Identification Of QTL For Effective Panicle Number In Rice(Oryza Sativa L.)via Association And Linkage Analyses

Rice?Oryza sativa L.?is the staple food for more than half of the global population.Realizing higher rice productivity is faced with challenges as the severe climate environment,increasing scarcity of land and water resources.Rice productivity is determined by three component traits including effective panicle numbers per plant?Epn?,spikelet number per plant,and kilo-grain weight.Epn is the most essential aspects among those three elements.Much work has focused on the"ideal plant type breeding"which has been proved an efficient new method to fulfill the third breakthrough in rice yield.Epn is an important part of the ideal plant type.Hence,it is very important to identify QTL controlling Epn.Two populations were used in this study,including 1090 rice accessions and secondary segregated population derived from two parents.The main results are summarized as follows:1.GWAS for Epn.We carried out a GWAS to identify QTL affecting Epn using a diverse panel of 1090 rice accessions which were cultivated in Sanya?SY?and Shenzhen?SZ?in 2016.Usinng 4.8M SNP,we identified 6 QTL in total,which were located in chromosome1,2,4 and 8.Then,we conducted haplotype analysis with those significant SNP located within CDS region which were non-synonymous SNP.Finally,we defined 2 important QTL and the corresponding 6 candidate genes.2.Fine-mapping of a major QTL Qpn4 through a high generation backcross near isogenic linesTQ,a high quality indica variety from south of China,which has more Epn than LT,a high quality japonica variety from the U.S.A.Previous study detected a major QTL Qpn4 through BRIL derived from TQ and LT.Comparing the result of association analysis and linkage analysis of BRIL,we found that the qEpn4 exactly contained Qpn4.Therefore,we used NIL-Qpn4^TQ to fine map the major QTL Qpn4 using the secondary population derived from TQ and LT.Finally,the Qpn4 locus was narrowed down to a region of 29.17 Kb from 31.19 to 31.21 Mb.which had two predicted genes according to the RADPB,including LOC_Os04g52460 and LOC_Os04g52479.The first gene was putative retrotransposon protein.LOC_Os04g52479 was a cloned gene which had been reported to have effect on polar transport activity of rice auxin.Hence,Nal1 was the most promising candidate gene for Qpn4considering auxin plays important roles in rice Epn.Futhermore,we conducted transgenetic analysis and confirmed Nal1 was the candidate gene for Qpn4.