A combination of upstream alleles involved in rice heading hastens natural long-day responses

Background: The female parental line Jinbuol (JBO, early heading) and two recombinant isogenic lines, JSRIL1 and JSRIL2, have been shown to flower 44, 34 and 16 days earlier, respectively, than the male parental line Samgwang (SG, late heading) in paddy fields. Objective: To explore how photoperiodicity-related genes are involved in differential heading among these lines. Methods: Deep sequencing was conducted for these lines, photoperiodicity-related genes (71) were categorized, and qRT-PCR was performed for some key genes. Results: Deep sequencing revealed a nearly even contribution of parental groups, with 48.5% and 45% of the chromosomes in JSRIL1 and JSRIL2, respectively, inherited from the female parent JBO; however, Chr6 contained the most biased parental contribution, with 99.4% inherited from the female parent. The variation in single-nucleotide polymorphisms (SNPs) among many known flower-inducing genes, including rice GIGANTEA (OsGI); grain number, plant height and heading date 7 (Ghd7); and EARLY HEADING DATE 1 (Ehd1), was minimal. In the JSRILs, HEADING DATE 1 (Hd1) and VERNALIZATION INSENSITIVE 3-LIKE 1 (OsVIL2) originated from JBO, whereas FLAVIN-BINDING, KELCH REPEAT, F BOX 1 (OsFKF1) originated from SG. Interestingly, HEN1 suppressor 1 (OsHESO1) originated from SG in JSRIL1 and JBO in JSRIL2. RNA sequencing and qRT‒PCR analyses of plants at the floral meristem stage revealed that transcriptional regulation through chromosomal restructuring and posttranscriptional regulation might control minute gene regulation, resulting in delayed heading in JSRILs. Conclusion: Our gene expression and SNP analyses of elite recombinant isogenic lines could be helpful in understanding how photoperiodicity-related genes in rice are modulated.