Analysis of diversity and linkage disequilibrium along chromosome 3B of bread wheat (Triticum aestivum L.)

Horvath, Aniko; Didier, Audrey; Koenig, Jean; Exbrayat, Florence; Charmet, Gilles; Balfourier, François

doi:10.1007/s00122-009-1153-8

Cited by 41 publications

(44 citation statements)

References 54 publications

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“…The many polymorphisms found in the promoter regions lead to differential expression during grain development of the haplotypes identified. The germplasm analyzed here included accessions from different geographical origins and represents a wide range of the natural diversity of wheat (Balfourier et al, 2007;Horvath et al, 2009). Significant associations were found between the alleles identified and dough viscoelasticity and grain hardness.…”

Section: Discussionmentioning

confidence: 99%

“…To reduce the rate of false positives, the structure components (i.e. the contribution of each line to the five ancestor groups) of the core collection (Horvath et al, 2009) were used as covariates (model I). As grain hardness is known to modify dough viscoelasticity (Eagles et al, 2006), the effects of Spa markers were then tested with grain hardness introduced into model I as covariate (model II).…”

Section: Discussionmentioning

confidence: 99%

“…The population structure of this core collection is characterized by five ancestor groups (Horvath et al, 2009). The whole core collection has recently been phenotyped for several quality traits (Bordes et al, 2008).…”

Section: Methodsmentioning

confidence: 99%

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Nucleotide Polymorphism in the Wheat Transcriptional ActivatorSpaInfluences Its Pattern of Expression and Has Pleiotropic Effects on Grain Protein Composition, Dough Viscoelasticity, and Grain Hardness

et al. 2009

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Storage protein activator (SPA) is a key regulator of the transcription of wheat (Triticum aestivum) grain storage protein genes and belongs to the Opaque2 transcription factor subfamily. We analyzed the sequence polymorphism of the three homoeologous Spa genes in hexaploid wheat. The level of polymorphism in these genes was high particularly in the promoter. The deduced protein sequences of each homoeolog and haplotype show greater than 93% identity. Two major haplotypes were studied for each Spa gene. The three Spa homoeologs have similar patterns of expression during grain development, with a peak in expression around 300 degree days after anthesis. On average, Spa-B is 10 and seven times more strongly expressed than Spa-A and Spa-D, respectively. The haplotypes are associated with significant quantitative differences in Spa expression, especially for Spa-A and Spa-D. Significant differences were found in the quantity of total grain nitrogen allocated to the gliadin protein fractions for the Spa-A haplotypes, whereas the synthesis of glutenins is not modified. Genetic association analysis between Spa and dough viscoelasticity revealed that Spa polymorphisms are associated with dough tenacity, extensibility, and strength. Except for Spa-A, these associations can be explained by differences in grain hardness. No association was found between Spa markers and the average single grain dry mass or grain protein concentration. These results demonstrate that in planta Spa is involved in the regulation of grain storage protein synthesis. The associations between Spa and dough viscoelasticity and grain hardness strongly suggest that Spa has complex pleiotropic functions during grain development.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Nucleotide Polymorphism in the Wheat Transcriptional ActivatorSpaInfluences Its Pattern of Expression and Has Pleiotropic Effects on Grain Protein Composition, Dough Viscoelasticity, and Grain Hardness

et al. 2009

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“…For example, genetic diversity parameters have been described at the whole-genome level for Arabidopsis (Nordborg et al, 2005;Kim et al, 2007), maize (Yan et al, 2009); http://www.panzea.org), rice (http://irfgc.irri.org), soybean (Lam et al, 2010) or at the chromosome level for wheat (Horvath et al, 2009). From these surveys of LD, Kim et al (2007) estimated that B140 000 single-nucleotide polymorphisms (SNPs) would be required for the whole scan of the 125-Mb genome of Arabidopsis, whereas Yan et al (2009) estimated this number between 240 000 and 480 000 SNPs for the 2400-Mb genome of maize.…”

Section: Introductionmentioning

confidence: 99%

The heterogeneous levels of linkage disequilibrium in white spruce genes and comparative analysis with other conifers

