The maize starch synthesis ZmSSIIa elongates amylopectin chains from degree of polymerization 6-10 to degree of polymerization 12-25 in the pathway of starch biosynthesis, and plays important roles in kernel yield and quality. The analysis of sequence polymorphism of maize ZmSSIIa gene will provide information for further detection of beneficial mutants associated with yield and quality. In order to reveal the sequence polymorphism of the maize ZmSSIIa gene, a total of 4836 bp sequence of this locus is captured in 86 elite maize inbred lines through a NimbleGensequence capture array. Analysis of the sequence polymorphism reveals that there are 78 SNPs and 19 Indels in this locus. The coding sequences of the maize ZmSSIIa gene contain 24 SNPs, which divide the coding regions into 9 haploytpes, and 7 different ZmSSIIa proteins are encoded by the tested inbred lines. At least 8 recombination events are found to contribute to the haplotype diversity and linkage disequilibrium between polymorphic sites in the maize ZmSSIIa gene. According to the results of the test of neutral evolution, there is no evidence of artificial selection for this gene in the tested inbred lines.
YANG Zefeng
,
ZHANG Enying
,
DU Cancan
,
MA Sijia
,
HU Yunyun
,
XIE Zhengwen
,
PAN Liang
,
CHEN Qing
,
XU Chenwu
. Analysis of Sequence Polymorphism for Maize Starch Biosynthesis Related Gene ZmSSIIa[J]. Science & Technology Review, 2014
, 32(36)
: 52
-58
.
DOI: 10.3981/j.issn.1000-7857.2014.36.008
[1] Tian Z, Qian Q, Liu Q, et al. Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualities[J]. Proceedings of the National Academy of Sciences of the United States of America,2009, 106(51): 21760-21765.
[2] Yang Z, Wang Y, Xu S, et al. Molecular evolution and functional divergence of soluble starch synthase genes in cassava (manihot esculenta crantz)[J]. Evolutionary Bioinformatics Online, 2013, 9: 239-249.
[3] Martin C, Smith A M. Starch biosynthesis[J]. The Plant cell, 1995, 7(7): 971-985.
[4] 谭彩霞, 封超年, 陈静, 等. 作物淀粉合成关键酶及其基因表达的研究 进展[J]. 麦类作物学报, 2008, 28(5): 912-919. Tan Caixia, Feng Chaonian, Chen Jing, et al. Progress on key enzymes involved in crop starch synthesis and their gene expression[J]. Journal of Triticeae Crops, 2008, 28(5): 912-919.
[5] Leterrier M, Holappa L D, Broglie K E, et al. Cloning, characterisation and comparative analysis of a starch synthase IV gene in wheat: Functional and evolutionary implications[J]. BMC Plant Biology, 2008, 8: 98.
[6] Grimaud F, Rogniaux H, James M G, et al. Proteome and phosphoproteome analysis of starch granule-associated proteins from normal maize and mutants affected in starch biosynthesis[J]. Journal of Experimental Botany, 2008, 59(12): 3395-3406.
[7] Zhang X, Colleoni C, Ratushna V, et al. Molecular characterization demonstrates that the Zea mays gene sugary2 codes for the starch synthase isoform SSIIa[J]. Plant Molecular Biology, 2004, 54(6): 865-879.
[8] Fulton T M, Chunwongse J, Tanksley S D. Microprep protocol for extraction of DNA from tomato and other herbaceous plants[J]. Plant Molecular Biology Reporter, 1995, 13(3): 207-209.
[9] Aiyar A. The use of CLUSTAL W and CLUSTAL X for multiple sequence alignment[J]. Methods in Molecular Biology, 2000, 132: 221-241.
[10] Librado P, Rozas J. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data[J]. Bioinformatics, 2009, 25(11): 1451-1452.
[11] 朱彩梅, 张京. 大麦糯性相关基因Wx 单核苷酸多态性分析[J]. 中国农 业科学, 2010, 43(5): 889-898. Zhu Caimei, Zhang Jing. Single nucleotide polymorphism of Wx gene associated with amylose content in barley germplasm[J]. Scientia Agricultura Sinica, 2010, 43(5): 889-898.
[12] Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism[J]. Genetics, 1989, 123(3): 585-595.
[13] Fu Y X, Li W H. Statistical tests of neutrality of mutations[J]. Genetics, 1993, 133(3): 693-709.
[14] Bradbury P J, Zhang Z, Kroon D E, et al. TASSEL: Software for association mapping of complex traits in diverse samples[J]. Bioinformatics, 2007, 23(19): 2633-2635.
[15] Remington D L, Thornsberry J M, Matsuoka Y, et al. Structure of linkage disequilibrium and phenotypic associations in the maize genome[J]. Proceedings of the National Academy of Sciences of the United States of America, 2001, 98(20): 11479-11484.
[16] Walbot V. 10 reasons to be tantalized by the B73 maize genome[J]. PLoS Genetics, 2009, 5(11): e1000723.
[17] Xu S, Yang Z, Zhang E, et al. Nucleotide diversity of Maize ZmBT1 gene and association with starch physicochemical properties[J]. PloS One, 2014, 9(8): e103627.
[18] Gore M A, Chia J M, Elshire R J, et al. A first-generation haplotype map of maize[J]. Science, 2009, 326(5956): 1115-1117.
[19] Yan J, Warburton M, Crouch J. Association mapping for enhancing maize (Zea mays L.) genetic improvement[J]. Crop Science, 2011, 51(2): 433-449.
[20] Ching A, Caldwell K S, Jung M, et al. SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines[J]. BMC Genetics, 2002, 3: 19.
[21] Doebley J F, Gaut B S, Smith B D. The molecular genetics of crop domestication[J]. Cell, 2006, 127(7): 1309-1321.
[22] Wang H, Nussbaum-Wagler T, Li B, et al. The origin of the naked grains of maize[J]. Nature, 2005, 436(7051): 714-719.
[23] Palaisa K, Morgante M, Tingey S, et al. Long-range patterns of diversity and linkage disequilibrium surrounding the maize Y1 gene are indicative of an asymmetric selective sweep[J]. Proceedings of the National Academy of Sciences of the United States of America, 2004, 101(26): 9885-9890.
