Genetic Dissection Of Plant Height Gene QPh3 And Grain Yield QTL QYd3 In Couple Phase And The Identification Of Intragenic Recombinant Of SD1

High yielding is one of the most important goals in rice breeding.Rice grain yield was composed by three components tiller number,1000-grain weight and grain number per panicle.In addition,the plant height also greatly affects rice yield.QTL mapping and map-based cloning was an important and efficient methd to isolating new genes.In our previous study,one major plant height QTL q Ph3 was mapped on chromosome 3 using the RILs between 02428 and Teqing.In this study,near isogneic lines for q Ph3 was developed by continuous backcross using a donor parent of TQ and recurrent parent of 02428.On the basis of NILs,map based cloning of q Ph3 and its function research was conducted.Meanwhile,the extremely high plant height line was found in the RILs from the cross between Zhenshan 97(ZS97)and Minghui 63(MH63).NILs for plant height was obtained through backcross to ZS97,and map based clone was conducted for the plant height gene.The main results presented as follows:1.Genetic analysis of q Ph3 revealed that 02428 allele had an additive effect of 6.2 cm and a dominant effect of 3.5 cm,and increasing yield.The q Ph3 was mapped in the interval between WPh1 and RM7389.To further fine mapping q Ph3,a large near isogenic line population was used to screen for recombinants,and the progeny test of recombinant plants was used for inferring the genotype of q Ph3.Finally,q Ph3 was mapped to a 19-kb interval between WPh10-1 and RM7389,where contained 2 genes,one is Os GA20Ox1.Comparative sequencing of two parents revealed that a SNP led to amino acid change from alanine(Ala)in02428 genotype to valine(Val)in TQ genotype.The expression of Os GA20Ox1 in the NIL-02428 was higher than the NIL-TQ.2.Overexpression of Os GA20Ox1 in Zhonghua 11 increaseed plant height which confirmed that Os GA20Ox1 was the candidate underlying q Ph3.Os GA20Ox1 encodes GA20 oxidase protein,which catalyzed GA12 and GA53 to GA9 and GA20,so the GAs content of NILs and transgenic was measured.Theresults show that the substrate of GA20 oxidase protein including GA12 and GA53 was accumulated in the NIL-TQ and transgenic negative plants.However,the products of GA20 oxidase protein such as GA20 was significantly increased in the NIL-02428 and transgenic positive plants.Finally,the active GAs in NIL-02428 and transgenic positive plants were increased.These results confirmed that Os GA20Ox1 regulated plant height through controlling the GAs content.3.Overexpression of Os GA20Ox1 in Zhonghua 11 had no effects on yield and yield related traits,which was contradict with the increasing grain yield performance of NIL-02428 plants.Therefore,there is likely another QTL for yield nearby q Ph3 in the NILs.The plant carried 02428 homozygous at Os GA20Ox1 was selected to backcross with 02428,and a BC5F2 population was obtained for fine mapping yield QTL q Yd3.Genetic analysis of q Yd3 revealed that the 02428 allele had an additive effect of 24 grains and a dominant effect of 14.9 grains on grains per panicle,an additive effect of 0.08 mm and a dominant effect of 0.03 mm on grain width,an additive effect of 0.7 g and a dominant effect of 1 g on grain weight,an additive effects of 4.1 g and a dominant effect of 4.3 g on yield.Futhermore,the positive alleles were all from 02428.Therefore,the linkage q Yd3 and q Ph3 was in coupling phase,and plant height and grain yield can be improved through selection of the genome fragment.4.QTL mapping showed that the semi-dwarf 1 was the most likely candidate gene for extreme plant height in RI92 from the cross between ZS97 and MH 63.Sequencing of sd1 in two parents and RI92 showed that intragenic recombination of two parent alleles between +1721 and +2575 was occurred,the premature termination codon TAG of ZS97 changed to MH63 TAC in the RI92 plants,whereas the SD1 coding was complete and can be translated to GA20 oxidase protein.Treatment of PBZ at seedling stage further proved that the SD1/SD1 had a stronger ability to synthesize GAs.The analysis of yield and related traits showed that SD1/SD1 plants increased yield per plant,but may decrease the harvest index and plant number per unit,and had high risk in lodging.5.Both qPh3 and SD1 were located in the telomere region.In both mapping populations,about 4 times higher recombination rates than the genome-wide average were observed,which was in agreement with the fact that the recombination hotspot was frequently located near the telomere.