與青花菜及花椰菜形態歧異相關之候選基因體區域

Abstract

青花菜(Brassica oleracea var. italica) 與花椰菜(B. oleracea var. botrytis)為世界重要蔬菜，兩者為同一個物種的不同變種。儘管兩者外觀相近皆為花球，但青花菜的花球大多由花苞構成，花椰菜則是未分化的花序分生組織。而兩者分化差異很可能是人為選拔造成，因此可以透由比較並追蹤選拔訊號，找出造成兩者分化差異的候選區域。本文針對National Center for Biotechnology Information (NCBI) 上一組全基因體定序資料，包含了20個花椰菜與23個青花菜，利用核苷酸多樣性比值以及hapFLK尋找族群內缺乏多樣性或者族群間分化顯著的區域，並且個別找到了88以及65個候選區域。而為了縮減候選區域數量，本文亦用多樣性的比值以及hapFLK分析了另一個來自台灣的族群以對上述的候選區域提供支持，包含53個青花菜與93個花椰菜自交系。最後多樣性的比值以及hapFLK分別找出了33個與16個在兩個資料組都有的候選區域。在這些區域裡，我們發現了至少8個與花序發展相關的候選基因，例如AINTEGUMENTA-like 6、APETALA1、BRANCHED 1、FILAMENTOUS FLOWER、LATE MERISTEM IDENTITY1、MONOPTEROS、 REPRODUCTIVE MERISTEM 1APETALA1與SUPPRESSOR OF OVEREXPRESSION OF CO 1；也發現了至少十個與側芽發展及分生組織相關的基因，例如BLADE ON PETIOLE 與JAGGED LATERAL ORGANS。本文提供了49個與青花菜、花椰菜分化相關的有利候選區域及其候選基因，更深入了解甘藍類的演化以及馴化；而這些區域也對花椰菜與花椰菜的分子育種有一定的幫助。

Broccoli (Brassica oleracea var. italica) and cauliflower (B. oleracea var. botrytis) belong to the same species but are recognized as different varieties. Albeit their edible heads have similar shapes, they are actually different anatomic structures, with cauliflower having clusters of inflorescence meristem while broccoli having clusters of floral buds for broccoli. The differentiation might be an outcome of artificial selection, which may leave signatures of selective sweeps at the genomic level. To uncover the genetic regions underlying the differentiation between broccoli and cauliflower, the resequencing population of 23 broccoli and 20 cauliflowers retrieved from National Center for Biotechnology Information were used to detect selective sweeps, by searching for regions with low nucleotide diversity in one population or significant divergence between populations using ratio of nucleotide diversity and hapFLK, respectively. Seventy-five and 65 candidate regions were discovered by ratio of nucleotide diversity and hapFLK, respectively. To narrow down candidate regions, the population with 53 broccoli and 93 cauliflowers inbred lines bred in Taiwan were also scanned for selective sweeps. Consequently, 33 and 16 regions were detected by ratio of nucleotide diversity and hapFLK, respectively. Within these regions, at least 8 genes were involved in the inflorescence meristem development: AINTEGUMENTA-like 6, APETALA1, BRANCHED 1, FILAMENTOUS FLOWER, LATE MERISTEM IDENTITY1, MONOPTEROS, REPRODUCTIVE MERISTEM 1, and SUPPRESSOR OF OVEREXPRESSION OF CO 1, and at least 10 genes were related to lateral organ and meristem development, e.g. BLADE ON PETIOLE and JAGGED LATERAL ORGANS. Our results reported 49 promising candidate genomic regions associated with the morphological differentiation between broccoli and cauliflower. These results could not only elucidate the evolutionary and domestication history of B. oleracea, but also provide candidate regions for crossing between broccoli and cauliflower in molecular breeding.