Comparative Genome Analysis of the Small-scale Duplication in Plants

Abstract

Mapping the genes against environmental changes is invaluable information for breeders to ensure the yield of cultivars, and become more important than ever before due to the global climate changes accompanying different biotic and abiotic stresses. However, the knowledge of the genes that provide resistance against such environmental stresses is still limited in crop plants. Previous researches showed that the genes related to response to biotic stress and secondary metabolism in Arabidopsis were retained after small and large scale duplication events and the tandemly duplicated genes corresponded to gene ontology (GO) category of stress response had high probability of retention and suggested their role of adaptive evolution against environments. In this dissertation, nucleotide-binding site and leucine-rich repeat (NBS-LRR) genes which are highly tandem-duplicated in G. max genome are suggested to contribute to soybean disease resistance by co-localization analysis with disease-related QTL and bacterial leaf pustule (BLP) treated transcriptome analysis. Moreover, genes underwent small scale duplication like tandem duplication and ectopic duplication were retrieved from 5 crop genomes and 2 non-crop genomes and investigated the QTL co-localization and the evolution rate by pair-wise calculation of Ks values in homologous gene groups, and we found the crop genome were commonly experienced recent tandem duplications while non-crop genome were not, which might implicate the domestication process could be influenced by tandem duplication process to optimize the adaptation to the environment and human needs.