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Acta Agron Sin ›› 2009, Vol. 35 ›› Issue (7): 1236-1243.doi: 10.3724/SP.J.1006.2009.01236


Development and Identification of InDel Marker Based on rhg1 Gene for Resistance to Soybean Cyst Nematode(Heterodera glycines Ichinohe)

NAN Hai-Yang,LI Ying-Hui**,CHANG Ru-Zhen,QIU Li-Juan*   

  1. National Key Facility for Crop Gene Resources and Genetic Improvement/Key Laboratory of Germplasm & Biotechnology/Institute of Crop Sciences,Chinese Academy of Agricultural Sciences,Beijing 100081,China
  • Received:2008-10-28 Revised:2009-03-16 Online:2009-07-12 Published:2009-05-19
  • Contact: QIU Li-Juan, E-mail: qiu_lijuan@263.net
  • About author:E-mail: haiyang_mei@163.com


Soybean cyst nematode (Heterodera glycaines, SCN) is one of the most important pests of soybean in the world. New molecular markers developed from resistance genes can provide marker resources for MAS (marker-assisted selection) breeding. Among four InDel loci detectedby comparing thesequences of candidate rhg1 conferringSCN resistance, three multiple-bases InDel loci were used to develop markers. A total of 11 alleles were detected in 33 cultivated soybean germplasm using three InDel markers developed. There were 5 alleles at rhg1-I1 locus, 2 and 4 at rhg1-I2 and rhg1-I4 respectively. Allelic variations at three InDel markers were assayed in the genotypes and discovered that rhg1-I4 marker was related to SCN resistance, which could distinguish 88.2% of resistant germplasm and 100% of the susceptible germplasm. Alleles of 288 and 294 bp presented in the SCN-resistant germplasm, and alleles 269 and 272 bp presented in the SCN-susceptible germplasm. In addition, rhg1-I4 could be used in MAS for the progenies of cross between typical southern US cultivar Lee crossed and the important resistant source PI88788. Combing with Satt309 which displayed the identical allele on these genotypes, rhg1-I4 would be higher effective in identifying germplasm with rhg1 conferring resistance in the MAS breeding.

Key words: Soybean, SCN, InDel marker

[1] Liu W-Z(刘维志), Liu Y(刘晔), Chen P-S(陈品三). Preliminary report of identify the races of SCN in some city & county of Northeast. J Shenyang Agric Coll (沈阳农学院学报), 1984, (2): 74-78(in Chinese)

[2] Liu H-Q(刘汉起), Shang S-G(商绍刚), Huo H(霍虹), Wu H-L(吴和礼). Resistance of soybean varieties to race 1,3 and 4 of soybean cyst nematode. Soybean Sci (大豆科学), 1989, 8(1): 113-114(in Chinese)

[3] Lu W-G(卢为国), Gai J-Y(盖钧镒), Li W-D(李卫东). Sample survey and identification of races of soybean cyst nematode (Heterodera glycines Ichinohe) in Huang-Huai valley. Sci Agric Sin (中国农业科学),2006, 39(2): 306-312(in Chinese with English abstract)

[4] Shang S-G(商绍刚), Liu H-Q(刘汉起). The distribution of races of soybean cyst nematode (Heterodera glycines Ichinohe) in Dongbei. Soybean Sci (大豆科学), 1989, 8(4): 382(in Chinese)

[5] Liu P-Y(刘佩印). Advances in study of screening and utilization for antigen to soybean cyst nematode. Heilongjiang Agric Sci (黑龙江农业科学), 2005, (6): 44-47 (in Chinese with English abstract)

[6] Riggs R D, Schmidt D P. Complete characterization of the race scheme for Heterodera glycines. J Nematol, 1988, 20: 392-395

[7] Caviness C E. Breeding of Resistance to Soybean Cyst Nematode. In: Riggs R D, Wrather J A, eds. Biology and Management of the Soybean Cyst Nematode. St. Paul, Minnesota: APS Press, 1992. pp 143-156

