Sequence Variation Analysis of Maize Starch Synthesis Related Gene ZmAGP2

doi:10.7668/hbnxb.20190786

Abstract

Abstract: The ZmAGP2 gene encoding ADP large subunit of glucose pyrophosphory is involved in the synthesis of corn starch,thus affecting the yield and quality of corn. Maize yield traits are controlled by multiple genes,and its genetic mechanism is very complex. This study aims to fully explore the excellent allelic variation of genes closely related to yield traits through gene sequence variation analysis,which provides a theoretical basis for improving the molecular level of maize breeding. The ZmAGP2 genes sequences of 103 inbred test populations were captured and sequenced using NimbleGen platform. ClustalX 2.0,DnaSP 6.0 and other software were used to analyze the nucleotide polymorphism of the target gene,and the neutral evolution test and haplotype analysis of the mutation site were carried out. The full-length sequence of 4 111 bp was obtained by resequencing the ZmAGP2 genes of 103 maize inbred lines. After nucleotide polymorphism analysis,a total of 112 mutation sites in the full-length sequence were detected,all of which SNP,nucleotide polymorphisms in 5' UTR segments were significantly higher than those in other segments. Polymorphism in the CDS region of the gene drived the ZmAGP2 gene into eight haplotypes encoding five different ZmAGP2 proteins. Neutral test did not detect obvious manually selected signals. The ZmAGP2 gene showed high variation,which accorded with the neutral evolution model hypothesis,was not subject to obvious artificial selection,and the protein sequence changed,which indicated that the sequence variation of the gene causes the change of the protein sequence,which lead to the change of the function of the gene.

Key words: Maize, ZmAGP2 gene, Starch synthesis, Nucleotides polymorphism, Neutral test, Haplotype

CLC Number:

S513.03
Q78

ZHANG Meng, ZHANG Hanhan, XU Min, HE Huan, WU Xueyi, Lü Yingying, ZHANG Enying. Sequence Variation Analysis of Maize Starch Synthesis Related Gene ZmAGP2[J]. ACTA AGRICULTURAE BOREALI-SINICA, 2020, 35(S1): 40-46. doi: 10.7668/hbnxb.20190786.

