基于QTL定位和全基因组关联分析挖掘甘蓝型油菜收获指数相关位点

doi:10.3724/SP.J.1006.2022.14159

Abstract

Abstract:

Harvest index (HI) is an important agronomic trait, and the HI of rapeseed (Brassica napus L.) remains much lowerer than that of other major crops, indicating there is large scope for improvement of this trait. It is important to explore the genetic mechanism of rapeseed harvest index for its genetic improvement. In this study, QTLs for HI using the 186 recombinant inbred lines (RIL) in the three environments (2016, 2017, and 2018) and best linear unbiased prediction (BLUP) were detected based on the high-density genetic linkage map. A total of 12 HI QTLs located on chromosomes A03, A05, A06, A07, A09, C04, and C05_random were detected, with the explained phenotypic variation of individual QTL range from 1.27% to 14.20%. GWAS for HI was performed using 588 resequencing natural populations established by our previous study. A total of 6 SNPs associated with HI were detected in three years (2016, 2017, and 2019) and BLUP, which located on chromosomes A09, C01, and C03. The S9_25882060 on chromosome A09 detected by the environment in 2019 overlapped with S9_25961704, and was close to S9_24834640 on chromosome A09 detected by the environment in 2016. In addition, 2016HI (S9_24834640) detected in 2016 was located in the interval region of q2017HI-9. Among these 18 loci, one locus was overlapped with reported HI-related QTLs, and six loci were contiguous to reported yield-related QTLs. Combining the results of transcriptome sequencing data of our laboratory, 36 primary candidate genes were selected and these genes involved in the photosynthesis, transmembrane transport, storage components synthesis, transcriptional regulation and so on. These results provide important theoretical basis for genetic improvement of HI in rapeseed.

Key words: Brassica napus, harvest index, GWAS, candidate genes

ZHANG Chao, YANG Bo, ZHANG Li-Yuan, XIAO Zhong-Chun, LIU Jing-Sen, MA Jin-Qi, LU Kun, LI Jia-Na. Mining harvest index loci based on QTL mapping and genome-wide association study in rapessed (Brassica napus L.)[J].Acta Agronomica Sinica, 2022, 48(9): 2180-2195.

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Table 5

Identification of candidate genes for harvest index"