[8] Cregan P B, Mudge J, Fickus E W, Denny R, Danesh R, Young N D. Two simple sequence repeat markers to select for soybean cyst nematode resistance conditioned by the rhg1 locus. Theor Appl Genet, 1999, 99: 811-818

[9] Arelli A P, Anand S C, Wrather J A. Soybean resistance to soybean cyst nematode race 3 is conditioned by an additional dominant gene. Crop Sci, 1992, 32: 862-864

[10] Concibido V C, Diers B W, Arelli P R. A decade of QTL mapping for cyst nematode resistance in soybean. Crop Sci, 2004, 44: 1121-1131

[11] Ruben E, Aziz J, Afzal J, Njiti V N, Triwitayakorn K, Iqbal M J, Yaegashi S, Arelli P, Town C, Meksem K, Lightfoot D A. Genomic analysis of the rhg1 locus: Candidate genes that underlie soybean resistance to the cyst nematode. Mol Genet Genome, 2006, 276: 503-516

[12] Concibido V C, Denny R L, Boutin S R, Hautea R, Orf J H, Young N D. DNA marker analysis of loci underlying resistance to soybean cyst nematode (Heterodera glycines Ichinohe). Crop Sci, 1994, 34: 240-246

[13] Concibido V C, Boutin S, Denny R L, Hautea R, Orf J, Young N D. Targeted comparative genome analysis and qualitative mapping of a major partial resistance gene to the soybean cyst nematode. Theor Appl Genet, 1996, 93: 234-241

[14] Webb D M, Baltazar B M, Arelli A P, Schupp J, Keim P, Clayton K, Ferreira A R, Owens T, Beavis W D. QTL affecting soybean cyst nematode resistance. Theor Appl Genet, 1995, 91: 574-581

[15] Chang S J C, Doubler T W, Kilo V, Suttner R J, Klein J, Schmidt M E, Gibson P T, Lightfoot D A. Association of loci underlying field resistance to soybean sudden death syndrome (SDS) and cyst nematode (SCN) race 3. Crop Sci, 1997, 372: 965-971

[16] Prabhu R R, Njiti V, Bell-Johnson B, Johnson J E, Schmidt M E, Klein J, Lightfoot D A. Selecting soybean cultivars for dual resistance to soybean cyst nematode and sudden death syndrome using two DNA markers. Crop Sci, 1999, 39: 982-987

[17] Meksem K, Ruben E, Hyten D L, Schmidt M E, Lightfoot D A. High-throughput genotyping for a polymorphism linked to soybean cyst nematode resistance gene Rhg4 by using Taqman (TM) probes. Mol Breed, 2001, 7: 63-71

[18] Yue P, Sleper D A, Arelli P R. Mapping resistance of multiple races of Heterodera glycines in soybean PI89772. Crop Sci, 2001, 41: 1589-1595

[19] Guo B, Sleper D A, Nguyen H T, Arelli P R, Shannon J G. Quantitative trait loci underlying resistance to three soybean cyst nematode populations in soybean PI404198A. Crop Sci, 2006, 46: 224-233

[20] Goffinet B, Gerber S. Quantitative trait loci: A meta-analysis.Genetics, 2000, 155: 463-473

[21] Guo B, Sleper D A, Lu P, Shannon J G, Nguyen H T, Arelli P R. QTLs associated with resistance to soybean cyst nematode in soybean: Meta-analysis of QTL locations. Crop Sci, 2006, 46: 595-602

[22] Lightfoot D A, Meksem K. Novel polynucleotides and polypeptides relating to loci underlying resistance to soybean cyst nematode and methods of use thereof. Patent pending # 09/772, 134. Filing date 2000-01-29

[23] Hauge B M, Wang M L, Parsons J D, Parnell L D. Nucleic acid molecules and other molecules associated with soybean cyst nematode resistance. WO 01/51627 PCT/US01/00552 Patent # 20030005491

[24] Concibido V C, Lange D A, Denny R L, Hautea R, Orf J, Young N D. Genome mapping soybean cyst nematode resistance genes in Peking, PI90763 and PI88788 using DNA markers. Crop Sci, 1997, 37: 258-264

