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Mapping of QTLs for ear-related traits and prediction of key candidate genes in maize

ZHENG Xue-Qing1,WANG Xing-Rong2,ZHANG Yan-Jun2,GONG Dian-Ming1,*,QIU Fa-Zhan1,*   

  1. 1 National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Wuhan, 430070, China; 2 Gansu Academy of Agricultural Sciences, Lanzhou 730070, Gansu, China
  • Received:2023-10-25 Revised:2024-01-12 Accepted:2024-01-12 Published:2024-02-19
  • Supported by:
    This study was supported by the Key Program of Action Plan to Revitalize Inner Mongolia through Science and Technology (2022EEDSKJXM011, 2022EEDSKJXM011-1) and the National Key Research and Development Program of Shandong Province (2022CXPT014).

Abstract:

Maize ear related traits are directly related to yield, and the analysis of their genetic basis is of great significance for guiding maize genetic improvement. In this study, the phenotypic characteristics of eight traits were identified in 168 high generation backcross recombinant inbred lines (AB-RILs) in six environments over three years. QTLs for eight traits were mapped with 11,407 SNP markers generated by 10 K liquid chip in maize. A total of 32 QTL related to eight ear traits were identified in this study, including five environmentally consistent QTLs and three pleiotropic QTL. Further, we used the genotypic and phenotypic data of 507 maize inbred lines to analyze the candidate regions of major QTL and identified 19 candidate genes that might be related to ear shape. We finally speculated four genes as candidate genes based on the analysis of evolution and expression of the genes. These results provide the important marker information for the genetic improvement of ear traits in maize breeding and offered guidance for the cloning of genes related to ear traits. 

Key words: maize, AB-RIL population, ear, kernel, QTL mapping, candidate regional association analysis

[1] Zhang H W, Lu Y T, Ma Y T, Fu J J, Wang G Y. Genetic and molecular control of grain yield in maize. Mol Breed, 2021, 41: 18.

[2] 李燕, 谭君, 李红梅, 魏明, 何立群, 赵后娟, 杜林, 刘可心, 邓路长, 杨俊品, 唐海涛. 高赖氨酸玉米F2:3群体穗部性状与产量的相关及通径分析. 安徽农业科学, 2020, 48(8): 41-42.

Li Y, Tan J, Li H M, Wei M, He L Q, Zhao H J, Du L, Liu K X, Deng L C, Yang J P, Tang H T. Correlation and path analysis of ear character in F2:3 population derived from high lysine content maize hybrid Quanyu No. 9. J Anhui Agric Sci, 2020, 48(8): 41-42 (in Chinese with English abstract).

[3] Chen Z L, Wang B B, Dong X M, Liu H, Ren L H, Chen J, Hauck A, Song W B, Lai J S. An ultra-high-density bin-map for rapid QTL mapping for tassel and ear architecture in a large F₂ maize population. BMC Genomics, 2014, 15: 433.

[4] Huo D A, Ning Q, Shen X M, Liu L, Zhang Z X. QTL Mapping of kernel number-related traits and validation of one major QTL for ear length in maize. PLoS One, 2016, 11: e0155506.

[5] Chen J F, Zhang L Y, Liu S T, Li Z M, Huang R R, Li Y M, Cheng H L, Li X T, Zhou B, Wu S W, Chen W, Wu J Y, Ding J Q. The genetic basis of natural variation in kernel size and related traits using a four-way cross population in maize. PLoS One, 2016, 11: e0153428.

[6] Hao D R, Xue L, Zhang Z L, Cheng Y J, Chen G Q, Zhou G F, Li P C, Yang Z F, Xu C W. Combined linkage and association mapping reveal candidate loci for kernel size and weight in maize. Breed Sci, 2019, 69: 420-428.

[7] Liu C L, Zhou Q, Dong L, Wang H, Liu F, Weng J F, Li X H, Xie C X. Genetic architecture of the maize kernel row number revealed by combining QTL mapping using a high-density genetic map and bulked segregant RNA sequencing. BMC Genomics, 2016, 17: 915.