位点 Locus	物理位置 Physical position	基因 Genes	拟南芥同源基因 Homologs in A. thaliana	功能注释 Functional annotation
q2016HI-6	chrA06: 2056287-2944745	BnaA06g04140D	AT1G47960	细胞壁/液泡果糖转化酶的抑制剂,在拟南芥中调节脱落酸响应和耐盐性,在碳水化合物新陈代谢、胁迫响应和糖信号中具有重要作用。 Cell wall/vacuolar inhibitor of fructosidase 1 regulates ABA response and salt tolerance in Arabidopsis, plays important roles in carbohydrate metabolism, stress responses, and sugar signaling.
		BnaA06g04150D	AT4G29120	6磷酸葡糖糖酸脱氢酶蛋白家族,具有辅酶结合域、氧化还原酶活性、具有磷酸葡糖糖酸脱氢、结合、还原活性。 6-phosphogluconate dehydrogenase family protein possesses coenzyme binding, oxidoreductase activity, phosphogluconate dehydrogenase (decarboxylating) activity, binding, and catalytic activity.
		BnaA06g04380D	AT1G07890	细胞质APX1,在植物干旱和高温胁迫的适应中具有重要作用。 Cytosolic APX1 plays a key role in the acclimation of plants to a combination of drought and heat stress.
		BnaA06g04820D	AT1G08380	编码光系统I的O亚基。 Encodes subunit O of photosystem I.
		BnaA06g05000D	AT1G08630	苏氨酸醛羧酶,涉及降解苏氨酸生成甘氨酸。主要在种子和幼苗中表达。 Threonine aldolase involved in threonine degradation to glycine is primarily expressed in seeds and seedlings.
q2016HI-7	chrA07: 14920316-15237451	BnaA07g18730D	AT3G60530	锌指结构转录因子中GATA家族。 GATA factor family of zinc finger transcription factors.
		BnaA07g19140D	AT3G62100	Aux/IAA蛋白家族,涉及生长素信号途径。促进体细胞胚胎化形成。 Aux/IAA family of proteins implicated in auxin signaling promotes somatic embryogenesis.
		BnaA07g19330D	AT3G62420	bZIP转录因子53,包含该蛋白的异源二聚体可显著增加种子成熟基因的转录。 The bZIP transcription factor 53 contains Heterodimers containing bZIP53 which participates in enhanceosome formation to produce a dramatic increase in seed maturation gene transcription.
q2016HI-14	chrC04:6005799-6099590	BnaC04g08090D	AT2G37170	PIP2质膜镶嵌蛋白亚家族的一个成员。位于质膜上,在爪蟾卵细胞中具有水分转运活性。在维管束中特异表达且蛋白水平在叶片发育过程中显著增加。 A member of the plasma membrane intrinsic protein subfamily PIP2 localized to the plasma membrane exhibites water transport activity in Xenopus oocyte and expresses specifically in the vascular bundles and protein level increases slightly during leaf development.
		BnaC04g08100D	AT2G37170
q2018HI-5-2	chrA05: 6778798-7543669	BnaA05g11950D	AT2G30490	突变该基因影响类苯丙烷的代谢,影响生长和发育。 Mutations in this gene impact phenylpropanoid metabolism, growth, and development.
		BnaA05g12160D	AT2G30250	WRKY转录因子。涉及响应各种非生物胁迫,特别是盐胁迫。 WRKY transcription Factor which involved in response to various abiotic stresses especially salt stress.
		BnaA05g12180D	AT2G30200	胚胎缺陷蛋白基因3147,细胞分裂必不可少并且超量表达该基因可增加储藏油脂含量。 Embryo defective 3147 is essential for cell division and its overexpression can increase the storage oil content.
		BnaA05g12360D	AT2G29980	内质网酶,负责将磷脂合成18:3脂肪酸。 Endoplasmic reticulum enzyme is responsible for the synthesis of 18:3 fatty acids from phospholipids.
		BnaA05g12390D	AT2G29650	编码位于类囊体膜上的无机磷酸盐转运蛋白PHT4;1。拟南芥中AtPHT4;1通过影响磷酸盐活性影响ATP合成和植物生长。 Encodes an inorganic phosphate transporter (PHT4;1) that is localized to the thylakoid membrane. AtPHT4;1 influences phosphate availability for ATP synthesis and plant growth.
		BnaA05g12530D	AT2G29500	编码热激蛋白,可以被非生物胁迫例如强光、活性氧、干旱等诱导。 Heat shock proteins encoded can be induced by abiotic stress such as high light, ROS, and drought.
qBLUPHI-3	chrA03: 10372839-10458202	BnaA03g22030D	AT2G28840	通过降解热敏元件ELF3来调控热敏性下胚轴生长。侧根萌动所必须。 Regulates thermoresponsive hypocotyl growth through mediating degradation of the thermosensor ELF3. It is required for lateral root initiation.
qBLUPHI-7-2	chrA07: 21687449-21719775	BnaA07g30760D	AT1G73260	丝氨酸蛋白酶(Kunitz型)抑制剂,在拟南芥中涉及调控植物病菌侵染的细胞程序性死亡。 Serine protease (Kunitz trypsin) inhibitor which is involved in modulating programmed cell death in plant-pathogen interactions in Arabidopsis.
2016HI (q2017HI-9)	chrA09: 24334640-25334640 (chrA09:24170241-24935073)	BnaA09g33290D	AT3G52930	果糖二磷酸醛缩酶8,拟南芥中其突变会影响胚发育和淀粉合成。 Fructose-bisphosphate aldolase 8, mutations in this gene, impacts embryo development and starch biosynthesis in Arabidopsis.
2016HI (q2017HI-9)	chrA09: 24334640-25334640 (chrA09:24170241-24935073)	BnaA09g33720D	AT3G53420	过氧化氢的跨膜转运、响应水分缺失、跨膜转运、水分转运。 Hydrogen peroxide transmembrane transport, response to water deprivation, transmembrane transport, and water transport.
