干旱胁迫下甘蓝型油菜籽粒含油量和蛋白质含量变化的全基因组关联分析

doi:10.3864/j.issn.0578-1752.2023.01.002

摘要/Abstract

摘要：

【目的】干旱是甘蓝型油菜生长发育过程中一种常见的非生物胁迫，严重影响了其产量和品质。联合全基因组关联分析和转录组差异表达分析，筛选干旱胁迫条件下影响甘蓝型油菜籽粒含油量和蛋白质含量变化的候选基因，为解释干旱胁迫下甘蓝型油菜籽粒含油量及蛋白质含量的变化提供理论基础。【方法】利用旱棚盆栽方式模拟干旱胁迫环境，使用183份甘蓝型油菜构成的自然群体，于2019和2020年在模拟干旱胁迫条件下收获2年的籽粒，并进行籽粒含油量以及蛋白质含量的测定，将得到的表型数据与60K芯片的基因型数据（包含34 103个SNP）进行全基因组关联分析，同时，结合相同处理下花后不同干旱时间段（30、40和50 d）的籽粒转录组差异基因数据，筛选共有基因，并利用甘蓝型油菜和拟南芥数据库注释信息、已报道的相关文献和转录组差异基因表达水平鉴定与干旱胁迫下甘蓝型油菜籽粒含油量及蛋白质含量变化相关的候选基因。【结果】通过对2年间籽粒含油量和蛋白质含量的分析，发现材料重复性较好，干旱胁迫造成甘蓝型油菜籽粒的含油量下降，蛋白质含量上升；全基因组关联分析得出的最佳模型主要为一般线性模型下的Q或naïve模型，共检测出38个显著关联位点（P<1/31597或P<1/31278），主要分布在A03（6个）、A04（8个）和C03（8个）染色体，各位点分别对含油量和蛋白质含量变化的贡献率均超过10%，其中含油量变化位点最大贡献率为23.97%，蛋白质含量变化位点最大贡献率为22.21%。通过整合全基因组关联分析和转录组分析，筛选出256个共有基因，根据基因注释和文献报道鉴定出与干旱胁迫下含油量及蛋白质含量变化相关的25个候选基因，其中包含转录因子（如bZIP transcription factor GBF6、TALE transcription factor ATH1、MYB-like Domain transcription factor MYBD、NAC transcription factor ANAC029和ERF transcription factor ERF111）、相关激酶（如与油脂相关的蛋白激酶CIPK9、水分胁迫响应激酶PIP5K1和代谢相关激酶PFK7）、相关蛋白（如与油脂相关转运蛋白ABCA9、与蛋白相关的存储蛋白CRU3、胁迫响应蛋白HUP26和M10、叶绿体蛋白DG238和CP12）等，涉及生长发育、光合反应、物质运输等多个生物学过程。【结论】鉴定出25个相关候选基因，可能响应干旱胁迫，并影响油菜籽粒蛋白质和含油量的积累。

关键词: 甘蓝型油菜, 干旱胁迫, 含油量, 蛋白质含量, 候选基因

Abstract:

【Objective】 Drought is one of the most adverse abiotic stresses that hinder growth and development of Brassica napus L., threatening its yield and quality. In this study, we identified the candidate genes that influence oil and protein content changes according to the results of the genome wide association mapping (GWAS) and differentially expressed genes (DEGs) under drought stress in B. napus. 【Method】 A natural population comprising 183 B. napus lines under drought stress across two years was genotyped with a Brassica 60K Illumina Infinium SNP array to perform GWAS. Combined with drought stressed seed transcriptome data from different treatment periods, the candidate genes related to the changes in oil and protein contents under drought stress were identified. 【Result】 The analysis showed that the best model for phenotypic data analysis in 2 years was mainly the Q or naïve model, and a total of 38 significant associated loci were detected (P<1/31597 or P<1/31278). By integrating GWAS and transcriptome results, 256 common genes were selected, and by comparing the database information of B. napus and Arabidopsis thaliana, 25 related candidate genes were identified. These genes, including transcription factors (e.g., bZIP transcription factor GBF6, TALE transcription factor ATH1, MYB-like Domain transcription factor MYBD, NAC transcription factor ANAC029, ERF transcription factor ERF111), related kinases (e.g., PIP5K1, PFK7), related proteins (e.g., seed stores protein CRU3, chloroplast protein DG238 and CP12, stress-responsive proteins HUP26 and M10), are involved in multiple biological processes such as photosynthetic reaction, substance transport, and stress response. For instance, oil-related protein kinase CIPK9, ABCA9 transporter, storage-related protein CRU3, may provide basis for explaining the changes in oil and protein contents of B. napus under drought stress. 【Conclusion】 The 25 identified candidate genes may affect the accumulation of protein and oil contents under drought stress during the seed development in B. napus.