/ / Recommend / Download Citations

URL: http://www.hbnxb.net/EN/10.7668/hbnxb.20190786

http://www.hbnxb.net/EN/Y2020/V35/IS1/40

References

[1] Qu J Z,Xu S T,Zhang Z Q,Chen G Z,Zhong Y Y,Liu L S,Zhang R H,Xue J Q,Guo D W.Evolutionary,structural and expression analysis of core genes involved in starch synthesis[J]. Sci Rep,2018,8(1):12736.doi:10.1038/s41598-018-30411-y.
[2] Yu G W,Lü Y N,Shen L Y,Wang Y B,Qing Y,Wu N,Li Y P,Huang H H,Zhang N,Liu Y H,Hu Y F,Liu H M,Zhang J J,Huang Y B.The proteomic analysis of maize endosperm protein enriched by Phos-tag(tm)reveals the phosphorylation of Brittle-2 subunit of ADP-Glc pyrophosphorylase in starch biosynthesis process[J]. Int J Mol Sci,2019,20(4):986.doi:10.3390/ijms20040986.
[3] Zhang S L,Guo H J,Irshad A,Xie Y D,Zhao L S,Xiong H C,Gu J Y,Zhao S R,Ding Y P,Liu L X.The synergistic effects of TaAGP.L-B1 and TaSSIVb-D mutations in wheat lead to alterations of gene expression patterns and starch content in grain development[J]. PLoS One,2019,14(10):e0223783. doi:10.1371/journal.pone.0223783.
[4] Deng X,Liu Y,Xu X X,Liu D M,Zhu G R,Yan X,Wang Z M,Yan Y M. Comparative analysis of AGPase genes and encoded proteins in eight monocots and three dicots with emphasis on wheat[J].Front Plant Sci,2017,8:19. doi:10.3389/fpls.2018.00425.
[5] Slattery C J,Kavakli I H and Okita T W,Engineering starch for increased quantity and quality[J]. Trends Plant Sci, 2000,5(7):291-298.doi:10.1016/s1360-1385(00)01657-5.c.
[6] Hou J,Li T,Wang Y M,Hao C Y,Liu H X,Zhang X Y. ADP-glucose pyrophosphorylase genes,associated with kernel weight,underwent selection during wheat domestication and breeding[J].Plant Biotechnol J, 2017,15(12):1533-1543.doi:10.1111/pbi.12735.
[7] Miao H X,Sun P G,Liu Q,Liu J H,Xu B Y,Jin Z Q. The AGPase family proteins in banana:Genome-wide identification,phylogeny,and expression analyses reveal their involvement in the development,ripening,and abiotic/biotic stress responses[J]. Int J Mol Sci, 2017,18(8):1581.doi:10.3390/ijms18081581.
[8] Zeeman S C,Kossmann J S,Alison M K,Smith A M.Starch:its metabolism,evolution,and biotechnological modification in plants[J]. Annu Rev Plant Biol, 2010,61:209-234.doi:10.1146/annurev-arplant-042809- 112301.
[9] Tiessen A,Nerlich A,Faix B,Hummer C,Fox S,Trafford K,Weber H,Weschke W,Geigenberger P.Sub cellular analysis of starch metabolism in developing barley seeds using a non-aqueous fractionation method[J].J Exp Bot, 2012,63(5):2071-2087.doi:10.1093/jxb/err408.
[10] Smidansky E D,Clancy M,Meyer F D,Lanning S P,Blake N K,Talbert L E,Giroux M J.Enhanced ADP-glucose pyrophosphorylase activity in wheat endosperm increases seed yield[J]. Proc Natl Acad Sci USA,2002,99(3):1724-1729. doi:10.1073/pnas.022635299.
[11] Rose M K,Huang X Q,BruleB A. Molecular characterization and sequence diversity of genes encoding the large subunit of the ADP-glucose pyrophosphorylase in wheat(Triticum aestivum L.)[J]. J Appl Genet, 2016,57(1):15-25.doi:10.1007/s13353-015-0298-1.
[12] Deng X,Liu Y,Xu X X,Liu D M,Zhu G R,Yan X,Wang Z M,Yan Y M.Comparative proteome analysis of wheat flag leaves and developing grains under water deficit[J]. Front Plant Sci,2018,9:425.doi:10.3389/fpls.2018.00425.
[13] Chen G X,Zhen S M,Liu Y L,Yan X,Zhang M,Yan Y M. In vivo phosphoproteome characterization reveals key starch granule-binding phosphoproteins involved in wheat water-deficit response[J]. BMC Plant Biol,2017,17(1):168.doi:10.1186/s12870-017-1118-z.
[14] Murray M G,Thompson W F.Rapid isolation of high molecular weight plant DNA[J]. Nucleic Acids Res,1980,8(19):4321-4325.doi:10.1093/nar/8.19.4321.
[15] Rozas J, Ferrer-Mata A, Sánchez-DelBarrio J C, Guirao-Rico S, Librado P, Ramos-Onsins S E, Sánchez-Gracia A. DnaSP 6:DNA sequence polymorphism analysis of large data pets[J]. Mol Biol Evol, 2017,34(12):3299-3302.doi:10.1093/molbev/msx248.
[16] Tajima F.Statistical method for testing the neutral mutation hypothesis by DNA polymorphism[J].Genetics,1989,123(3):585-595.
[17] Fu Y X,Li W H.Statistical tests of neutrality of mutations[J]. Genetics,1993,133(3):693-709.
[18] Xiao Y J,Liu H J,Wu L J,Warburton M,Yan J B. Genome-wide association studies in maize:praise and stargaze[J].Mol Plant, 2017,10(3):359-374.doi:10.1016/j.molp.2016.12.008.
[19] Mafra G S,Amaral J,Antonio T D,Almeida F,Janeo E D,Vivas M,Santos P H A D,Santos J S,Pena G F,Lima V J D,Kamphorst S H,Oliveira FT D,Souza Y P D,Schwantes I A,Santos T D,Oliveira B,Rosimeire B,Maldonado C,Mora F. SNP-based mixed model association of growth-and yield-related traits in popcorn[J]. PLoS One,2019,14(6):e0218552. doi:10.1371/journal.pone.0218552.
[20] Ching A,Caldwell K S,Jung M,Dolan M,Smith O S,Tingey S,Morgante M,Rafalski A J.SNP frequency,haplotype structure and linkage disequilibrium in elite maize inbred lines[J]. BMC Genet,2002,3:19.doi:10.1186/1471-2156-3-19.
[21] Zhang E Y,Yang Z F,Wang Y F,Hu Y Y,Song X Y,Xu C W. Nucleotide polymorphisms and haplotype diversity of RTCS gene in China elite maize inbred lines[J]. PLoS One,2013,8(2):e56495.doi:10.1371/journal.pone.0056495.

Please choose a citation manager

Content to export