		BnaA09g34460D	AT3G54620	正调控种子成熟,正调控基因转录、DNA模板化。 Positive regulation of seed maturation, positive regulation of transcription, and DNA-templated.
2017HI-1	chrC01: 16923943-17923943	BnaC01g23350D	AT3G51520	编码二酰甘油酰基辅酶A转移酶,具有不同骨架酰基辅酶A偏好性,比AtDGAT1将二酰甘油转化成二酰甘油的效率更高。可以在消耗C16:3的基础上增加C18:2和C18:3多不饱和脂肪酸。 Encodes a functional acyl-CoA:diacylglycerol acyltransferase with different acyl-CoA substrate preferences which has higher DAG to TAG conversion rate than AtDGAT1. It increases both C18:2 and C18:3 polyunsaturated fatty acids at the expense of C16:0.
		BnaC01g23800D	AT3G50820	编码光系统II的外来亚基,对维持具有催化活性的锰离子簇稳定性至关重要。在类囊体上光系统II中的PsbO2不仅对维持光系统II的功能起作用也对调节光系统I与光系统II的比率起作用。 Encodes a protein which is an extrinsic subunit of photosystem II and which has been proposed to play a central role in stabilization of the catalytic manganese cluster. The presence of PsbO₂ isoform in the PSII centers has consequences not only to the function of PSII but also to the PSI/PSII ratio in thylakoids.
2017HI-2	chrC03: 9934536-10934536	BnaC03g19670D	AT2G35860	类成束阿拉伯半乳聚糖蛋白16前体,在植物次生细胞壁的合成中具有重要作用并且可能涉及胚胎形成和种子发育。 FASCICLIN-like arabinogalactan protein 16 precursor (FLA16) plays a role in plant secondary cell wall synthesis and possibly involved in embryogenesis and seed development.
		BnaC03g20550D	AT2G37170	PIP2质膜镶嵌蛋白亚家族的一个成员。位于质膜上,在爪蟾卵细胞中具有水分转运活性。在维管束中特异表达且蛋白水平在叶片发育过程中显著增加。 A member of the plasma membrane intrinsic protein subfamily PIP2 which is localized to the plasma membrane has water transport activity in Xenopus oocyte and increases the expressed specifically in the vascular bundles and protein level increases slightly during leaf development.
2019HI-1	chrA09: 25382060-26382060	BnaA09g34720D	AT3G54890	编码与光系统I相关的光收集复合体组件。 Encodes a component of the light harvesting complex associated with photosystem I.
		BnaA09g34930D	AT3G55360	涉及在超长链脂肪酸延长反应中烯脂酰的还原,为表皮蜡质、储藏油脂和鞘脂类代谢所必须。 Enoyl-CoA reductase is involved in all very long chain fatty acids (VLCFA) elongation reactions that are required for cuticular wax, storage lipid, and sphingolipid metabolism.
		BnaA09g35240D	AT3G55620	涉及在种子休眠过程中响应脱落酸刺激、调控胚胎发育的终止。 Cellular response is related with abscisic acid stimulus and embryo development ending in seed dormancy.
		BnaA09g35380D	AT3G55800	编码叶绿体酶景天庚酮糖-1,7-二磷酸酶,涉及卡尔文循环的碳还原。增加其活性的转基因株系比对照多积累了50%的蔗糖和淀粉。 The chloroplast enzyme sedoheptulose-1,7-bisphosphatase (SBPase), which involves in the carbon reduction of the Calvin cycle, increases in SBPase activity in transgenic lines accumulate up to 50% more sucrose and starch than wild-type.
		BnaA09g35590D	AT3G56130	负调控脂肪酸的合成过程。 Negative regulation of fatty acid biosynthetic process.
		BnaA09g36130D	AT3G56850	编码一个具有bZIP结构域的脱落酸响应元件结合蛋白。定位于细胞核中,在拟南芥种子成熟的胚中表达并涉及调控AtSUC1的表达。 An ABA-responsive element binding protein encodes with a bZIP domain located in the nucleus can regulate the expressed in the embryo during seed maturation and involved in the regulation of AtSUC1 expression in Arabidopsis.
		BnaA09g36160D	AT3G56860	涉及脱落酸活化信号途径、细胞死亡、防卫反应、乙烯合成过程、叶片衰老、mRNA的稳定化。 Involves abscisic acid-activated signaling pathway, cell death, defense response, ethylene biosynthetic process, leaf senescence, mRNA stabilization.
		BnaA09g36180D	AT3G56880	响应渗透胁迫、盐胁迫、水分缺失胁迫。 Response to osmotic stress, salt stress and water deprivation.
2019HI-2	chrA09: 25461704-26461704	BnaA09g36610D	AT3G57260	响应冷胁迫、系统获得性抗性。 Response to cold, systemic acquired resistance.
		BnaA09g36620D	AT3G57280	编码位于叶绿体内囊膜的Tmemb-14蛋白家族的一个成员,涉及脂肪酸和油脂的平衡,可能具有从质体中跨膜转运脂肪酸的功能。 A chloroplast inner envelope localized member of the Tmemb-14 gene family is involved in fatty acid and lipid homeostasis, which has likely functions as a fatty acid transporter that exports fatty acids from the plastid.
BLUP_HI	chrC01: 27593591-28593591	BnaC01g29930D	AT1G61800	葡萄糖-6-磷酸转运,磷酸烯醇式丙酮酸转运,磷酸甘油酸酯跨膜转运,光合作用适应,跨膜运输,磷酸丙糖跨膜转运。 Glucose-6-phosphate transport, phosphoenolpyruvate transport, phosphoglycerate transmembrane transport, photosynthetic acclimation, transmembrane transport, and triose phosphate transmembrane transport.

