| Onion (Allium cepa L.) is a biennial vegetable. It is widely grown throughout the world and known as the queen of vegetables. China posses the largest production area and output quantity of onions in the world, which occupy above 30% of the world (FAO,2008). It is well known, analysising genetic diversity is a helpful method to comprehend the relationship among the onion breeding lines, and it is also a foundational work for improvement onion variety. Onion is main sources of food to obtain flavonoids for human. Flavonoids have an important impact on human health. It has extensive biological activity and important medicinal value,such as preventing cardiovascular disease,antitumor,anti-free radical, antioxidation, anallergies, antiphlogistic, antivirusand so on.Therefore bioflavonoids has aroused wide attention of scholars at home and abroad and become a hot spot in research and development. Due to the different colors (red skin, yellow skin, white skin) breed, flavonols content in onions change greatly.The red skin varieties is obviously higher than white and yellow.The research of Chalcone synthase is the basis of studying skeleton formation in flavonoid. which regulating many physiological and biochemical processes such as the plant's pigment synthesis, defense responses, fertility and so on. In this research we studied the genetic diversity of onion germplasm and analyze the result of Chalcone synthase after being cloned and sequenced.The summarized results are as fllows:1. sequence related amplified polymorphism (SRAP) markers were employed to analyze the genetic diversity of onion varieties. 44 germplasm of onion were analyzed by 12 highly polymorphic and stable primer pairs selected form 462 pairs of SRAP primer. A total of 103 SRAP bands were obtained including 90 polymorphic ones. The percentage of polymorphic bands is 87.38%, and the average polymorphism bands were 7.5 per primer pairs. The results demonstrated that SRAP had higher polymorphism in the tested onion varieties. Based on cluster analysis with the SRAP makers, the genetic distance range among the tested 44 varieties was form 0.1591 to 0.4116. At the genetic distance of 0.36, 44 varieties were clustered into 4 main groups, and 36 varieties were clustered into 1 group,which demonstrated the inheritance variation of the 44 germplasm of onion was low,and inheritance background is narrow in onion.2. Two chalcone synthase genes AcCHS1 and AcCHS2 were isolated from onionBLAST analysis indicates that both genes have unabridged open reading frames(ORFs).The ORF of AcCHS1 gene contained 1182 bp encoding a protein of 393 aminoacids and ORF of AcCHS2 gene contained 1176 bp encoding a protein of 391 aminoacids . Comparison of the nucleotide sequences of AcCHS1 with AcCHS2 showed thatheir homology is 78.43% . Comparison of the amino acids sequences of the two geneswith the corresponding CHS protein of rice and Arabidopsis showed they are highlyconserved, including all amino acids resides of activity center (AcCHS1:Cys166, Phe217His305, Asn338; AcCHS2 Cys164, Phe215, His303, Asn336). To investigate theexpressions of the two genes in different onions (different bulb color with differenfertility), RT-PCR method were employed.The results indicated that the AcCHS2 geneexpression is obviously higher than AcCHS1.
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