Association of nucleotide variation, transcriptome, and phytohormones with tillering in Malaysian upland rice varieties (Oryza sativa l.)

Rice is being consumed by more than half of the world's population. Since tiller is a specialized grain-bearing branch, increasing its number may increase the panicle number and improve total rice yield. The objectives of this study are to analyze the single nucleotide polymorphisms (SNPs) in genes related to tillering by focusing the genes involved in phytohormone biosynthesis; to validate the tillering-associated SNPs among the rice varieties from Malaysia by using the whole genome sequencing (WGS) data; and to investigate the effects of cytokinin and growth conditions on tiller production, gene expression, and phytohormone level of upland and lowland rice varieties, respectively. A total of 180 and 29 SNPs in 74 genes related to tillering were found to be significantly associated with the rice tiller number in japonica and indica subpopulations from the Rice SNP-Seek database, respectively. These SNPs were further validated by using the WGS data from six low tillering upland and seven high tillering lowland rice varieties, which are closely related to the japonica and indica subpopulations, respectively (based on the phylogenetic analysis). The low-tiller-associated allele of 61 SNPs from the japonica subpopulation matched with the major allele of the upland rice varieties, while the high-tiller-associated allele of one SNP from the indica subpopulation matched with the major allele of the lowland rice varieties. The application of kinetin (1.0-2.5 mg/L), a synthetic cytokinin, through in vitro culture was found to increase the tiller number of lowland and upland rice varieties earlier than the untreated rice cultures. Kinetin-treated Bokilong and Gonsulak (upland rice varieties) in the greenhouse also initiated earlier tillering but did not significantly increase the total tiller number at maturity compared to the untreated rice plants. Based on the gene expression analysis by using NanoString nCounterÒ, the early tillering induced by kinetin may be associated with the differential expression of the genes involved in abscisic acid (ABA) signaling (SAPK10), gibberellin biosynthesis (SD1/OsGA20ox2), and strigolactone biosynthesis (D27) at the beginning of tillering phase. In addition, the upregulation of ABA biosynthetic gene (OsABA4) in kinetin-treated Bokilong and Gonsulak may negatively regulate tiller formation during the tillering phase. However, based on the high-performance liquid chromatography analysis, the ABA level was found to be significantly increased in Bokilong but significantly decreased in Gonsulak treated with kinetin, compared to the untreated plants. Nevertheless, a higher level of indole acetic acid (IAA) in these plants during tillering may also inhibit tiller formation. In addition, the total tiller number of two lowland rice varieties i.e., Kadaria and MR269, were found to reduce by 59.5% and 40.7%, respectively, when grown under upland condition, compared those grown under lowland condition; possibly due to the differential expression of the genes encoding auxin efflux carrier (OsPIN9) and strigolactone receptor protein (D14). Moreover, a higher ABA and IAA levels (as observed in Kadaria), along with a lower trans-zeatin level (as observed in MR269), may account for the reduction in tiller number of lowland rice plants grown under upland condition. In conclusion, the findings of this research have advanced the knowledge on the key genetic markers and phytohormonal mechanisms affecting tillering that are useful for future breeding programs of Malaysian rice varieties with high yields and climate-resilience.

Text 125115 - Full Text.pdf Download (21MB) Official URL or Download Paper: http://ethesis.upm.edu.my/id/eprint/18810

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