Chin Bull Bot ›› 2018, Vol. 53 ›› Issue (4): 487-501.doi: 10.11983/CBB17082

• EXPERIMENTAL COMMUNICATIONS • Previous Articles     Next Articles

Analysis of Meta-quantitative Trait Loci and Their Candidate Genes Related to Leaf Shape in Maize

Guo Shulei1,2, Zhang Jun1, Qi Jianshuang1, Yue Runqing1, Han Xiaohua1, Yan Shufeng1, Lu Caixia1, Fu Xiaolei1, Chen Nana1, Ku Lixia2,*(), Tie Shuanggui1,*()   

  1. 1Henan Provincial Key Lab of Maize Biology, Cereal Crops Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
    2Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agriculture University, Zhengzhou 450002, China
  • Received:2017-04-13 Accepted:2017-10-25 Online:2018-09-11 Published:2018-07-01
  • Contact: Ku Lixia,Tie Shuanggui E-mail:kulixia0371@163.com;tieshuanggui@126.com
  • About author:† These authors contributed equally to this paper

Abstract:

Leaf length, width, area, and angle are important components of plant architecture but also affect the efficiency of photosynthesis in maize. In this study, 620 quantitative trait loci (QTL) were used to construct an integrated map related to maize leaf shape; 22 maize QTL (mQTL) for leaf length, 22 for leaf width, 12 for leaf area and 17 for leaf angle were estimated by meta-analysis. Further bioinformatics analysis identified 44 candidate genes closely related to leaf shape within the mQTL region, with some unintegrated QTL. However, only 13 candidate genes, including NAL7-like, YABBY6-like, and GRF2, were located in the mQTL region. Most of the candidate genes, such as the cloned genes KNOTTED1, AN3/GIF1, rgd1/lbl1 and mwp1 in maize and SRL2-like, HYL1-like, and CYCB2;4-like in rice and Arabidopsis thaliana homologous genes were projected onto the interval of unintegrated QTL. The regulation mechanism of 44 candidate genes is summarized and analyzed in the development of leaf length, width and thickness, by proximal-distal, central-marginal and adaxial-abaxial. Only a few known genes revealed part of the molecular mechanism of leaf deve- lopment in maize. Further research of the mQTL/QTL and related genes will create a global view of the genetic architecture of maize leaf shape, provide useful biological information for fine mapping QTL, and identify more candidate genes to clarify the molecular mechanism of leaf morphogenesis and provide a theoretical base for ideal plant-architecture improvement of maize marker-assisted breeding.

Key words: maize (Zea mays), leaf length, leaf width, leaf area, leaf angle, meta-analysis, meta-QTL, candidate gene

Table 1

Summary of the QTL of leaf shape in maize reported previously"

Parents Type of Pop. Pop.
size
No. of
QTL for
LL
No. of
QTL for
LW
No. of
QTL for
LAr
No. of QTL for LA No./type
of marker
Analysis method Reference
B73×G79 F2:3 214 7 185/RFLP IM Agrama et al., 1999
B73×Mo17 RIL 180 9 192/SSR CIM Mickelson et al., 2002
H21×Mo17 F2:3 120 7 102/SSR CIM 于永涛等, 2006
Zi330×K36 F2:3 114 2 90/SSR CIM 于永涛等, 2006
Ye478×Dan340 F2:3 397 6 138/SSR CIM 路明等, 2007
Mo17×Huangzao4 RIL 239 4 2 5 98/SSR CIM 郑祖平等, 2007
Ye478×Wu312 RIL 218 7 184/SSR ICIM 刘建超等, 2010
Yu82×Shen137 F2:3 229 3 4 13 3 222/SSR CIM Ku et al., 2010, 2012a
Yu82×Yu87-1 F2:3 256 5 5 5 216/SSR CIM Ku et al., 2012b
B73/Mo17 etc. NAM 4892 36 34 30 203000/SNP GWAS Tian et al., 2011
N6×BT-1 RIL 250 6 207/SSR CIM 李贤唐等, 2011
Y105×Y106 F2 189 5 7 6 8 215/SSR ICIM 郭莹, 2012
Y114×Y115 F2 189 1 1 2 3 204/SSR ICIM 郭莹, 2012
Ye478×Wu312 RIL 218 14 7 9 184/SSR CIM Cai et al., 2012
Yu82×D132 F2:3 245 18 204/SSR CIM Ku et al., 2012
B73×1212 RIL 325 67 62 208/SSR ICIM 唐登国, 2013
B73×Mo17 RIL 93 1 2 3 IBM2 map CIM Wassom, 2013
CY5×YL106 F2:3 144 8 212/SSR CIM 刘正等, 2014
Z58/87-1//
PH6WC/Zi330
CP 228 13 225/SSR IM 张姿丽等, 2014b
T4×T19 F2:3 232 4 81/SSR CIM 张姿丽等, 2014a
Yu82×Yu87-1 RIL 208 18 1370/SNP CIM Guo et al., 2015
Yu82×Shen137 RIL 197 9 1411/SNP CIM Guo et al., 2015
Zong3×Yu87-1 RIL 223 10 1479/SNP CIM Guo et al., 2015
Yu537A×Shen137 RIL 212 9 1371/SNP CIM Guo et al., 2015
B73×Mo17 DH 221 9 17 16 12 5935/bin markers ICIM 张志腾, 2015
Xu178×K12 RIL 150 34 191/SSR CIM 常立国等, 2016
M1-7×SYF F2 259 36 218/SSR CIM 安允权等, 2016
Yu82×D132 RIL 234 5 7 4 1226/SNP CIM Wei et al., 2016

