Abstract
A maize genetic linkage map was generated using SSR and SNP markers in a F7:8 recombinant inbred line (RIL) population derived from a cross of waxy corn (KW7) and dent corn (Mo17). A total of 465 markers, including 459 SSR and 6 SNP markers, were assigned to 10 linkage groups which spanned 2,656.5 cM with an average genetic distance between markers of 5.7 cM, and the number of loci per linkage group ranged from 39 to 55. The SSR (85.4%) and SNP (83.3%) markers showed Mendelian segregation ratios in the RIL population at a 5% significance threshold. In linkage analysis of six SNP loci associated with kernel starch synthesis genes (ae1, bt2, sh1, sh2, su1, and wx1), all six loci were successfully mapped and are closely linked with SSR markers in chromosomes 3 (sh2), 4 (su1 and bt2), 5 (ae1), and 9 (sh1 and wx1). The SSR markers linked with genes in starch synthesis may be utilized in marker assisted breeding programs. The resulting genetic map will be useful in dissection of quantitative traits and the identification of superior QTLs from the waxy hybrid corn. Additionally, these data support further genetic analysis and development of maize breeding programs.
Similar content being viewed by others
References
Akagi H, Yokozaki Y, Inagaki A and Fujimura T (1997) Highly polymorphic microsatellites of rice consist of AT repeats, and a classification of closely related cultivars with these microsatellite loci. Theor. Appl. Genet. 94: 61–67.
Austin DF and Lee M (1998) Detection of quantitative trait loci for grain yield and yield components in maize across generations in stress and nonstress environments. Crop Sci. 38: 1296–1308.
Blair MW, Muñoz C, Buendía HF, Flower J, Bueno JM and Cardona C (2010) Genetic mapping of microsatellite markers around the arcelin bruchid resistance locus in common bean. Theor. Appl. Genet. 121: 393–402.
Buckler ES and Thornberry JM (2002) Plant molecular diversity and applications to genomics. Curr. Opin. Plant Biol. 5: 107–111.
Burr B, Burr FA, Thompson KH, Albertson MC and Stuber CW (1988) Gene Mapping with Recombinant Inbreds in Maize. Genetics 118: 519–526.
Casa A, Brouwer C, Nagei A, Wang L, Zhang Q, Kresovich A and Wessler SL (2000) The MITE family Heartbreaker (Hbr): Molecular markers in maize. Proc. Natl. Acad. Sci. USA 97: 10083–10089.
Cho RJ, Mindrinos M, Richards DR, Sapolsky RJ, Anderson M, Theologis A, Yang W-H, Hubbell E, Au M, et al. (1999) Genome-wide mapping with biallelic markers in Arabidopsis thaliana. Nat. Genet. 23: 203–207.
Davis GL, McMullen MD, Baysdorfer C, Musket T, Grant D, Staebell M, Xu G, Polacco M, Koster L, et al. (1999) A maize map standard with sequenced core markers, grass genome reference points and 932 expressed sequence tagged sites (ESTs) in a 1736 locus map. Genetics 152: 1137–1172.
Dellaporta SL, Wood J and Hicks JB (1983) A simple and rapid method for plant DNA preparation. Version II. Plant Mol. Biol. Rep. 1: 19–21.
Drenkard E, Richeter BG, Rozen S, Stutitius LM, Angell NA, Mindrinos M, Cho RJ, Oefner PJ, Davis RW and Ausubel FM (2000) A simple procedure for the analysis of single nucleotide polymorphisms facilitates map-based cloning in Arabidopsis. Plant Physiol. 124: 1483–1492.
Frova C, Krajewski P, di Fonzo N, Villa M and Sari-Gorla M (1999) Genetic analysis of drought tolerance in maize by molecular markers I. Yield components. Theor. Appl. Genet. 99: 280–288.
Gardiner JM, Coe EH, Melia-Hancock S, Hoisington DA and Chao S (1993) Development of a core RFLP map in maize using an immortalized F2 population. Genetics 134: 917–930.
