2017年6月5日，中国农业科学院蔬菜花卉研究所甘蓝青花菜研究团队在期刊genes（2023IF=3.5，Q2）上发表了题为“Fine Mapping and Transcriptome Analysis Reveal Candidate Genes Associated with Hybrid Lethality in Cabbage (Brassica Oleracea)”的研究论文。论文第一作者是肖志亮博士，通讯作者是吕红豪研究员和庄木研究员。

杂种致死是一种有害的表型，对物种进化至关重要。作者先前报道了甘蓝的杂种致死性，并对相关基因进行了初步定位。在本研究中，对杂交致死基因的精细定位表明，BoHL1位于第1染色体上，介于BoHLTO124和BoHLTO130之间，间隔为101kb。BoHL2位于C4上的插入-缺失标记HL234和HL235之间，标记间隔为70kb。在BoHL1和BoHL2两个区间内分别发现了28个和9个注释基因。作者还应用RNA-Seq技术对甘蓝的杂种致死性进行了分析。

在BoHL1区发现了7个差异表达基因(Degs)和5个抗病相关基因(Bo1g153320和Bo1g153380)，而在BoHL2区发现了2个degs和4个抗病相关基因(2个共同，Bo4g173780和Bo4g173810)。

随着抗病基因在其他植物中经常与杂交致死有关的研究，这些有趣的差异表达的抗病基因可能是与杂交致死相关的很好的候选基因。作者还使用了SNP/Indel分析和实时定量聚合酶链式反应来验证结果。这项工作为研究甘蓝杂种致死机理提供了新的思路。

Figure 1. Phenotypes of the parental lines and F1 hybrids and the segregating population strategy. (A)
Phenotypes of the parental lines 09-211 and 09-222 and the F1 hybrids; (B) Segregating population
strategies used to map BoHL1; (C) Segregating population strategies used to map BoHL2

Figure 2. Fine mapping and analysis of BoHL1. (A) A genetic map and corresponding physical map
of BoHL1. The BoHL1 gene was delimited to an interval between BoHLTO124 and BoHLTO130, with
an estimated length of 101 kb. N: normal phenotype; (B) Twenty-eight genes were annotated in
the ‘TO1000’ reference genome; (C) R-related gene analysis and differentially expressed genes (DEG)
analysis for 28 genes

Figure 3. Fine mapping and analysis of BoHL2. (A) A genetic map and corresponding physical map of
BoHL2. The BoHL2 gene was delimited to an interval between HL234 and HL235, with an estimated
length of 70 kb. N: normal phenotype; (B) Nine genes were annotated in the ‘TO1000’ reference genome;
(C) R-related gene analysis and DEG analysis for nine genes.

Figure 4. Screening of DEGs and DEG functional analysis. (A) Significantly up-or down-regulated
genes using the q-value threshold of <0.05; (B) GO enrichment analysis of the DEGs; (C) The top
20 Kyoto encyclopedia of genes and genomes (KEGG) pathways with the highest representation
of DEGs.

Figure 5. Schematic of the pathway category ‘Plant-pathogen interaction’.

Figure 6. Validation of RNA-Seq data by qRT-PCR. Twelve genes were selected for validation and
showed the same tendencies as revealed by the RNA-Seq data. FPKM: Fragments per kilobase of exon
model per million mapped reads.

Figure 7. Collinearity analysis. (A) Collinearity analysis of the C1 chromosome in the ‘TO1000’ and
’02-12’ reference genomes. (B) The physical position and collinearity analysis of the two mapping
positions of BoHL1.

点评：定位+RNA-seq，感觉发genes有点可惜了？