Key words: Brassica napus L., candidate genes, drought stress, oil content, protein content

胡盛,李阳阳,唐章林,李加纳,曲存民,刘列钊. 干旱胁迫下甘蓝型油菜籽粒含油量和蛋白质含量变化的全基因组关联分析[J]. 中国农业科学, 2023, 56(1): 17-30.

HU Sheng,LI YangYang,TANG ZhangLin,LI JiaNa,QU CunMin,LIU LieZhao. Genome-Wide Association Analysis of the Changes in Oil Content and Protein Content Under Drought Stress in Brassica napus L.[J]. Scientia Agricultura Sinica, 2023, 56(1): 17-30.

图/表 8

表1

表2

图1

图2

表3

干旱胁迫下油菜籽粒含油量和蛋白质含量变化显著关联的SNP位点"

性状 Trait	SNP标记 SNP marker	染色体 Chr.	位置 Site (bp)	P值 P-value	贡献率 R² (%)	置信区间 Confidence interval (500 kb up/downstream)
重庆2019含油量 CQ2019_ Oil	Bn-scaff_16888_1-p1803454	C04	45940031	2.80E-05	14.13	45440031—46440031
	Bn-A06-p19292104	A06	15319939	2.99E-05	10.82	14819939—15819939
	Bn-A06-p14864165	A06	16344344	5.07E-06	16.40	15844344—16844344
	Bn-scaff_16755_1-p1357741	C03	59428822	1.01E-05	15.61	58928822—59928822
	Bn-A06-p5279490	A04	3858538	1.38E-05	15.25	3358538—4358538
	Bn-scaff_16755_1-p1427195	C03	59368418	1.53E-05	15.13	58868418—59868418
	Bn-A04-p4978478	A04	5117185	1.79E-05	14.95	4617185—5617185
	Bn-scaff_19193_1-p527597	C01	5772854	2.46E-05	12.95	5272854—6272854
	Bn-scaff_15712_8-p121910	C04	28592068	2.73E-05	14.46	28092068—29092068
	Bn-A04-p4418670	A04	4543027	3.12E-05	14.30	4043027—5043027
重庆2020含油量 CQ2020_ Oil	Bn-A04-p17845366	A04	17948897	9.77E-07	23.97	17448897—18448897
	Bn-scaff_23107_1-p47992	C05	44218	8.06E-06	19.52	0—544218
	Bn-A04-p18595858	A04	18723761	2.38E-05	17.89	18223761—19223761
	Bn-A04-p18639840	A04	18762292	3.09E-05	17.20	18262292—19262292
	Bn-A04-p18620226	A04	18746954	3.16E-05	17.17	18246954—19246954
	Bn-A07-p16423207	A07	18399689	1.36E-05	18.82	17899689—18899689
重庆2019蛋白质含量 CQ2019_ Pro	Bn-A06-p5260549	A04	3866976	2.70E-06	16.69	3366976—4366976
	Bn-scaff_16142_1-p714220	C01	34837361	1.00E-05	13.43	34337361—35337361
	Bn-scaff_16092_1-p205960	C03	27846928	1.82E-05	14.07	27346928—28346928
	Bn-scaff_18181_1-p1691208	C05	6102902	1.87E-05	14.11	5602902—6602902
	Bn-scaff_18549_1-p129072	C06	1368140	2.20E-05	12.97	868140—1868140
	Bn-A05-p21188442	A05	19340595	3.18E-06	16.92	18840595—19840595
	Bn-A03-p15615278	A03	14676315	1.52E-05	15.14	14176315—15176315
	Bn-A03-p24688180	A03	23155012	1.58E-05	15.10	22655012—23655012
	Bn-scaff_16755_1-p1327949	C03	59461983	3.03E-05	14.34	58961983—59961983
	Bn-scaff_16755_1-p1427195	C03	59368418	3.04E-05	14.33	58868418—59868418
重庆2020蛋白质含量 CQ2020_ Pro	Bn-A08-p18820218	A08	16173557	5.73E-07	22.21	15673557—16673557
	Bn-A08-p18789560	A08	16143836	6.06E-07	21.58	15643836—16643836
	Bn-scaff_16231_1-p203872	C08	21771676	6.26E-07	21.36	21271676—22271676
	Bn-A03-p21505530	A03	20289512	9.18E-06	19.44	19789512—20789512
	Bn-A03-p21478889	A03	20250601	9.32E-06	18.72	19750601—20750601
	Bn-A03-p21357849	A03	20131639	9.79E-06	19.68	19631639—20631639
	Bn-A08-p18827698	A08	16181029	1.83E-05	17.08	15681029—16681029
	Bn-scaff_18322_1-p2150739	C03	6946175	2.35E-05	17.38	6446175—7446175
	Bn-scaff_18322_1-p2147199	C03	6948511	2.73E-05	14.41	6448511—7448511
	Bn-A03-p21505363	A03	20289679	3.12E-05	16.20	19789679—20789679
	Bn-A01-p1890102	A01	1424609	1.08E-05	15.34	924609—1924609
	Bn-scaff_21778_1-p364556	C03	5155386	2.01E-05	18.89	4655386—5655386