[25] Heer J A, Knap H T, Mahalingam R, Shipe E R, Arelli P R, Matthews B F. Molecular markers for resistance to Heterodera glycines in advanced soybean germplasm. Mol Breed, 1998, 4: 359-367

[26] Meksem K, Pantazopoylos P, Niti V N, Hyten L D, Arelli P R. ‘Forrest’ resistance to soybean cyst nematode is bigenic: Saturation mapping of the Rhg1 and Rhg4 loci. Theor Appl Genet, 2001, 103: 710-714

[27] Mudege J, Cregan P B. Two microsatellite markers that flank the major soybean cyst nematode resistance locus. Crop Sci, 1997, 37: 1611-1615

[28] Qiu B X, Arelli P R, Sleper D A. RFLP markers associated with soybean cyst nematode resistance and seed composition in a ‘Peking’× ‘Essex’ population. Theor Appl Genet, 1999, 98: 356-364

[29] Ma Y S, Wang W H, Wang L X, Ma F M, Wang P W, Chang R Z, Qiu L J. Genetic diversity of soybean and the establishment of a core collection focused on resistance to soybean cyst nematode. J Integr Plant Biol, 2006, 48: 722-731

[30] Liu M S, Amirkhanian V D. DNA fragment analysis by an affordable multiple-channel capillary electrophoresis system (Short communication). Electrophoresis-Weinheim, 2003, 24: 93-95

[31] Mills R E, Luttig C T, Larkins C E, Beauchamp A, Tsui C, Pittard W S, Devine S E. An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res,2006, 16: 1182-1190

[32] Shen Y J, Jiang H, Jin J P, Zhang Z B, Xi B, He Y Y, Wang G, Wang C, Lily Q, Yu Q B, Liu H J, Chen D H, Gao J H, Huang H, Shi T L, Yang Z N. Development of genome-wide DNA polymorphism database for map-based cloning of rice genes. Plant Physiol, 2004, 135: 1198-1205

[33] Feltus F A, Wan J, Schulze S R, Wan J, Estill J C, Jiang N, Paterson A H. An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments. Genome Res, 2004, 14: 1812-1819

[34] Dinakar B, Maureen D, Mike H, Robin W, Dave V, James C R. Insertion-deletion polymorphisms in 3' regions of maize genes occur frequently and can be used as highly informative genetic markers. Plant Mol Biol, 2002, 48: 539-547

[35] Choi I Y, Hyten D L, Matukumalli L K, Song Q, Chaky J M, Quigley C V, Chase K, Lark K G, Reiter R S, Yoon M S, Hwang E Y, Yi S I, Young N D, Shoemaker R C, Van Tassell C P, Specht J E, Cregan P B. A soybean transcript map: Gene distribution, haplotype and SNP analysis. Genetics, 2007, 176: 685-696

[36] Ellegren H. Microsatellites: Simple sequences with complex evolution. Nat Rev Genet, 2004, 5: 435-445

[37] Li Y H, Guan R X, Ma Y S, Wang L X, Li L H, Lin F Y, Luan W J, Chen P Y, Yan Z, Guan Y, Zhu L, Ning X C, Smulders M J M, Li W, Piao R H, Cui Y H, Yu Z M, Guan M, Chang R Z, Liu Z X, Hou A F, Shi A N, Zhang B, Zhu S L, Qiu L J. Genetic structure and diversity of cultivated soybean

[Glycine max (L.) Merr.] landraces in China. Theor Appl Genet, 2008, 117: 857-871

Feng F-J(冯芳君), Luo L-J(罗利军), Li-Y(李荧), Zou L-G(周立国), Xu X-Y(徐小艳), Wu J-H(吴金红), Chen H-W(陈宏伟), Chen L(陈亮), Mei H-W(梅捍卫). Comparative analysis of polymorphism of InDel and SSR markers in rice. Mol Plant Breed (植物分子育种), 2005, 3(5): 725-730(in Chinese with English abstract)
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