High-throughput SNP genotyping is widely used for plant genetic studies. Recently, a RICE6K SNP array has been developed based on the Illumina Bead Array platform and Infinium SNP assay technology for genome-wide evaluation of allelic variations and breeding applications. In this study, the RICE6K SNP array was used to genotype a recombinant inbred line （RIL） population derived from the cross between the indica variety, Zhenshan 97, and the japonica variety, Xizang 2. A total of 3324 SNP markers of high quality were identified and were grouped into 1495 recombination bins in the RIL population. A high-density linkage map, consisting of the 1495 bins, was developed, covering 1591.2 cM and with average length ofl.1 cM per bin. Segregation distortions were observed in 24 regions of the 11 chromosomes in the RILs. One half of the distorted regions contained fertility genes that had been previously reported. A total of 23 QTLs were identified for yield. Seven QTLs were firstly detected in this study. The positive alleles from about half of the identified QTLs came from Zhenshan 97 and they had lower phenotypic values than Xizang 2. This indicated that favorable alleles for breeding were dispersed in both parents and pyramiding favorable alleles could develop elite lines. The size of the mapping population for QTL analysis using high throughput SNP genotyping platform is also discussed.
To enhance understanding of the genetic basis of trait correlation in rice,a recombinant inbred line(RIL)population(F6 and F7) from a cross between Zhenshan97 and HR5 was employed to identify main quantitative trait loci(QTLs)and epistatic QTL(E-QTL).Highly significant positive correlations were detected among five traits of heading date(HD),plant height(PH),panicle length(PL),flag leaf length(FLL)and flag leaf width(FLW)in 2 environments.Four to 8 main QTLs were detected for an individual trait.No E-QTL was detected for PH.One,4,4 and 5 E-QTLs were detected for FLL,HD,FLW and PL,respectively.Each E-QTL individually explained less than 3%of trait variation except E-QFll1.Comparison of QTL results was made in order to dissect the genetic basis of trait correlation.We found that main QTLs with pleiotropic effects and QTL clusters were the main genetic basis of trait correlation.No E-QTL had pleiotropic effects.E-QTL played an important role in the genetic basis of individual trait,but it made a little contribution to trait correlation.
