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Comparing to white cotton, the colored cotton has the disadvantages of bad quality, lower specific fiber strength, shorter fiber length, etc. Although domestic and international of experts cotton breeding have done a lot of work in selecting and improving the breed of colored cotton, up to now, there are still some differences in yield and quality between colored cotton and white cotton, and it is difficult to achieve breakthrough progress by common breeding methods, because it is hard to break the negative correlation between color and velvet length.Therefore, by marking the genetic differences between colored cotton and white cotton , we could provide some information for reference for breeding of new colored cotton cultivars and use the colored cotton resources reasonably.Genetic difference analysis between Colored Cotton and White Cotton by SRAP markers and Morphologica markers, the main results were followed:1. Analysis on the 10 morphological characters of the 30 spices of cotton materials showed that the average coefficient variation was 19.57%,the biggest was the number of fruit(27.83%), and the smallest was growth period of boll abscission(6.35%). The cluster analysis of morphological character showed that the 30 spices of cotton materials could be divided into 7 groups: there were 6 in the first group and only one white cotton, 10 in the second group, there were 6 colored cotton in the third group, there was 1 colord cotton in the forth、sixth、seventh group, there were 5 white cotton in the fifth.2. To gain a suitable system for SRAP marker method of cotton, the experimental profile and parameters were optimized. The optimal reaction system was as follows: 25reaction system containing 30ng template, 10mmol/L primers 1.5 l, 10mmol/L dNTPs0.5 l, 25mmol/L Mg2+ 2.0 l, Taq polymerase 0.2 l. The optimal amplificationprogram was as follows: 5min at 94oC, followed by 94oC for 1min, 35oC for 1min, 72oCfor 1min, 5 cycles, 1min at 94oC, 50oC for 1min, 35 cycles, and final extension time for7min at 72oC.3. A total of 1067 amplified fragments and 132 polymorphic framents were detectedby applying 29 SRAP primer combinations. The polymorphic fragment percentage was14.1%. The number of amplified fragments and polymorphic fragments per primercombination were 36.8 and 4.55 respectively. 30 spices of cotton materials were dividedintoⅠandⅡat genetic distance of 0.65, 28 spices of cotton materials were classified intogroupⅠ. GroupⅠcould also be divided into A、B sub-groups at genetic distance of0.72. There were 19 in the A subgroup and 9 in the B subgroup. 4. By comparing the two clustering results of morphology and SRAP, we found that, the genetic relationship of colored cotton Brown1-61 and white cotton Huakang-6 which morphological trait index of the cultivars are the best among all the observed cotton material is distant according to the result of morphology clustering and SRAP clustering. Similarly, the genetic relationship is far betwwen corlored cotton Zongcaixuan-1 and MeiV81-052, and they have good morphological trait too. As a result, we could conclude that we may recombinent the good traits of the parents and breed new cultivars by distant hybridization between the four cultivars, which could promote the breeding of new colored cotton cultivars and use colored cotton resources reasonably.
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