Heun M, Anderson JA, Lapitan NLV, Sorrells ME and Tanksley SD (1991) Construction of a restriction fragment length polymorphism map for barley (Hordeum vulgare). Genome 34: 437–447.
Kosambi D (1944) The estimation of map distances from recombination values. Ann. Eugen. 12: 172–175.
Kruglyak L (1997) The use of a genetic map of biallelic markers in linkage studies. Nat. Genet. 17: 21–24.
Li G, Hu W, Qin R, Jin H, Tan G, Zhu L and He G (2008) Simple sequence repeat analyses of interspecific hvbrids and MAALs of Oryza officinalis and Oryza sativa. Genetica 134: 169–180.
Lagercrantz U, Ellegren H and Andersson L (1993) The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates. Nucl. Acids. Res. 21: 1111–1115.
Lee C and Wu XL (2001) Interval mapping of quantitative trait loci in complex pedigrees. Korean J. Genetics 23: 349–357.
Lee JK, Park JY, Kim JH, Kwon SJ, Shin JH, Hong SK, Min HK and Kim NS (2006) Genetic mapping of the Isaac-CACTA transposon in maize. Theor. Appl. Genet. 113: 16–22.
Liedl B and Anderson NO (1993) Reproductive barriers: identification, uses and circumvention. Plant Breed. Rev. 11: 11–154.
Lincoln S, Daly M and Lander ES (1992) Constructing genetic maps with MAPMAKER/EXP 3.0. Whitehead Institute Technical Report. 3rd edition. Cambridge, MA.
Liu G, Bernhardt JL, Jia MH, Wamishe YA and Jia Y (2008) Molecular characterization of the recombinant inbred line population derived from a japonica-indica rice cross. Euphytica 159: 73–82.
Lu H, Romero-Severson J and Bernardo R (2002) Chromosomal regions associated with segregation distortion in maize. Theor. Appl. Genet. 105: 622–628.
Moreno-Vázquez S, Ochoa OE, Faber N, Chao S, Jacobs JME, Maisonneuve B, Kesseli R and Michelmore RW (2003) SNP-based codominant markers for a recessive gene conferring resistance to corky root rot (Rhizomonas suberifaciens) in lettuce (Lactuca sativa). Genome 46: 1059–1069.
Myers AM, Morell MK, James MG and Ball SG (2000) Recent progress toward understanding biosynthesis of the amylopectin crystal. Plant Physiol. 122: 989–997.
Nelson OE and Rines HW (1962) The enzymatic deficiency in the waxy mutant of maize. Biochem. Biophys. Res. Commun. 9: 297–300.
Nelson O and Pan D (1995) Starch synthesis in maize endosperms. Annu. Rev. Plant Phys. Plant Mol. Biol. 46: 475–496.
Neuffer MG, Coe EH and Wessler SR (1997) Mutants of maize. Cold spring harbor laboratory, New York. pp. 468.
Ni J, Colowit PM and Mackill DJ (2002) Evaluation of genetic diversity in rice subspecies using microsatellite markers. Crop Sci. 42: 601–607.
Park YJ, Lee JK and Kim NS (2009) Simple sequence repeat polymorphisms (SSRPs) for evaluation of molecular diversity and germplasm classification of minor crops. Molecules 14:4546–4569; doi: 10.3390/molecules14114546.
Peng JH, Korol AB, Fahima T, Roder MS, Ronin YI, Li YC and Nevo E (2000) Molecular genetic maps in wild emmer wheat, Triticum dicoccoides: genome-wide coverage, massive negative interference, and putative quasi-linkage. Genome Res. 10: 1509–1531.
Piquemal J, Cinquin E, Couton F, Rondeau C, Seignoret E, Doucet I, Perret D, Villeger MJ, Vincourt P and Blanchard P (2005) Construction of an oilseed rape (Brassica napus L.) genetic map with SSR markers. Theor. Appl. Genet. 111: 1514–1523.
