Simple sequence repeat-based association analysis of fruit traits in eggplant (Solanum melongena)

Ge, Heng; Liu, Y.; Zhang, J.; Han, Hongqiang; Li, H.Z.; Shao, W.T.; Chen, H.Y.

doi:10.4238/2013.november.18.14

Cited by 16 publications

(11 citation statements)

References 37 publications

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“…This was provided by the r 2 sv model, which achieved a 30 fold reduction in associations between unlinked markers, leaving high LD values only between pairs of genetically linked SNP loci. The end estimate for the extension of LD was 3.4 cM, which matches reasonably well with the level reported for eggplant by Ge et al [ 16 ], and also with those documented in other self-pollinating species such as the near-relative tomato (6–8 cM; [ 51 ]), Arabidopsis thaliana (10 kb; [ 52 ]), barley (3.5 cM; [ 26 ]) and wheat (1–5 cM; [ 27 ]). LD was not uniformly distributed along the genome (Figure 3 ), a phenomenon which has also been noted elsewhere [ 27 , 51 , 53 , 54 ].…”

Section: Discussionsupporting

confidence: 90%

“…QTL discovery in eggplant has to date been achieved using linkage mapping in bi-parental inter and intra-specific populations [ 6 , 7 , 10 , 11 , 56 ]. A first attempt to apply GWA has been published recently [ 16 ], in which 49 marker associations related to eight traits were reported. Some potentially fatal weaknesses in the analysis can, however, be identified.…”

Section: Discussionmentioning

confidence: 99%

“…To date only one GWA-based study of variation in eggplant has been performed [ 16 ] but the present study used a larger number of accessions (191 vs 141 ) and a more densely populated genetic map (384 SNPs (single nucleotide polymorphisms) vs 105 microsatellites) and targeted traits related to anthocyanin accumulation and fruit color.…”

Section: Introductionmentioning

confidence: 99%

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Linkage disequilibrium and genome-wide association analysis for anthocyanin pigmentation and fruit color in eggplant

et al. 2014

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BackgroundThe genome-wide association (GWA) approach represents an alternative to biparental linkage mapping for determining the genetic basis of trait variation. Both approaches rely on recombination to re-arrange the genome, and seek to establish correlations between phenotype and genotype. The major advantages of GWA lie in being able to sample a much wider range of the phenotypic and genotypic variation present, in being able to exploit multiple rounds of historical recombination in many different lineages and to include multiple accessions of direct relevance to crop improvement.ResultsA 191 accessions eggplant (Solanum melongena L.) association panel, comprising a mixture of breeding lines, old varieties and landrace selections originating from Asia and the Mediterranean Basin, was SNP genotyped and scored for anthocyanin pigmentation and fruit color at two locations over two years. The panel formed two major clusters, reflecting geographical provenance and fruit type. The global level of linkage disequilibrium was 3.4 cM. A mixed linear model appeared to be the most appropriate for GWA. A set of 56 SNP locus/phenotype associations was identified and the genomic regions harboring these loci were distributed over nine of the 12 eggplant chromosomes. The associations were compared with the location of known QTL for the same traits.ConclusionThe GWA mapping approach was effective in validating a number of established QTL and, thanks to the wide diversity captured by the panel, was able to detect a series of novel marker/trait associations.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-896) contains supplementary material, which is available to authorized users.

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Section: Discussionsupporting

confidence: 90%

Section: Discussionmentioning

confidence: 99%

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Linkage disequilibrium and genome-wide association analysis for anthocyanin pigmentation and fruit color in eggplant

et al. 2014

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“…First association mapping experiments have also been performed, which identified associations of SSR and SNP markers with a number of fruit and plant characters. QTLs that have been detected previously by linkage mapping were confirmed, and novel QTL were also found (Cericola et al 2014; Ge et al 2013; Portis et al 2015). A draft genome sequence of the typical Asian eggplant cultivar ‘Nakate-Shinkuro’ was published recently (Hirakawa et al 2014).…”

Section: Eggplantsupporting

confidence: 65%

The historical role of species from the Solanaceae plant family in genetic research

