|Abstract: ||水晶蝦（Caridina cantonensis）因其鮮豔的體色和多變的條紋表現而廣受水族市場歡迎，在台灣觀賞水族產業重要的經濟物種。然而過往對觀賞蝦的顯色調節和代謝機制的研究較少，顯色成因仍須進一步探討。現今商業模式中，繁殖業者仍依循傳統選育的道路，並產業升級成分子標記輔助選育及系統化育種管理。故不論是學術或是產業中，水晶蝦的分子輔助選育都極具發展潛力。 本研究構建了四種水晶蝦品系的轉錄組數據庫，包括紅白水晶蝦純系（Pure Crystal Red Shrimp，PR）、黑白水晶蝦純系（Pure Crystal Black Shrimp，PB）、紅白金水晶蝦（Crystal Red Golden Shrimp，RG）及金蝦（Golden Bee Shrimp，GS）純系等四個品系，並以紅白水晶蝦純系、黑白水晶蝦純系、紅白金水晶蝦純系三組轉錄體進行比較。在比較的三組轉錄體中，共有82,471個具差異表現的Unigenes，其中有12,125個Unigenes被註釋到六大資料庫且具有微衛星序列。通過差異表現基因比較以PR對PB（PR/PB）和RG對PB（RG/PB）兩組比對組，以差異表現量篩選微衛星標記，設計出13組微衛星引子；並參考相關研究中的顯色相關基因後，對轉錄體進行註釋的結果篩選微衛星標記，設計出17組微衛星引子。並且進一步使用來自三個不同來源的紅白（n = 75）和黑白（n = 75）共6組水晶蝦進行微衛星標記基因型分析。共有9組標記的基因頻率在紅白與黑白群間顯示出顯著差異（p <0.05），有4組為差異表現量篩選之微衛星標記，另外5組標記Ug40579、Ug40269、Ug2427、CL6891_2、Ug19742則與顯色相關基因APOD、CYP450和ABCG相關。透過本研究開發的功能性微衛星分子標記，有助於優質水晶蝦種苗的選育，還可以幫助繁殖業者在選育高等級商業蝦種及新品系開發，並對甲殼類的顯色相關研究提供重要的參考依據。|
The crystal shrimp (Caridina cantonensis) is widely welcomed by the aquarium market for its bright body color and varied stripes, and it is an important economic species in the aquarium industry in Taiwan. However, there were only few studies on the color regulation and metabolic mechanism of ornamental shrimp in the past, and the cause of color development still needs further investigation. In today's business model, breeders continue to follow the path of traditional breeding methods, and upgrade the sub-marker-assisted selection and systematic breeding management. Therefore, whether it is in academy or industry, the molecular-assisted breeding of crystal shrimp has great potential.This study constructed a transcriptome database of four crystal shrimp strains, including Pure Crystal-Red Shrimp (PR), Pure Crystal-Black Shrimp (PB), and Crystal Red-Golden Shrimp (RG) and Golden Bee Shrimp (GS) pure line and other four lines. By comparing red-crystal shrimp strain, black-crystal shrimp strain and red-gold-crystal shrimp strain three groups of transcriptomes, there were 82,471 differentially expressed Unigenes, of which 12,125 Unigenes were annotated into six databases and had microsatellite sequences.By comparing the differentially expressed genes of PR with PB (PR/PB) and RG with PB (RG/PB) two groups, the microsatellite markers were screened by differential expression, and 13 microsatellite primers were designed. By referring researches of color-related gene, the microsatellite markers were screened for the annotation of the transcripts, and 17 microsatellite primers were designed. Furthermore, microsatellite genotype analysis was performed using a total of 6 sets of crystal shrimp from red crystal (n = 75) and black crystal (n = 75) from three different sources. The frequency of the gene with 9 groups of markers showed significant difference between red crystal and black crystal groups (p <0.05), 4 groups were microsatellite markers for differential expression screening, and 5 groups were labeled Ug40579, Ug40269, Ug2427, CL6891_2, Ug19742. Related to the color-related genes APOD, CYP450 and ABCG.The functional microsatellite molecular markers developed in this study will help the breeding of high quality crystal shrimp seedlings, and also help breeders to develop high-grade commercial shrimp species and new strains, and to study the color development of crustaceans. Provide an important reference.