玉米雌穗性状遗传分析与形成机制<sup>*</sup>

doi:10.13523/j.cb.2111004

中国生物工程杂志

2021, Vol. 41

Issue (12): 30-46 DOI: 10.13523/j.cb.2111004

玉米生物育种基础研究与关键技术专辑

玉米雌穗性状遗传分析与形成机制^*

殷芳冰^1,²,王成^1,²,龙艳^1,^2,³,董振营^1,^2,^**(

),万向元^1,^2,^3,^**(

)

1 北京科技大学生物与农业研究中心化学与生物工程学院顺德研究生院北京 100083
2 北京中智生物农业国际研究院北京 100192
3 北京首佳利华科技有限公司主要作物生物育种北京市工程实验室生物育种北京市国际科技合作基地北京 100192

Progress on Dissecting Genetic Architecture and Formation Mechanism of Maize Ear Traits

YIN Fang-bing^1,²,WANG Cheng^1,²,LONG Yan^1,^2,³,DONG Zhen-ying^1,^2,^**(

),WAN Xiang-yuan^1,^2,^3,^**(

)

1 Research Center of Biology and Agriculture, Shunde Graduate School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
2 Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
3 Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co., Ltd., Beijing 100192, China

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摘要：

雌穗是玉米重要的生殖器官,雌穗发育决定成熟果穗大小及单穗粒重,进而直接影响玉米产量。雌穗性状主要包括穗长、穗粗、穗行数、行粒数、穗重、单穗粒重等,均为多基因控制的数量遗传性状,且其遗传结构各不相同。解析雌穗性状的遗传基础,优化雌穗结构,是玉米增产的重要途径。前人通过数量性状位点(quantitative trait locus mapping,QTL)定位和全基因组关联分析(genome-wide association study, GWAS)等方法,已经鉴定出较多雌穗性状相关的遗传位点,但是目前已鉴定功能的基因较少,所建立的遗传位点一致性图谱并不完整,因此难以全面揭示雌穗性状遗传结构。通过综合前人雌穗性状遗传定位进展,现将已鉴定QTL位点和显著关联SNP整合至玉米B73参考基因组V4版本,并鉴定出雌穗性状定位热点区间,对深入解析雌穗性状遗传结构、指导雌穗性状基因克隆和理解雌穗发育分子机制均具有重要意义。

关键词： 雌穗性状; QTL定位; 全基因组关联分析; 遗传结构; 基因

Abstract:

Ear is an important reproductive organ of maize. The development of ear determines the size of mature ear and the weight of single ear, and then directly affects the yield of maize. Ear traits include ear length, ear diameter, kernel row number, kernel number per row, ear weight, and kernel weight per ear, which are quantitative genetic traits controlled by multiple genes, and their genetic structures are different. It is effective to increase maize yield by analyzing the genetic basis of the traits of ear and optimizing the structure of ear. Through quantitative trait locus(QTL) mapping, genome-wide association study (GWAS) and other approaches, many loci related to ear traits have been identified, but at present, there are few ear-trait-related genes were cloned, and the consistent map of the identified genetic loci is not complete, so it is difficult to reveal the genetic structure of ear traits comprehensively. Based on the previous progress in genetic mapping of ear traits, the identified QTLs and significantly associated SNPs were integrated into the V4 version of maize B73 reference genome, and the genetic hotspots for ear traits were identified. The work is valuable for further analysis of the genetic structure of ear traits, cloning ear-trait-related genes and dissecting the molecular mechanism of ear development.

Key words: Ear traits Quantitative trait locus(QTL) mapping Genome-wide association study(GWAS) Genetic structure Gene

收稿日期: 2021-10-31 出版日期: 2022-01-13

ZTFLH:

Q819

基金资助: * 中央高校基本科研业务费专项资金(06500060);国家“万人计划”科技创新领军人才特殊支持经费(201608)

通讯作者: 董振营,万向元 E-mail: zydong@ustb.edu.cn;wanxiangyuan@ustb.edu.cn

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引用本文:

殷芳冰,王成,龙艳,董振营,万向元. 玉米雌穗性状遗传分析与形成机制^*[J]. 中国生物工程杂志, 2021, 41(12): 30-46.

