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The Japanese murrelet ( Synthliboramphus wumizusume ) is an endangered small seabird species in Japan. Molecular sexing using PCR targeting of the gene encoding  chromodomain helicase DNA-binding protein 1 ( CHD1 ) has been used for sex identification. Specifically, PCR using any of three commonly used primer sets (CHD1F/1R, 2550F/2718R and P2/P8) has permitted sexing in many bird species. CHD1F/1R and 2550F/2718R permitted molecular sexing in Japanese murrelet; however, P2/P8 did not permit. To generate a primer pair that permits efficient molecular sexing in this species, a new primer set, CHD1F1/1R1, was prepared to permit amplification of smaller products from degraded DNA samples. The electrophoretic patterns of PCR products amplified with the new primer set were easily classified as female or male. Additionally, the PCR product indicated the presence of a polymorphism in the fragment from chromosome W. The PCR fragments of long-type (WL) and short-type (WS) polymorphisms were observed only in females. When the distribution of the  CHD1  gene on chromosome W of 61 female Japanese murrelet on Biroujima Island in Miyazaki Prefecture, WL and WS were observed in 90.2% and 9.8%. The DNA polymorphism is derived from the number of copies of a 32-bp-repeat unit, with WL and WS corresponding to two and one 32-bp-repeats, respectively.

Molecular sexing in Japanese murrelet (Synthliboramphus wumizusume) and a tandem-repeat polymorphism on the W chromosome