Analysis Of Genetic Diversity And Gene Mapping Of Panicle Traits In Japonica Rice Of Northern China

With the development of molecular marker technology, the traditional breeding in combination with marker-assistant selection has become the mainstream of the crop breeding in recent years. Germplasm resource is the base of parents selection. Genetic diversity of the germplasm resources provides us with the theoretical reference to the utilization of the germplasm,The panicle traits decides the yield and quality of rice directly which is regarded as an important factor in new variety selection for breeders. In this study, the genetic diversity of japonica rice cultivars released from1970’s to now and the fine mapped gene controlling the panicle traits in the northeast of China were analyzed which will benefit the breeding community in japonica rice.The major results are as follows:1.There is a lower genetic diversity level of’the japonica rice cultivars in northern China and the cultivars genetic diversity are different among release years and geographic locations. A total of195alleles (Na) are detected with an average of3.61alleles per locus. Further analysis showed that the genetic diversity of the cultivars from Jilin province is the highest among the three geographic distribution zones while the Heilongjiang is lower. According to the genetic diversity among different release years, it is showed that the cultivars genetic diversity increased slightly these years. The Analysis of molecular variance (AMOVA) reveals that genetic differentiations are more diverse within the population than that among the populations and the intraspecific variation in different location and release year are88.18%and96.86%, respectively. The Neighbor-joining (NJ) tree indicates that cultivar clusters based on geographic distribution represent three independent groups, with on behalf of Heilongjiang, Jilin and Liaoning province. The population structure of Heilongjiang cultivars is significantly different to the cultivars from Liaoning, a significant differentiation of population structure in japonica rice collection.2. Many of functional gene related yield were used in japonica rice breeding in northern China. Eight of functional gene tags were detected in japonica rice cultivars, which showed that most of functional gene tags had allelic variation in japonica rice cultivars except for IPA1and GW2. It implied that these6functional genes such as GS3, GS5, qSW5, Gnla, qGW8and DEP1are fixed into the modem japonica rice varieties.3. There is a gradually increasing of indica-allele frequencies in northern China. To analyze the genetic components of super japonica rice, we found that indica linage have already introgressed into the genomes of 15super-rice varieties at different level which represented by indica-type frequency (F,). The F, variation of super-rice varieties reflected registration periods difference, varieties bred in2005-2011are highest (F,=0.068), followed by1977-1999(F1=0.03) and rarely in1963-2000(0.011).4. A total of14QTLs which control panicle traits were detected, including2QTLs for PL,1QTL for PW,2QTLs for PBN,2QTLs for SBN,2QTLs for SNP,3QTLs for SSR,1QTL for GD and1QTL for TGW, which were identified on chromosomes1,3,4,5,6,7,11and12. Further analysis showed that the number of QTLs which detected on chromosome1accounted for more than40%of the totals. It is implied that the expression of gene on chromosome1plays an important role in rice panicle traits. Furthermore, the contribution of single QTL in this study was between8.06%-58.62%, and there were8efficiency alleles from the typical japonica rice’Akihilari’and6efficient alleles from indica rice’Qishanzhan’.5. From2011to2013, a total of27QTLs of grain shape traits were detected on chromosomes1,2,3,4,5,11and12, including3QTLs for grain length,11QTLs for grain width and13QTLs for grain thickness, which explained the phenotypic variation14.45-38.48%,28.98-52.36%and38.77-44.23%, respectively. Seven QTLs were detected in2011including3QTLs of grain width and4QTLs of grain thickness; Eleven QTLs were detected in2012including2QTLs of grain length,5QTLs of grain width and4QTLs of grain thickness; Nine QTLs were detected in2013including1QTL of grain length,3QTLs of grain width and5QTLs of grain thickness. The qGW5a and qGT12c were detected in three years, which implied that they were stable expression and stronger repeatability. Further analysis showed that the QTL controlling grain traits are mainly located on chromosome3and12, and accounted for more than44.44%of QTLs. The contribution of single QTL in this study was between5.58-26.90%. There were6efficient alleles from ’Qishanzhan’and14efficient alleles from ’Akihikari’.6. sp mutant is a spreading panicle mutant material with the panicle branch extending outward, the angle between primary branch and rachis increasing and the panicle growing around. Comparing with wild type parents, the plant height of sp significantly increased and the panicle weight has significantly decreased. The genetic analysis showed that the phenotype of sp was controlled by a single dominant nuclear gene. Primary mapping based on the F2derived line between sp and02428showed that the sp gene was located on the long arm of chromosome4, narrowed down to a62.9kb region between marker E3and RM17578and included two BAC such as OSJNBb0022F16and OSJNBa0071I13.7. A lax panicle natural mutant lax(i) was found from the recombinant inbred lines (RILs) which derived from a cross between ’Akihikari’(japonica) and ’Qishanzhan’(indica). From phenotype identification in the field, we find that the lax(i) mutant showed the second branch disappearance and lateral spikelet degradation. Genetic analysis showed that lax(t) phenotype was controlled by a single recessive nuclear gene. By map-based cloning based on BERCA, the target gene was located on a159.6kb region between marker RM16883and MM1466on the chromosome4. Fine mapping by expanding the mapping population and designing new markers, we finally narrowed down to a47.8kb region between markers MM1406and RM16890. Gene prediction shows that there was only one candidate gene Iax2in this region and it guide the AM formation. Sequence analysis revealed that there were three mutant locates between lax(t) and Nippobare, it is indicated that lax(t) is anew allelic genes of lax2possibly.