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作物学报

作物学报 ›› 2023, Vol. 49 ›› Issue (7): 1829-1842.doi: 10.3724/SP.J.1006.2023.24188

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

甘蓝型油菜SGR基因家族的全基因组鉴定与功能分析

唐玉凤(), 姚敏, 何昕, 官梅, 刘忠松, 官春云, 钱论文*()   

  1. 湖南农业大学农学院 / 南方粮油作物协同创新中心, 湖南长沙 410128
  • 收稿日期:2022-08-11 接受日期:2022-11-25 出版日期:2023-07-12 网络出版日期:2022-12-06
  • 通讯作者: *钱论文, E-mail: qianlunwen@163.com
  • 作者简介:E-mail: tyf331213@163.com
  • 基金资助:
    本研究由国家自然科学基金项目(31801399);湖南省教育厅科学研究重点项目(21A0135)

Genome-wide identification and functional analysis of SGR gene family in Brassica napus L.

TANG Yu-Feng(), YAO Min, HE Xin, GUAN Mei, LIU Zhong-Song, GUAN Chun-Yun, QIAN Lun-Wen*()   

  1. College of Agronomy, Hunan Agricultural University / Collaborative Innovation Center of Grain and Oil Crops in South China, Changsha 410128, Hunan, China
  • Received:2022-08-11 Accepted:2022-11-25 Published:2023-07-12 Published online:2022-12-06
  • Contact: *E-mail: qianlunwen@163.com
  • Supported by:
    The National Natural Science Foundation of China(31801399);The Research Foundation of Education Bureau of Hunan Province(21A0135)

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摘要：

叶绿素是植物进行光合作用的一类绿色色素, 对植物生长有着直接的影响。本研究利用生物信息学方法在全基因组水平上对甘蓝型油菜(Brassica napus)、白菜(Brassica rapa)、甘蓝(Brassica oleracea)和拟南芥(Arabidopsis thaliana)中滞绿基因(STAY-GREEN, SGR)家族成员进行分析发现, 28个SGR基因大多数包含4个外显子, 编码碱性蛋白。染色体定位和共线性分析显示, 甘蓝型油菜SGR基因家族成员中不存在串联复制, SGR基因家族成员之间具有线性关系, 高度同源, 且在进化过程中非常保守。此外, 利用60K SNP对203份半冬性甘蓝型油菜自交系的叶绿素含量进行全基因组关联分析(Genome-wide association study, GWAS), 检测到2个单体型区域Chr.A01: 6,193,165~ 6,317,757 bp和Chr.C01: 9,059,861~9,906,618 bp携带的BnaSGR1a-A01和BnaSGR1-C01与叶绿素含量显著相关。同时, 结合50份半冬性甘蓝型油菜重测序数据, 对这2个单体型进行进区域关联分析, 检测到1个SNP定位在BnaSGR1a-A01的外显子2区域, 并与叶绿素含量显著关联。共表达网络分析结果验证了BnaSGR1a-A01与BnaSGR2-A03直接相连, 与BnaSGR1-C01、BnaSGR1-A08、BnaSGR2-C03、BnaSGR1-C07、BnaSGRL-C06、BnaSGRL-A10等基因间接相连形成了一个网络体系, 共同调节叶绿素含量。T2拟南芥转BnaSGR1a-A01基因超表达植株的叶绿素a、叶绿素b和总的叶绿素含量相比野生型显著降低, 表明BnaSGR1调控叶绿素降解。本研究为油菜SGR基因的功能研究和利用奠定了基础。

关键词: 甘蓝型油菜, SGR基因, 全基因组关联分析, 叶绿素含量

Abstract:

Chlorophyll is a kind of green pigment for plant photosynthesis, which has a direct effect on plant growth. In this study, bioinformatics methods were used to identify the members of SGR gene family in Brassica napus, Brassica rapa, Brassica oleracea, and Arabidopsis thaliana. Most of the 28 SGR genes contained four exons, encoding basic proteins. Chromosome mapping and syntenic analysis showed that there was no tandem duplication in the SGR gene family members of Brassica napus. SGR gene family members had a linear relationship, highly homologous in evolution, and very conserved in the evolutionary process. Moreover, a genome-wide association study (GWAS) of chlorophyll content was performed using a Brassica 60K Illumina Infinium SNP array in 203 Brassica napus accessions. Two haplotype regions (Chr.A01: 6,193,165-6,317,757 bp and Chr.C01: 9,059,861-9,906,618 bp) carrying two SGR genes (BnaSGR1a-A01 and BnaSGR1-C01) were detected, which were significantly associated with chlorophyll content. Meanwhile, the regional association analysis of 50 resequenced rapeseed inbred lines revealed that a SNP located in exon 2 of BnaSGR1a-A01 significantly associated with chlorophyll content. Co-expression network analysis revealed that BnaSGR1a-A01 were directly linked with BnaSGR2-A03, and indirectly linked with BnaSGR1-C01, BnaSGR1-A08, BnaSGR2-C03, BnaSGR1-C07, BnaSGRL-C06, and BnaSGRL-A10, thus forming a molecular network involved in the potential regulation of chlorophyll content. Chlorophyll a, chlorophyll b, and the total chlorophyll content of T2 Arabidopsis transgenic plants overexpressing BnasSGR1a-A01 were significantly lower than wild type, indicating that BnaSGR1a-A01 regulated chlorophyll degradation. This study laid a foundation for the functional research and utilization of SGR gene in Brassica napus L.