Table 2

Candidate genes for maize leaf shape of mQTL/QTL"

Bin mQTL/QTL CI (cM) Candidate gene Annotation Homologous gene E-value Reference
1.02 mQTLW1-1 153.8-158.3 GRMZM2G480386 NAL7-like Os03g0162000/YUCCA7 0 Fujino et al., 2008
1.04 q12SevLW1 270.6-286.2 GRMZM2G011483 SRL2-like Os03g19520/SRL2 0 Liu et al., 2016
1.05 mQTLW1-2 485.9-505.6 GRMZM2G141955 YABBY6-like Os12g42610/YAB6 3E-88 Toriba et al., 2007;
Zhang et al., 2009
GRMZM2G003509 PHB-like AT2G34710/AtHB14 0 Kim et al., 2003; Mallory et al., 2004
1.09 mQTLW1-3 820.6-845.5 GRMZM2G018414 GRF8 AT4G37740/AtGRF2 4E-37 Debernardi et al., 2014
1.10 q4LWm139 873.7-902.1 GRMZM2G017087 KNOTTED1 AT4G08150/KN1 2E-114 Ramirez et al., 2009
GRMZM2G178261 GRF1-like AT2G22840/AtGRF1 2E-66 Kim et al., 2003
GRMZM2G180246 AN3/GIF1 AT5G28640/AtAN3/GIF1 1E-36 Nelissen et al., 2015
1.11 q4LLm155 941.6-1022.3 GRMZM2G135447 OSH43-like Os03g0771500/OsH43 4E-99 Sentoku et al., 2000
2.02 q3LAr2a 67.5-79.7 GRMZM2G174784 AP2-like AT4G36920/AP2 7E-102 Würschum et al., 2006; Mlotshwa et al., 2006
2.02 mQTLW2-1 118.3-147.8 GRMZM2G102346 NAL1-like Os04g52479/NAL1 0 Kubo et al., 2017
GRMZM2G041223 GRF6 AT3G13960/AtGRF5 1E-36 Horiguchi et al., 2006; Debernardi et al., 2014
2.06 q4RLAr2 355.7-374.4 GRMZM2G444808 HYL1-like AT1G09700/HYL1 6E-56 Liu et al., 2011
2.06 q8SecLW2 370.0-381.6 GRMZM2G083972 LNG2-like AT3G02170/LNG2 6E-57 Lee et al., 2006
GRMZM2G161382 CYCD3;3-like AT3G50070/CYCD3;3 5E-56 Dewitte et al., 2007
2.07 q7LL2b 450.0-461.9 GRMZM2G004619 GRF4 AT4G37740/AtGRF2 5E-28 Kim et al., 2003
2.10 q12LAr2 713.1-732.4 GRMZM2G146688 ANT-like AT4G37750/ANT 1E-131 Mizukami and Fis- cher, 2000
3.02 q4LWm309 69.6-90.3 GRMZM2G143235 ROT3-like AT4G36380/ROT3 1E-176 Kim et al., 1998
3.06 mQTLW3-2 368.5-390.3 GRMZM2G118250 AS2-like AT1G65620/AS2 1E-66 Iwakawa et al., 2007
3.08 q4LWm410 613.6-653.7 GRMZM2G437460 ARF3-like AT2G33860/ARF3/ETT 1E-169 Kelley et al., 2012
4.04 q13NLW4 220.5-230.6 GRMZM2G402653 OSH1-like Os03g0727000/OsH1 1E-75 Matsuoka et al., 1993
4.06 mQTLW4 373.7-399.4 GRMZM2G124566 GRF9-like AT2G36400/AtGRF3 1E-36 Kim et al., 2003
4.08 q7LL4 429.5-451.0 GRMZM2G075117 CYCD3;1-like AT4G34160/CYCD3;1 4E-47 Dewitte et al., 2007
GRMZM2G105335 GRF3 AT3G13960/AtGRF5 8E-49 Horiguchi et al., 2006; Debernardi et al., 2014
5.03 q4LWm602 268.8-295.0 GRMZM2G361518 AGO10-like AT5G43810/AGO10/ZLL 0 Zhu et al., 2011; Roodbarkelari et al., 2015
5.03 q4LLm605 280.1-296.1 GRMZM2G171349 COW1-like AT4G34580/COW1 3E-66 Woo et al., 2007