Gebhardt

2016

Theor Appl Genet

102

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Key message This article evaluates the main contributions of tomato, tobacco, petunia, potato, pepper and eggplant to classical and molecular plant genetics and genomics since the beginning of the twentieth century. AbstractSpecies from the Solanaceae family form integral parts of human civilizations as food sources and drugs since thousands of years, and, more recently, as ornamentals. Some Solanaceous species were subjects of classical and molecular genetic research over the last 100 years. The tomato was one of the principal models in twentieth century classical genetics and a pacemaker of genome analysis in plants including molecular linkage maps, positional cloning of disease resistance genes and quantitative trait loci (QTL). Besides that, tomato is the model for the genetics of fruit development and composition. Tobacco was the major model used to establish the principals and methods of plant somatic cell genetics including in vitro propagation of cells and tissues, totipotency of somatic cells, doubled haploid production and genetic transformation. Petunia was a model for elucidating the biochemical and genetic basis of flower color and development. The cultivated potato is the economically most important Solanaceous plant and ranks third after wheat and rice as one of the world’s great food crops. Potato is the model for studying the genetic basis of tuber development. Molecular genetics and genomics of potato, in particular association genetics, made valuable contributions to the genetic dissection of complex agronomic traits and the development of diagnostic markers for breeding applications. Pepper and eggplant are horticultural crops of worldwide relevance. Genetic and genomic research in pepper and eggplant mostly followed the tomato model. Comparative genome analysis of tomato, potato, pepper and eggplant contributed to the understanding of plant genome evolution.

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“…Depending on the presence of loci: F (van Eck et al 1993Eck et al , 1994, D (I) (Salaman 1910;De Jong 1987) or Pf ( de Jong 1987), the QTL on chromosome V may cause enhancement of violet colour in corolla, tuber skin and flesh, respectively, which may be useful information for breeding potatoes with pigmented tubers. The eggplant chromosomes V and X harbor QTL for anthocyanin distribution in tissues and organs such as fruit skin, stem, leaf, calyx, corolla, venation or fruit peduncle (Barchi et al 2012;Ge et al 2013;Toppino et al 2016). Although direct comparisons with eggplant QTL maps are hampered by the differences in genome organization between this plant and potato (Wu and Tanksley 2010), this may be an indication of conserved character of QTL on chromosome V (Fukuoka et al 2012;Rinaldi et al 2016), has an upper part orthologous to chromosome V (inversed in tomato) and lower part orthologous to chromosome XII.…”

Section: Discussionmentioning

confidence: 99%

Quantitative trait loci affecting intensity of violet flower colour in potato

et al. 2017

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Anthocyanins occur in potato tuber skin and flesh, sprouts, leaves, stems and flowers. The goal of this study was to identify genomic regions and candidate gene alleles key for accumulation of anthocyanins in potato corolla in various quantities. QTL analyses were performed in two mapping populations segregating for flower colour intensity and candidate genes were identified on the basis of function and location (chalcone isomerase, chi; chalcone synthase, chs) or location (RNA-dependent RNA polymerase 1, RDR1). We detected three and four QTL affecting the violet flower colour intensity using the two mapping populations, respectively. In both populations a locus F, necessary for violet flower colour, segregated and we used different approaches to differentiate the qualitative effect of this locus and to detect the genetic factors affecting the quantitative flower colour intensity. The strongest QTL and the only one common for the two mapping populations was located on chromosome V. The role of all three candidate genes, chi, chs and RDR1, in control of flower colour intensity is supported to different extents by the performed genetic analyses. The most important QTL on chromosome V is most likely in the same position as the QTL for anthocyanin tuber flesh coloration described previously, which indicates that the natural variation in some biosynthetic and/or regulatory genes may influence anthocyanin levels in multiple tissues.

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Simple sequence repeat-based association analysis of fruit traits in eggplant (Solanum melongena)

Cited by 16 publications

References 37 publications

Linkage disequilibrium and genome-wide association analysis for anthocyanin pigmentation and fruit color in eggplant

Linkage disequilibrium and genome-wide association analysis for anthocyanin pigmentation and fruit color in eggplant

The historical role of species from the Solanaceae plant family in genetic research

Quantitative trait loci affecting intensity of violet flower colour in potato

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