| Rice is one of the most important staple crops in the world.With the increase of the living standard,people have paid more and more attention on rice quality.The Yangtze River Basin is a most important rice production area in China,and most rice in this area is cultivated in middle season.In recent years,middle season rice in this area has been largely affected by high temperature during flowering and filling stage,resulting in loss of rice yield and poor rice quality.Higher temperature during filling stage mainly leads to decrease of thousand grain weight and head milled rice rate,and increase of percentage of grains with chalkiness and chalkiness degree.Thus,it’s urgent to dissect the genetic basis of rice heat tolerance during filling quality,and breed elite varieties with heat tolerance and high quality at both high and normal temperature conditions.In the present study,a set of rice germplasm consisting of 388 varieties from 3K RGP were evaluated their thousand grain weight,head milled rice rate,percentage of grains with chalkiness and chalkiness degree under both high and normal temperature conditions during filling stage across 2021 and 2022 at Jinghzou,to investigate their heat tolerance ability.Then,combined with high-density genotypes data,genome-wide association strategy was used to identify QTL for rice heat tolerance during filling stage.Finally,candidate genes and favorable alleles were mined by association at candidate regions and haplotypes analysis.The main results are as follows:(1)The rice germplasm was divided into three subpopulations,and there were196,165 and 27 varieties in indica,japonica and Aus,respevtively.(2)There were large variations of thousand grain weight,head milled rice rate,percentage of grains with chalkiness and chalkiness degree under both high and normal temperature conditions.Among them,chalkiness had largest variations,and variation of head milled rice was larger than thousand grain weight.Moreover,ratio of thousand grain weight rate and ratio of head milled rice rate were below 1.00,while ratio of percentage of grains with chalkiness and ratio of chalkiness degree were above 1.00,indicating that high temperature during filling stage leads to decrease of thousand grain weight and head milled rice rate,and increase of percentage of grains with chalkiness and chalkiness degree.(3)The appearance quality of Aus varieties from South Asia was excellent under both high and normal temperature,while they had low thousand geain weight and milling quality.The appearance quality of indica was more stable than japonica under both high and normal temperature conditions.Indica rice from East Asia had poor appearance quality.(4)Three Aus varieties with good quality and heat tolerant at filling stage were mined.They come from India and Bangladesh.Their head milled rice were all above50%,percentage of grains with chalkiness and chalkiness degree were 0.Most importantly,the ratios of four traits between high temperature and normal temperature conditions were between 0.8-1.2,which means they were heat tolerant during filling stage.(4)Correlations of the same trait between high and normal temperature conditions were significantly positive,while there were low or even no correlations among thousand grain weight,head milled rice rate and chalkiness.The reults suggested that there were low genetic overlaps among these three traits.(6)A total of 41 QTLs on all 12 chromosomes for thousand grain weight were identified using genome-wide association strategy,which explained 0.18% to 15.07%of phenotypic variations.Of them,the region of 21 Mb on chromosome 8simultaneously affected thousand grain weight under both high and normal temperature conditions.Two regions of 39.59-39.76 Mb on chromosome 1 and 20 Mb on chromosome 2 controlled both thousand grain weight under normal temperature condition and ratio of thousand grain weight.(7)A total of 68 QTLs on all 12 chromosomes for head milled rice rate were identified,which explained 0.11% to 15.44% of phenotypic variations.Of them,ten regions of 10.39 Mb and 32.26 Mb on chromosome 1,0.12-0.22 Mb,19.73 Mb and32.61-32.80 Mb on chromosome 2,8.90-8.95 Mb on chromosome 6,1.51-1.56 Mb and26.72-27.80 Mb on chromosome 8,17.41-18.06 Mb on chromosome 10 and23.83-24.93 Mb on chromosome 11 simultaneously affected head milled rice rate under both high and normal temperature conditions.Two regions of 1.14-1.52 Mb on chromosome 1 and 14.59-15.37 Mb on chromosome 7 controlled both head milled rice rate under normal temperature condition and ratio of head milled rice rate.16.43-18.15 Mb on chromosome 9 controlled all of head milled rice rate under high and normal temperature conditions and ratio of head milled rice rate.(8)A total of 46 QTLs on all 12 chromosomes for percentage of grains with chalkiness were identified,which explained 0.13% to 13.10% of phenotypic variations.Of them,four regions of 27.78-27.89 Mb on chromosome 1,20.11-20.69 Mb on chromosome 4,19.13-19.65 Mb on chromosome 8 and 16.38-17.69 on chromosome 9 simultaneously affected percentage of grains with chalkiness under both high and normal temperature conditions.Two regions of 16.60-16.62 Mb on chromosome 5 and 23.44-23.64 Mb on chromosome 11 controlled both percentage of grains with chalkiness under normal temperature condition and ratio of percentage of grains with chalkiness.(9)A total of 34 QTLs on 11 chromosomes except chromosome 11 for chalkiness degree were identified,which explained 0.32% to 15.53% of phenotypic variations.Of them,three regions of 3.77-3.81 Mb on chromosome 3,32.06-32.18 Mb on chromosome 4 and 6.17 Mb on chromosome 8 simultaneously affected chalkiness degree under both high and normal temperature conditions.28.14-29.96 Mb on chromosome1 controlled both chalkiness degree under normal temperature condition and ratio of chalkiness degree.(10)A total of 32 QTL regions affected different quality traits.Of them,6 QTL regions on chromosome 2,4,5,8,and 11 simultaneously affected thousand grain weight and head milled rice rate,9 QTL regions on chromosome 2,3,6,7,8 and 10 affected both thousand grain weight and chalkiness,9 QTL regions on chromosome 4,7,8,9,10 and 11 controlled both head milled rice rate and chalkiness,7 QTL regions on chromosome1,5,8,10,11 and 12 had pleiotropic effects on both percentage of grains with chalkiness and chalkiness degree.(11)Using association analysis in candidate regions and haplotype analysis,a total of 37 candidate genes at 6 QTL regions on chromosome 1,3,5,8 and 11 were identified,and 37 favorable alleles were mined. |
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