YIN Fang-bing,WANG Cheng,LONG Yan,DONG Zhen-ying,WAN Xiang-yuan. Progress on Dissecting Genetic Architecture and Formation Mechanism of Maize Ear Traits. China Biotechnology, 2021, 41(12): 30-46.

链接本文:

https://manu60.magtech.com.cn/biotech/CN/10.13523/j.cb.2111004 或 https://manu60.magtech.com.cn/biotech/CN/Y2021/V41/I12/30

图1 玉米雌穗性状定位QTL(a)及显著关联SNP(b)染色体分布

表1 玉米雌穗相关性状QTL、显著关联SNP位点数量总结

图2 玉米雌穗性状QTL、SNP热点区间及已克隆基因染色体分布

表2 雌穗性状QTL及SNP共同定位热点区间

调控途径	基因名称	基因ID	位置/bp	编码蛋白	参考文献
CLV-WUS	TD1	Zm00001d014793	Chr5:63456839~63460120	LRR蛋白激酶	[68]
负反馈途径	FEA2	Zm00001d051012	Chr4:136765871~136767712	LRR蛋白激酶	[69-70]
	CT2	Zm00001d027886	Chr1:16722714~16730676	GTP结合蛋白	[71]
	FEA3	Zm00001d040130	Chr3:28711131~28713722	LRR受体样蛋白	[72]
	FCP1	Zm00001d003320	Chr2:40126366~40127328	CLE蛋白	[72]
	ZmWUS1	Zm00001d001948	Chr2:3416796~3418004	Wuschel相关同源异型框蛋白	[73-74]
	ZmWUS2	Zm00001d026537	Chr10:147855536~147856873	Wuschel相关同源异型框蛋白	[73]
激素途径	SPI1	Zm00001d044069	Chr3:218287295~218289461	黄素单加氧酶	[75]
	VT2	Zm00001d008700	Chr8:17394723~17398865	色氨酸氨基转移酶	[76]
	BIF1	Zm00001d008749	Chr8:18951758~18953833	AUX/IAA转录因子	[64,77]
	BIF2	Zm00001d031068	Chr1:175807851~175809432	丝氨酸/苏氨酸蛋白激酶	[78-79]
	BIF4	Zm00001d037691	Chr6:134088831~134092670	AUX/IAA转录因子	[64]
	PIN1a	Zm00001d044812	Chr9:3291763~3295059	PIN蛋白	[80-81]
	FEA4	Zm00001d037317	Chr6:120724112~120726773	bZIP转录因子	[82]
	BA1	Zm00001d042989	Chr3:186014629~186015264	bHLH转录因子	[75-76,78, 83-84]
	BA2	Zm00001d003897	Chr2:65742713~65755466	与BA1共定位并异二聚化的蛋白质	[85]
	BAF1	Zm00001d045427	Chr9:21786350~21787375	AT-hook蛋白	[86]
	KN1	Zm00001d033859	Chr1:276073335~276081242	同源异型结构域转录因子	[87-90]
