Discovering The "Hidden" Plant Height Genes Related To SD1 In Rice

Plant height is one of the most important agronomic traits in plant architecture and yield.The first“green revolution”of rice benefited from the ustilization of semi-dwarf gene sd1.However,the extensive use of sd1 in practice has caused severe problems such as narrowed genetic base and yield bottleneck.Therefore,it is very important to clarify the mechanism of sd1 and find more genes regulating plant height.The japonica rice variety nipponbare（NIP）contains a functional SD1 gene but its plant height is of semi-dwarf,when the gene SD1 from NIP introduced into the indica rice variety Zhenshan 97（ZS97）,it makes a higher plant height of introgression lines.In this study,we used NIP（semi-dwarf）and near-isogenic line NIL-SD1^NIP（high）with a background of ZS97 to develop a segregating population.We have identified several loci associated with plant height in the presence of SD1 using an integrated strategy of next-generation sequencing and bulk segregant analysis（NGS-BSA）,and then fine-mapped a major locus q PH8-1.The main results are as follows:1. Using the NGS-BSA analysis method,three loci controlling rice plant height were detected,of which q PH6 distributed on chromosome 6（physical location 26.07-27.41 Mb）,q PH8-1 and q PH8-2 mapped on chromosome 8（8.92-11.79 Mb,and 14.76-15.58 Mb）,respectively.The NIP alleles at the three detected loci decreased plant height.The G’values of these three QTLs are 5.44,6.38,and 5.16,respectively.2. To fine map qPH8-1,the markers 08C9110 and 08C9500 were firstly used to select recombinant plants in the segregating population,and then nine markers were developed for further genotyping the recombinant plants.q PH8-1 was narrowed into a 145 kb interval between markers 08C9260-08C9405.3. According to the rice website,there are 24 functional genes annotated in the small region of 145 kb and three cytochrome genes LOC＿08g15292（CYTB6）、LOC＿08g15322（CYTB559）、LOC＿08g15280（CYTF）all exist in NIP but absent in ZS97.Thus,these three genes would be candidate genes for q PH8-1.4. Transgenic experiments reveal that the lines overexpressing CYTB6,CYTB559,CYTF is shorter in plant height than the recipient NIL-SD1^NIP.These results indicate that CYTB6,CYTB559,CYTF may negatively regulate plant height in rice.5. The expressions of CYTB6,CYTB559,CYTF are transiently induced by GA（GA₃treatment）and repressed by a GA inhibitor（paclobutrazol）.These results suggest that the three genes may be involved with the GA homeostasis in rice.