表3

图3

表4

候选基因鉴定"

候选基因 Candidate genes	物理位置 Physical position(bp)	拟南芥同源基因 Homologs in Arabidopsis	功能注释 Function annotation
BnaC05g00760D	Chr.C05:398202-401549	AT1G01140	CBL相互作用蛋白激酶，在油菜以及拟南芥中调节种子油含量 CBL-interacting protein kinase (CIPK9), involved in seed oil regulation in Brassica napus L. and Arabidopsis
BnaA03g40520D	Chr.A03:20244987-20246636	AT5G61730	ABC转运蛋白，其过表达能提高油料植物种子含油量和产量 ABC transporter protein (ABCA9), ABCA9-OEs can increase the oil content and yield of oil plant seeds
BnaC01g09900D	Chr.C01:5867929-5870050	AT4G28520	种子储藏蛋白，对蛋白积累起到重要作用 Seed storage protein (CRU3) plays a key role in protein accumulation
BnaA06g24040D	Chr.A06:16613640-16616541	AT5G65110	编码一种参与长链脂肪酸生物合成的酰基辅酶 Encodes an acyl-CoA (ACX2) that involves in long chain fatty acid biosynthesis
BnaA01g03890D	Chr.A01:1798245-1799923	AT4G32980	TALE转录因子，参与光形态建设 TALE transcription factor (ATH1) involved in photomorphogenesis
BnaA01g02570D	Chr.A01:1280574-1281038	AT4G34590	bZIP转录因子，参与氨基酸代谢 bZIP transcription factor (GBF6) involved in amino acid metabolism
BnaA07g24010D	Chr.A07:17937117-17938262	AT1G70000	MYB类结构域转录因子，响应光合细胞分裂素，增加花青素积累 MYB-like Domain transcription factor (MYBD) that responses to light, cytokinins and anthocyanin accumulation
BnaA07g24270D	Chr.A07:18152148-18153317	AT1G69490	NAC转录因子，响应ABA，调节叶片衰老 NAC transcription factor (ANAC029) that responses to ABA signal and regulates leaf senescence
BnaA06g23710D	Chr.A06:16462716-16465107	AT5G64750	ERF转录因子，参与植物发育过程和胁迫响应 ERF transcription factor (ERF111) that involves in plant development processes and stress responses
BnaA04g25300D	Chr.A04:18254430-18255160	AT2G43670	碳水化合物结合X8结构域超家族蛋白 Carbohydrate-binding X8 domain superfamily protein
BnaC01g09810D	Chr.C01:5790810-5791936	AT4G28660	类植物光系统Ⅱ中PsbW亚基，参与组装和修复光系统Ⅱ复合体 Similar to PsbW subunit of photosystem II(PSB8), implicated in the assembly and repair of the photosystem II complex
BnaA05g26270D	Chr.A05:19264359-19265918	AT3G12930	一种新型叶绿体蛋白，参与叶绿体发育 A novel chloroplast protein (DG238) that involves in chloroplast development
BnaA04g26990D	Chr.A04:19060731-19061503	AT2G47400	一种叶绿体蛋白，响应光反应，参与碳代谢过程 A chloroplast protein (CP12) that responds to a light response and is involved in carbon metabolism processes
BnaA01g02610D	Chr.A01:1304663-1306004	AT4G34540	叶片衰老的遗传变异，与还原酶相似，GSV1变异在发育中起着重要作用 Genetic Variants in leaf Senescence (GVS1), similarity to reductase, GSV1 variant plays an important role in development
BnaA03g30440D	Chr.A03:14777856-14781737	AT3G10020	缺氧反应未知蛋白，增强环境耐受性 Hypoxia response unknown protein 26 (HUP26), enhances environment tolerance
BnaA03g40640D	Chr.A03:20311931-20313526	AT5G67500	编码一个电压依赖性阴离子通道蛋白，在拟南芥中参与生长发育，响应干旱胁迫以及盐胁迫 Encodes a voltage-dependent anion channel (VDAC2), involved in growth and response to drought stress and salt stress
BnaA04g23790D	Chr.A04:17566194-17567208	AT2G41280	类晚期胚胎丰富蛋白，能被脱落酸、盐胁迫以及干旱胁迫抑制表达 Similar to Late Embryogenesis Activated (LEA) protein (M10), Inhibited expression by ABA, salt stress and drought stress
BnaC03g10560D	Chr.C03:5070625-5073146	AT5G21280	一种响应氧化反应和非生物胁迫的特异性基因 A specific gene (ATR7) that responses to oxidative and abiotic stresses
BnaA08g21050D	Chr.A08:15685703-15689509	AT1G21980	编码Ⅰ型磷脂酰肌醇-4-磷酸5-激酶，响应水分胁迫信号 Encodes Type I phosphatidylinositol-4-phosphate 5-kinase (PIP5K1) that responses to water-stress signal
BnaC03g13370D	Chr.C03:6467762-6470298	AT5G56630	磷酸果糖激酶7，调节叶片代谢，促进生长发育 Phosphofructokinase 7(PFK7), Regulates leaf metabolism and promotes development
BnaA03g40200D	Chr.A03:20093860-20095203	AT5G61440	定位在叶绿体中的氧硫还家族蛋白 The thioredoxin family protein(ACHT5), located in the chloroplast
BnaA03g41120D	Chr.A03:20618565-20619734	AT3G51030	定位在胞质中的氧硫还家族蛋白 The thioredoxin family protein(TRX1), located in the cytosolic
BnaA08g21800D	Chr.A08:16019052-16021113	AT5G38120	AMP依赖性合成酶与连接酶家族蛋白 AMP-dependent synthetase and ligase family protein (4-CL8)
BnaC01g09540D	Chr.C01:5573226-5579124	AT3G23890	定位在细胞核中的拓扑异构酶Ⅱ蛋白 A topoisomerase II protein (TOP II), located in nucleus
BnaA04g26710D	Chr.A04:18885632-18889024	AT2G46700	钙依赖蛋白激酶3促进靶蛋白磷酸化 CDPK kinase 3 (CRK3) promotes phosphorylation of target proteins