[8] Liu M, Tan X L, Yang Y, Liu P, Zhang X X, Zhang Y C, Wang L, Hu Y, Ma L L, Li Z L, Zhang Y L, Zou C Y, Lin H J, Gao S B, Lee M, Lübberstedt T, Pan G T, Shen Y O. Analysis of the genetic architecture of maize kernel size traits by combined linkage and association mapping. Plant Biotechnol J, 2020, 18: 207-221.

[9] Yang C, Zhang L, Jia A M, Rong T Z. Identification of QTL for maize kernel yield and kernel-related traits. J Genet, 2016, 95: 239-247.

[10] Yang X H, Gao S B, Xu S T, Zhang Z X, M. Prasanna B, Li L, Li J S, Yan J B. Characterization of a global germplasm collection and its potential utilization for analysis of complex quantitative traits in maize. Mol Breed, 2011, 28: 511–526.

[11] Yang N, Liu J, Gao Q, Gui S T, Chen L, Yang L F, Huang J, Deng T Q, Luo J Y, He L J, Wang Y B, Xu P W, Peng Y, Shi Z X, Lan L, Ma Z Y, Yang X, Zhang Q Q, Bai M Z, Li S, Li W Q, Liu L, Jackson D, Yan J B. Genome assembly of a tropical maize inbred line provides insights into structural variation and crop improvement. Nat Genet, 2019, 51: 1052–1059.

[12] Bernardi J, Lanubile A, Li Q B, Kumar D, Kladnik A, Cook S D, Ross J J, Marocco A, Chourey P S. Impaired auxin biosynthesis in the defective endosperm18 mutant is due to mutational loss of expression in the ZmYuc1 gene encoding endosperm-specific YUCCA1 protein in maize. Plant Physiol, 2012, 160:1318-1328.

[13] 席先梅. 基于导入系群体玉米遗传图谱构建及重要农艺性状QTL定位. 内蒙古农业大学博士学位论文, 内蒙古呼和浩特, 2018.

Xi X M. Construction of Genetic Linkage Map and Identification of QTLs for Important Agronomic Traits in Introgression Lines of Maize. PhD Dissertation of Graduate School of Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China, 2018 (in Chinese with English abstract).

[14] Liu J, Huang J, Guo H, Lan L, Wang H Z, Xu Y C, Yang X H, Li W Q, Tong H, Xiao Y J, Pan Q C, Qiao F, Raihan M S, Liu H J, Zhang X H, Yang N, Wang X Q, Deng M, Jin M L, Zhao L J, Luo X, Zhou Y, Li X, Zhan W, Liu N N, Wang H, Chen G S, Li Q, Yan J B. The conserved and unique genetic architecture of kernel size and weight in maize and rice. Plant Physiol, 2017, 175: 774-785.

[15] Lu X, Zhou Z Q, Yuan Z H, Zhang C S, Hao Z F, Wang Z H, Li M S, Zhang D G, Yong H J, Han J N, Li X H, Weng J F. Genetic dissection of the general combining ability of yield-related traits in maize. Front Plant Sci, 2020, 11: 788.

[16] Zhang X X, Guan Z R, Li Z L, Liu P, Ma L L, Zhang Y C, Pan L, He S J, Zhang Y L, Li P, Ge F, Zou C Y, He Y C, Gao S B, Pan G T, Shen Y O. A combination of linkage mapping and GWAS brings new elements on the genetic basis of yield-related traits in maize across multiple environments. Theor Appl Genet, 2020, 133: 2881-2895.

[17] Chen L, An Y X, Li Y X, Li C H, Shi Y S, Song Y C, Zhang D F, Wang T Y, Li Y. Candidate loci for yield-related traits in maize revealed by a combination of metaQTL analysis and regional association mapping. Front Plant Sci, 2017, 8: 2190.

[18] 郭海平. 玉米穗粗主效 QTL qED3 的精细定位和候选基因克隆. 河南农业大学硕士学位论文, 河南郑州, 2018.

