Genome Wide Association Study on the Germination Ability at Low Temperature and Preharvest Sprouting Resistance in Rice
xii, 143 p.
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ABSTRACT* A large portion of world population relies on energy calorie supplied from rice. For that reason, there is no bout that sustainable rice production is vital for the food security of the world. Nowadays, more and more challenges including the biotic and abiotic stress are coming to rice production. Cold stress is one of the challenging factors, affecting the different growth stages of rice plant, which can ultimately cause tremendous loss in crop productivity. Among the different growth stages affected by cold stress, germination stage is not the least important growth stage because getting uniform seed germination and good performance of early seedling at low temperature is vital for the high crop productivity. Therefore, understanding and investigating the mechanism of the germination ability at low temperature is prerequisite as a basic step to develop new varieties with improved cold tolerance. Preharvest sprouting resistance (PHS) could render the huge economic losses in crop production. PHS usually occurs in the region where there are occasional rains at harvest time. However, global weather changes cause the unexpected and unusual rain at harvest time everywhere. Therefore, effort to improve PHS resistance in rice should be paid attention and prepared in advance in the rice breeding. Traditional breeding takes time to develop new varieties with desired traits. Molecular genetics and biotechnology can help to accelerate the development of new improved varieties. Accordingly, the alleles which can confer the PHS resistance should be mined as much as possible although several studies on PHS in cereals have been conducted. Therefore, the candidate genes associated with the germination ability at low temperature and PHS resistance in rice were investigated through genome wide association study (GWAS) using the whole genome resequencing data. 1. Genome Wide Association Study on the Germination Ability of Rice at Low Temperature Cold stress at the germination stage is one of the limitations for the crop production causing the poor crop stand and seedling performance. Understanding the cold tolerance mechanism and detecting the associated candidate genes fortify the efforts in improving the cold tolerance at germination stage. This GWAS study could detect many candidate genes associated with the germination ability at low temperature. Among the associated candidate genes, OsWR2 was associated with all traits related with low temperature, which seems to be mediated cold tolerance through the lipid composition in plasma membrane. Many genes involving in cellular respiration and electron transport chain processes were also found to be associated with the low temperature germination traits in the present study. In overall, radicle and coleoptile emergence were associated with the same candidate genes, which can assume the same mechanism is controlling the early phase of seed germination (i.e. emergence of radicle and coleoptile from the seed) at low temperature. For the post emergence growth of seedling, candidate genes which are different from that of early phase of germination, were observed. At the optimal temperature also, the same candidate genes were associated with both coleoptile and radicle emergence whereas candidate genes different from that of emergence phase were found to be associated with post emergence growth. Moreover, radicle elongation and coleoptile elongation were probably steered by different mechanisms. Taken together, this study could provide insight of the molecular mechanisms underlying regulation of seed germination. The GWAS results presented in this study not only could confirm the previous molecular works related to the cold tolerance in rice and other crops but also explore the potential genome-wide alleles which may confer the cold tolerance at germination and probably other growth stages in future breeding works. 2. Genome Wide Association Study on the Preharvest Sprouting Resistance in Rice Preharvest sprouting resistance (PHS) might be a serious problem for rice production in very near future because of the global weather changes which leads to coincide occasional and unusual rain at harvest time. The available genetic resources conferring the PHS resistance should be explored as much as possible. GWAS on PHS resistance in rice was performed using the diverse rice germplasm accessions and genome wide resequencing data. This study not only could detect the previously identified dormancy and PHS associated genes but also the new candidate genes associated with the PHS and related traits. Some of them were associated with more than one trait. Among these genes, OsERF1, OsERF94, GMPK2, and Os04g0546100 (Similar to OSIGBa0101C23.10 protein) genes were found to be most significantly associated with PHS, D7, D14, and GI. Among the hormonal signaling underlined PHS and germination process, ethylene response factor was found to be most prominent. Many other candidate genes which have potential implication in improving the PHS resistance in rice were also detected in this study. Os05g0180600 (PI3K) and Os04g0546500 (similar to Oleosin) are examples of them. Haplotype analysis of some selected genes could identify the promising functional allele which may confer the PHS resistance in irce. To confirm the GWAS associated signals, further research on gene expressions are needed. This study point out many physiological aspects of germination and could provide the useful information on the associated candidate genes which might be very useful to future attempts improving the PHS resistance in rice.