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DINH THI LAM. 2021. Studies on wild genetic resources to improve phosphorus deficiency tolerance in rice (Oryza sativa L.).
Thứ hai, 08-08-2022 | 08:07:21

PhD Thesis Abstract. The United Graduate School of Agricultural Sciences - Iwate University, JAPAN


E-mail: lamiasvn@gmail.com


Advisor: Prof. Ryuji Ishikawa


The wild species of genus Oryza is regarded as a valuable resource for rice improvement because of its high genetic diversity.


Chloroplast genome variations (maternal lineage) mentioning Oryza rufipogon populations collected were evaluated through 8 cpINDELs.


166 accessions from Vietnam comprises 10 plastid types, carrying 5 that were unique and different from the controls.


Re-sequencing of the mitochondrial genome yielded two absence/deletion markers, which were confirmed by PCR amplification. The PCR products of orf153 and its upstream region weare used as probes to confirm the deletion by Southern blot. The two deletions were present in a single maternal lineage.


Genetic diversity and phylogenetic relationship evaluated using SSR markers (20 SSRs) obtained the highest diversity of Dong Thap population, He=0.659; the lowest of Cantho population, He=0.300.


The wild rice at Cantho is unique in comparison to Dong Thap, My Tho, Intermediate sites.


Genetic analysis conferring tolerance to P deficiency inherited from wild rice (AS996, a derivative of O. rufipogon) into cultivated rice (IR64) was carried out.


The F2 population includes 391 individuals derived from the cross between  IR64 (susceptible) x AS996 (tolerant). The hydroponic screening used a nutrient culture solution with P deficiency (0.5 mg/L) and P adequate (10.0 mg/L).  To investigate the presence of PSTOL1 gene, four primer-pairs covering 975 bp CDS region of the gene.


Eventually, AS996 had a higher number of tillers than IR64 in P depleted condition. P content in root, stem, primary leaves and upper leaves was measured at booting and harvesting stage.


The sequence alignment, RNA-seq analysis and PCR were applied to examine presence of PSTOL1 in AS996, IR64, Oryza rufipogon (Acc. 106412). They were performed by CLC Genomics Workbench. Kasalath specific Pup sequence was used as a reference to detect and determine SNPs among PSTOL1 gene. The DEGs, which had the same expressed pattern with neither P deficiency and P sufficiency in AS996 and IR64, were identified as P-independent genes. 276 DEGs in shoot and 184 DEGs in root were retained after filtering for DEGs and excluded P-independent genes.


Estimation of the introgressed segments originated from O.rufipogon by NGS (next generation sequencing) addressed higher SNPs frequencies in AS996 more than IR64. Large segments were detected at chromosome 4 in AS996 as compared to IR64. Other candidate regions were also found such as 9.5-10.13 Mb region on chr.2; 6.16-6.2 Mb and 24.1-24.7 Mb on chr.5. From chr.7 to chr.12, two candidate regions were found in flanking 21.74-21.80 Mb region on chr.11 and 22.24-13-39 on chr.12.


The P deficiency tolerance in AS996 beyond P uptake efficiency to high P utilization to meet the demand of rice productivity increase when P supply is limited.


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