Flowering time or heading date of cultivated rice (Oryza sativa) is an important agricultural trait for yield production. In general, rice is known as a short-day plant that induces transition from the vegetative phase to the reproductive phase when it senses a decrease in day length (Takahashi et al. 2009). Initially, the molecular genetic pathway for short-day flowering in cultivated rice has been illustrated (Hayama et al. 2006; Takahashi et al. 2009; Purwestri et al. 2017), and several studies or reviewed articles has been provided on the regulation of rice flowering (Tsuji et al. 2013; Shrestha et al. 2014; Wu et al. 2020). According to these studies, three key genes including Early heading date 1 (Ehd1), Hd3a and grain number, plant height, and heading date 7 (Gh7) were affected rice flowering time. In addition, results from studies of gene expression of Takahashi et al. (2009), they found that Heading date 1 (Hd1) is a major determinant of variation in flowering time of cultivated rice. In addition, results from experimental studies were strongly suggest that under short-day length, three key genes including GIGANTEA (OsGI), heading date 1 (Hd1) and Heading date 3a (Hda3) function for flowering promotion of rice (Kojima et al. 2002; Tamaki et al. 2007; Komiya et al. 2008).
Up to date, the mutations that caused morphological and physiological change, followed by human selection in rice as well as the molecular mechanisms generating the diversity of flowering time in cultivated rice are under investigation. For example, Wu et al. (2020) reported that the DNA sequence information of Heading date1 gene associated with flowering phenotypes of cultivated rice in different regions, and photoperiod sensitivity controlled by cooperation and competition among genes of Hd1, Ghd7 and DTH8 (Zong et al. 2021). Hd1 gene of rice has two exons and was identified as Arabidopsis orthologue CONSTANS and encodes zinc-finger type transcriptional activators with the CO, CO-like, and TOC1 (CCT) domains (Yano et al. 2000). The DNA sequence of exon2 contains the CCT domain, with function as a nuclear localization signal Furthermore, the mutant without the CCT domain in CO showed a defect in protein function (Robson et al. 2001). In addition, Hd1 protein functioned as suppressing flowering under Long day (LD) conditions and promoting flowering under short day (SD) conditions. Genetic pathway suggested that Hd1 upstream regulates the expression of Hd3a (Takahashi et al. 2009). A current study reported that Hd1 has a much higher level of polymorphism than the other genes (Hd3a, Ehd1, OsMADS51), and it is a main source of flowering time diversity in cultivated rice, and type of alleles associated with major agronomic traits (Takahashi et al. 2009; Mo et al. 2021).
In temperate region, results from physiological experiment by Izawa et al. (2002) reported that the expression of Hd3 is repressed, while Ehd1 is a key regulator of floral transition in temperate regions. In addition, the areas south of 31N(31degreeN), flowering is regulated by both Hd1 and Ehd1 promotion and resulted in short-day flowering, while in areas north of 31N the expression of Hd3a is regulated by Hd1 repression and Ehd1 promotion (Izawa et al. 2002), which resulted in early flowering under long-day conditions (Doi 2004). (Izawa et al. 2002). Historically, some areas of Thailand have been archeological recorded of different cultivated rice varieties during the development of the country as early as the Metal/Iron Age (Castillo 2011). There are more than 10,000 rice seed samples of Thai rice cultivars with 3,500 different cultivars named which were collected for germplasm conservation around the country by the Pathum Thani Rice Research Institute during 1982–1986. These cultivars attribute to the dissimilar ecological environments and/or agroecological conditions found in northern region (mountain areas) through central (large central plain), northeastern and southern region (lower areas) of the country. Each region has a number of minority tribes, such as Khamu, Mein, Lisu, Hmong and Karen in northern region. Traditionally, these people have cultivated local upland rice cultivars. The upland rice cultivars grown under rainfed conditions in rainfall season (start on May) and these rice cultivars have a characteristic of early maturity (flowering time on September). For Thai low land rice cultivars, they have characteristics of early-, middle-, and late-maturity, depends on genetic background of each cultivar. In addition, almost of these upland rice cultivars have classified as tropical japonica rice type by using DNA markers (i.e., ORF100, plastid subtype ID sequences). There are several previous reports to characterize upland rice and lowland rice cultivars from Thailand (i.e. Prathepha 2008; Prathepha and Baimai 2004; Fongfon et al. 2021). Nowadays a very few rice traditional rice cultivars have grown in some areas of northern and northeastern regions of the country, some of them have no appear in rice fields. Knowledge of the variation of genes that associated with agronomic traits of local rice germplasm collections is an important information for genetic improvement. Furthermore, the overall population structure of global O. sativa germplasm has been well characterized, more detailed analyses of rice germplasm on a regional or country-specific basis have only just begun (Thomson et al. 2007). For such example is Thailand—a country with a wealth of rice diversity that is largely untapped. A long history of traditional rice production across numerous environments in Thailand has led to a diverse array of traditional rice cultivars.
Existence of traditional rice cultivars reflex to food security and health benefits of local people. For example, the temperate regions in north India have been an abode of traditional rice varieties since prehistoric times and were used recommended for medical uses by traditional healers and local farmers. Theses varieties thus fit into the description of healthy and functional foods. Furthermore, local varieties need to be conserved and promote them by commercialize and through general public awareness about their medicinal benefits (Bhat and Riar 2015)
In Thailand, some traditional rice cultivars both tropical japonica and indica rice type have been made in breeding programs and recommended to farmers since 1963, such as KDML105 (non-glutinous and indica rice), Khao Pong Krai (glutinous and tropical japonica rice). To date, traditional rice cultivars have been mostly disappeared from paddy fields of local farmers. These rice cultivars were replaced by modern or new release varieties which recommended by the Department of Rice. Moreover, it might be loss and scientists pay no attention to carry out research as well. However, some traditional rice cultivars had been collected and genomic DNA were extracted and kept at long term storage (-80℃) for research purposes (Prathepha 2009). It would be interesting to figure out whether this gene is conserved between different rice types (indica and tropical japonica). Future studies could use similar genetic tools in other local rice landraces to identify DNA sequence differences that respond to photoperiod sensitivity. Currently, the studies of Hd1 gene of local rice landraces in Thailand have no reports. In addition, studies in plant molecular population genetics requires additional sampling of local populations (Wright and Gaut 2005). The study of DNA sequence polymorphism in the Hd1gene in the two types of Asian cultivated rice, i.e., tropical japonica type and indica type rice will help us gain more insight into the genetic background of this gene. In addition, to address this paucity of information of this gene, re-sequenced of the Hd1 gene of traditional rice cultivars were carried out. The objective of this study aims to explore the DNA sequence variation and comparison of Hd1 gene between tropical japonica type which grown by ethnic groups in northern region of Thailand and indica type of traditional lowland rice cultivars from northeastern region of the country.