| Rice(Oryza sativa L.)is one of the largest crops in China.With the improvement of people’s living standard,the cultivation of high yield and high quality has become an important goal of breeding in the world.The grain appearance and milling quality are typical quantitative traits,which are controlled by genes and environment.So far,some important QTL loci and genes about rice appearance and milling quality have been cloned by different populations and analysis methods,but few applied to the rice breeding practice.The germplasm resources have abundant favorable alleles and the genome-wide association analysis based on the rich variation of germplasm resources is a popular analysis method in the present.However,there are few studies on the grain appearance and milling quality traits.In this study,we carried out an association analysis to identify QTL affecting eight rice grain appearance and milling quality related traits including brown rice rate,milled rice rate,head milled rice rate,grain length,grain width,grain length to width ratio,the percentage of grains with chalkiness and degree of endosperm chalkiness using the 404 k SNP genotype and a diverse panel consisting of 732 accessions selected from 3k Rice Genome Project and evaluated in two environments Sanya and Shenzhen,China,respectively.The main conclusions are as follows:1.732 materials from 56 countries or regions have abundant phenotypic variation.In Hainan,the phenotype of brown rice rate(BRR)ranged from 75.01% to 84.96%,the milled rice rate(MRR)ranged from 53.24% to 74.31%,the head milled rice rate(HMRR)ranged from 34.04% to 73.93%,the grain length(GL)range from 3.44 mm to 7.51 mm,the grain width(GW)ranged from 1.64 mm to 3.01 mm,the grain length to width ratio(GLWR)ranged from 1.41 to 3.62,the percentage of grains with chalkiness(PGWC)ranged from 3.61% to 100% and the degree of endosperm(DEC)chalkiness ranged from 0.38% to 79.03%.In Shenzhen,the BRR ranged from 59.18% to 91.21%,the MRR ranged from 47.81% to 81.35%,the HMRR range from 30.13% to 71.69%,the GL ranged from 3.90 mm to 7.38 mm,the GW ranged from 1.59 mm to 3.16 mm,the GLWR ranged from 1.52 to 3.68,the PGWC ranged from 17.86% to 100% and the DEC ranged from 3.52% to 83.07%.2.The correlation analysis between different traits showed that the correlation between appearance and milling quality was stable in different environments,and the correlation between different types of traits was complicated.Grain length and grain width were closely related to the two milling quality traits(BRR and HMRR),which was a significant correlation in two environments.The correlation between grain shape and appearance quality was relatively stable and not affected by environment,which performed long grain decreased the chalkiness and the grain width increased the chalkiness.The BRR has no relationship about chalkiness,but the MRR had a significant negative correlation with chalkiness.3.The mapping results showed that there were 48,67 and 77 QTL in indica rice,japonica rice and total samples,respectively.Among which 13,16 and 15 QTLs were detected in two environments from above groupand 37,41 and 51 QTLs were new loci.Among the new loci,9 QTLs of them were detected in two environments,including qB RR1.1,qG L1,qGLWR2,qG L12,qG LWR6,qP GWC5,qG W6,qDEC11.2 and qH MRR11.And 21 new loci were expressed in two or more populations,including 3 QTLs were detected in the indica and japonica populations,5 QTLs identified respectively in the indica and total populations as well as the same in the japonica and total populations.4.In the indica populations,the qG L1 is in the region of 41752290-42069152 bp on 1 chromosome by fine-mapping,about 316 kb.And the qB RR1.2 was also located in the interval,indicating that this 2 QTL may be affected by the same gene.Through finemapping,the qG LWR2 is located in 21181849-21191798 bp interval on 2 chromosome,about 9.9 kb.The qD EC11.2 was fine-mapped in the region of 28778120-28899327 on 11 chromosome,about 121 kb,and the qPGWC11.3 overlap with this interval among all samples.5.There was a pleiotropic effect of locus or gene for controlling rice appearance and processing quality,such as qG L12,qG LWR6,qP GWC5.3 and qG W6 in the new loci.In the known loci,the most important is 5007414-5887782 bp interval on 5 chromosome which GW5 / qSW5 and GSE5 genes located on.The region plays an important role in grain shape and chalkiness. |
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