Chinas production of indica hybrid rice accounts for more than 16 million hectares peryear, which makes up 52％ of the total cultivated rice area.Japonica rice cultivation onlycovers 8.28 million hectares per annum making up another 27％ of the total rice acreage.Japonica hybrid rice acreage is 3％ of the total japonica rice acreage as compared to indicahybrid rice.Main reasons for the slow development of hybrid japonica rice were due to itsproperties of weaker competitive advantages and lower seed production.Improvement ofhybrid japonica rice lines is very critical in China as there are reasonable comparativeadvantage between indica rice production and japonica rice production.Although researchon the utilization of heterosis in rice has made tremendous gains during the last 30 years, itis, from a strategic point of view, still in its infancy because the outcrossing characteristicpotential has not been fully tapped yet.Improving japonica seed production is very vital inChina.In order for higher seed productions in japonica rice, characteristics of out-crossingrelated traits in rice must be well studied and understood.A variety with good stigma traitsand good architectural traits would have an advantage of giving high and stable F1 seedproduction yield.Therefore, genetic and breeding studies at this level provide a platform forincrease hybrid japonica seeds production.
　　For the experiment on the evaluation procedure, a total of 462 different rice varieties fromTaihu Lake and other areas were used as testing materials.Investigative study was done onthe following traits: flag leaf angle, filament length, stigma length, anther length andpercentage exerted stigma.For the genotyping, 263 SSR molecular markers coveting the 12chromosomes of rice were used to screen the 462 rice varieties.TASSEL software GeneralLinear Model (GLM) was used to identify association between markers and traits.Theresults obtained are as follows:
　　(1) Percentage Exerted Stigma recorded the highest co-efficient of variation with90.49％ in 2011.This was followed by flag leaf angle with a co-efficientvariation of 49.09％ in 2011 and 48.09％ in 2012.
　　(2) In analysis of genetic diversity, 263 SSR molecular markers detected a total of730 alleles.The number of alleles varied from 2 to 25 with an overall mean of9.35 alleles per locus indicating polymorphism within the population.Theaverage genetic diversity is 0.0832 and the genetic diversity ranged from 0.009to 0.2015.Polymorphic Information Content (PIC) values ranged from 0.0269to 0.9329 with an average value of 0.699.
　　(3) Analysis of population structure revealed that 5 sub-population existed in thetotal population of 462 varieties.
　　(4) SSR molecular markers detected 730 alleles.
　　(5) Flag leaf angle has 3 SSR loci associated with the trait in both 2011 and 2012.They are RM212, RM5951, and RM405.RM212 was associated with allelesRM212-120 in both 2011 and 2012.Their ai was 0.941 and 0.948 respectively.The carrier varieties were found to be mudanjiang27 and ligengqing.Thelargest allele effect ai was 0.94 identifying ligengqing.RM5951 was associatedwith alleles RM5951-75 and RM5951-80 in 2011 and 2012 but associated withallele RM5951-100 only in 2012.The ai for RM5951-71 was 3.608 (2011) andRM5951-71 was 3.611 (2012).RM5951-100 ai Was 0.1.The allele with thelargest effect is RM5951-80 and the variety identified was longdao6.RM405was associated with alleles RM405-95, RM405-110, RM405-115 and RM405-150.The allele with the largest ai effect was RM405-110 identifying the carriervariety mudanjiang27.In all, allele RM5951-80 has the largest ai effect of4.067 reasonably above all other alleles in flag leaf angle, thus identifyinglongdao6 as the elite cartier variety.
　　Stigma length has 3 SSR loci associated with the trait in both 2011 and 2012.They are RM129, RM140 and RM212.RM129 is associated with RM129-90.The largest allele effect ai value of allele RM129-90 is 0.062 identifyingzhonghua3 as the carrier variety.RM140 is associated with alleles RM140-265,RM140-270 and RM140-285.Allele RM140-285 has the largest allele effectidentifying yue82 (17.11-2) as the carrier variety.RM212 is associated withalleles RM212-80 and RM212-135.RM212-80 has the largest ai effectidentifying zhonghua3 as the carrier variety.In all, RM140-285 has the largestai of all other alleles in SL thus identifying yue82 (17.11-2) as the carriervariety.
　　Anther length has 3 SSR loci associated with the trait in both 2011 and 2012.They are RM129, RM545 and RM212.RM129 was associated with alleleRM129-190 and RM129-105.Allele Rm129-190 has the larger ai valueidentifying carrier variety kuobanzhong.RM545 was associated with allelesRM545-175, RM545-180 and RM545-185.RM545-185 has the larger ai effectidentifying variety zijianwujing.RM212 was associated with alleles RM212-80 and RM212-135.RM212-135 has the higher ai of 0.068 identifying carriervariety yue36 (17.10-1).In all, allele RM545-185 has the largest ai effect of allother alleles in anther length thus identifying zijianwujing as the carrier variety.
　　In filament length, there were no identical SSR loci markers associated with thetrait both in 2011 and including 2012.However, 8 SSR loci markers wereassociated independently in two years.The alleles found to be associatedinclude RM269-170, RM269-175, RM269-180, RM280-100, RM280-175,RM129-190, RM7163-225, RM437-275, RM545-175, RM545-185, RM433-185,and RM304-135.The elite of all alleles with the largest ai was RM545-185which identified the cartier variety zijianwujing.
　　Percentage exerted stigma have 5 SSR loci associated with the trait.The allelesin association were RM159-150, RM159-230, RM159-240, RM159-250,RM159-255, RM159-260, RM225-115, RM225-225, RM225-235, RM281-115,RM281-130, RM259-155 RM281-285, RM259-135, RM259-145 and RM281-220.Allele RM281-115 has the largest ai effect identifying Chiguhong as thecarrier variety.