An EST-based linkage map reveals chromosomal translocation in Capsicum

Park, Soung-Woo; Jung, Jin-Kee; Choi, Eun A; Kwon, Jae-Hoon; Kang, Jin‐Ho; Jahn, Molly M.; Kang, Byoung−Cheorl

doi:10.1007/s11032-014-0089-0

Cited by 16 publications

(11 citation statements)

References 37 publications

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“…The two groups clustered together due to linkage of markers in the middle of the large linkage block to those of the smaller linkage block. This pseudolinkage suggested that this cluster included the chromosomal translocation pair P1 and P8, as observed in previous interspecific maps ( Tanksley et al 1988 ; Livingstone et al 1999 ; Wu et al 2009 ; Park et al 2014 ). This was confirmed by linkage group assignment that used FA COSII markers.…”

Section: Resultssupporting

confidence: 79%

Ultra-High Density, Transcript-Based Genetic Maps of Pepper Define Recombination in the Genome and Synteny Among Related Species

Hill

Ashrafi

Chin-Wo

et al. 2015

G3 Genes|Genomes|Genetics

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Our ability to assemble complex genomes and construct ultradense genetic maps now allows the determination of recombination rates, translocations, and the extent of genomic collinearity between populations, species, and genera. We developed two ultradense genetic linkage maps for pepper from single-position polymorphisms (SPPs) identified de novo with a 30,173 unigene pepper genotyping array. The Capsicum frutescens × C. annuum interspecific and the C. annuum intraspecific genetic maps were constructed comprising 16,167 and 3,878 unigene markers in 2108 and 783 genetic bins, respectively. Accuracies of marker groupings and orders are validated by the high degree of collinearity between the two maps. Marker density was sufficient to locate the chromosomal breakpoint resulting in the P1/P8 translocation between C. frutescens and C. annuum to a single bin. The two maps aligned to the pepper genome showed varying marker density along the chromosomes. There were extensive chromosomal regions with suppressed recombination and reduced intraspecific marker density. These regions corresponded to the pronounced nonrecombining pericentromeric regions in tomato, a related Solanaceous species. Similar to tomato, the extent of reduced recombination appears to be more pronounced in pepper than in other plant species. Alignment of maps with the tomato and potato genomes shows the presence of previously known translocations and a translocation event that was not observed in previous genetic maps of pepper.

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Section: Resultssupporting

confidence: 79%

Ultra-High Density, Transcript-Based Genetic Maps of Pepper Define Recombination in the Genome and Synteny Among Related Species

Hill

Ashrafi

Chin-Wo

et al. 2015

G3 Genes|Genomes|Genetics

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“…Additionally, other nine regions were noted in both parents with 3 to 7 markers (Table 4 ). Similarly, in Capsicum , a chromosomal translocation event between chromosome 01 and 08, between wild and cultivated Capsicum , respectively, had been reported based on an EST-based linkage map [ 51 ]. The validation and biological significance of chromosome structural variations are often analyzed using fluorescence in situ hybridization [ 51 , 52 ], and we have already been working on it and the results could be expected soon.…”

Section: Discussionmentioning

confidence: 99%

A dense SNP genetic map constructed using restriction site-associated DNA sequencing enables detection of QTLs controlling apple fruit quality

Sun

Chang

Yang³

et al. 2015

BMC Genomics

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BackgroundGenetic map based quantitative trait locus (QTL) analysis is an important method for studying important horticultural traits in apple. To facilitate molecular breeding studies of fruit quality traits in apple, we aim to construct a high density map which was efficient for QTL mapping and possible to search for candidate genes directly in mapped QTLs regions.MethodsA total of 1733 F1 seedlings derived from ‘Jonathan’ × ‘Golden Delicious’ was used for the map constructionand QTL analysis. The SNP markers were developed by restriction site-associated DNA sequencing (RADseq). Phenotyping data of fruit quality traits were calculated in 2008-2011. Once QTLs were mapped, candidate genes were searched for in the corresponding regions of the apple genome sequence underlying the QTLs. Then some of the candidate genes were validated using real-time PCR.ResultsA high-density genetic map with 3441 SNP markers from 297 individuals was generated. Of the 3441 markers, 2017 were mapped to ‘Jonathan’ with a length of 1343.4 cM and the average distance between markers was 0.67 cM, 1932 were mapped to ‘Golden Delicious’ with a length of 1516.0 cM and the average distance between markers was 0.78 cM. Twelve significant QTLs linked to the control of fruit weight, fruit firmness, sugar content and fruit acidity were mapped to seven linkage groups. Based on gene annotation, 80, 64 and 17 genes related to fruit weight, fruit firmness and fruit acidity, respectively, were analyzed.Among the 17 candidate genes associated with control of fruit acidity, changes in the expression of MDP0000582174 (MdMYB4) were in agreement with the pattern of changes in malic acid content in apple during ripening, and the relative expression of MDP0000239624 (MdME) was significantly correlated withfruit acidity.ConclusionsWe demonstrated the construction of a dense SNP genetic map in apple using next generation sequencing and that the increased resolution enabled the detection of narrow interval QTLs linked to the three fruit quality traits assessed. The candidate genes MDP0000582174 and MDP0000239624 were found to be related to fruit acidity regulation. We conclude that application of RADseq for genetic map construction improved the precision of QTL detection and should be utilized in future studies on the regulatory mechanisms of important fruit traits in apple.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1946-x) contains supplementary material, which is available to authorized users.

