Genetic Analysis Of The Grain Shape And Plant Architecture Using A Four-parent MAGIC Population In Rice

Rice is a major food crop in China.Its small size of genome and abundant genetic diversity make it an ideal model monocot plant in genetic and genomic research.The genetic analysis of grain shape and plant architecture of rice has been the targets in the study of plant breeders.Meanwhile mapping more quantitative trait locus?Q TLs?associated with grain shape and plant architecture and identification of the superior alleles are helpful to guide a design for molecular breeding.C lassical bi-parental mapping population has been made great contribution to gene identification,but suffered a shortage of diversity and recombination events.Multi-parent advanced generation inter-cross?MAGIC?as a new style of mapping population,has abundant genetic makeup and smaller population structure,which can be directly or indirectly applied to the breeding process.Because of these advantages,MAGIC population has been generated in most cereal crops.In this study,we developed a MAGIC population consisting of 248 recombinant inbred lines?RILs?using four elite diverse indica rice varieties.We obtained about 1231431 high quality single-nucleotide polymorphism?SNPs?based on whole genome resequencing,we also conducted genetic diversity analysis,principal component analysis?PCA?and linkage disequilibrium?LD?analysis.Besides that,we conducted a genome-wide analysis?GWAS?with the phenotypic data.In order to further validated the results,association analysis was conducted at the bin level developed by Han Zhongming.We compared the results from two mapping methods and made multi-comparison among the al eles at bin level.The main results were below:1.We sequenced parents with 10 X genome sequence per parent and the population with 2X genome sequence per line through Hiseq-3000 platform.1231431 SNPs were identified with the bioinformational tools of bwa,samtools and vcftools.Using Mendel_Impute software,we filled a vacancy of the genotype data based on the family kinship.2.The phenogenic tree analysis indicated that the MAGIC population had a lower population structure.PCA analysis results showed that the top 10 components together explained only 25% of the sample variance.And there was no stratification phenomenon,namely population structure was not obvious.The LD decay-rate for MAGIC population was faster than the bi-parent mapping populations.3.QTL detecting for three sets of grain shape in two years was conducted by both association mapping at SNP level and at bin level.5 and 4 Q TLs were detected by these two methods with grain length data,respectively.The known genes GS3 and GL3.2 were detected by both methods.And GS3 was confined in bins of size 10 kb by association map at bin level,which harbored the single gene GS3.GL7 was detected by association mapping at SNP level alone.Besides those,two new SNP locis chr03₁9636931 and chr03₂2449318 were detected in all the three environments.The bin B2₂75 and B8₃50 were associated with grain length,and there was no known grain shape gene reported at this locus.With the same two methods,7 and 6 QTLs were detected with grain width data.The known genes GW5 and GL7 were shared with the two methods,GW5 was limited in size to 10 kb bin interval at the bin level.5 newly SNPs were associated only in one environment at SNP level,and 4 newly QTLs were associated at least in two environments in bin level.Interestingly,the new site chr10₁0645936 located very close to the bin of B10₉3 which detected in bin level,regarded as a new QTL.4.Using the phenotype of plant architecture,we conducted GWAS at two methods with plant height,tiller angel and flag leaf angel.Both 4 QTLs were associated with plant height at SNP level and bin level.The cloned gene of TAD1 was associated by both methods,and Psd1 was detected by association mapping at SNP level alone.The new site chr07₂4813588 located in the interval of the bin B10₉3 which detected in bin level with plant height.There were no known plant height genes reported at this locus,so B10₉3 was an new heading date QTL.Corresponding to the two methods in tiller in angle phenotypes,besides these 2 known Q TLs ONAC106 and TAC1 detected in the SNP level,additional one QTL was mapped at bin level,which was close to the QTL of ta9.9 and 2 Q TLs were detected in two methods,respectively.The new site chr07₂1605018 located closely to the bin B7₂10.5.We further made multiple comparisons for the bins of GS3,GW5,TAC1,ONAC106 and B10₉3,B7₂47.Each of these four loci in population was contributed by all the four parents.Confirming the elite alleles and the origin of parent lines may have a significant phenotypic effect on rice grain traits and pant architecture improvements.