High-density genetic map and QTL analysis of soluble solid content, maturity date, and mealiness in peach using genotyping by sequencing

Núñez-Lillo, Gerardo; Balladares, Cristóbal; Pavez, Catalina; Urra, Claudio; Sanhueza, Dayán; Vendramin, Elisa; Dettori, Maria Teresa; Arús, Pere; Verde, Ignazio; Blanco‐Herrera, Francisca; Campos-Vargas, Reinaldo; Meneses, Claudio

doi:10.1016/j.scienta.2019.108734

Cited by 36 publications

(46 citation statements)

References 70 publications

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“…SNPs are known to be associated with many quantitative trait loci in plants 20,[30][31][32][33] and an individual SNP can have a large impact on the phenotype 34,35 . We found 2180 SNPs located in coding regions and 26,271 in noncoding regions of the papaya genome.…”

Section: Discussionmentioning

confidence: 99%

“…DNA variants such as SNPs and InDels are very abundant in all genomes and are thought to bring out the phenotypic differences among individuals of a species, including differences related to yield and fruit quality traits [18][19][20][21] . SNPs and InDels are quickly identified through Next Generation Sequencing (NGS) technologies and numerous studies in climacteric fruit crops revealed the potential of NGS-based markers for the genetic mapping of fruit quality traits 17,[22][23][24] .…”

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confidence: 99%

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Discovery of SNPs and InDels in papaya genotypes and its potential for marker assisted selection of fruit quality traits

Bohry

Ramos

Santos

et al. 2021

Sci Rep

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Papaya is a tropical and climacteric fruit that is recognized for its nutritional benefits and medicinal applications. Its fruits ripen quickly and show a drastic fruit softening, leading to great post-harvest losses. To overcome this scenario, breeding programs of papaya must invest in exploring the available genetic variation to continue developing superior cultivars with improved fruit quality traits. The objective of this study was to perform a whole-genome genotyping (WGG) of papaya, predict the effects of the identified variants, and develop a list of ripening-related genes (RRGs) with linked variants. The Formosa elite lines of papaya Sekati and JS-12 were submitted to WGG with an Illumina Miseq platform. The effects of variants were predicted using the snpEff program. A total of 28,451 SNPs having Ts/Tv (Transition/Transversion) ratio of 2.45 and 1,982 small insertions/deletions (InDels) were identified. Most variant effects were predicted in non-coding regions, with only 2,104 and 138 effects placed in exons and splice site regions, respectively. A total of 106 RRGs were found to be associated with 460 variants, which may be converted into PCR markers to facilitate genetic mapping and diversity studies and to apply marker-assisted selection (MAS) for specific traits in papaya breeding programs.

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Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

Discovery of SNPs and InDels in papaya genotypes and its potential for marker assisted selection of fruit quality traits

Bohry

Ramos

Santos

et al. 2021

Sci Rep

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“…These LGs have been also identified as key genome regions for fruit quality traits in other Prunus species including almonds [ 176 ], peaches [ 177 , 178 , 179 , 180 , 181 ], and Japanese plums [ 170 , 182 ]. The most significant QTLs are located in LG4 for soluble solid contents and ripening dates, as well as in LG3 for skin ground and flesh color in different analyzed Prunus species [ 183 , 184 , 185 , 186 ]. Flesh color around the stone, flower color, and other color have been mapped to LG 3, fruit skin color and leaf color have been mapped to LG6, blood flesh has been mapped to the top of LG4, and dominant blood flesh has been mapped to the top of LG5 [ 63 , 187 , 188 ].…”

Section: Application Of New Molecular Tools To Prunus mentioning

confidence: 99%

Molecular Bases of Fruit Quality in Prunus Species: An Integrated Genomic, Transcriptomic, and Metabolic Review with a Breeding Perspective