Key words: Brassica napus, STAY-GREEN gene, GWAS, chlorophyll content

表1

本研究中所用的引物序列"

引物名称
Primer name		 引物序列
Sequence (5°-3°)
BnaNYE1a-qRT F: TCTTCACATATTTACAGTAGAGGCC
R: GTTAGACATTTTCCCTCGGCC
AtACT2 F: CGCTCTTTCTTTCCAAGCTC
R: AACAGCCCTGGGAGCATC
19OV141T1 F: CTCTCTCGAGCTTTCGCGAGCTCTATTTTTGTTGATTATGCTTTTCAT
R: TAATGGAGTGAGAAATAGCTAAAGT
19OV141T2 F: CAGTGACATTACTGCTAAATTAACT
R: CCTGCAGGTCGACTCTAGAGGATCCTCAATAGAGTTTCTCTGGACTAGGA
HPT II F: ACACTACATGGCGTGATTTCAT
R: TCCACTATCGGCGAGTACTTCT

表2

SGR基因信息汇总"

拟南芥
Arabidopsis thaliana		 基因编号
Gene ID		 基因名称
Gene name		 核苷酸长度
Gene length		 氨基酸长度
Length of amino acids		 等电点
pI		 分子量
Molecular weight (kD)		 内含子数目
No. of introns		 外显子数目
No. of exons		 亚细胞定位
Predicted subcellular localization
AT4G22920/SGR1
甘蓝型油菜 Brassica napus BnaA01g12570D BnaSGR1a-A01 1874 332 9.35 37.82 5 6 叶绿体Chloroplast
甘蓝型油菜 Brassica napus BnaA01g22870D BnaSGR1b-A01 1063 114 9.86 13.18 2 3 叶绿体Chloroplast
甘蓝型油菜 Brassica napus BnaA03g45630D BnaSGR1-A03 1484 266 8.67 29.83 3 4 叶绿体Chloroplast
甘蓝型油菜 Brassica napus BnaA08g10510D BnaSGR1-A08 1341 273 8.32 30.67 3 4 叶绿体Chloroplast
甘蓝型油菜 Brassica napus BnaCnng29210D BnaSGR1-Cnn 1378 264 8.85 29.57 3 4 叶绿体Chloroplast
甘蓝型油菜 Brassica napus BnaC01g14360D BnaSGR1-C01 5975 999 8.65 112.40 11 12 质膜Plasma membrane
甘蓝型油菜 Brassica napus BnaC07g37710D BnaSGR1-C07 1616 266 8.60 29.92 3 4 叶绿体Chloroplast
白菜 Brassica rapa Bra013656 BraSGR1a-A01 5705 950 8.48 106.87 10 11 质膜Plasma membrane
白菜 Brassica rapa Bra028385 BraSGR1b-A01 804 113 10.02 13.00 1 2 叶绿体Chloroplast
白菜 Brassica rapa Bra019346 BraSGR1-A03 1125 264 8.60 29.73 3 4 叶绿体Chloroplast
白菜 Brassica rapa Bra020829 BraSGR1-A08 982 254 8.57 28.55 3 4 叶绿体Chloroplast
甘蓝Brassica oleracea Bol014983 BoSGR1-C01 1252 269 9.01 30.49 3 4 叶绿体Chloroplast
甘蓝Brassica oleracea Bol010654 BoSGR1-C03 1018 264 8.85 29.57 3 4 叶绿体Chloroplast
甘蓝Brassica oleracea Bol042063 BoSGR1-C07 1106 266 8.41 29.78 3 4 叶绿体Chloroplast
AT4G11910/SGR2
甘蓝型油菜 Brassica napus BnaA03g24900D BnaSGR2-A03 1776 262 9.28 29.96 4 5 叶绿体Chloroplast
甘蓝型油菜 Brassica napus BnaC03g72930D BnaSGR2-C03 1654 274 9.00 31.14 3 4 叶绿体Chloroplast
白菜 Brassica rapa Bra000755 BraSGR2-A03 1335 274 9.22 31.08 3 4 叶绿体Chloroplast
甘蓝Brassica oleracea Bol030516 BoSGR2-C03 1194 263 8.94 30.15 3 4 叶绿体Chloroplast
AT1G44000/SGRL
甘蓝型油菜 Brassica napus BnaA10g08850D BnaSGRL-A10 1387 257 9.15 29.28 3 4 叶绿体Chloroplast
甘蓝型油菜 Brassica napus BnaC06g00560D BnaSGRL-C06 1455 257 9.15 29.17 3 4 叶绿体Chloroplast
白菜 Brassica rapa Bra036938 BraSGRL-Scaffold000123 1067 257 9.24 29.34 3 4 叶绿体Chloroplast
甘蓝Brassica oleracea Bol006958 BoSGRL-Scaffold000269 1096 259 8.40 29.29 3 4 叶绿体Chloroplast
AT4G11911/SGLP
甘蓝型油菜 Brassica napus BnaCnng70460D BnaSGLP-Cnn 983 246 7.99 28.05 3 4 叶绿体Chloroplast
甘蓝Brassica oleracea Bol044955 BoSGLP-C02 982 267 8.44 28.13 3 4 叶绿体Chloroplast

