Liu Xiao-Ping, Gao Bao-Zhen, Han Feng-Qing, Fang Zhi-Yuan, Yang Li-Mei, Zhuang Mu, Lv Hong-Hao, Liu Yu-Mei, Li Zhan-Sheng, Cai Cheng-Cheng, Yu Hai-Long, Li Zhi-Yuan, Zhang Yang-Yong
Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12# ZhongGuanCun Nandajie, 100081, Beijing, People's Republic of China.
BMC Genomics. 2017 Mar 14;18(1):230. doi: 10.1186/s12864-017-3613-x.
Due to its variegated and colorful leaves, ornamental kale (Brassica oleracea L. var. acephala) has become a popular ornamental plant. In this study, we report the fine mapping and analysis of a candidate purple leaf gene using a backcross population and an F population derived from two parental lines: W1827 (with white leaves) and P1835 (with purple leaves).
Genetic analysis indicated that the purple leaf trait is controlled by a single dominant gene, which we named BoPr. Using markers developed based on the reference genome '02-12', the BoPr gene was preliminarily mapped to a 280-kb interval of chromosome C09, with flanking markers M17 and BoID4714 at genetic distances of 4.3 cM and 1.5 cM, respectively. The recombination rate within this interval is almost 12 times higher than the usual level, which could be caused by assembly error for reference genome '02-12' at this interval. Primers were designed based on 'TO1000', another B. oleracea reference genome. Among the newly designed InDel markers, BRID485 and BRID490 were found to be the closest to BoPr, flanking the gene at genetic distances of 0.1 cM and 0.2 cM, respectively; the interval between the two markers is 44.8 kb (reference genome 'TO1000'). Seven annotated genes are located within the 44.8 kb genomic region, of which only Bo9g058630 shows high homology to AT5G42800 (dihydroflavonol reductase), which was identified as a candidate gene for BoPr. Blast analysis revealed that this 44.8 kb interval is located on an unanchored scaffold (Scaffold000035_P2) of '02-12', confirming the existence of assembly error at the interval between M17 and BoID4714 for reference genome '02-12'.
This study identified a candidate gene for BoPr and lays a foundation for the cloning and functional analysis of this gene.
观赏羽衣甘蓝（Brassica oleracea L. var. acephala）因其叶片色彩斑斓，已成为一种受欢迎的观赏植物。在本研究中，我们利用回交群体和由两个亲本系W1827（白叶）和P1835（紫叶）衍生的F群体，对一个候选紫叶基因进行了精细定位和分析。
遗传分析表明，紫叶性状由单个显性基因控制，我们将其命名为BoPr。利用基于参考基因组“02 - 12”开发的标记，BoPr基因初步定位到C09染色体上一个280 kb的区间，侧翼标记M17和BoID4714的遗传距离分别为4.3 cM和1.5 cM。该区间内的重组率几乎比正常水平高12倍，这可能是由于参考基因组“02 - 12”在此区间的组装错误所致。基于另一个甘蓝参考基因组“TO1000”设计了引物。在新设计的InDel标记中，发现BRID485和BRID490与BoPr最接近，分别在基因两侧，遗传距离为0.1 cM和0.2 cM；两个标记之间的区间为44.8 kb（参考基因组“TO1000”）。44.8 kb的基因组区域内有7个注释基因，其中只有Bo9g058630与AT5G42800（二氢黄酮醇还原酶）具有高度同源性，该基因被鉴定为BoPr的候选基因。Blast分析表明，这个44.8 kb的区间位于“02 - 12”的一个未锚定支架（Scaffold000035_P2）上，证实了参考基因组“02 - 12”在M17和BoID4714之间的区间存在组装错误。
本研究鉴定了BoPr的一个候选基因，为该基因的克隆和功能分析奠定了基础。