	IFA1	Zm00001d028216	Chr1:26771165~26776231	C2C2-yabby转录因子	[91]
	AN1	Zm00001d032961	Chr1:244858795~244867417	ent-焦磷酸古巴酯合成酶	[92]
	BD1	Zm00001d022488	Chr7:178605958~178606905	ERF转录因子	[93]
miRNA途径	CG1	zma-MIR156b	Chr3:6928278~6928401	两个串联miRNA156	[65]
	TGA1	Zm00001d049822	Chr4:46350597~46355118	SBP-box转录因子	[94-95]
	TU1	Zm00001d052180	Chr4:181857308~181864042	MADS-box转录因子	[96]
	TSH4	Zm00001d020941	Chr7:137273600~137277139	SBP-box转录因子	[97]
	UB2	Zm00001d031451	Chr1:190382866~190386589	SBP-box转录因子	[98-99]
	UB3	Zm00001d052890	Chr4:203611347~203615518	SBP-box转录因子	[98-100]
	GIF1	Zm00001d033905	Chr1:278134999~278138569	GRF相互作用因子	[101]
	IDS1/TS6	Zm00001d034629	Chr1:298422859~298427050	AP2转录因子	[66,102-103]
	SID1	Zm00001d019230	Chr7:23054461~23065589	AP2转录因子	[103]
RAMOSA途径	RA1	Zm00001d020430	Chr7:113572410~113572937	C2H2锌指蛋白	[104-105]
	RA2	Zm00001d039694	Chr3:12158280~12159065	LOB结构域蛋白	[106]
	RA3	Zm00001d022193	Chr7:172484959~172489194	海藻糖-6-磷酸磷酸酯酶	[107]
	REL2	Zm00001d024523	Chr10:75993828~76002912	转录辅阻遏物	[67]
其他途径	KNR6	Zm00001d036602	Chr6:94190254~94199686	丝氨酸/苏氨酸蛋白激酶	[108]
	KRN5b	Zm00001d013603	Chr5:15168335~15173013	核酸内切酶/核酸外切酶/磷酸酶家族蛋白	[109]
调控途径	基因名称	基因ID	位置/bp	编码蛋白	参考文献
	ZFL1	Zm00001d026231	Chr10:141561862~141564767	LEAFY同源蛋白	[110-111]
	ZFL2	Zm00001d002449	Chr2:12914091~12917068	LEAFY同源蛋白	[110-111]
	ID1	Zm00001d032922	Chr1:243201405~243204865	IDD家族蛋白	[112-113]
	ZAG1	Zm00001d037737	Chr6:135893605~135901920	MADS-box转录因子	[114]
	TB1	Zm00001d033673	Chr1:270553676~270554776	TCP家族转录因子	[115-117]
	TRU1	Zm00001d042111	Chr3:151328862~151332856	BTB/POZ结构域转录因子	[118]