图1

甘蓝型油菜、白菜、甘蓝和拟南芥SGR基因家族的系统进化树分析"

图2

拟南芥、白菜、甘蓝和甘蓝型油菜SGR基因的系统比较分析"

图3

白菜、甘蓝、甘蓝型油菜染色体上SGR基因的分布 染色体编号标记在每个染色体的左侧。A和C分别是白菜和甘蓝的染色体; chrA和chrC分别是甘蓝型油菜的A亚组和C亚组染色体; Random意味着基因被随机分配到一个特定的染色体上, chrCnn表示属于C亚基因组但不确定染色体信息。"

图4

甘蓝型油菜、甘蓝、白菜和拟南芥的SGR基因共线性分析 同一条粉色曲线上的2个基因是甘蓝型油菜内的线性关系, 同一条绿色曲线是甘蓝型油菜对白菜、甘蓝的线性关系, 同一条棕色曲线是拟南芥对甘蓝型油菜、白菜和甘蓝的线性关系。"

图5

203份油菜苗期和抽薹期叶绿素含量全基因组关联分析 单体型区域(6,193,165~6,317,757 bp)和单体型区域(9,059,861~9,906,618 bp)与叶绿素含量显著相关。这2个单体型区域包含2个拟南芥直系同源基因BnaSGR1a-A01 (BnaA01g12570D)和BnaSGR1-C01 (BnaC01g14360D), 这些基因涉及到叶绿素合成。热图显示了这些SNPs之间存在强的连锁不平衡。水平红色虚线表示临界值(-log10(P)=4.0)。ss_GH: 在光照培养室调查苗期叶绿素含量指数, bs_GH: 在光照培养室调查抽薹期叶绿素含量指数。"

图6

50个重测序材料叶绿素含量候选基因关联分析 A: 单体型(6,193,165~6,312,172 bp; r2=0.55)区域叶绿素含量的关联分析。蓝色虚线表示全基因组显著性的阈值P值为1.0×10-3。B: BnaSGR1a-A01基因区域变异位点分析。该SNP chrA01:6306874定位于BnaSGR1a-A01基因外显子2区域。C和D: 比较分析等位基因G和T对应材料的表达和叶绿素表型分析。等位基因在群体中的频率大于0.05将被用于此分析。箱型图显示了等位基因G对应的材料有较高的叶绿素含量和相对高的基因表达水平。"

图7

BnaSGR1a-A01在拟南芥中超表达分析 A: 超表达骨架载体示意图; B: 野生型拟南芥与超表达拟南芥1个月苗龄第4~6片真叶对比, 标尺为5 mm; C: 野生型拟南芥与超表达拟南芥的qRT-PCR检测; D~F: 野生型拟南芥与超表达拟南芥的叶绿素a、叶绿素b及总叶绿素测定。Col-0: 非转基因植株, OE-BnaSGR1-13和OE-BnaSGR1-14: 转基因植株。用Excel软件的数据统计分析对数据进行t检验(Student’s t-test), *表示平均值间差异显著(P < 0.05), **表示平均值间差异极显著(P < 0.01), 误差线表示标准差(SD)。"

图8

BnaSGR1a-A01基因共表达网络分析 A: 甘蓝型油菜长角果中BnaSGR1a-A01的共表达网络。红色节点表示BnaSGR候选基因, 青绿色三角形节点代表着与BnaSGR基因直接相连接的基因。B: 在甘蓝型油菜长角果中的部分BnaSGR1a-A01共表达网络。基于功能注释, BnaSGR1a-A01共表达网络中的基因被分为以下3类: 叶绿素(浅蓝色节点)、光系统(青绿色节点)和转录因子(深橄榄绿节点)。C: BnaSGR1a-A01基因GO pathway分析网络。颜色的深浅表示BnaSGR1a-A01与这些代谢路径相关性的强弱。"

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