Genetics Distance Bias on Domesticated Gene Region Among Rice Accessions Collected in Taiwan

Domestication is the selection process depending on human being’s demand. The domesticated genes are the heredity unit to represent these selected traits. We would like to study how diversity the domestication genes and their nearby regions among the rice landraces with widely different characters but all been adopted in Taiwan.

Totally 20 rice accessions, ranged from thousands of years to modern varieties which may be classified as landraces, upland races, old varieties and modern elite varieties, of Indica or Japonicarice. After quality control, mapping quality and variant calling quality, the mapped NGS data and BAM files were then transformed to variant calling format, the VCF files. Then we further processed decreasing false negative possibility on SNP-relative non-variant variety. The generic distance among whole genome and domesticated gene region were calculated and analyzed.  A total of 25 domesticated genes, including heading day, grain and plant morphology, abiotic tolerance, etc., were examined.

The genetic distances of genome-wide, chromosome-wide or regions around domestication genes showed in difference between them. The variation of phylogenetic clades revealed the evolutionary changes during domestication along genomics. Integration and comparison of resulted phylogeny gave more information about the genetic resources of domestication.