5.06 q4LLm661 500.7-521.1 GRMZM2G034876 GRF1 AT3G13960/AtGRF5 1E-47 Horiguchi et al., 2006; Debernardi et al., 2014
5.07 mQTLW5-3 556.7-578.5 GRMZM5G893117 GRF9 AT3G13960/AtGRF5 1E-27 Horiguchi et al., 2006; Debernardi et al., 2014
6.01 q8FirLW6-1 82.3-93.9 GRMZM2G122537 PRS1-like AT2G28610/PRS1 6E-29 Matsumoto and Ok- ada, 2001; Nakata
et al., 2012
GRMZM2G020187 rgd1/lbl1 AT5G23570/SGS3 1E-157 Dotto et al., 2014
mQTL/QTL CI (cM) Candidate gene Annotation Homologous gene E-value Reference
6.01 mQTLAr6 92.8-108.9 GRMZM2G098594 GRF14 AT3G13960/AtGRF5 1E-36 Horiguchi et al., 2006; Debernardi
et al., 2014
6.02 q7PLL6 123.0-144.8 GRMZM2G073671 CYCB2;3-like AT1G20610/CYCB2;3 1E-144 Eloy et al., 2011
GRMZM2G157820 CLF-like AT2G23380/CLF 0 Menges et al., 2005; Schatlowski et al., 2010
6.04 q4LWm706 158.2-205.1 GRMZM5G850129 GRF7 AT3G13960/AtGRF5 4E-41 Horiguchi et al., 2006; Debernardi et al., 2014
7.00 q4LWm762 8.0-93.0 GRMZM2G028041 OSH15-like Os07g0129700/OsH15 1.E-168 Nagasaki et al., 2001
GRMZM2G019200 DRL1-like Os11g0312782/DRL1 0 Jun et al., 2015
7.02 q12EigLW7 200.7-217.9 GRMZM2G107377 CYCD3;2-like AT5G67260/CYCD3;2 8E-49 Dewitte et al., 2007
7.02 q12FirLW7 229.3-246.3 GRMZM2G082264 mwp1 Os09g23200/SLL1/Kan1 2E-170 Candela et al., 2008
7.03 q3LW7 380.6-498.2 GRMZM2G096709 GRF10 AT4G37740/AtGRF2 4E-29 Kim et al., 2003; Deb- ernardi et al., 2014
8.08 q3LW8 599.1-603.8 GRMZM5G874163 ARF4-like AT5G60450/ARF4 7E-120 Pekker et al., 2005;
Hunter et al., 2006
9.03 mQTLW9 206.1-230.6 GRMZM2G119359 GRF12 AT2G06200/AtGRF6 1E-30 Kim et al., 2003;
Liang et al., 2014
GRMZM5G870176 NRL-like Os12g36890/CSLD4 0 Hu et al., 2010
10.04 mQTLW10 295.6-327.3 GRMZM2G078641 GRF2 GRAT3G13960/AtGRF7 3E-156 Horiguchi et al., 2006; Debernardi et al., 2014
10.06 q1HNLAr10 367.0-383.9 GRMZM2G061287 CYCB2;4-like AT1G76310/CYCB2;4 9E-148 Menges et al., 2005; Eloy et al., 2011

Figure 1

Distribution of leaf shape mQTL on maize chromosomes in the integrated mapChr: Chromosome. The red region is the identified location of the overlaps of mQTL on the chromosome; The position distribution and the name for mQTL are listed in the left of chromosome; Marker name and genetic distance (cM) are listed in the right of chromosome."

Figure 2

Phylogenetic trees of amino acid sequences of 44 candidate genes related to leaf shape of maizeFunction of candidate genes which have been known and cloned related to maize leaf shape are highlighted in the box"

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