Inferring Genome Ancestry and Estimating Molecular Relatedness Among 187 Chinese Maize Inbred Lines

National Key Facility of Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China

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Corresponding author: E-mail address: cshzhang2000@yahoo.com.cn (Shihuang Zhang)

摘要

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Abstract: The inference of genome ancestry and the estimation of molecular relatedness are of great importance for breeding efficiency and association studies. Seventy SSR loci, evenly distributed in 10 chromosomes, were assayed for polymorphism among 187 commonly used maize (Zea mays L.) inbreds which represent the genetic diversity in China. The identified 290 alleles served as raw data for estimating population structure using the coalescent linked loci, based on the ADMIXTURE model. Population number, K, has been inferred to be between five and seven. Specifying five subpopulations (K = 5) led to a distinct decrease and specifying K to be greater than six resulted in only minimal increases in the likelihood value. Therefore, population number, K, has been inferred into six subpopulations, which are PA, BSSS (includes Reid), PB, Lan (Lancaster Sure Crop), LRC (Luda Reb Cob, a Chinese landrace, and its derivatives), and SPT (Si-ping-tou, a Chinese landrace and its derivatives). The Kullback-Leibler distance of pairwise subpopulation was also inferred as n × p (187 × 6) Q matrices, which gave a detailed percentage of genetic composition of six subpopulations and molecular relatedness of each line. The genome-wide linkage disequilibrium (LD) indicated that the association studies in QTLs and/or candidate genes might avoid nonfunctional and spurious associations, as most of the LD blocks were broken among diverse germplasm. The defined population structure has given us a clear genetic structure of these lines for breeding practice and established a good basis for association analysis.
- maize /
- genetic diversity /
- relatedness /
- linkage disequilibrium /
- association analysis

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[1]	Smith, OS, Smith, et al. Measurement of genetic diversity among maize hybrids–a comparison of isozymic, RFLP, pedigree, and heterosis data Maydica, 37 (1992),pp. 53-60
[2]	Smith, JSC, Chin, et al. Theor Appl Genet, 95 (1997),pp. 163-173
[3]	Doebley, J, Wendel, et al. The origin of corn belt maize: the isozyme evidence Econ Bot, 42 (1988),pp. 120-131
[4]	Rafalski, JA, Vogel, et al.
[5]	Lu, H, Bernardo, et al. Molecular marker diversity among current and historical maize inbreds Theor Appl Genet, 103 (2001),pp. 613-617
[6]	Pejic, I, Ajmore-Marsan, et al. Comparative analysis of genetic similarity among maize inbred lines detected by RFLPs, RAPDs, SSRs, and AFLPs Theor Appl Genet, 97 (1998),pp. 1248-1255
[7]	Senior, ML, Murphy, et al. Utility of SSRs for determining genetic similarities and relationships in maize using an agarose gel system Crop Sci, 38 (1998),pp. 1088-1098
[8]	Liu, K, Goodman, et al. Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites Genetics, 165 (2003),pp. 2117-2128
[9]	Vigouroux, Y, Mitchell, et al. An analysis of genetic diversity across the maize genome using microsatellites Genetics, 169 (2005),pp. 1617-1630
[10]	Reif, JC, Warburton, et al. Grouping of accessions of Mexican races of maize revisited with SSR markers Theor Appl Genet, 113 (2006),pp. 177-185
[11]	Li, Y, Du, et al. Genetic diversity and relationships among Chinese maize inbred lines revealed by SSR markers Maydica, 47 (2002),pp. 93-101
[12]	Li, XH, Fu, et al. Genetic variation of inbred lines of maize detected by SSR markers Sci Agric Sin, 33 (2000),pp. 1-9
[13]	Yuan, LX, Fu, et al. Comparison of genetic diversity in maize inbreds based on RFLP, SSR, AFLP and RAPD markers Acta Genet Sin, 27 (2000),pp. 725-733
[14]	Corder, EH, Saunders, et al. Protective effect of apolipoprotein E type 2 allele for late onset Alzheimer disease Nat Genet, 7 (1994),pp. 180-184
[15]	Kerem, B, Rommens, et al. Identification of the cystic fibrosis gene: genetic analysis Science, 245 (1989),pp. 1073-1080
[16]	Thornsberry, JM, Goodman, et al. Nat Genet, 28 (2001),pp. 286-289
[17]	Andersen, JR, Schrag, et al. Theor Appl Genet, 111 (2005),pp. 206-217
[18]	Camus-Kulandaivelu, L, Veyrieras, et al. Genetics, 172 (2006),pp. 2449-2463
[19]	Flint-Garcia, SA, Thornsberry, et al. Structure of linkage disequilibrium in plants Annu Rev Plant Biol, 54 (2003),pp. 357-374
[20]	Stich, B, Melchinger, et al. Linkage disequilibrium in European elite maize germplasm investigated with SSRs Theor Appl Genet, 111 (2005),pp. 723-730
[21]	Remington, DL, Thornsberry, et al. Structure of linkage disequilibrium and phenotypic associations in the maize genome Proc Natl Acad Sci USA, 98 (2001),pp. 11479-11484
[22]	Saghai-Maroof, MA, Soliman, et al. Ribosomal DNA spacer length polymorphism in barley: Mendelian inheritance, chromosomal location and population dynamics Proc Natl Acad Sci USA, 81 (1984),pp. 8014-8018
[23]	Falush, D, Stephens, et al. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies Genetics, 164 (2003),pp. 1567-1587
[24]	Pritchard, JK, Stephens, et al. Inference of population structure using multilocus genotype data Genetics, 155 (2000),pp. 945-959
[25]	Kullback, S, Leibler, et al. On information and sufficiency Ann Math Stat, 22 (1951),pp. 79-86
[26]	Garris, AJ, Tai, et al. Genetics, 169 (2005),pp. 1631-1638
[27]	Li, Y Development and germplasm base of maize hybrids in China Maydica, 43 (1998),pp. 259-269
[28]	Kraakman, ATW, Niks, et al. Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars Genetics, 168 (2004),pp. 435-446

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doi: 10.1016/S1673-8527(07)60083-6

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Inferring Genome Ancestry and Estimating Molecular Relatedness Among 187 Chinese Maize Inbred Lines

Corresponding author: E-mail address: cshzhang2000@yahoo.com.cn (Shihuang Zhang)

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doi: 10.1016/S1673-8527(07)60083-6

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Inferring Genome Ancestry and Estimating Molecular Relatedness Among 187 Chinese Maize Inbred Lines

Corresponding author: E-mail address: cshzhang2000@yahoo.com.cn (Shihuang Zhang)

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