García-Gómez

Salazar

Nicolás-Almansa

et al. 2020

IJMS

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In plants, fruit ripening is a coordinated developmental process that requires the change in expression of hundreds to thousands of genes to modify many biochemical and physiological signal cascades such as carbohydrate and organic acid metabolism, cell wall restructuring, ethylene production, stress response, and organoleptic compound formation. In Prunus species (including peaches, apricots, plums, and cherries), fruit ripening leads to the breakdown of complex carbohydrates into sugars, fruit firmness reductions (softening by cell wall degradation and cuticle properties alteration), color changes (loss of green color by chlorophylls degradation and increase in non-photosynthetic pigments like anthocyanins and carotenoids), acidity decreases, and aroma increases (the production and release of organic volatile compounds). Actually, the level of information of molecular events at the transcriptional, biochemical, hormonal, and metabolite levels underlying ripening in Prunus fruits has increased considerably. However, we still poorly understand the molecular switch that occurs during the transition from unripe to ripe fruits. The objective of this review was to analyze of the molecular bases of fruit quality in Prunus species through an integrated metabolic, genomic, transcriptomic, and epigenetic approach to better understand the molecular switch involved in the ripening process with important consequences from a breeding point of view.

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“…Du et al revealed the genetic architecture of growth traits in poplars using linkage analysis and association studies [17]. Other traits, such as bud burst timing [18], lignin content [19], reproduction-related traits [20], and fruit-related traits [21, 22], have also been subjected to linkage-based QTL mapping in forest species and other woody plants. According to QTL studies, genetic mapping is still one of the most efficient methods for studying genetic characteristics.…”

Section: Introductionmentioning

confidence: 99%

Construction of a high-density genetic map and QTL mapping of leaf traits and plant growth in an interspecific F1 population of Catalpa bungei × Catalpa duclouxii Dode

Zhang

Xiao

et al. 2019

BMC Plant Biol

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BackgroundCatalpa bungei is an important tree species used for timber in China and widely cultivated for economic and ornamental purposes. A high-density linkage map of C. bungei would be an efficient tool not only for identifying key quantitative trait loci (QTLs) that affect important traits, such as plant growth and leaf traits, but also for other genetic studies.ResultsRestriction site-associated DNA sequencing (RAD-seq) was used to identify molecular markers and construct a genetic map. Approximately 280.77 Gb of clean data were obtained after sequencing, and in total, 25,614,295 single nucleotide polymorphisms (SNPs) and 2,871,647 insertions-deletions (InDels) were initially identified in the genomes of 200 individuals of a C. bungei (7080) × Catalpa duclouxii (16-PJ-3) F1 population and their parents. Finally, 9072 SNP and 521 InDel markers that satisfied the requirements for constructing a genetic map were obtained. The integrated genetic map contained 9593 pleomorphic markers in 20 linkage groups and spanned 3151.63 cM, with an average distance between adjacent markers of 0.32 cM. Twenty QTLs for seven leaf traits and 13 QTLs for plant height at five successive time points were identified using our genetic map by inclusive composite interval mapping (ICIM). Q16–60 was identified as a QTL for five leaf traits, and three significant QTLs (Q9–1, Q18–66 and Q18–73) associated with plant growth were detected at least twice. Genome annotation suggested that a cyclin gene participates in leaf trait development, while the growth of C. bungei may be influenced by CDC48C and genes associated with phytohormone synthesis.ConclusionsThis is the first genetic map constructed in C. bungei and will be a useful tool for further genetic study, molecular marker-assisted breeding and genome assembly.

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High-density genetic map and QTL analysis of soluble solid content, maturity date, and mealiness in peach using genotyping by sequencing

Cited by 36 publications

References 70 publications

Discovery of SNPs and InDels in papaya genotypes and its potential for marker assisted selection of fruit quality traits

Discovery of SNPs and InDels in papaya genotypes and its potential for marker assisted selection of fruit quality traits

Molecular Bases of Fruit Quality in Prunus Species: An Integrated Genomic, Transcriptomic, and Metabolic Review with a Breeding Perspective

Construction of a high-density genetic map and QTL mapping of leaf traits and plant growth in an interspecific F1 population of Catalpa bungei × Catalpa duclouxii Dode

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