臺灣水鹿 (Rusa unicolor swinhoei) 為臺灣特有亞種，有 63 條染色體，原棲息於臺灣山區林地，現以民間圈養為主。鹿茸 (velvet antler) 供食用歷史已久，且為我國養鹿產業主要收入來源。本試驗旨在估計臺灣水鹿產茸相關遺傳參數，並發展產茸相關基因檢測平台。試驗I：應用 2003 至 2015 年間出生之 62 頭臺灣水鹿 184 筆剪茸紀錄，以動物模式-限制性最大似然法進行茸重累加性遺傳、永久環境與殘差變方-共變方估計後，預測茸鹿產茸育種價。臺灣水鹿產茸能力具高遺傳性與重複性，遺傳變異率與重複勢估值分別為 0.488 與 0.735；其中父方影響效應約為母方兩倍。同時，年改進趨勢評估顯示，茸重表型改進量較遺傳改進大；此可能係因飼養管理提升與鹿農主觀式留種所致。試驗II：依白尾鹿基因序列設計七組引子，進行臺灣水鹿 ALYREF 基因序列解碼。完成臺灣水鹿該基因序列串接，全長共 3,432 bp；並已登錄於 NCBI GenBank 基因組核苷酸資料庫，登錄號 MN006827 (Accession number)。本研究發現臺灣水鹿 ALYREF 基因七個點突變，其中五個具多態性。進一步比較五個多態性位點之不同基因型對其產茸性能之影響發現：ALYREF-in2-C910T 顯著影響三至五歲齡茸重，且 TT 為有利基因型。ALYREF-in2-A1381G 與 ALYREF-in5-C2922T 組合基因型中，GGCC 基因型茸鹿有顯著較重茸重。同時，ALYREF-in2-C910T、ALYREF-in2-A1381G 與 ALYREF-in5-C2922T 三個多態性位點之不同組合基因型茸鹿產茸量比較顯示，具 TTGGCC 基因型之茸鹿有最佳產茸量。綜合言之，鹿茸重屬於高度遺傳與重複性狀，預期個體選拔且輔以標記選拔應可有效地提升臺灣水鹿產茸量與提升養鹿產業競爭力。

Formosan sambar (Rusa unicolor swinhoei) is an endemic subspecies of Taiwan with 63 of chromosome. Although Formosan sambar were originally inhabited in the woodlands of mountain areas in Taiwan, they are now mainly in captivity by farmers. Velvet antler has been used for over thousands of year as tonic in traditional Chinese medicine, which is the main source of income for the deer industry in Taiwan. The objectives of this study were to estimate genetic parameters related to velvet antler production of Formosan sambar, and to develop a genotyping platform for marker genes related to antler production. Experiment I: A total of 184 antler velvet weight (AVW) records from 62 bucks born during 2003 and 2015 was used for analysis. Animal model-restricted maximum likelihood method was used to estimate the additive genetic, permanent environment, and residual variance-covariance components, and breeding value of velvet antler weight was then predicted. Velvet antler weight was high heritable and repeatable with estimates of heritability and repeatability being 0.488 and 0.735, respectively. The paternal effect (sire) was about twice that of the maternal (dam). Furthermore, the evolution of phenotype and genotype indicated more progress was shown in phenotype than that of genotype, which might be due to the improvement of management, including feeds and feeding, and no selection conducted during the years. Experiment II: Seven sets of primers based on the whitetail deer gene sequence were used to decode the ALYREF gene of Formosan sambar. Whole sequence of ALYREF gene for Formosan sambar was concatenated completely with a total length of 3,432 bp; and registered in the NCBI GenBank genomic nucleotide database, accession number MN006827. Seven point mutations were observed in ALYREF gene of Formosan sambar with five polymorphic sites. Effects of ALYREF-in2-C910T polymorphism on velvet antler weight showed TT genotype was the favorable one. Also, genotype combination of GGCC was preferred when ALYREF-in2-A1381G and ALYREF-in5-C2922T were evaluated jointly. Moreover, TTGGCC was the most favorable genotype combination for velvet antler weight when three polymorphism sites were considered. In conclusions, velvet antler weight of Formosan sambar was a highly inherited and repetitive trait, and thus mass selection could be effective. Also, significant ALYREF gene polymorphic effects showed marker assisted selection incorporated into breeding program should effectively increase the velvet antler production and enhance the competitiveness of the Taiwan’s deer industry.

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