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“…As one of the most important downstream application of DNA marker, genetic map is also a basic tool necessarily for QTL analysis and marker-assisted selection (MAS) in breeding. In Capsicum , genetic maps (Qin et al 2014 ; Park et al 2014 ; Kim et al 2014 ; Sugita et al 2013 ; Mimura et al 2012 ; Lu et al 2012b ; Wu et al 2009 ; Barchi et al 2007 ; Yi et al 2006 ; Minamiyama et al 2006 ; Sugita et al 2005 ; Paran et al 2004 ; Kang et al 2001 ; Livingstone et al 1999 ; Tanksley et al 1988 ) based on intraspecific or interspecific populations were constructed using various marker systems mentioned above. Even though the SNP brought the density of pepper map to an unprecedented height (Qin et al 2014 ; Kim et al 2014 ), the total number of PCR-based anchored marker is still limited (Sugita et al 2013 ).…”

Section: Introductionmentioning

confidence: 99%

An InDel-based linkage map of hot pepper (Capsicum annuum)

Cheng

et al. 2015

Mol Breeding

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Two independent pepper (Capsicum annuum) genomes were published recently, opening a new era of molecular genetics research on pepper. However, pepper molecular marker technologies are still mainly focusing on the simple sequence repeats derived from public database or genomic library. The development and application of the third generation marker system such as single nucleotide polymorphisms, structure variations as well as insertion/deletion polymorphisms (InDels) is still in its infancy. In the present study, we developed InDel markers for pepper genetic mapping with the convenience of two whole-genome re-sequenced inbred lines BA3 (C. annuum) and B702 (C. annuum). A total of 154,519 and 149,755 InDel (1–5 bp) sites were identified for BA3 and B702, respectively, by the alignment of re-sequencing reads to Zunla-1 reference genome. Then, 14,498 InDel sites (only 4 and 5 bp) that are different between BA3 and B702 were predicted. Finally, within a random set of 1,000 primer pairs, 251 InDel markers were validated and mapped onto a linkage map using F2 population derived from the intraspecific cross BA3 × B702. The first InDel-based map, named as BB-InDel map, consisted of 12 linkage groups, covered a genetic distance of 1,178.01 cM and the average distance between bin markers was 5.01 cM. Compared to the Zunla-1 reference physical map, high consistency was observed on all 12 chromosomes, and the total length of scaffold anchored and physical distance covered by this map was 299.66 and 2,558.68 Mb, respectively, which accounted for 8.95 and 76.38 % of the Zunla-1 reference genome (3.35 Gb), respectively. Furthermore, 37 scaffolds (total length of 36.21 Mb) from the pseudo-chromosome (P0) of the current genome assembly were newly assigned to the corresponding chromosomes by 40 InDel markers. Thus, this map provided good genome coverage and would be useful for basic and applied research in pepper.Electronic supplementary materialThe online version of this article (doi:10.1007/s11032-015-0219-3) contains supplementary material, which is available to authorized users.

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An EST-based linkage map reveals chromosomal translocation in Capsicum

Cited by 16 publications

References 37 publications

Ultra-High Density, Transcript-Based Genetic Maps of Pepper Define Recombination in the Genome and Synteny Among Related Species

Ultra-High Density, Transcript-Based Genetic Maps of Pepper Define Recombination in the Genome and Synteny Among Related Species

A dense SNP genetic map constructed using restriction site-associated DNA sequencing enables detection of QTLs controlling apple fruit quality

An InDel-based linkage map of hot pepper (Capsicum annuum)

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