Pavy

Gagnon

et al. 2011

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In plants, knowledge about linkage disequilibrium (LD) is relevant for the design of efficient single-nucleotide polymorphism arrays in relation to their use in population and association genomics studies. Previous studies of conifer genes have shown LD to decay rapidly within gene limits, but exceptions have been reported. To evaluate the extent of heterogeneity of LD among conifer genes and its potential causes, we examined LD in 105 genes of white spruce (Picea glauca) by sequencing a panel of 48 haploid megagametophytes from natural populations and further compared it with LD in other conifer species. The average pairwise r 2 value was 0.19 (s.d.¼0.19), and LD dropped quickly with a half-decay being reached at a distance of 65 nucleotides between sites. However, LD was significantly heterogeneous among genes. A first group of 29 genes had stronger LD (mean r 2 ¼0.28), and a second group of 38 genes had weaker LD (mean r 2 ¼0.12). While a strong relationship was found with the recombination rate, there was no obvious relationship between LD and functional classification. The level of nucleotide diversity, which was highly heterogeneous across genes, was also not significantly correlated with LD. A search for selection signatures highlighted significant deviations from the standard neutral model, which could be mostly attributed to recent demographic changes. Little evidence was seen for hitchhiking and clear relationships with LD. When compared among conifer species, on average, levels of LD were similar in genes from white spruce, Norway spruce and Scots pine, whereas loblolly pine and Douglas fir genes exhibited a significantly higher LD.

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“…LD-based association studies have been conducted for various traits including kernel size, milling quality (Breseghello and Sorrels 2006), yellow pigment (Reimer et al 2008), drought tolerance (Maccaferri et al 2011) and late maturity α-amylase activity (Emebiri et al 2010). In common wheat LD pattern has been assessed for chromosomes 2D, 5A (Breseghello and Sorrels 2006), and 3B (Horvath et al 2009). …”

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confidence: 99%

Analysis of Genetic Diversity in Synthetic Wheat Assemblage (T. turgidum^|^times;Aegilops tauschii; 2n=6x=42; AABBDD) for Winter Wheat Breeding

et al. 2014

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Summary An unconventional genetic resource for bread wheat improvement is the diploid D genome donor to bread wheat; Aegilops tauschii (2n=2x=14, DD). Bridge crossing the Triticum turgidum/Aegilops tauschii results in synthetic hexaploid (SH) wheats; the most common method of wheat improvement that efficiently utilizes the diversity of this diploid wheat progenitor of the primary gene pool. SH wheats exhibit spring or winter growth habits, depending on the parental durum germplasm. This study focuses on the molecular diversity among 58 winter synthetic hexaploid wheat (WSH) combinations that have been produced to facilitate winter wheat breeding programs. Genetic diversity and genome-wide linkage disequilibrium (LD) were investigated for all D-genome chromosomes using SSR markers. LD analysis based on 71 microsatellite loci represented a mean marker density of 7.1 cm. A total of 738 alleles ranging from 3 to 20 per locus were characterized in WSHs. The mean PIC and MI values were 0.61 and 3.41, ranging from 0.14 to 0.86 and 0.02 to 9.6, respectively. The analysis of molecular variance and Wright s fixation index further established significant genetic diversity among different clusters and durum groups leading to the conclusion that diversity within WSHs is well validated. The population structure also partially validated the cluster analysis by forming eight (K=6) sub-populations. The variable patterns of LD independent of the genetic distance (cm) in some cases provided critical information for these resynthesized winter wheat genetic resources for their future deployment and association mapping studies. Molecular analyses, thus, have established ample diversity that is present within these winter SHs and generated information for effectively introducing new diversity from these unique genetic resources into the prevalent winter wheat germplasm.

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Analysis of diversity and linkage disequilibrium along chromosome 3B of bread wheat (Triticum aestivum L.)

Cited by 41 publications

References 54 publications

Nucleotide Polymorphism in the Wheat Transcriptional ActivatorSpaInfluences Its Pattern of Expression and Has Pleiotropic Effects on Grain Protein Composition, Dough Viscoelasticity, and Grain Hardness

Nucleotide Polymorphism in the Wheat Transcriptional ActivatorSpaInfluences Its Pattern of Expression and Has Pleiotropic Effects on Grain Protein Composition, Dough Viscoelasticity, and Grain Hardness

The heterogeneous levels of linkage disequilibrium in white spruce genes and comparative analysis with other conifers

Analysis of Genetic Diversity in Synthetic Wheat Assemblage (T. turgidum^|^times;Aegilops tauschii; 2n=6x=42; AABBDD) for Winter Wheat Breeding

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