzed the function of LH2. LH2 was fine‐mapped to a 53‐kb genomic region. Sequencing analysis revealed that there were differences in the coding sequence of LOC_Os08g07740 between the varieties 'Bo B' and 'Yuefeng B'. Therefore, LOC_Os08g07740 was identified as a candidate gene for LH2 and subsequently determined that LH2 is a Type 3 allele of Days To Heading 8. Transgenic plants of Yuefeng B carrying LH2 from Bo B significantly delayed the heading date under short‐day and long‐day conditions. A yeast two‐hybrid analysis revealed that LH2 physically interacted with Heme Activator Protein (HAP) 5A, ‐H, ‐I, ‐L, ‐K, and HAP5‐LIKE. The HAP5 domain of HAP5 family members has various functions. Further analysis revealed that LH2 represses photoperiodic flowering by controlling the expression of Early Heading Date 1, Heading date 3a, and Rice Flowering Locus T1 in rice. Core Ideas: LH2 delayed heading by 17.6 d in short‐day conditions and >32.7 d in long‐day conditions.LH2 physically interacted with HAP5A, ‐H, ‐I, ‐L, ‐K, and HAP5‐LIKE.The HAP5 domain of the HAP5 family exhibited functional differentiation.LH2 is a Type 3 allele of DTH8. [ABSTRACT FROM AUTHOR]

Leaf‐color mutants have been extensively studied in rice (Oryza sativa L.) and many corresponding genes have been identified and cloned. However, the mechanism of complex leaf‐color mutations requires further study. In this study, we obtained an introgression line (TIL22) from a set of introgression lines raised using African cultivated rice (O. glaberrima Steud.) as the donor parent and O. sativa subsp. indica Teqing as the recipient. Compared with Teqing, TIL22 showed a yellow‐green leaf phenotype at the seedling stage, but the leaves gradually changed to green after the five‐leaf stage. The photosynthetic pigment contents of yellow‐green leaves at the seedling stage were significantly reduced and chloroplast development was retarded compared with those of Teqing. Genetic analysis indicated that the introgression line phenotype was controlled by a single nuclear gene, temporarily designated YGL22. Map‐based cloning and sequence analysis suggested that the candidate gene was likely to be LOC_Os01g15390, which encodes a chloroplast protein. Real‐time quantitative polymerase chain reaction (qPCR) analysis revealed that the YGL22 transcript level was significantly lower in TIL22 than that of Teqing at the seedling stage. We generated the ygl22 knockout mutant using the CRISPR/Cas9 system. The ygl22 mutants showed a similar phenotype to that of TIL22 at the seedling stage, suggesting that YGL22 may be involved in the early development of chloroplasts in rice. In addition, plant height, number of panicles per plant, and grain yield per plant of ygl22 were not significantly affected. The results indicate that YGL22 can be used as a trait marker gene in hybrid rice production. [ABSTRACT FROM AUTHOR]