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Acta Agron Sin ›› 2011, Vol. 37 ›› Issue (10): 1724-1734.doi: 10.3724/SP.J.1006.2011.01724

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Analysis of Gene Glyma13g21630 Diversity in Cultivated (G. max) and Wild (G. soja) Soybeans

ZHANG Le,Li Ying-Hui**,LIU Zhang-Xiong,QIU Li-Juan*   

  1. National Key Facility for Crop Gene Resources and Genetic Improvement / Key Laboratory of Germplasm Utilization, Ministry of Agriculture / Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
  • Received:2011-03-15 Revised:2011-06-25 Online:2011-10-12 Published:2011-07-28
  • Contact: 邱丽娟, E-mail: qiu_lijuan@263.net, Tel: 010-82105841

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Abstract: Glyma13g21630 from soybean is homologous with a gene related to leaf size from Arabidopisis thaliana, and it experienced man-made selection during domestication in small sample test. This paper aims at analyzing single nucleotide polymorphism of Glyma13g21630 in large sample test and providing the foundation for tracing back to soybean domestication and analyzing the genetic basis of domesticated traits. According to Sanger method, PCR products of Glyma13g21630 from 49 wild soybean and 84 cultivars (including 46 landraces and 38 cultivars) were sequenced. The distribution patterns of single nucleotide polymorphism (SNP) for Glyma13g21630 were summarized. Using DNAStar, Mega, DNAsp and Tassel software tools, a total of 29 polymorphism sites were identified, which included 22 SNPs and seven InDels with frequencies of 1SNP/138 bp and 1InDel/434 bp, respectively. There were rich regions for nucleotide variation in intron three and intron five and less variations in other regions. Haplotype analysis indicated that the number of polymorphic loci was reducing from wild soybean to cultivated soybean, and the distribution range was correspondingly narrowed. Linkage disequilibrium analysis demonstrated that 42.86% of SNP sites in wild soybean were at significant linkage disequilibrium levels. The high ratio of Ka/Ks illustrated that some sites suffered strong positive selection pressure, which resulted in the reduction of polymorphism. The favored variation of Glyma13g21630 has been fixed in cultivated soybean, showing a bottleneck effect simultaneously.