Guo H P. Fine Mapping and Cloning of the Ear Diameter QTL qED3 in Maize. MS Thesis of Henan Agricultural University, Zhengzhou, Henan, China, 2018 (in Chinese with English abstract).

[19] 涂亮, 高媛, 刘鹏飞, 郭向阳, 王安贵, 何兵, 刘颖, 祝云芳, 吴迅, 陈泽辉. 玉米穗长主效QTL q21EL-GZ 的精细定位. 植物遗传资源学报, 2021, 22: 13941401.

Tu L, Gao Y, Liu P F, Guo X Y, Wang A G, He B, Liu Y, Zhu Y F, Wu X, Chen Z H. Fine mapping of the ear length major QTL q21EL-GZ in maize. J Plant Genet Res, 2019, 22: 1394–1401 (in Chinese with English abstract).

[20] 赵强. 基于两个F2:3家系的玉米产量相关性状QTL定位及候选基因分析. 贵州大学硕士学位论文, 贵州贵阳, 2020

Zhao Q. QTL Mapping and Candidate Gene Analysis of Maize Yield-Related Traits by Using Two Maize F2:3 Families. MS Thesis of Guizhou University, Guiyang, Guizhou, China, 2020 (in Chinese with English abstract).

[21] 赵强, 陈柔屹, 王安贵, 郭向阳, 刘鹏飞, 祝云芳, 吴迅, 陈泽辉. 基于高密度 SNP 标记对玉米穗部相关性状的QTL定位及候选基因分析. 玉米科学, 2021, 29: 3641 (in Chinese with English abstract).

Zhao Q, Chen R Y, Wang A G, Guo X Y, Liu P F, Zhu Y F, Wu X, Chen Z H. QTL mapping and candidate gene analysis about ear-related traits in maize based on high density SNP markers. J Maize Sci, 2012, 29: 36–41 (in Chinese with English abstract).

[22] Gong D M, Tan Z D, Zhao H L, Pan Z Y, Sun Q, Qiu F Z. Fine mapping of a kernel length-related gene with potential value for maize breeding. Theor Appl Genet, 2021, 134: 1033-1045.

[23] Han X S, Qin Y, Sandrine AMN, Qiu F Z. Fine mapping of qKRN8, a QTL for maize kernel row number, and prediction of the candidate gene. Theor Appl Genet, 2020, 133: 3139-3150.

[24] Huang J, Lu G, Liu L, Raihan M S, Xu J T, Jian L M, Zhao L X, Tran T M, Zhang Q H, Liu J, Li W Q, Wei C X, Braun D M, Li Q, Fernie A R, Jackson D, Yan J B. The kernel size-related quantitative trait locus qKW9 encodes a pentatricopeptide repeat protein that affects photosynthesis and kernel filling. Plant Physiol, 2020, 183: 1696-1709.

[25] Li W L, Bai Q H, Zhan W M, Ma C Y, Wang S Y, Feng Y Y, Zhang M D, Zhu Y, Cheng M, Xi Z Y. Fine mapping and candidate gene analysis of qhkw5-3, a major QTL for kernel weight in maize. Theor Appl Genet, 2019, 132: 2579-2589.

[26] Nie N N, Ding X Y, Chen L, Wu X, An Y X, Li C H, Song Y C, Zhang D F, Liu Z Z, Wang T Y, Li Y, Li Y X, Shi Y S. Characterization and fine mapping of qkrnw4, a major QTL controlling kernel row number in maize. Theor Appl Genet, 2019, 132: 3321-3331.

[27] Wang G Y, Zhao Y M, Mao W B, Ma X J, Su C F. QTL analysis and fine mapping of a major QTL conferring kernel size in maize (Zea mays). Front Genet, 2020, 11: 603920.

[28] Wang C, Li H G, Long Y, Dong Z Y, Wang J H, Liu C, Wei X, Wan X Y. A systemic investigation of genetic architecture and gene resources controlling kernel size-related traits in maize. Int J Mol Sci, 2023, 24: 1025.

