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作物学报 ›› 2024, Vol. 50 ›› Issue (5): 1136-1146.doi: 10.3724/SP.J.1006.2024.34152

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

转录组结合区域关联分析挖掘油菜含油量积累的候选基因

曹松(), 姚敏, 任睿, 贾元, 向星汝, 李文, 何昕, 刘忠松, 官春云, 钱论文*(), 熊兴华*()   

  1. 湖南农业大学农学院, 湖南长沙 410128
  • 收稿日期:2023-09-08 接受日期:2024-01-12 出版日期:2024-05-12 网络出版日期:2024-01-25
  • 通讯作者: 熊兴华, E-mail: xiongene@hunau.edu.cn; 钱论文, E-mail: qianlunwen@163.com
  • 作者简介:E-mail: c18890046232@163.com
  • 基金资助:
    湖南省杰出青年科学基金项目(2022JJ10027);湖南省教育厅科学研究重点项目(21A0135);国家科技重大专项项目(2022ZD04009)

A combination of genome-wide association and transcriptome analysis reveal candidate genes affecting seed oil accumulation in Brassica napus

CAO Song(), YAO Min, REN Rui, JIA Yuan, XIANG Xing-Ru, LI Wen, HE Xin, LIU Zhong-Song, GUAN Chun-Yun, QIAN Lun-Wen*(), XIONG Xing-Hua*()   

  1. College of Agronomy, Hunan Agricultural University, Changsha 410128, Hunan, China
  • Received:2023-09-08 Accepted:2024-01-12 Published:2024-05-12 Published online:2024-01-25
  • Contact: E-mail: xiongene@hunau.edu.cn; E-mail: qianlunwen@163.com
  • Supported by:
    Science Foundation for Distinguished Youth Scholars of Hunan Province, China(2022JJ10027);Research Foundation of Education Bureau of Hunan Province, China(21A0135);National Key Science and Technology Project(2022ZD04009)

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摘要：

油菜(Brassica napus L.)是中国食用植物油的主要来源, 提高种子含油量是增加菜籽油供应最为有效的方法。本研究利用4个油菜自交系授粉后25 d、35 d、45 d的种子转录组数据分析, 筛选出43个与油脂合成相关基因, 其中33个基因持续上调表达, 10个基因持续下调表达, 主要基因包括BnLEC1、BnABI5、BnOLEO4和BnOBAP1a等。同时, 结合50份半冬性甘蓝型油菜重测序数据, 检测到与含油量显著相关3个SNP、9个SNP分别定位到BnOBAP1a-A10和BnABI5-A05, 其中BnOBAP1a-A10_Hap1对应材料含油量显著高于Hap2, BnABI5-A05_Hap1对应材料含油量显著高于Hap3。此外, 利用WGCNA构建基因共表达网络发现, BnOBAP1a与BnABI5通过3个转录因子LEC1、HMGB3、HTA11间接相连, 形成了潜在调控的分子网络, 影响种子油脂积累。这些结果有利于我们开发单体型功能标记进一步提高油菜籽含油量。

关键词: 甘蓝型油菜, 含油量, 转录组分析, 共表达分析, 区域关联分析

Abstract:

Rapeseed (Brassica napus L.) is the main source of edible vegetable oil in China, and increasing seed oil content is the most effective way to increase the supply of rapeseed oil. In this study, 43 genes related to lipid synthesis were selected by analyzing the seed transcriptome data of 4 rapeseed inbred lines 25, 35, and 45 days after pollination. Among them, 33 genes were continuously up-expressed and 10 genes were continuously down-expressed from 25 to 45 days of seed development. The main genes included BnLEC1, BnABI5, BnOLEO4, and BnOBAP1a. At the same time, combined with the resequencing data of 50 semi-winter Brassica napus, 3 SNPs and 9 SNPs significantly related to oil content were detected to BnOBAP1a-A10 and BnABI5-A05, respectively, and the oil content of BnOBAP1A-A10_Hap1 was significantly higher than Hap2. The oil content of BnABI5-A05_Hap1 was significantly higher than Hap3. In addition, WGCNA was used to construct gene networks, and we found that BnOBAP1a and BnABI5 were indirectly connected through three transcription factors LEC1, HMGB3, and HTA11, which together formed a molecular network involved in the potential regulation of seed oil accumulation. The results of this study provide valuable insights for the development of haplotype functional markers, aiming to further enhance oil content in B. napus.

