Linkage disequilibrium and sequence diversity in a 500-kbp region around the adh1 locus in elite maize germplasm

Jung, Mark; Ching, Ada; Bhattramakki, Dinakar; Dolan, M. Eileen; Tingey, Scott V.; Morgante, Michèle; Rafalski, Antoni

doi:10.1007/s00122-004-1695-8

Cited by 71 publications

(40 citation statements)

References 41 publications

(42 reference statements)

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“…Similar studies on haplotyping were conducted earlier in bread wheat (Caldwell et al 2004;Beales et al 2005), barley (Bundock & Henry 2004;Russell et al 2004) and maize (Ching et al 2002;Palaisa et al 2003). Taken together, these studies suggest that on average there are fewer SNPs/haplotype in inbreeders like wheat and barley than in outbreeders like maize (Clark et al 2004;Jung et al 2004;Palaisa et al 2004;Buntjer et al 2005). This has been attributed to selective constraints, absence of recombination and narrow genetic base of the inbreeders (Kanazin et al 2002;Zhu et al 2003;Bundock & Henry 2004;Caldwell et al 2004;Russell et al 2004).…”

Section: Haplotype Structuresupporting

confidence: 57%

EST-SNPs in bread wheat: discovery, validation, genotyping and haplotype structure

Rustgi¹,

Bandopadhyay²,

Balyan³

et al. 2009

CZECH J GENET PLANT

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Abstract:The present study involves discovery, validation and use of single-nucleotide polymorphisms (SNPs) in bread wheat utilizing 48 EST-contigs (individual contigs having 20-89 ESTs, derived from 2 to 11 different genotypes). In order to avoid a problem due to homoeologous relationships, the ESTs in each contig were classified into 175 sub-contigs (3.7 sub-contigs/EST-contig) using characteristic homoeologue sequence variants (HSVs), which had a density of 1 HSV every 136.7 bp. In silico analysis of sub-contigs led to the discovery of 230 candidate EST-SNPs with a density of 1SNP/273.9 bp. Locus specific primers (each primer pair flanking 1-18 SNPs) were designed utilizing one sub-contig each from 42 EST-contigs that contained SNPs, the remaining 6 contigs having no SNPs. To provide locus specificity to the PCR products, each primer was tagged with an HSV at its 3' end. Only 10 primer pairs, which gave each a characteristic solitary band, were utilized to validate EST-SNPs over 30 diverse bread wheat genotypes; 7 SNPs were validated through resequencing the PCR products. Allele specific primers were designed and utilized for genotyping of 50 diverse bread wheat accessions (including 30 bread wheat genotypes previously used for validation of SNPs), with an aim to test their utility in genotyping and map construction. The allele specific primers allowed the classification of 50 genotypes in two alternative allele groups for each SNP as expected, thus suggesting their utility for genotyping. Of the above 7 validated SNPs, 4 belonged to a solitary locus (PKS37); 7 haplotypes were available at this locus. Altogether, the results suggested that EST-SNPs constitute an important source of molecular markers for studies on wheat genomics.

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Section: Haplotype Structuresupporting

confidence: 57%

EST-SNPs in bread wheat: discovery, validation, genotyping and haplotype structure

Rustgi¹,

Bandopadhyay²,

Balyan³

et al. 2009

CZECH J GENET PLANT

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“…Significant genetic diversity has apparently been preserved in a small number of highly divergent B-and R-line haplotypes in sunflower, where haplotype divergence is greater between than within heterotic groups (supplemental Figure 1). While heterotic groups seem to be much less sharply differentiated in sunflower than maize, patterns of genetic diversity and haplotype divergence seem to be similar within and between heterotic groups in both species (Tenaillon et al 2001(Tenaillon et al , 2002Yu et al 2002Yu et al , 2003Liu et al 2003;Reif et al 2003;Jung et al 2004;Ching et al 2002). By contrast, haplotypes seem to be unstructured in the wild progenitor of maize (White and Doebley 1999;Liu et al 2003) and wild sunflower Tang and Knapp 2003;Kolkman et al 2004;Liu and Burke 2006).…”

