| CCRI 48 is a new hybrid variety with the high yield line S9708 as female and big boll mutant S9108 as male bred by Cotton Research Institute of Chinese Academy of Agricultural Sciences.The hybrid with big bolls, good fiber quality and high lint output was accepted by majority of farmers. In this study the above two parents were used to establish a mapping population with 261 F2 population. Based on the linkage maps constructed using this population, some QTLs contralling the boll weight,lint percentage and fiber quality were located, which may be helpful in molecular maker assistied selection of cotton. The fellowing were the main methods and results.1. A total of 4961 pairs of different sources SSR primers were used to screen polymorphism between two parents,86 pairs of them were polymorphic.71 pairs of them with stable amplification and clear bands were used to amplify among the 261 F2 and resulted into 71 polymorphism loci. Thirty three distorted SSR markers including 26 pairs biased to the heterozygote,5 makers distorted to female parent and 2 to male parent were detected, occuping 46.5% among the polymorphic primers including. These distorted segregation maybe resulted from the enviroment factors. With the Joinmap 3.0 software with LOD of 3.0. a total of 48 loci was grouped into 14 linkage groups and covered 498.7cM, approximately 10.0% of the total recombinational length of the cotton genome.13 groups have been anchored to the chromosomes.2. A total of 11 stable QTLs.2 for boll weight.4 for lint percentage and 5 for fiber quality including 2 for fiber uniform.2 for micronaire and 1 for fiber elongation, were detected in F2 population of CCRI48. By Complex Interval Mapping (CIM) method with the software of Win QTL Cartographer 2.5. The QTLs for fiber length and fiber strength were not detected. The stable QTLs with greater phenotypic variations could be used for maker assisted selection for yield and fiber quality. Two lint percentage QTL (qLP1-2,qLP3-1). one QTL for boll weight (qBW1-1) and one for fiber uniformity (qLU1-1) were closely linked with the SSR markers NAU3903. BNL2960, BNL3502 and BNL4082 respectively with a distance of 0.3-3cM which could be used as molecular marker assisted breeding. 3. CCRI 48 and its parents were amplified with 25 pairs of core primers which had been screened by our lab. Digital fingerprint of CCRI 48 was constructed with the amplification result by changing binary system into decimal system. It provides a method for seed genuineness and purity detection of hybrids.4. Six F2 populations with same female parent as that of CCRI 48 and different male parents with different boll weight were planted in 2005 and 2006. Traits of boll weight, lint percentage and fiber quality in these populations were analyzed by using SAS 8.0 software.The result showed:All fiber traits were highly significant in all F2 populations. The coefficient of variation for boll weight and micronaire was the lighest which was 15-20% among the 6 populations. It indicated boll weight and fiber micronaire had a greater degree of genetic variation. The second greater variation was lint percentage and fiber strength with the variation coefficient of 6-9%. While the variation coefficients of fiber length, elongation and fiber uniformity was less.5. The result also showed that the average boll weight and lint percentage of F2 population were determined by the male parent sincce the same female parent. The larger was the boll weight and lint percentage of the male parent, the greater was that in their offspring, vice versa. The average fiber quality in F2 has little different, but the variation range in F2 was larger. So the selection method for offspring of boll weight, lint percentage and fiber quality should be different. The elite characters of bigger bolls, higher lint percentage, longer and stronger fiber etc. of the parent was still performed. Therefore, it is important to select the germplasm with big boll, high lint percentage, better fiber quaity during the procession of parent selection in the heterosis.
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