Population structure and linkage disequilibrium of a mini core set of maize inbred lines in China

Wang, Ronghuan; Yu, Yangyang; Zhao, Jiuran; Shi, Yunsu; Song, Yi; Wang, Tianyu; Yu, Li

doi:10.1007/s00122-008-0852-x

Cited by 83 publications

(83 citation statements)

References 29 publications

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“…The heterotic pools identified by Xie et al (2008) included four North American and two Chinese germplasms. The heterotic pools obtained by Wang et al (2008) were consistent with the pedigree information and the probable origin of the Chinese maize germplasm (Lancaster, Reid, TSPT, and P). Based on the analysis of SSR markers and five populations from Central Europe that were widely used in breeding in the pre-hybrid age, Reif et al (2005) concluded that each population corresponds to a heterotic pool.…”

Section: Discussionsupporting

confidence: 78%

“…All founder and elite European and North American inbred lines were obtained by the French company Limagrain. Xie et al (2008) and Wang et al (2008) analyzed Chinese inbred lines that were genotyped for SSR loci. The population structure analyses revealed six and four heterotic pools, respectively.…”

Section: Discussionmentioning

confidence: 99%

“…The average value relative to tropical/subtropical and temperate gene pools was 0.16. In the studies of Yang et al (2011b), Van Inghelandt et al (2010), Wang et al (2008), Reif et al (2005), and Liu et al (2003), the ranges for the estimates of the number of alleles per locus, gene diversity, and private alleles were 2.7-21.7, 0.31-0.82, and 9-765, respectively. The superior number of alleles per locus and private alleles in the former and the latter studies is due to the high number of inbreds from broad geographic origins.…”

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confidence: 99%

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Population structure and genetic diversity of maize inbreds derived from tropical hybrids

Lanes¹,

Viana²,

Paes³

et al. 2014

Genet. Mol. Res.

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ABSTRACT. The objectives of this study were to identify the population structure and to assess the genetic diversity of maize inbreds. We genotyped 81 microsatellite loci of 90 maize inbreds that were derived from tropical hybrids and populations. The population structure analysis was based on a Bayesian approach. Each subpopulation was characterized for the effective number of alleles, gene diversity, and number of private alleles. We also performed an analysis of molecular variance and computed a measure of population differentiation (F ST ). The genetic distances were computed from the similarity index of Lynch and the dissimilarity measures proposed by Smouse and Peakall. The cluster analyses were based on the unweighted pair-group method using arithmetic averages and Tocher method. The clustering efficiency was assessed by the error rate of the discriminant analysis. We also performed a principal coordinates analysis. The population structure analysis revealed three tropical heterotic pools, which have been used by worldwide and Brazilian maize seed companies. The degree of genetic differentiation and of intra-and inter-population genetic diversity for these tropical heterotic pools are comparable to that observed for temperate and subtropical heterotic pools. The higher allelic frequency variation within each tropical heterotic pool and the high genetic diversity between the inbreds were evidence of heterotic groups within the main tropical heterotic pools.

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Section: Discussionsupporting

confidence: 78%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

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Population structure and genetic diversity of maize inbreds derived from tropical hybrids

Lanes¹,

Viana²,

Paes³

et al. 2014

Genet. Mol. Res.

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“…Li et al 2009) and genotyping technologies have simplified the generation of genetic maps and the analysis of recombinants (Shifman et al 2006). Dense maps in economically important crops will be invaluable for marker-assisted selection programs (Prigge et al 2009), analyzing linkage disequilibrium (Kruglyak 2008;Wang et al 2008), detection of intraspecies cisregulatory variation (Stupar and Springer 2006), and other quantitative genetic studies (Cookson et al 2009).…”

mentioning

confidence: 99%

High-Throughput Genetic Mapping of Mutants via Quantitative Single Nucleotide Polymorphism Typing