[29] Wang J, Lin Z L, Zhang X, Liu H Q, Zhou L N, Zhong S Y, Li Y, Zhu C, Lin Z W. krn1, a major quantitative trait locus for kernel row number in maize. New Phytol, 2019, 223: 1634–1646.

[30] Luo Y, Zhang M L, Liu Y, Liu J, Li W Q, Chen G S, Peng Y, Jin M, Wei W J, Jian L M, Yan J, Fernie A R, Yan J B. Genetic variation in YIGE1 contributes to ear length and grain yield in maize. New Phytol, 2022, 234: 513–526.

[31] Liu L, Du Y F, Shen X M, Li M F, Sun W, Huang J, Liu Z J, Tao Y S, Zheng Y L, Yan J B, Zhang Z X. KRN4 controls quantitative variation in maize kernel row number. PLoS Genet, 2015, 11: e1005670.

[32] Chen L, Li YX, Li C, Shi Y, Song Y, Zhang D, Wang H, Li Y, Wang T. The retromer protein ZmVPS29 regulates maize kernel morphology likely through an auxin-dependent process(es). Plant Biotechnol J, 2020, 18: 1004–1014

[33] Jia H T, Li M F, Li W Y, Liu L, Jian Y N, Yang Z X, Shen X M, Ning Q, Du Y F, Zhao R, Jackson D, Yang X H, Zhang Z X. A serine/threonine protein kinase encoding gene KERNEL NUMBER PER ROW6 regulates maize grain yield. Nat Commun, 2020, 11: 988.

[34] Ning Q, Jian Y N, Du Y F, Li Y F, Shen X M, Jia H T, Zhao R, Zhan J M, Yang F, Jackson D, Liu L, Zhang Z X. An ethylene biosynthesis enzyme controls quantitative variation in maize ear length and kernel yield. Nat Commun, 2021, 12: 5832.

[35] Sun Q, Li Y F, Gong D M, Hu A Q, Zhong W S, Zhao H L, Ning Q, Tan Z D, Liang K, Mu L Y, Jackson D, Zhang Z X, Yang F, Qiu F Z. A NAC-EXPANSIN module enhances maize kernel size by controlling nucellus elimination. Nat Commun, 2022, 13: 5708.

[36] Zhang S, Deng L, Cheng R, Hu J, Wu C Y. RID1 sets rice heading date by balancing its binding with SLR1 and SDG722. J Integr Plant Biol, 2022, 64: 149-165.

[37] Stelpflug S C, Sekhon R S, Vaillancourt B, Hirsch C N, Buell C R, de Leon N, Kaeppler S M. An expanded maize gene expression atlas based on RNA sequencing and its use to explore root development. Plant Genome, 2016, 9: plantgenome2015.04.0025.

[38] Walley J W, Sartor R C, Shen Z, Schmitz R J, Wu K J, Urich M A, Nery J R, Smith L G, Schnable J C, Ecker J R, Briggs S P. Integration of omic networks in a developmental atlas of maize. Science, 2016, 353: 814-818.

[39] Ohta M, Takaiwa F. OsERdj7 is an ER-resident J-protein involved in ER quality control in rice endosperm. J Plant Physiol, 2020, 245: 153109.

[40] Scholl S, Hillmer S, Krebs M, Schumacher K. ClCd and ClCf act redundantly at the trans-Golgi network/early endosome and prevent acidification of the Golgi stack. J Cell Sci, 2021, 134: jcs258807.

[41] Derkacheva M, Liu S J, Figueiredo DD, Gentry M, Mozgova I, Nanni P, Tang M, Mannervik M, Köhler C, Hennig L. H2A deubiquitinases UBP12/13 are part of the Arabidopsis polycomb group protein system. Nat Plants, 2016, 2: 16126.

[42] Cui X, Lu F L, Li Y, Xue Y M, Kang Y Y, Zhang S B, Qiu Q, Cui X K, Zheng S Z, Liu B, Xu X D, Cao X F. Ubiquitin-specific proteases UBP12 and UBP13 act in circadian clock and photoperiodic flowering regulation in Arabidopsis. Plant Physiol, 2013, 162: 897-906.

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