Mapping And Cloning Of AWN-2 Controlling Long Awn In Rice

Rice is one of the earliest domesticated and the most important food crops in the world. Cultivated rice was domesticated form wild rice, that has experienced a long process. Awn is an important domestication trait in rice and it is common existence in rice. It is important for the field survival and dispersal of wild rice. However, awn has been gradually being eliminated on the process of domestication and artificial selection. Most of cultivated rice selected is awnless or short awn. It is great significance to explore the process of rice domestication through mapping and cloning the genes related to the awn development and regulation. In this study, one accession of Guangxi common wild rice (Oryza rufipogon Griff.) as donor parent and an indica rice variety 9311 as receptor parent were used to develop a set of rice chromosome segment substitution lines (CSSLs), from which we characterized a long-awn line CSSL5. Results obtained are as follow:(1)There was no difference in plant and panicle phenotypes. Awrr length(AL) and Percentage of awned spikelets per panicle(AP) were investigated:AL and AP Both showed significant differences between 9311 and CSSL5 by student’s t-test. The surface of the awn was also obviously different between 9311 and CSSL5. The surface of the awn of CSSL5 was densely covered with numerous sharp barbs, and that of 9311 was smooth.(2) By analysis of 9311/CSSL5 derived BC5F1 and BC5F2 populations it was found that the phenotype of awn in F1 generation was similar to the long awn parent CSSL5. The ratio of long awn to short awn plants in the BC5F2 population fitted 3:1 segregation ratio, suggesting that the long awn phenotype was controlled by a pair of dominant nuclear genes. This gene is designated as AWN-2 in this study.(3) The number of 408 polymorphic molecular markers between DP30 and 9311 were obtained from 1663 molecular markers covering the 12 chromosomes. These polymorphic markers were used to detect substitution segments from donor parent DP30 in CSSL5. It was found that there were only five substitution segments from DP30. This gene AWN-2 and molecular markers MY land MY2 on chromosome 4 are linked through linkage analysis. The AWN-2 was located to a 1.32-Mb region between markers M1 and M6 on chromosome 4 by analysis of 96 plants with short awn.(4) A F3 population was expanded and 6 new polymorphic markers developed between the M1 and M2 were used to further mapping the gene. Finally, the AWN-2 was located to a 12.14-kb narrow region between markers M7 and M8 on chromosome 4 by use of 5480 lines with short awn.(5) The region of fine mapping included only one predicted gene in Nipponbare Genome annotation database, which is lysine decarboxylase (LOC_Os04g43840). Comparison of the coding sequences of the predicted gene in CSSL5, Nipponbare and 9311, it was revealed that a 29-bp deletion and a 2-bp mutation of LOC_Os04g43840 were present in CSSL5. Therefore, we speculate LOC_Os04g43840 is the candidate gene.