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GENOME-WIDE ASSOCIATION STUDIES FOR DRY-DIRECT-SEEDED RICE TRAITS AND GENE EDITING TO VALIDATE THE GENES UNDERLYING PURPLE LEAF COLOR IN RICE
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Rice (Oryza sativa L.) is the major source of calories for more than half of the world population. Dry direct-seeded rice is becoming increasingly popular in rainfed and irrigated ecosystems worldwide mainly due to labor and water scarcities. Addressing constraints in the DDSR ecosystem is a key to develop high-yielding cultivars suitable for this ecosystem. Toward this goal, we performed a genome-wide association study (GWAS) using a subset of 300 indica/aus accessions from the 3,000 Rice Genomes Project. The 300 accessions were phenotyped for 23 traits, including nutrient, root, grain yield and yield-related traits components at the International Rice Research Institute, Philippines experimental fields in replicated trials during the dry and wet seasons of 2018. A total of 265,650 SNPs were used for the GWAS analysis using the Compressed Mixed Linear Model in R/GAPIT. For the 23 traits evaluated, a total of 55 QTLs were detected with the false discovery rate (FDR) values of < 0.001. Many previously reported genes and QTLs potentially colocalized with our significant GWAS sites, while some potentially novel QTLs were also detected. More QTLs were detected during the dry season compared to the wet season, partly due to a less favorable environment which leads to lower heritability for nearly all the traits examined. This study offers key insights into the prospective links between grain yield, yield components, and its environment using high-resolution association mapping. Our results demonstrate the complex nature of the genetic architecture of yield and related traits, which may assist lay the foundation to develop high-yielding varieties. In another experiment, we designed an approach to validate the genes underlying purple leaf color. Out of the various color pigments produced by plants, anthocyanins are the essential secondary metabolites that protect plants against biotic and abiotic stresses. Toward this goal, we have successfully designed and validated guide RNAs for OSB1 and OSB2, which subsequently will be used to knock out the purple leaf color via gene editing.
Dry direct-seeded rice
Genome-wide association study (GWAS)
Purple rice, CRISPR/Cas9
Mankar, Sumeet Prabhakar (2021). GENOME-WIDE ASSOCIATION STUDIES FOR DRY-DIRECT-SEEDED RICE TRAITS AND GENE EDITING TO VALIDATE THE GENES UNDERLYING PURPLE LEAF COLOR IN RICE. Doctoral dissertation, Texas A&M University. Available electronically from