Genotyping by Sequencing for SNP-Based Linkage Map Construction and QTL Analysis of Chilling Requirement and Bloom Date in Peach [Prunus persica (L.) Batsch]

Bielenberg, Douglas G.; Rauh, B.; Fan, Shenghua; Gašić, Ksenija; Abbott, Albert G.; Reighard, G.L.; Okie, W.R.; Wells, Christina E.

doi:10.1371/journal.pone.0139406

Cited by 105 publications

(109 citation statements)

References 31 publications

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“…These methods involve next-generation sequencing near restriction sites in genome sequences and are collectively described as reduced representation library sequencing (Davey et al, 2011;Jiang et al, 2016). SNP-based linkage map construction and QTL analysis using GBS have been carried out in several plant species (Bielenberg et al, 2015). The genotyping-by-sequencing method (GBS; Sonah et al, 2013) is a simple library preparation method that can be used along with restriction site-associated DNA sequencing (Baird et al, 2008).…”

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confidence: 99%

Genotyping-by-sequencing for construction of a new genetic linkage map and QTL analysis of growth-related traits in Pacific bluefin tuna

et al. 2017

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Pacific bluefin tuna (Thunnus orientalis) has high market value, but its wild populations have decreased in recent years. The broodstock of Pacific bluefin tuna that were hatched artificially and reared under aquaculture conditions is beginning to be used for production. The creation of broodstock with commercially valuable traits, such as rapid growth, is therefore of great interest. Genetic linkage map-based identification of markers associated with quantitative trait loci (QTLs) facilitates marker-assisted selection (MAS) breeding and allows efficient genetic improvement of broodstock. Single nucleotide polymorphism (SNP)-based genetic linkage map construction using the genotyping-by-sequencing method can expand the number of mapped markers and help identify growth-related QTLs. In this study, we constructed sex-specific maps for 24 linkage groups consisting of 677 SNP and 651 microsatellite markers. The total lengths of 93 progenies in the mapping population followed normal distribution, with an average length of 9.4 mm. We performed composite interval mapping in the mapping population. QTL analysis revealed one significant QTL in LG10 on the female linkage map. The genetic linkage map-the second such map generated for Pacific bluefin tuna-and the growth-related QTLs detected in this study will be useful for tuna aquaculture MAS programs. K E Y W O R D Sgenotyping-by-sequencing, growth-related trait, Pacific bluefin tuna, QTL

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confidence: 99%

Genotyping-by-sequencing for construction of a new genetic linkage map and QTL analysis of growth-related traits in Pacific bluefin tuna

et al. 2017

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“…Additionally, GBS has been shown to be a valid tool for genomic diversity studies (Fu and Peterson, 2011). Recently this approach was reported for quantitative trait loci (QTL) analyses in peach and other species (Ward et al, 2013; Bielenberg et al, 2015). Several microarrays using the Infinium R platform for SNP genotyping are available in different Rosaceae species such as peach, apple, and cherry (Chagné et al, 2012; Verde et al, 2012).…”

Section: Next Generation Sequencingmentioning

confidence: 99%

“…Similarly to fruit quality, high-throughput sequencing helped to dissect complex traits and to identify candidate genes for other traits such as adaptability to chilling (Bielenberg et al, 2015), and resistance to brown rot (Martínez-García et al, 2013), bacterial spot (Yang et al, 2013), and PPV (Zuriaga et al, 2013). …”

Section: Impact Of Ngs On Breedingmentioning

confidence: 99%

Application of Genomic Technologies to the Breeding of Trees

et al. 2016

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The recent introduction of next generation sequencing (NGS) technologies represents a major revolution in providing new tools for identifying the genes and/or genomic intervals controlling important traits for selection in breeding programs. In perennial fruit trees with long generation times and large sizes of adult plants, the impact of these techniques is even more important. High-throughput DNA sequencing technologies have provided complete annotated sequences in many important tree species. Most of the high-throughput genotyping platforms described are being used for studies of genetic diversity and population structure. Dissection of complex traits became possible through the availability of genome sequences along with phenotypic variation data, which allow to elucidate the causative genetic differences that give rise to observed phenotypic variation. Association mapping facilitates the association between genetic markers and phenotype in unstructured and complex populations, identifying molecular markers for assisted selection and breeding. Also, genomic data provide in silico identification and characterization of genes and gene families related to important traits, enabling new tools for molecular marker assisted selection in tree breeding. Deep sequencing of transcriptomes is also a powerful tool for the analysis of precise expression levels of each gene in a sample. It consists in quantifying short cDNA reads, obtained by NGS technologies, in order to compare the entire transcriptomes between genotypes and environmental conditions. The miRNAs are non-coding short RNAs involved in the regulation of different physiological processes, which can be identified by high-throughput sequencing of RNA libraries obtained by reverse transcription of purified short RNAs, and by in silico comparison with known miRNAs from other species. All together, NGS techniques and their applications have increased the resources for plant breeding in tree species, closing the former gap of genetic tools between trees and annual species.

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“…The QTLs for apricot blooming initiation time were located on LG1 and LG4 (Dirlewanger et al, ; Olukolu et al, ; Socquet‐Juglard et al, ). In peach, major QTLs for chilling requirements and blooming time were detected on LG1, LG4, and LG7 (Bielenberg et al, ; Fan et al, ; Zhebentyayeva et al, ). Genome‐wide association studies for CR in peach identified seven association peaks, located on LG 1, 3, 7, and 8.…”

Section: Introductionmentioning

confidence: 99%

Association between blooming time and climatic adaptation in Prunus mume

Shi

Luo

et al. 2019

Ecology and Evolution

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Prunus mume Sieb. et Zucc. is an important fruit crop of the subtropical region, originating in China. It blooms earlier than other deciduous fruit trees, but different regions have different blooming periods. The time of anthesis is related to the dormancy period, and a certain amount of chilling promotes bud break and blooming. To identify the relationship between blooming time and the climatic adaptation of P. mume cultivars in China, the nuclear and chloroplast genomes of 19 cultivars from the main cultivation areas of P. mume in China were resequenced. The average depth of coverage was 34X–76X, and a total of 388,134 single nucleotide polymorphisms were located within the coding regions of the gene (CDs). Additionally, the 19 cultivar accessions were divided into three groups based on their blooming time: early, mid, and late. Associated with the blooming time groups, 21 selective sweep regions were identified, which could provide evidence supporting the possible model of P. mume domestication originating due to natural selection. Furthermore, we identified a flowering gene, FRIGIDA‐LIKE 3 (FRL3), seems to affect the blooming time and the climatic adaptation of P. mume cultivars. This study is a major step toward understanding the climatic adaptation of P. mume cultivars in China.

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Genotyping by Sequencing for SNP-Based Linkage Map Construction and QTL Analysis of Chilling Requirement and Bloom Date in Peach [Prunus persica (L.) Batsch]

Cited by 105 publications

References 31 publications

Genotyping-by-sequencing for construction of a new genetic linkage map and QTL analysis of growth-related traits in Pacific bluefin tuna

Genotyping-by-sequencing for construction of a new genetic linkage map and QTL analysis of growth-related traits in Pacific bluefin tuna

Application of Genomic Technologies to the Breeding of Trees

Association between blooming time and climatic adaptation in Prunus mume

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