Key words: Brassica napus, oil content, transcriptome analysis, coexpression analysis, regional association analysis

表1

长沙地区4个油菜品种成熟种子含油量统计表"

品种
Variety		 最小值
Min.		 最大值
Max.		 平均值±标准差
Mean±SD		 变异系数
CV (%)
XY777 31.60 36.06 33.32±1.67 5.02
XY015 38.83 42.56 40.39±1.28 3.16
CS136 47.51 51.52 49.50±1.30 2.62
CS115 46.24 50.18 48.84±1.21 2.32

图1

持续上调或下调表达基因筛选统计 (a) 长沙地区4个油菜品种, 25~35 d、35~45 d持续上调或下调基因数量统计图。(b) 4个品种持续上调基因维恩图。(c) 4个品种持续下调基因维恩图。"

图2

383个差异基因通路富集分析 圆圈大小表示基因数量, 热图表示-log10(P-value)的值。"

图3

热图显示与含油量相关差异表达基因的表达量(DEGs) RNA-seq数据的表达值进行了log10(fpkm+1)转换, 并显示为填充块, 从蓝色到黄色, 再到红色。"

图4

50个重测序材料中单体型(1,944,128~1,994,025 bp)区域含油量关联分析 (a) 单体型(1,944,128~1,994,025 bp; R2=0.99)区域的含油量关联分析。蓝色实线表示全基因组显著性的阈值P值为1.0×10-4。(b)和(c) 3个SNP (Chr.A10: 1,969,139; Chr.A10: 1,969,444; Chr.A10: 1,969,452, P=1.35×10-5)与含油量显著相关, 并定位在BnOBAP1a-A10基因启动子区域。热图显示这些SNPs存在强的连锁不平衡。在BnOBAP1a-A10单倍型区检测到2个单倍型等位基因。(d) 比较分析2个单体型等位基因对应材料的含油量。单体型等位基因在群体中的频率大于0.01将被用于此分析。箱型图显示BnOBAP1a-A10_Hap1等位基因对应的材料含油量显著高于BnOBAP1a-A10_Hap2对应的材料含油量。*、**、***分别表示在0.05、0.01和0.001概率水平差异显著。"

图5

50个重测序材料中单体型(4,389,567~4,439,432 bp)区域的含油量关联分析 (a) 单体型(4,389,567~4,439,432 bp; R2=0.99)区域的含油量关联分析。蓝色实线表示全基因组显著性的阈值P值为1.0×10-4。(b)和(c) 9个SNP (A05: 4414567; P =1.42×10-4)与含油量显著相关, 并定位在BnABI5-A05基因区域。热图显示这些SNPs存在强的连锁不平衡。在BnABI5-A05单倍型区检测到3个单倍型等位基因。(d) 比较分析3个单体型等位基因对应材料的含油量。单体型等位基因在群体中的频率大于0.01将被用于此分析。箱型图显示BnABI5-A05_Hap1等位基因对应的材料有较高的含油量。*、**、***分别表示在0.05、0.01和0.001水平差异显著。"

图6

共表达网络分析 (a) 模块系统树图。(b) 模块与含油量相关性。(c) 模块中基因数目对比。(d) 基因网络图。八边形红色节点代表候选基因, 根据功能标注, 共表达网络分为油脂生物合成过程(红色节点)、油脂转运(紫色节点)、油脂氧化(橙色节点)、光合作用(绿色节点)和碳水化合物代谢过程(灰色节点)。"

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