Linkage disequilibrium in European elite maize germplasm investigated with SSRs

Stich, Benjamin; Melchinger, Albrecht E.; Frisch, Matthias; Maurer, Hans Peter; Heckenberger, Martin; Reif, Jochen C.

doi:10.1007/s00122-005-2057-x

Cited by 175 publications

(136 citation statements)

References 30 publications

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“…Four markers mentioned a significant association with the flowering time (P \ 0.0001). The success of association mapping depends on the possibility of detecting LD between DNA marker alleles and alleles affecting phenotypic expression (Stich et al 2005). These results can be explained by the small number of germplasm and the number of markers used for this association.…”

Section: Discussionmentioning

confidence: 99%

Variation in flowering time in sorghum core collection and mapping of QTLs controlling flowering time by association analysis

Mannai

Shehzad

Okuno

2011

Genet Resour Crop Evol

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A wide range of variation in flowering time was observed within a diversity research set of 107 sorghum accessions ranging from 56 to 133 days. Accessions were classified into early medium and late flowering groups. 45 accessions were grown under three different environments of photoperiod (11, 12 and 15 h). Sorghum accessions gradually responded to the decreasing of day-length. The 12 h of photoperiod could be considered as a threshold above which day-length delays the flowering time in sorghum. Association analysis was performed to identify the QTLs controlling flowering time and photoperiod sensitivity using 107 accessions of sorghum grown under natural condition and 45 accessions grown under controlled conditions. Four QTLs controlling flowering time were detected under natural condition of day-length at threshold 2.5 using K model. A total of seven flowering time loci were detected under controlled conditions of day-length. One QTL controlling photoperiod sensitivity was detected on chromosome 1 and one QTL controlling photoperiod insensitivity was detected on chromosome 4.

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Section: Discussionmentioning

confidence: 99%

Variation in flowering time in sorghum core collection and mapping of QTLs controlling flowering time by association analysis

Mannai

Shehzad

Okuno

2011

Genet Resour Crop Evol

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“…Linkage disequilibrium SSR markers have been used for primary evaluation of LD across the genome of crops, including maize (Remington et al 2001;Liu et al 2003;Stich et al 2005) and durum wheat (Maccaferri et al 2005). As a selWng species, soybean was supposed to have a high level of LD, but Zhu et al (2003) detected low genome-wide LD in soybean (Glycine max L.…”

Section: Genetic Diversitymentioning

confidence: 99%

“…Information on the extent and structure of linkage disequilibrium (LD) within the population under consideration is a prerequisite for association mapping. A panel of a large number of SSR markers is suitable to establish LD patterns, as was shown in maize (Remington et al 2001;Liu et al 2003;Stich et al 2005) and durum wheat (Maccaferri et al 2005). Gametic phase disequilibrium can be the result of a number of factors next to recombination, and the population structure resulting from selection, population admixture, and genetic drift is more likely to remain intact over time in a selWng species such as soybean, in which recombination is very low or absent.…”

mentioning

confidence: 99%

Genetic structure and diversity of cultivated soybean (Glycine max (L.) Merr.) landraces in China

et al. 2008

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The Chinese genebank contains 23,587 soybean landraces collected from 29 provinces. In this study, a representative collection of 1,863 landraces were assessed for genetic diversity and genetic diVerentiation in order to provide useful information for eVective management and utilization. A total of 1,160 SSR alleles at 59 SSR loci were detected including 97 unique and 485 low-frequency alleles, which indicated great richness and uniqueness of genetic variation in this core collection. Seven clusters were inferred by STRUCTURE analysis, which is in good agreement with a neighbor-joining tree. The cluster subdivision was also supported by highly signiWcant pairwise F st values and was generally in accordance with diVerences in planting area and sowing season. The cluster HSuM, which contains accessions collected from the region between 32.0 and 40.5°N, 105.4 and 122.2°E along the central and downstream parts of the Yellow River, was the most genetically diverse of the seven clusters. This provides the Wrst molecular evidence for the hypotheses that the origin of cultivated soybean is the Yellow River region. A high proportion (95.1%) of pairs of alleles from diVerent loci was in LD in the complete dataset. This was mostly due to overall population structure, since the number of locus pairs in LD was reduced sharply within each of the clusters compared to the complete dataset. This shows that population structure needs to be accounted for in association studies conducted within this collection. The low value of LD within the clusters can be seen as evidence that much of the recombination events in the past have been maintained in soybean, Wxed in homozygous self-fertilizing landraces.

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“…The unlinked r 2 were obtained by analysis of all pairs of adjacent loci were in LD (Stich et al 2005). Three LD blocks were detected on 4A.…”

Section: Linkage Disequilibriummentioning

confidence: 99%

Association mapping of six agronomic traits on chromosome 4A of wheat (<em>Triticum aestivum</em> L.)

Liu¹,

Wang²,

Yao³

et al. 2010

mpb

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Association mapping is a powerful approach to identify associations between traits of interest and genetic markers. In this study, 103 wheat germplasm accessions from China were genotyped using 76 SSR markers and 40 EST-SSR markers. The phenotyping of plant height, spike length, spikelets per spike, spikelets density, grains per spike and thousand-kernel weight were carried out in three locations for three years. Six subpopulations were identified among these accessions by population structure analysis based on 49 SSR and 40 EST-SSR markers. Linkage disequilibrium (LD) on chromosome 4A extended up to ~3 cM with r 2 =0.054. Based on the mixed linear model considering population structure and relative kinship, a total of 10 SSR markers (p<0.01) on chromosome 4A were significantly associated with six agronomic traits, and six of them were associated with multiple traits. Some of the associated markers were in agreement with previous quantitative trait loci (QTL) analysis. This study demonstrated that association mapping can be successfully applied in wheat breeding context for detection of marker-traits associations. Furthermore, association mapping can enhance previous QTL information and provide additional QTL information for marker-assisted selection.

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Linkage disequilibrium in European elite maize germplasm investigated with SSRs

Cited by 175 publications

References 30 publications

Variation in flowering time in sorghum core collection and mapping of QTLs controlling flowering time by association analysis

Variation in flowering time in sorghum core collection and mapping of QTLs controlling flowering time by association analysis

Genetic structure and diversity of cultivated soybean (Glycine max (L.) Merr.) landraces in China

Association mapping of six agronomic traits on chromosome 4A of wheat (<em>Triticum aestivum</em> L.)

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