Construction of Commercial Sweet Cherry Linkage Maps and QTL Analysis for Trunk Diameter

Wang, Jing; Zhang, Kaichun; Zhang, Xiaoming; Yan, Guohua; Zhou, Yu; Feng, Laibao; Ni, Yang; Duan, Xiaoqun

doi:10.1371/journal.pone.0141261

Cited by 14 publications

(15 citation statements)

References 42 publications

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“…Recently, the SLAF-seq technology has been used successfully to develop a large number of SLAF markers and for the construction of high-density genetic maps for many plants, including soybean [43], sweet cherry [24], cucumber [44], watermelon [45], red sage [46], and willow [47]. …”

Section: Discussionmentioning

confidence: 99%

Construction of a high-density genetic map for grape using specific length amplified fragment (SLAF) sequencing

et al. 2017

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Genetic maps are important tools in plant genomics and breeding. We report a large-scale discovery of single nucleotide polymorphisms (SNPs) using the specific length amplified fragment sequencing (SLAF-seq) technique for the construction of high-density genetic maps for two elite wine grape cultivars, ‘Chardonnay’ and ‘Beibinghong’, and their 130 F1 plants. A total of 372.53 M paired-end reads were obtained after preprocessing. The average sequencing depth was 33.81 for ‘Chardonnay’ (the female parent), 48.20 for ‘Beibinghong’ (the male parent), and 12.66 for the F1 offspring. We detected 202,349 high-quality SLAFs of which 144,972 were polymorphic; 10,042 SNPs were used to construct a genetic map that spanned 1,969.95 cM, with an average genetic distance of 0.23 cM between adjacent markers. This genetic map contains the largest molecular marker number of the grape maps so far reported. We thus demonstrate that SLAF-seq is a promising strategy for the construction of high-density genetic maps; the map that we report here is a good potential resource for QTL mapping of genes linked to major economic and agronomic traits, map-based cloning, and marker-assisted selection of grape.

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Section: Discussionmentioning

confidence: 99%

Construction of a high-density genetic map for grape using specific length amplified fragment (SLAF) sequencing

et al. 2017

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“…An initial scan with marker CPDCT037 and EPPB4221‐PR110 mapped this locus onto sweet cherry LG 3. Two new specific‐locus amplified fragment sequencing (SLAF‐seq) markers (marker 1637 and marker 3823) were developed, and the site of the locus was identified based on the results of BLAST peach genome analyses (Dirlewanger et al ., ; Verde et al ., ; Wang et al ., ,b).…”

Section: Methodsmentioning

confidence: 99%

“…Many reports show that the R2R3‐MYB TFs interact with common bHLH and WDR factors form a MYB–bHLH–WD40 (MBW) transcriptional activator complex to regulate the anthocyanin biosynthesis. The MBW activator complex regulates anthocyanin biosynthesis by directly activating the expression of the anthocyanin biosynthesis genes (Albert et al ., , ; D'Amelia et al ., ; Gonzalez et al ., ; Lowry et al ., ; Matsui et al ., ; Schaart et al ., ; Starkevič et al ., ; Wang et al ., ,b).…”

Section: Introductionmentioning

confidence: 99%

TheR2R3MYBtranscription factorPavMYB10.1involves in anthocyanin biosynthesis and determines fruit skin colour in sweet cherry (Prunus aviumL.)

Jin

Wang

et al. 2016

Plant Biotechnology Journal

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162

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SummarySweet cherry is a diploid tree species and its fruit skin has rich colours from yellow to blush to dark red. The colour is closely related to anthocyanin biosynthesis and is mainly regulated at the transcriptional level by transcription factors that regulate the expression of multiple structural genes. However, the genetic and molecular bases of how these genes ultimately determine the fruit skin colour traits remain poorly understood. Here, our genetic and molecular evidences identified the R2R3 MYB transcription factor PavMYB10.1 that is involved in anthocyanin biosynthesis pathway and determines fruit skin colour in sweet cherry. Interestingly, we identified three functional alleles of the gene causally leading to the different colours at mature stage. Meanwhile, our experimental results of yeast two‐hybrid assays and chromatin immunoprecipitation assays revealed that PavMYB10.1 might interact with proteins PavbHLH and PavWD40, and bind to the promoter regions of the anthocyanin biosynthesis genes PavANS and PavUFGT; these findings provided to a certain extent mechanistic insight into the gene's functions. Additionally, genetic and molecular evidences confirmed that PavMYB10.1 is a reliable DNA molecular marker to select fruit skin colour in sweet cherry.

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“…This genetic map, with an average inter-marker distance of 0.37 cM, represents, to our knowledge, the most extensive orchardgrass genetic map to date. This map also has a much higher marker density than most genetic maps constructed with SLAF markers 23 34 38 39 40 41 42 . HighMap software and collinearity with the genome sequence 32 were used to evalute the quality of previous genetic maps.…”

Section: Discussionmentioning

confidence: 99%

Construction of high-density genetic linkage map and identification of flowering-time QTLs in orchardgrass using SSRs and SLAF-seq

Zhao

Huang

Zhang

et al. 2016

Sci Rep

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Orchardgrass (Dactylis glomerata L.) is one of the most economically important perennial, cool-season forage species grown and pastured worldwide. High-density genetic linkage mapping is a valuable and effective method for exploring complex quantitative traits. In this study, we developed 447,177 markers based on SLAF-seq and used them to perform a comparative genomics analysis. Perennial ryegrass sequences were the most similar (5.02%) to orchardgrass sequences. A high-density linkage map of orchardgrass was constructed using 2,467 SLAF markers and 43 SSRs, which were distributed on seven linkage groups spanning 715.77 cM. The average distance between adjacent markers was 0.37 cM. Based on phenotyping in four environments, 11 potentially significant quantitative trait loci (QTLs) for two target traits–heading date (HD) and flowering time (FT)–were identified and positioned on linkage groups LG1, LG3, and LG5. Significant QTLs explained 8.20–27.00% of the total phenotypic variation, with the LOD ranging from 3.85–12.21. Marker167780 and Marker139469 were associated with FT and HD at the same location (Ya’an) over two different years. The utility of SLAF markers for rapid generation of genetic maps and QTL analysis has been demonstrated for heading date and flowering time in a global forage grass.

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Construction of Commercial Sweet Cherry Linkage Maps and QTL Analysis for Trunk Diameter

Cited by 14 publications

References 42 publications

Construction of a high-density genetic map for grape using specific length amplified fragment (SLAF) sequencing

Construction of a high-density genetic map for grape using specific length amplified fragment (SLAF) sequencing

TheR2R3MYBtranscription factorPavMYB10.1involves in anthocyanin biosynthesis and determines fruit skin colour in sweet cherry (Prunus aviumL.)

Construction of high-density genetic linkage map and identification of flowering-time QTLs in orchardgrass using SSRs and SLAF-seq

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