表4

图4

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环境/年份 Environment/Year	性状 Trait	处理 Treatment	范围 Range (%)	均值±标准差 Mean± SD	变异系数 CV (%)
重庆2019 CQ2019	油脂含量 Oil content	WW	26.92—44.82	38.26±3.31	8.65
		DS1	27.14—44.07	33.53±2.59**	7.72
		DS2	23.90—42.30	32.88±2.44**	7.41
	蛋白质含量 Protein content	WW	21.75—33.96	28.16±2.18	7.75
		DS1	26.90—36.70	31.18±1.48**	4.75
		DS2	27.18—35.91	31.41±1.45**	4.60
重庆2020 CQ2020	油脂含量 Oil content	WW	28.81—47.14	36.45±3.10	8.52
		DS1	26.53—38.23	31.86±2.43**	7.63
		DS2	25.08—39.49	30.71±2.58**	8.40
	蛋白质含量 Protein content	WW	24.51—32.98	29.31±1.60	5.45
		DS1	27.15—36.02	31.42±1.43**	4.56
		DS2	27.62—36.12	32.30±1.66**	5.14

年份/性状 Year/Trait		2019含油量2019_Oil		2019蛋白质含量2019_Pro		2020含油量2020_Oil		2020蛋白质含量2020_Pro
年份/性状 Year/Trait		DS1	DS2	DS1	DS2	DS1	DS2	DS1	DS2
2019含油量2019_Oil	DS1	1
2019含油量2019_Oil	DS2	0.788**	1
2019蛋白质含量2019_Pro	DS1	-0.744**	-0.656**	1
2019蛋白质含量2019_Pro	DS2	-0.580**	-0.768**	0.846**	1
2020含油量2020_Oil	DS1	-0.008	-0.049	0.099	0.115	1
2020含油量2020_Oil	DS2	0.036	-0.076	0.090	0.134	0.576**	1
2020蛋白质含量2020_Pro	DS1	0.041	0.080	-0.065	-0.079	-0.742**	-0.512**	1
2020蛋白质含量2020_Pro	DS2	0.069	0.108	-0.086	-0.081	-0.340**	-0.666**	0.605**	1