Table 5

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材料 Material	环境 Environment	平均值±标准偏差 Mean±SD	范围 Range (%)	变异系数 CV (%)
父本中油821 Male parent Zhongyou 821	2016	17.68±0.95
	2017	18.17±4.50
	2018	19.68±0.68
母本GH06 Female parent GH06	2016	15.83±0.40
	2017	13.06±1.04
	2018	16.07±0.42
重组自交系 RIL	2016	20.57±3.29	11.87-32.83	16.01
	2017	19.68±4.35	9.33-33.66	22.09
	2018	18.50±2.81	9.05-24.02	15.17
	BLUP	19.53±1.10	16.03-23.32	5.62
自然群体 NP	2016	17.99±4.35	6.44-29.08	24.18
	2017	17.25±4.65	3.55-28.74	26.97
	2019	23.14±4.94	5.64-32.73	21.35
	BLUP	18.91±3.13	7.80-25.94	16.55

	重组自交系 RIL					自然群体 NP
	2016HI	2017HI	2018HI	BLUP		2016HI	2017HI	2019HI	BLUP
2016HI	1.000				2016HI	1.000
2017HI	0.354^**	1.000			2017HI	0.571^**	1.000
2018HI	0.269^*	0.438^**	1.000		2019HI	0.542^**	0.594^**	1.000
BLUP	0.698^**	0.866^**	0.733^**	1.000	BLUP	0.798^**	0.782^**	0.800^**	1.000

位点 QTL	染色体 Chr.	加性效应 Additive effect	LOD阈值 LOD score	贡献率 R² (%)	标记区间 SNP interval	物理区间 Physical position (bp)
q2016HI-6	A06	-0.9225	2.5258	7.74	SNP13605-SNP14257	2056287-2944745
q2016HI-7	A07	-1.1539	3.5976	11.18	SNP15424-SNP15485	14920316-15237451
q2016HI-14	C04	3.1475	3.5999	11.53	SNP27560-SNP27571	6005799-6099590
q2017HI-2	A07	-1.1705	2.9408	7.08	SNP3321-SNP3325	12808959-12813162
q2017HI-9	A09	-1.0928	2.7174	5.89	SNP20565-SNP20632	24170241-24935073
q2018HI-5-1	A05	-1.5749	6.0438	14.20	SNP12592-SNP12692	7315852-7543669
q2018HI-5-2	A05	-1.6657	5.2083	11.77	SNP12692-SNP12548	6778798-7543669
q2018HI-15-1	C05_random	0.7312	2.7726	1.27	SNP46328-SNP46308	1679049-1734366
q2018HI-15-2	C05_random	0.7312	2.7726	6.62	SNP46315-SNP46336	1731384-1749200
qBLUPHI-3	A03	-0.4181	3.1453	4.71	SNP5280-SNP5570	10372839-10458202
qBLUPHI-7-1	A07	0.4047	2.7985	5.49	SNP16354-SNP16358	21782147-21797231
qBLUPHI-7-2	A07	0.4000	2.7037	5.31	SNP16342-SNP16345	21687449-21719775

位点 Locus	染色体 Chr.	关联标记 Associate marker	物理位置 Physical position	贡献率 R²(%)	阈值 -log₁₀ (P)	最佳模型 Best model
2016HI	A09	S9_24834640	24,834,640	11.26	5.60	K+Q
2017HI-1	C01	S11_17423943	17,423,943	5.84	5.92	K+Q
2017HI-2	C03	S13_10434536	10,434,536	6.55	5.72	K+Q
2019HI-1	A09	S9_25882060	25,882,060	6.20	5.87	K+PCA
2019HI-2	A09	S9_25961704	25,961,704	5.79	5.69	K+PCA
BLUP_HI	C01	S11_28093591	28,093,591	6.36	5.76	K+Q

Mining harvest index loci based on QTL mapping and genome-wide association study in rapessed (Brassica napus L.)

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