Pradhan AK, Gupta V and Mukhopadhyay A (2003) A high-density linkage map in Brassica juncea (Indian mustard) using AFLP and RFLP markers. Theor. Appl. Genet. 106: 607–614.
Rafalski JA, Vogel JM, Morgante M, Powell W, Andre C and Tingey SV (1996) Generating and using DNA markers in plants. In: Birren B, Lai E (eds), Non-mammalian genomic analysis. A practical guide. Academic Press, San Diego, pp 75–134.
Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr. Opin. Plant Biol. 5: 94–100.
Senior ML, Chin ECL, Smith JSC and Stuber CW (1996) Simple sequence repeat developed from maize sequences found in the GenBank database: map construction. Crop Sci. 36: 1676–1683.
Séne M, Thévenot C, Hoffmann D, Bénétrix MC and Prioul J-L (2001) QTLs for grain dry milling properties, composition and vitreousness in maize recombinant inbred lines. Theor. Appl. Genet. 102: 591–599.
Shin JH, Kwon SJ, Lee JK, Min HW and Kim NS (2006) Genetic diversity of maize kernel starch-synthesis genes with SNAPs. Genome 49: 1287–1296.
Sprague GF, Brimhall B and Hixon RM (1943) Some effects of the waxy gene in corn on properties of the endosperm starch. J. Am. Soc. Agron. 35: 817–822.
Syvänen A-C (2001) Accessing genetic variation: genotyping single nucleotide polymorphisms. Nat. Rev. 2: 930–942.
Tanksley SD (1984) Linkage relationships and chromosomal locations of enzyme-coding genes in pepper, Capsicum annum. Chromosoma 89: 352–360.
Tanksley SD, Ganal MW, Prince JP, de Vincent MC, Bonierbale MW, Brown P, Fulton TM, Giovanni JJ, Grandillo S, et al. (1992) High density molecular linkage maps of the tomato and potato genomes. Genetics 132: 1141–1160.
Tanksley SD, Grandillo S, Fulton TM, Zamir D, Eshed Y, Petiard V, Lopez J and Beck-Bunn T (1996) Advanced backcross QTL analysis in a cross between an elite processing line of tomato and its wild relative L. pimpinellifolium. Theor. Appl. Genet. 92: 213–224.
Tsukazaki H, Yamashita KI, Yaguchi S, Masuzaki S, Fukuoka H, Yonemaru J, Kanamori H, Kono I, Hang TTM, et al. (2008) Construction of SSR-based chromosome map in bunching onion (Allium fistulosum). Theor. Appl. Genet. 117: 1213–1223.
Wilson LM, Whitt SR, Ibáñez AM, Rocheford TR, Goodman MM and Buckler ES (2004) Dissection of Maize Kernel Composition and Starch Production by Candidate Gene Association. Plant Cell. 16: 2719–2733.
Xu Y, Zhu L, Xiao J, Huang N and McCouch SR (1997) Chromosomal regions associated with segregation distortion of molecular markers in F2, backcross, doubled-haploid, and recombinant inbred populations in rice (Oryza sativa L.). Mol. Gen. Genet. 253: 535–545.
Yang X, Guo Y, Yan J, Zhang J, Song T, Rocheford T and Li JS (2010) Major and minor QTL and epistasis contribute to fatty acid compositions and oil concentration in high-oil maize. Theor. Appl. Genet. 120: 665–678.
Yu J, Hu S, Wang J, Wong GKS, Li S, Hu S, Liu B, Deng Y, Dai L, et al. 2002. A draft sequence of the rice genome (Oryza sativa L. spp. Indica). Science 296: 79–92.
Author information
Authors and Affiliations
Corresponding author
Additional information
K. J. Sa, J. Y. Park, and K.-C. Park contributed equally to this work.
Rights and permissions
About this article
Cite this article
Sa, K.J., Park, J.Y., Park, KC. et al. Analysis of genetic mapping in a waxy/dent maize RIL population using SSR and SNP markers. Genes Genom 34, 157–164 (2012). https://doi.org/10.1007/s13258-011-0208-9
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s13258-011-0208-9