Liu

Chen²,

Makarevitch

et al. 2010

Genetics

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Advances in next-generation sequencing technology have facilitated the discovery of single nucleotide polymorphisms (SNPs). Sequenom-based SNP-typing assays were developed for 1359 maize SNPs identified via comparative next-generation transcriptomic sequencing. Approximately 75% of these SNPs were successfully converted into genetic markers that can be scored reliably and used to generate a SNPbased genetic map by genotyping recombinant inbred lines from the intermated B73 3 Mo17 population. The quantitative nature of Sequenom-based SNP assays led to the development of a time-and costefficient strategy to genetically map mutants via quantitative bulked segregant analysis. This strategy was used to rapidly map the loci associated with several dozen recessive mutants. Because a mutant can be mapped using as few as eight multiplexed sets of SNP assays on a bulk of as few as 20 mutant F 2 individuals, this strategy is expected to be widely adopted for mapping in many species. W ITH the availability of a sequenced genome it is feasibletoundertakechromosomewalking projects to clone genes responsible for mutant phenotypes (Alleman et al. 2006;Briggs et al. 2007;Menzel et al. 2007;Song et al. 2007) and quantitative trait loci (QTL) (Glazier et al. 2002;Korstanje and Paigen 2002;Salvi et al. 2007). However, it can be logistically difficult and time-consuming to map mutants with current technologies. A high-throughput system to map phenotypic mutants would be very useful in converting the wealth of phenotypic mutants into an understanding of the molecular basis.Single nucleotide polymorphisms (SNPs) can be converted into genetic markers that are scored in mapping populations using various high-throughput SNP-typing technologies ( Maize (Zea mays L.) is an important model organism with substantial economic value. In this species, SNPs occur at a rate of one per 28-214 bp (Tenaillon et al. 2001;Barbazuk et al. 2007). Using our 454-based SNP discovery pipeline, we identified .7000 putative SNPs, .85% (94/ 110) of which could be validated via Sanger sequencing (Barbazuk et al. 2007). Here, we report the analysis of 1359 of these putative SNPs. Approximately 75% of the tested SNPs could be converted into genetic markers, and only 3% were deemed to be false positives. These SNP-based markers were used to construct a genetic map that can be used to address diverse biological questions. Finally, we apply the combination of quantitative SNP typing and bulked segregant analysis (BSA) (Michelmore et al. 1991) to efficiently map phenotypic mutants. MATERIALS AND METHODSGenetic materials: Using a high-throughput protocol (Dietrich et al. 2002) (Table S1, supporting information), the 25 non-B73 parents of the nested association mapping (NAM) population , and mutant and non-mutant pools of DNAs for BSA. For BSA, tissues from all mutant (or non-mutant) individuals from within the same F 2 family were pooled, and a single DNA isolation was performed or DNA was isolated from each individual and then equal amounts from each individ...

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“…What reason is for highest value in the whole population is that there is population structure existed in it, which causes spurious LD. For example, Wang et al (2008) found that 63.89% LDs of loci pairs at a 1% level were in the entire sample, but a range of 18.75-40.28% was in the subgroups. We selected unstructured populations for further analyzing of LD, Many LDs of loci pairs in unstructured populations were detected, which explained that natural populations might have experienced genetic bottleneck from their progenitor and natural selection for a long time, and self-compatible individuals generated genetic drift because some deadly genes became homogeneous.…”

Section: Discussmentioning

confidence: 99%

Population Structure, Linkage Disequilibrium and Selective Loci in Natural Populations of Prunus davidiana

Cheng¹,

Gašić²,

Wang³

2013

JAS

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Prunus davidiana (Carrie're) Franch is a very important resource for the restoration in dry and arid areas, genetic improvement of peach, and extraction of health-promoting components. To effectively use the resource, we must have a measure of genetic diversity of P. davidiana and its population structure. LD (Linkage disequilibrium) provides information for association mapping underlying the phenotypic variation observed. Selective loci reveal adaptive evolution processes resulting from natural selection. A set of 190 genotypes from seven natural populations（SXTB, SIYQ, SXFX, NXXJ, SIJC, GSHT, GSHS) of P. davidiana collected from the range of P. davidiana in China was fingerprinted with 23 SSR markers, and analyzed with spatial structure, pairwise Fst (differentiation coefficient), PCA (principal coordinate analysis), estimation of groups of populations with STRUCTURE software, selective loci obtained from lnRH tested by standardization distribution and Grubbs. Our results demonstrate that population structure of four groups existed among populations through complementary analyses of the above mentioned methods; significant LD numbers from 22 to 129 between loci within unstructured populations were detected; there were five selective loci in all populations and two common selective loci for local natural selection between populations. We should conserve four populations among seven populations; these selective loci may provide information for disclosing adaption evolution and candidate genes according to selective loci and alleles; LDs inform how to use them for association analysis.

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Population structure and linkage disequilibrium of a mini core set of maize inbred lines in China

Cited by 83 publications

References 29 publications

Population structure and genetic diversity of maize inbreds derived from tropical hybrids

Population structure and genetic diversity of maize inbreds derived from tropical hybrids

High-Throughput Genetic Mapping of Mutants via Quantitative Single Nucleotide Polymorphism Typing

Population Structure, Linkage Disequilibrium and Selective Loci in Natural Populations of Prunus davidiana

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