Key words: Soybean, Glyma13g21630, Single nucleotide polymorphism, Haplotype

[1]Wang X J, Reyes J L, Chua N H, Gassterland T. Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets. Genome Biol, 2004, 5: 1–15
[2]Jin J, Huang W, Gao J P, Yang J, Shi M, Zhu M Z, Luo D, Lin H X. Genetic control of rice plant architecture under domestication. Nat Genet, 2008, 40: 1365–1369
[3]Thubrer C S, Reagon M, Rross B L, Olsen K M, Jia Y L, Caicedo A L. Molecular evolution of shattering loci in US weedy rice. Mol Ecol, 2010, 19: 3271–3284
[4]Zhou X-A(周新安), Peng Y-H(彭玉华), Wang G-X(王国勋), Chang R-Z(常汝镇). Preliminary studies on the centres of genetic diversity and origination of cultivate soybeans in China. Sci Agric Sin (中国农业科学), 1998, 31(3): 37–43 (in Chinese with English abstract)
[5]Zhao T-J(赵团结), Gai J-Y(盖钧镒), Li W-H(李旺海), Xing H(邢邯), Qiu J-X(邱家驯). Advances in breeding for super high-yielding soybean cultivars. Sci Agric Sin (中国农业科学), 2006, 39(1): 29–37 (in Chinese with English abstract)
[6]Palatnik J, Allen E, Wu X L, Schommer C, Schwab R, Currington J C, Weigel D. Control of leaf morphogenesis by microRNAs. Nature, 2003, 425: 257–263
[7]Gorou H, Ali F, Ushio F, Hirokazu T. Coordination of cell proliferation and cell expansion in the control of leaf size in Arabidopsis thaliana. J Plant Res, 2006, 119: 37–42
[8]Ascencio-Ibanez J T, Sozzani R, Lee T J, Chu T M, Wolfinger R D, Cella Rino, Hanley-Bowdoin L. Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminvirus infection, Plant Physiol, 2008, 148: 436–454
[9]Wang L, Hao L, Li X, Hu S, Ge S, Yu J. SNP deserts of Asian cultivated rice: genomic regions under domestication. Evol Biol, 2009, 22: 751–761
[10]Joseph A H, Walter R F, Randy C S, Grace A W, Susan L J, Silvia R C. Molecular marker analysis of seed size in soybean. Crop Sci, 2003, 43: 68–74
[11]Mian M A R, Bailey M A, Tamulonis J P, Shipe E R, Carter T E, Parrott W A, Ashley D A, Hussey R S, Boerma H R. Molecular markers associated with seed weight in two soybean populations. Theor Appl Genet, 1996, 93: 1011–1016
[12]Hyten D L, Pantalone V R, Sams C E, Saxton A M, Landau-Ellis D, Stefaniak T R. Seed quality QTL in a prominent soybean population. Theor Appl Genet, 2004, 109: 552–561
[13]Specht J E, Chase K, Macrander M, Graef G L, Chung J, Markwell J P, Germann M, Orf J H, Lark K G. Soybean response to water: a QTL analysis of drought tolerance. Crop Sci, 2001, 41: 493–509
[14]Qiu L-J(邱丽娟), Li Y-H(李英慧), Guan R-X(关荣霞), Liu Z-X(刘章雄), Wang L-X(王丽侠), Chang R-Z(常汝镇). Establishment, representative testing and research progress of soybean core collection and mini core collection. Acta Agron Sin (作物学报), 2009, 35(4): 571–579 (in Chinese with English abstract)
[15]Rozas J, Sánchez-DelBarrio J C, Messeguer X, Rozas R. DnaSP, DNA polymorphism analysis by the coalescent and other methods. Bioinformatics, 2003, 19: 2496–2497
[16]Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol, 2007, 24: 1596–1599
[17]Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 1989, 123: 585–95
[18]Fisher R A. The mathematical distribution used in the common tests of significance. Econometrica, 1935, 98: 39–54
[19]Nielsen R. Molecular signatures of natural selection. Ann Rev Genet, 2005, 39: 197–218
[20]Hyten D L, Choi I Y, Song Q J, Shoemaker R C, Nelson R L, Costa J M, Specht J E, Cregan P B. Highly variable patterns of linkage disequilibrium in multiple soybean populations. Genetics, 2007, 175: 1937–1944
[21]Zhu Y L, Song Q J, Hyten D L, Van Tassell C P, Matukumalli L K, Grimm D R, Hyatt S M, Fickus E W, Young N D, Cregan P B. Single-nucleotide polymorphisms in soybean. Genetics, 2003, 163: 1123–1134
[22]Choi I Y, Hyten D L, Matukumalli L K, Song Q J, Chaky J M, Quigley C V, Chase K, Lark K G, Reiter R S, Yooh M S, Hwang E Y, Yi S I, Yong N D, Shoemaker R C, Tassll C P, Specht J E. A soybean transcript map: gene distribution, haplotype and SNP analysis. Genetics, 2007, 176: 685–696
[23]Liu C-G(刘传光), Zhang G-Q(张桂权). Single nucleotide polymorphism (SNP) and its application in rice. Hereditas, 2006, 28(6): 737–744 (in Chinese with English abstract)
[24]Guillet-Claude C, Birolleau-Touchard C, Manicacci D, Rogowsky P M, Rigau J, Murigneux A, Martinant J P, Barriere Y. Nucleotide diversity of the ZmPox3 maize peroxidase gene: relationships between a MITE insertion in exon 2 and variation in forage maize digestibility. BMC Genet, 2004, 16, 5: 19
[25]Sachidanandam R, Weissman D, Schmidt S C, Kakol J M, Stein L D, Marth G, Sherry S, Mullikin J C, Mortimore B J, Willey D L, Hunt S E, Cole C G, Coggill P C, Rice C M, Ning Z, Rogers J, Bentley D R, Kwok P Y, Mardis E R, Yeh R T, Schultz B, Cook L, Davenport R, Dante M, Fulton L, Hillier L, Waterston R H, McPherson J D, Gilman B, Schaffner S, Van Etten W J, Reich D, Higgins J, Daly M J, Blumenstiel B, Baldwin J, Stange-Thomann N, Zody M C, Linton L, Lander E S, Altshuler D. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature, 2001, 15, 409: 928–933
[26]Chen J-B(陈吉宝), Jing R-L(景蕊莲), Yuan H-Y(员海燕), Wei B(卫波), Chang X-P(昌小平). Single nucleotide polymorphism of TaDREB1 gene in wheat germplasm. Sci Agric Sin (中国农业科学), 2005, 38: 2387–2394 (in Chinese with English abstract)
[27]Wang A-P(王爱萍), Mao X-G(毛新国), Jing R-L(景蕊莲), Chang X-P(昌小平), Yang W-D(杨武德). Single nucleotide polymorphism of TaMyb2-II gene in common wheat (Triticum aestivum L.) and its relatives. Acta Agron Sin (作物学报), 2006, 32(12): 1809–1816 (in Chinese with English abstract)
[28]Rickert A M, Kim J H, Meyer S, Nagel A, Ballvora A, Oefner P J, Gebhardt C. First-generation SNP/InDel markers tagging loci for pathogen resistance in the potato genome. Plant Biotechnol J, 2003, 1: 399–410
[29]Tian Z X, Wang X B, Lee R, Li Y H, Specht J E, Nelson R L, McClean P E, Qiu L J, Ma J X. Artificial selection for feterminate growth habit in soybean. Proc Natl Acad Sci USA, 2010, 107: 8563-8568.
[30]Wu X-L(吴晓雷), He C-Y(贺超英), Chen S-Y(陈受宜), Zhuang B-C(庄炳昌), Wang K-J(王克晶), Wang X-C(王学臣). Phylogenetic analysis of interspecies in genus Glycine through SSR markers. Acta Genet Sin (遗传学报), 2001, 28: 359–366 (in Chinese with English abstract)
[31]Hyten D L, Song Q J, Zhu Y L, Choi I Y, Nelson R L, Costa J M, Specht J E, Shoemaker R C, Cregan P B. Impacts of genetic bottlenecks on soybean genome diversity. Proc Natl Acad Sci USA, 2006, 103: 16666–16671
[32]Tenaillon M, Sawkins M C, Long A D, Gaut R L, Doebley J F, Gaut B S. Patterns of DNA sequence polymorphisms along chromosome 1 of maize (Zea mays ssp. may L). Proc Natl Acad Sci USA, 2001, 98: 9161–9166
[33]Ching A, Katherine S C, Mark J, Maurine D, Oscar S S, Scott T, Michele M, Rafalski J. SNP frequency haplotype structure and linkage diseqilibrium in elite maize inbred lines. BMC Genet, 2002, 3: 19
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