Whole Genome Resequencing for Capturing Biodiversity, Rediscovering Domestication and Beyond.

Obtaining the genome sequence of a wide range of individuals of a species will generate vast amounts of informative datasets and enable the rapid discovery of much greater genome-wide sequence variation than has been identified previously. With the decreasing cost of sequencing, the genetic maps of many species are getting increasingly dense, a great improvement for plant breeding and selection. Also, a wealth of knowledge will be gained from comparative genomic analyses within and across species, as how plants grow, function and survive different ecological conditions and various environmental stresses. Whole genome resequencing approach has been successfully used in rice and maize studies to identify evolution patterns during domestication and to develop efficient ways to discover domestication genes. We re-sequenced 25 representative cultivated rice and 25 wild rice, and developed the genome variation maps containing about 8.4 million SNPs. With a combination of conventional population genetic methods and a new tree-thinking method, about 500 genes were detected with strong selection signals in cultivated rice and thus could be candidate domestication genes. Many of them have functions related to growth, architecture, maturity, productivity or resistance and can be further applied in breeding programs. Similar study has been carried out in maize for whole genome resequencing of several maize inbred lines. A large number of SNPs and InDels were identified. Hundreds of genes that are present in one haplotype but absent in another were detected. More than 100 large chromosomal intervals with low-sequence-diversity represent putative selective sweeps which may be related with domestication. Limited amounts of intra-chromosomal recombination during pedigree breeding were identified. Whole genome resequencing will have far reaching implications for improving breeding strategies and plant varieties to meet the worldĄŻs growing demand on plant production.