青花菜(Brassica oleracea var. italica Plenck)與花椰菜(B. oleracea var. botrytis L.)二種十字花科蔬菜因其缺乏足夠的分子標誌，難以進行遺傳連鎖分析與分子輔助育種的研究。本研究為建立B. oleracea 的分子輔助育種研究及品種鑑定良好基礎，將來自蕓苔屬內四個物種的402 個簡單重複序列(SSR, Simple Sequence Repeat)分子標誌及阿拉伯芥100 個內含子多型性(IP, Intron Polymorphism)分子標誌應用於青花菜和花椰菜之多型性與親緣關係研究。SSR 分子標誌來自AA、BB、CC 和AACC基因體等不同物種之成功擴增率分別為69.4%、80%、83.6%和87.2%，可見來自與
B. oleracea 同為CC 基因體物種之SSR 分子標誌之轉移力較高。IP 分子標誌之成功擴增率為96%，故依IP 分子標誌之轉移力高於SSR 分子標誌，且IP 多型性比例63.5%)較SSR 分子標誌(54.4%)高。有58.3%的IP 分子標誌及81%的SSR 分子標誌偵測到一個基因座，而41.7%的IP 分子標誌及19%的SSR 分子標誌偵測出兩個以上基因座；推測有基因體雙倍化的現象。利用多型性分子標誌分析12 個青花菜品系及12 個花椰菜品系間之親緣關係之結果，顯示本研究所篩選之多型性分子標誌可成功將青花菜與花椰菜兩變種分群，且花椰菜的遺傳相似度高於青花菜。在本研究中觀察到蕓苔屬物種間之分子標誌具有高轉移力，可將其應用在分子標誌缺乏之其他物種研究上，而所得之多型性分子標誌，可於日後應用在種原親緣關係分析、品種鑑定、構築遺傳連鎖圖譜、基因定位及分子輔助育種。

Broccoli (Brassica oleracea var. italica Plenck) and cauliflower (B. oleracea var. botrytis L.), the two important flower vegetables in Taiwan, were in short of molecular markers for linkage analysis, gene mapping and marker-assisted selection in breeding programs. Therefore, we applied 402 SSR (Simple Sequence Repeat) markers from four Brassica species and 100 IP (Intron Polymorphism) markers from Arabidopsis in polymorphic and phylogenetic analyses of broccoli and cauliflower. Approximately 69.4%,
80%, 83.6%, and 87.2% of SSR markers from AA, BB, CC, and AACC genomes, respectively, were amplified successfully in broccoli and cauliflower. In comparison with the SSR markers, higher transferability of IP markers was noted with a successful amplification of 96%. A higher degree of
polymorphism was also observed in IP (63.5%) than in SSR (54.4%).The marker transferability of IP markers was higher than that of SSR markers as the result of that 96% of IP markers amplified successfully. A majority of IP (58.3%) and SSR (81%) markers detected one locus. Nevertheless, a smaller portion of IP (41.7%) and SSR (19%) markers detected two or more loci, indicating genome duplication occurred in B. oleracea during evolution. Polymorphic markers were used to genotype 12 broccoli accessions and 12 cauliflower accessions while they were clustered into two distinct groups. As revealed by phylogenetic and PCoA analyses in this study, cauliflower possesses higher genetic similarity than broccoli. The high marker transferability among Brassica species implies that the markers could be applied on other species which are also in short of molecular markers. The polymorphic markers uncovered here can be employed in phylogenetic analysis, variety identification, construction of linkage maps, mapping of gene or QTLs, and marker-assisted breeding.