Candidate gene prediction via quantitative trait locus analysis of fruit shape index traits in apple

Cao, Ke; Chang, Yuansheng; Sun, Rui; Shen, Fei; Wu, Ting; Wang, Yi; Zhang, Xinzhong; Han, Zhenhai

doi:10.1007/s10681-015-1488-y

Cited by 15 publications

(13 citation statements)

References 38 publications

(44 reference statements)

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“…Cao et al . 22 reported a large effect QTL for apple fruit shape index on LG11, suggesting an orthologous region between apple and pear genomes. A QTL for AVFW was mapped on LG7 21 , which agrees with our results, but some studies 3,4 mapped QTLs for AVFW on different linkage groups – suggesting this trait has a complex polygenic nature.…”

Section: Discussionmentioning

confidence: 99%

Marker-trait associations and genomic predictions of interspecific pear (Pyrus) fruit characteristics

Kumar

Kirk

Deng

et al. 2019

Sci Rep

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Interspecific pear ( Pyrus spp.) hybrid populations are often used to develop novel cultivars. Pear cultivar breeding is a lengthy process because of long juvenility and the subsequent time required for reliable fruit phenotyping. Molecular techniques such as genome-wide association (GWA) and genomic selection (GS) provide an opportunity to fast-forward the development of high-value cultivars. We evaluated the genetic architecture of 10 pear fruit phenotypes (including sensory traits) and the potential of GS using genotyping-by-sequencing of 550 hybrid seedlings from nine interrelated full-sib families. Results from GWA suggested a complex polygenic nature of all 10 traits as the maximum variance explained by each marker was less than 4% of the phenotypic variance. The effect-size of SNPs for each trait suggested many genes of small effect and few of moderate effect. Some genomic regions associated with pear sensory traits were similar to those reported for apple – possibly a result of high synteny between the apple and pear genomes. The average (across nine families) GS accuracy varied from 0.32 (for crispness) to 0.62 (for sweetness), with an across-trait average of 0.42. Further efforts are needed to develop larger genotype-phenotype datasets in order to predict fruit phenotypes of untested seedlings with sufficient efficiency.

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Section: Discussionmentioning

confidence: 99%

Marker-trait associations and genomic predictions of interspecific pear (Pyrus) fruit characteristics

Kumar

Kirk

Deng

et al. 2019

Sci Rep

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“…The fruit shape development has been confirmed to be essentially determined by fruit genotype (Cao et al, 2015;Kurian & Peter, 1997). Climate, soil type, and management strategy also play important roles in altering the shape of fruits.…”

Section: Physicochemical and Chemical Propertiesmentioning

confidence: 92%

Comparison of physical and chemical composition of three chinese jujube (Ziziphus jujuba Mill.) cultivars cultivated in four districts of Xinjiang region in China

Chen

Fan

et al. 2019

Food Sci. Technol

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This study investigated the physical and chemical composition of three jujube fruits cultivated in China. The objective was to explore the effect of jujube genotype and cultivation districts on the quality of jujube fruits. Results showed significant differences on their physical and chemical composition. The Junzao cultivar contained relatively low level on the total dietary fiber, protein, total sugar, and total titratable acids. The Huizao cultivar possessed the mediate level of the sugar-to-acid ratio and ascorbic acid. The Dazao cultivar showed high level of the total dietary fiber, protein, sugar, and total acids. The cultivation districts exerted important roles in altering the physicochemical indexes of the same jujube cultivar. The Junzao cultivar harvested in the Hami and Kashi districts showed the significant difference on the level of the sugar-to-acid ratio and ascorbic acid compared with that in the Akesu and Hetian districts. The Huizao cultivar in the Kashi area possessed higher content of the total soluble dietary fiber than that in the Akesu and Hetain districts. Principal component analysis indicated that the parameters that differentiated these jujube cultivars appeared to be the total dietary fiber, protein, total sugar, fructose, glucose, sucrose, and total titratable acids.

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“…A benefit of such high-density maps is that they can narrow the confidence intervals of QTLs for target traits, thus increasing the efficiency to find candidate genes. For example, based on dense SNP genetic maps of apple, potential genes for fruit texture, acidity and shape have been revealed, respectively [ 18 – 20 ]. Although researchers have identified QTLs for the indices of photosynthetic gas exchange under atmospheric drought stress, as well as the production of vegetative tissue and fruit under soil water-deficit conditions, the associated genes have not been screened because the density of single sequence repeats (SSRs) on their genetic maps has been insufficient [ 21 , 22 ].…”

Section: Introductionmentioning

confidence: 99%

Mapping QTLs for water-use efficiency reveals the potential candidate genes involved in regulating the trait in apple under drought stress

et al. 2018

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BackgroundImprovement of water-use efficiency (WUE) can effectively reduce production losses caused by drought stress. A better understanding of the genetic determination of WUE in crops under drought stress has great potential value for developing cultivars adapted to arid regions. To identify the genetic loci associated with WUE and reveal genes responsible for the trait in apple, we aim to map the quantitative trait loci (QTLs) for carbon isotope composition, the proxy for WUE, applying two contrasting irrigating regimes over the two-year experiment and search for the candidate genes encompassed in the mapped QTLs.ResultsWe constructed a high-density genetic linkage map with 10,172 markers of apple, using single nucleotide polymorphism (SNP) markers obtained through restriction site-associated DNA sequencing (RADseq) and a final segregating population of 350 seedlings from the cross of Honeycrisp and Qinguan. In total, 33 QTLs were identified for carbon isotope composition in apple under both well-watered and drought-stressed conditions. Three QTLs were stable over 2 years under drought stress on linkage groups LG8, LG15 and LG16, as validated by Kompetitive Allele-Specific PCR (KASP) assays. In those validated QTLs, 258 genes were screened according to their Gene Ontology functional annotations. Among them, 28 genes were identified, which exhibited significant responses to drought stress in ‘Honeycrisp’ and/or ‘Qinguan’. These genes are involved in signaling, photosynthesis, response to stresses, carbohydrate metabolism, protein metabolism and modification, hormone metabolism and transport, transport, respiration, transcriptional regulation, and development regulation. They, especially those for photoprotection and relevant signal transduction, are potential candidate genes connected with WUE regulation in drought-stressed apple.ConclusionsWe detected three stable QTLs for carbon isotope composition in apple under drought stress over 2 years, and validated them by KASP assay. Twenty-eight candidate genes encompassed in these QTLs were identified. These stable genetic loci and series of genes provided here serve as a foundation for further studies on marker-assisted selection of high WUE and regulatory mechanism of WUE in apple exposed to drought conditions, respectively.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1308-3) contains supplementary material, which is available to authorized users.

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Candidate gene prediction via quantitative trait locus analysis of fruit shape index traits in apple

Cited by 15 publications

References 38 publications

Marker-trait associations and genomic predictions of interspecific pear (Pyrus) fruit characteristics

Marker-trait associations and genomic predictions of interspecific pear (Pyrus) fruit characteristics

Comparison of physical and chemical composition of three chinese jujube (Ziziphus jujuba Mill.) cultivars cultivated in four districts of Xinjiang region in China

Mapping QTLs for water-use efficiency reveals the potential candidate genes involved in regulating the trait in apple under drought stress

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