Mining Of Excellent Genes For Nitrogen Use Efficiency And Nitrogen Deficiency Tolerance And Creation Of Germplasm In Rice

Phenotypic traits related to nitrogen use efficiency(NUE)and nitrogen deficiency tolerance(NDT)were implemented using multi-parents advanced generation inter-cross(MAGIC),which were produced from eight diverse rice varieties collected from different countries under different levels of nitrogen for two years.A set of 55K high throughput SNP chip developed from the 3K Rice Project was used for genome wide association study for QTL affecting NUE and NDT in combination with phenotypic data collected under environments with different levels of nitrogen.Total of 35 main effect QTL were detected for the yield and yield related traits in 2015 and 2016.Among them,a main effect QTL(qNGY6)identified on the short arm end of chromosome 6 for NUE was a very important locus with pleiotropy and stability.A segregation population was further developed for fine-mapping of qNGY6.An interconnected breeding(IB)population was developed using HHZ as recurrent parent and eight elite lines as donor parents.A total of 497 lines plus the HHZ,were tested in the field experiment for three seasons under different nitrogen treatments.Based on re-sequencing SNP data of IB population,7,388 SNP bins was constructed for detection of main effect QTL and excellent alleles for low nitrogen tolerance by genome wide association study(GWAS)approach.Total of 35 main-effect QTL were detected for yield and yield related traits under different nitrogen conditions.Binl6 on chromosome 1 and bin2183-2186 on chromosome 3 were significantly associated with the main effect QTL for yield,biomass,harvest index and spikelet fertility.Among them,QTL(qTGW 2-1)for 1000-grain wight was fine mapped on the bin 1459 with the region of 50 kb by graphic genotypic overlapping method.The main effect QTL qGY1 and qSP8-3 were progeny tested then further pyramided by the linked KASP SNP markers.Finally,the pyramided lines carrying qGY1 and qSP8-3 showed much better in NDT than Huanghuazhan and their pyramiding parents.The IB population was used to identify cold tolerance(CT)QTL at booting stage.For two years,the spikelet fertility was measured under natural low temperature treatment at the high altitude localities(Xundian,Songming and Yuxi in Yunnan).A total of 8 CT QTL were identified.The main effect QTL qCT-3-2 was located on the short arm of chromosome 3.It was a stable expression QTL under four environments.The qCT-3-2 was mapped to the physical range of 192 kb by physical mapping,and its favorable allele came from recurrent parent Huanghuazhan.In addition,we found that qCT-3-2 also played a role in cold tolerance during rice seedling stage.Therefore,this locus will be great application value in cold tolerant molecular breeding of rice.