Section: Discussionmentioning

confidence: 99%

Single Nucleotide Polymorphisms and Linkage Disequilibrium in Sunflower

Kolkman

Berry²,

Leόn³

et al. 2007

Genetics

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Genetic diversity in modern sunflower (Helianthus annuus L.) cultivars (elite oilseed inbred lines) has been shaped by domestication and breeding bottlenecks and wild and exotic allele introgression -the former narrowing and the latter broadening genetic diversity. To assess single nucleotide polymorphism (SNP) frequencies, nucleotide diversity, and linkage disequilibrium (LD) in modern cultivars, alleles were resequenced from 81 genic loci distributed throughout the sunflower genome. DNA polymorphisms were abundant; 1078 SNPs (1/45.7 bp) and 178 insertions-deletions (INDELs) (1/277.0 bp) were identified in 49.4 kbp of DNA/genotype. SNPs were twofold more frequent in noncoding (1/32.1 bp) than coding (1/ 62.8 bp) sequences. Nucleotide diversity was only slightly lower in inbred lines (u ¼ 0.0094) than wild populations (u ¼ 0.0128). Mean haplotype diversity was 0.74. When extraploted across the genome ($3500 Mbp), sunflower was predicted to harbor at least 76.4 million common SNPs among modern cultivar alleles. LD decayed more slowly in inbred lines than wild populations (mean LD declined to 0.32 by 5.5 kbp in the former, the maximum physical distance surveyed), a difference attributed to domestication and breeding bottlenecks. SNP frequencies and LD decay are sufficient in modern sunflower cultivars for very high-density genetic mapping and high-resolution association mapping.

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“…Even within a species, LD decay can vary significantly. In maize (Zea mays), for example, LD decays within 1 kb in land races (Tenaillon et al, 2001), within 2 kb in diverse inbred lines (Remington et al, 2001), and can extend up to 500 kb in commercial elite inbred lines (Rafalski, 2002;Jung et al, 2004). Finally, LD decay also varies among loci within a population, sometimes due to positive selection, which can generate LD that extends much farther than the genome-wide average (e.g., Whitt et al, 2002).…”

Section: Why Linkage Disequilibrium Mattersmentioning

confidence: 99%

Association Mapping: Critical Considerations Shift from Genotyping to Experimental Design

et al. 2009

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The goal of many plant scientists' research is to explain natural phenotypic variation in terms of simple changes in DNA sequence. Traditionally, linkage mapping has been the most commonly employed method to reach this goal: experimental crosses are made to generate a family with known relatedness, and attempts are made to identify cosegregation of genetic markers and phenotypes within this family. In vertebrate systems, association mapping (also known as linkage disequilibrium mapping) is increasingly being adopted as the mapping method of choice. Association mapping involves searching for genotype-phenotype correlations in unrelated individuals and often is more rapid and cost-effective than traditional linkage mapping. We emphasize here that linkage and association mapping are complementary approaches and are more similar than is often assumed. Unlike in vertebrates, where controlled crosses can be expensive or impossible (e.g., in humans), the plant scientific community can exploit the advantages of both controlled crosses and association mapping to increase statistical power and mapping resolution. While the time and money required for the collection of genotype data were critical considerations in the past, the increasing availability of inexpensive DNA sequencing and genotyping methods should prompt researchers to shift their attention to experimental design. This review provides thoughts on finding the optimal experimental mix of association mapping using unrelated individuals and controlled crosses to identify the genes underlying phenotypic variation. GENETIC MAPPING: IT'S ALL ABOUT RECOMBINATIONThe aim of many genetic mapping studies is to identify quantitative trait loci (QTL) that are responsible for phenotypic variation. Although often viewed as fundamentally different, linkage and association mapping share a common strategy that exploits recombination's ability to break up the genome into fragments that can be correlated with phenotypic variation. The key difference between the two methods is the control the experimenter has over recombination. On the one hand, linkage mapping is a highly controlled experiment: individuals are crossed to generate a mapping population in which relatedness is known. In plants, these are generally biparental crosses, while in humans these populations may be extended pedigrees. The experimenter thereby creates a closed system and uses a small number of genetic markers to infer the locations of the relatively few recombination breakpoints. With genotype data from across the genome, the experimenter can then determine if a chromosomal fragment between two specific breakpoints is associated with a phenotype. Association mapping, on the other hand, is not a controlled experiment, but rather a natural experiment. Genotype and phenotype data are collected from a population in which relatedness is not controlled by the experimenter, and correlations between genetic markers and phenotypes are sought within this population. This open system design provides higher mapping resol...

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Linkage disequilibrium and sequence diversity in a 500-kbp region around the adh1 locus in elite maize germplasm

Cited by 71 publications

References 41 publications

EST-SNPs in bread wheat: discovery, validation, genotyping and haplotype structure

EST-SNPs in bread wheat: discovery, validation, genotyping and haplotype structure

Single Nucleotide Polymorphisms and Linkage Disequilibrium in Sunflower

Association Mapping: Critical Considerations Shift from Genotyping to Experimental Design

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