Genome-wide Association Analysis Of Rice Some Agronomic And Quality Traits Based On MAGIC Population

Rice(Oryza sativa L.)is one of the most important food crops in the world,feeding more than half of the world ’s population.Many important agronomic traits quality traits of rice,such as heading date,yield,and grain shape and chalkiness,are complex quantitative traits controlled by multiple genes and are affected by the environment.To explore the relevant trait loci and their associated markers of rice agronomic and rice appearance varieties,to screen important germplasm carrying a large number of excellent alleles,and to select high-yielding,high-quality varieties through the marker-assisted selective(MAS)method.It is the most economical and effective way to improve rice yield and quality.In this study,a group of eight-parent Advanced Generation Inter-Crosses population(MAGIC)and eight parents were used as materials.They were planted in Changsha,Hunan,for two consecutive years in 2017 and 2018.Yield traits and rice appearance quality phenotype survey,based on genotyping by sequencing(GBS),Genome-wide association analysis(GWAS)was conducted to discover the effects of rice sowing duration and yield traits(effective per plant)QTL(Quantitative trait loci,QTL)such as number of panicles,number of grains per panicle,seed setting rate,thousand-grain weight and yield per plant)and rice appearance quality(grain length,grain width,grain length-width ratio,chalkiness of endosperm and percentage of grain with chalkiness).The main findings are as follows:1.In the two years of this study,a total of 6 QTLs for controlling the the sowing-to-heading days were detected,located on chromosomes 2,3,6,7,8 and 12,respectively,and four QTLs were located in both years(QHD3,q HD6,q HD7,and q HD8)cover the cloned genes Oscp SRP43,HGW,GHD7.1,and DTH8 respectively,and the other two QTLs(q HD2,q HD12)that are significantly associated with the rice seeding period may be new sites.A total of 20 QTLs controlling yield traits were detected in two years,including the number of effective ears per plant,number of grains per ear,seed setting rate,thousand-grain weight,and yield per plant were 3,4,3,5,and 5,respectively.Among them,there are cloned genes in or near 11 mapping intervals,and 9 QTLs(q NTP7,q NTP9,q GNP1.2,q SR9,q GW7,q YD1.2,q YD7,q YD11 and q YD12)that are significantly associated with rice yield traits are new location.The locus q NTP9,which is significantly associated with the number of grains per ear,was located in the 12 M-14 Mb interval on chromosome 9 and was detected in two years,indicating that the locus is less affected by the environment and can be used for further refinement location and gene cloning.2.A total of 16 QTLs controlling rice appearance quality traits were detected in two years,including the number of grain length,grain width,grain length-width ratio,chalkiness of endosperm and percentage of grain with chalkiness were 3,3,2,4,and 4,respectively.Among them,there are cloned genes in or near 8 mapping intervals,and8 QTLs(q GL3.2、q DEC1、q DEC2、q DEC4、q DEC7、qCR1、qCR2 和 qCR7)that are significantly associated with rice appearance quality traits are new location.The locus q GL3.2 significantly associated with the grain length and the locus q DEC1 and qDEC2 significantly associated with chalkiness of endosperm,were detected in two years,indicating that the locus is less affected by the environment and can be used for further refinement location and gene cloning.3.According to the correlation analysis results of this experiment,combined with the phenotypic data of the experiment and SNP genotype,five double-gene aggregated lines of the sowing-to-heading days and yield traits were selected,namely GID4170482,GID4172993,GID4173982,GID4173992 and GID4171060;three excellent rice linescarrying more favorable alleles were selected,namely GID4171776,GID4172677,and GID4172985 respectively;three high-yielding and low-chalkiness lines were screened,namely GID4173717,GID4170433,and GID4172349,which can be used for future ricebreeding.