表3 已克隆雌穗性状相关基因汇总

性状	染色体	QTL热点区间/Mb (区间内不同独立研究检测次数)	SNP热点区间/Mb (区间内所含SNP个数)	已知基因
KRN	1	54.028~55.710(3)、202.063~204.150(3)、218.463~227.220(3)、272.978~276.046(3)、293.102~295.562(4)、298.217~298.423²(3)	0.048~7.812(17)、25.925~34.948¹(12)	IFA1¹、IDS1²
	2	4.863~5.588(3)、8.807~9.481(3)、15.192~16.422(3)、18.322~20.399(5)、22.071~26.774(5)、34.887~38.310(4)、41.524~42.235(4)、195.475~202.580(3)	0.177~7.426¹(13)、21.579~28.986(15)	ZmWUS1¹
	3	148.152~154.065(3)、203.609~210.466(3)、223.243~234.079(3)	0.007~5.007(5)、16.335~21.384(6)、219.823~224.823(5)	无
	4	7.251~7.619(4)、10.673~10.957(3)、40.318~41.687(5)、46.784~64.228(4)、64.550~73.911(3)、168.623~170.065(3)、178.365~183.236(5)、189.139~192.081(3)、200.053~208.887¹(9)、241.458~242.137(3)	0.245~16.220(30)、23.546~29.978(11)、199.295~209.466¹(17)	UB3¹
	5	10.405~15.269¹(5)、19.174~23.270(4)、87.878~110.560(3)、113.117~119.770(3)、149.402~155.423(4)、170.626~171.220(3)、173.409~176.147(3)、177.649~182.372(4)、191.441~192.945(4)、197.020~200.074(4)、209.645~212.244(4)、213.924~216.610(3)	0.002~7.166(18)、14.522~20.319¹(7)	KRN5b¹
	6	39.080~81.971(3)、152.846~153.541(3)、154.368~155.603(3)、158.522~166.027(3)	0.158~5.476(6)、8.757~13.757(5)	无
	7	42.931~87.966(3)、101.645~104.576(3)、128.987~130.295(3)、	11.524~18.250(11)	无
	8	13.559~14.747(3)、16.339~17.187(3)、17.464~17.753(3)、18.752~19.243²(3)、19.243~20.793(3)、21.818~23.742(3)、27.676~34.289(3)、102.416~103.345(3)、113.493~115.665(4)、164.803~165.678(3)、166.280~167.568(3)、175.434~176.323(3)	0.002~6.298(6)、13.973~21.469^1,2(8)	VT2¹、BIF1²
	9	13.811~15.042(3)、23.174~27.778(3)、99.139~102.441(3)、102.441~112.272(3)、144.051~145.548(4)	0.016~6.248¹(13)、11.834~16.834(5)	PIN1a¹
	10	85.277~87.401(3)、87.401~93.374(3)、93.374~93.611(4)、93.611~103.654(3)、144.228~146.895(3)	11.397~16.397(5)、140.145~145.145¹(5)	ZFL1¹
EL	1	无	0.028~12.702(28)、23.342~33.261(18)、253.363~258.363(5)、261.460~267.978(6)	无
	2	107.210~138.761(3)	0.052~23.871¹(37)、189.668~195.769(6)、227.400~237.864(11)	ZmWUS1¹
	3	无	0.024~8.434¹(13)、18.223~26.596(7)、219.822~226.875(8)	CG1¹
	4	无	1.277~6.277(5)、213.077~218.077(8)	无
	5	无	0.063~12.244(29)、211.154~217.577(8)	无
	6	无	1.345~6.345(5)、132.529~141.427¹(10)、141.663~146.998(6)、152.955~157.955(5)	BIF4¹
性状	染色体	QTL热点区间/Mb (区间内不同独立研究检测次数)	SNP热点区间/Mb (区间内所含SNP个数)	已知基因
	7	无	159.934~167.687(9)	无
	8	无	11.862~18.246¹(7)、163.265~169.416(8)	VT2¹
	9	150.000~150.672(4)	7.308~19.148(16)、122.253~127.253(5)	无
	10	148.671~149.279(3)	0.154~8.731(10)、12.794~17.898(6)、135.064~141.798(7)、143.632~150.987(6)	无
CD	1	无	0.023~9.496(28)、19.435~33.699(12)	无
	2	无	0.156~7.484(15)、11.955~27.976(16)	无
	3	无	0.148~7.120¹(10)、21.268~27.365(7)、211.859~221.389²(9)	CG1¹、SPI1²
	4	无	0.065~7.113(13)、17.586~28.191(11)	无
	5	无	0.069~10.715(12)	无
	6	无	0.0834~5.375(6)、14.877~20.162(7)、144.695~154.634(9)	无
	7	无	12.743~21.353(8)	无
	8	无	1.272~7.549(9)	无
	9	无	0.025~6.946(13)、11.889~17.943(6)	无
	10	无	6.925~11.925(5)、13.767~18.856(7)	无
ED	4	无	239.765~246.020(6)	无
EW	1	284.975~286.103(3)	无	无
	2	42.673~50.144(3)	无	无
KNR	5	82.611~87.033(3)、92.674~142.584(3)、142.584~170.514(3)	无	无
FL	1	无	25.156~31.889¹(11)	IFA1¹
	9	无	7.308~12.380(7)	无
SR	4	无	136.449~141.449(6)	无
	5	无	70.628~76.070(9)	无

表S1 雌穗性状QTL及SNP热点区间分布汇总

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