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中国生物工程杂志

China Biotechnology
China Biotechnology  2021, Vol. 41 Issue (12): 30-46    DOI: 10.13523/j.cb.2111004
    
Progress on Dissecting Genetic Architecture and Formation Mechanism of Maize Ear Traits
YIN Fang-bing1,2,WANG Cheng1,2,LONG Yan1,2,3,DONG Zhen-ying1,2,**(),WAN Xiang-yuan1,2,3,**()
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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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 wordsEar traits      Quantitative trait locus(QTL) mapping      Genome-wide association study(GWAS)      Genetic structure      Gene     
Received: 31 October 2021      Published: 13 January 2022
ZTFLH:  Q819  
Corresponding Authors: Zhen-ying DONG,Xiang-yuan WAN     E-mail: zydong@ustb.edu.cn;wanxiangyuan@ustb.edu.cn
Cite this article:

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.

URL:

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

Fig.1 Chromosomal distribution of ear-trait-related QTLs and SNPs in maize CD:Cob diameter;CW:Cob weight;ED:Ear diameter;EL:Ear length;ETB:Ear tip-barrenness;EW:Ear weight;FL:Fruit length;KNR:Kernel number per row;KRN:Kernel row number;KWE:Kernel weight per ear;SR:Setting rate
性状 Chr1 Chr2 Chr3 Chr4 Chr5 Chr6 Chr7 Chr8 Chr9 Chr10 合计
EL 24/91 17/89 12/36 7/32 21/61 8/39 6/29 6/37 10/38 10/40 121/492
ED 6/6 3/1 3/5 1/10 2/5 1/2 2/4 3/4 10/1 4/0 35/38
EW 8/7 9/2 4/3 9/2 7/5 2/2 9/0 5/3 6/4 1/1 60/29
KRN 26/50 28/47 22/33 40/72 38/49 11/23 18/27 27/23 24/32 11/26 245/382
KNR 6/2 5/7 3/4 5/1 9/3 2/1 1/1 4/2 4/2 5/1 44/24
CW 8/6 10/10 3/6 3/3 7/5 5/3 5/5 6/5 4/2 1/1 52/46
CD 8/64 7/43 0/39 4/40 2/32 3/33 2/24 3/23 7/27 1/19 37/344
ETB 0/5 5/0 1/1 0/0 0/0 0/3 3/0 0/0 0/1 3/0 12/10
KWE 0/0 2/2 1/0 1/0 2/1 1/1 3/1 0/2 2/0 0/0 12/7
FL 0/18 0/11 0/0 0/0 0/2 0/2 0/1 0/6 0/8 0/1 0/49
SR 0/9 0/0 0/0 0/7 0/16 0/1 0/3 0/3 0/8 0/0 0/47
合计 86/258 86/212 49/127 70/167 88/179 33/110 49/95 54/108 67/123 36/89 618/1 468
Table 1 Summary of the number of maize ear-trait-related QTLs and SNPs
Fig.2 Chromosomal distribution of ear-trait-related QTL and SNP hotspots and cloned genes in maize
性状 染色体 QTL与SNP共同定位热点区间/Mb 热点区间内所含基因
KRN 2 4.863~5.588、22.071~26.774
3 223.243~224.823
4 7.251~7.619、10.673~10.957、200.053~208.8871 UB31
5 14.522~15.2691、19.174~20.319 KRN5b1
8 13.973~14.747、16.339~17.187、17.464~17.753、18.752~19.2431、19.243~20.793 BIF11
9 13.811~15.042
10 144.228~145.145
EL 10 148.671~149.279
Table 2 Chromosomal distribution of the overlaps of maize ear-trait-related QTL and SNP hotspots
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]
Table 3 Summary of the cloned ear-trait-related genes
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) IFA11IDS12
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)
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)
7 42.931~87.966(3)、101.645~104.576(3)、128.987~130.295(3)、 11.524~18.250(11)
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)、13.973~21.4691,2(8) VT21BIF12
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 0.028~12.702(28)、23.342~33.261(18)、253.363~258.363(5)、261.460~267.978(6)
2 107.210~138.761(3) 0.052~23.8711(37)、189.668~195.769(6)、227.400~237.864(11) ZmWUS11
3 0.024~8.4341(13)、18.223~26.596(7)、219.822~226.875(8) CG11
4 1.277~6.277(5)、213.077~218.077(8)
5 0.063~12.244(29)、211.154~217.577(8)
6 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
7 159.934~167.687(9)
8 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)
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)
CD 1 0.023~9.496(28)、19.435~33.699(12)
2 0.156~7.484(15)、11.955~27.976(16)
3 0.148~7.1201(10)、21.268~27.365(7)、211.859~221.3892(9) CG11SPI12
4 0.065~7.113(13)、17.586~28.191(11)
5 0.069~10.715(12)
6 0.0834~5.375(6)、14.877~20.162(7)、144.695~154.634(9)
7 12.743~21.353(8)
8 1.272~7.549(9)
9 0.025~6.946(13)、11.889~17.943(6)
10 6.925~11.925(5)、13.767~18.856(7)
ED 4 239.765~246.020(6)
EW 1 284.975~286.103(3)
2 42.673~50.144(3)
KNR 5 82.611~87.033(3)、92.674~142.584(3)、142.584~170.514(3)
FL 1 25.156~31.8891(11) IFA11
9 7.308~12.380(7)
SR 4 136.449~141.449(6)
5 70.628~76.070(9)
Table S1 Summary of the chromosomal distribution of maize ear-trait-related QTL and SNP hotspots
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