Mapping of a major gene for the slow ripening character in peach: co-location with the maturity date gene and development of a candidate gene-based diagnostic marker for its selection

Eduardo, Iban; Picañol, Roger; Rojas, Eugenia Ibarra; Batlle, I.; Howad, Werner; Aranzana, María José; Arús, Pere

doi:10.1007/s10681-015-1445-9

Cited by 51 publications

(41 citation statements)

References 23 publications

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“…A marker developed for this locus cosegregated with the SR trait and showed no amplification in the case of the srsr genotypes, suggesting that there is a large deletion in the MD region including the ppa008301m sequence. Hence, it is possible that the absence of the product of the PpNAC1 gene causes the SR phenotype (Eduardo et al, 2015). These results all confirm that LG4 has a major effect on biochemical processes related to fruit maturation in peach.…”

Section: Introductionsupporting

confidence: 60%

Correspondence between maturity date and molecular variations in a NAC transcription factor of diploid and polyploid Prunus species

Balogh¹,

Halász²,

Szani³

et al. 2018

Turk J Agric For

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The maturity date (MD) of Prunus stone fruit has been long known to be a quantitatively inherited trait. A NAC-type gene indicated as PpNAC1 (ppa008301m) has been found recently to be a strong candidate of a major gene influencing MD in peach. A 9-bp insertion in this gene resulted in earlier MD in two segregating peach populations. This study was carried out to test whether this mutation in the PpNAC1 gene can be used as a reliable functional marker for MD in a wide range of peach cultivars of various origins and phenotypic characters. A total of 125 peach cultivars were examined using a 3 × 3 custom chi-square contingency table according to their NAC genotype and MD (early, midseason, and late). Cramér's V equaled 0.478 and the Goodman-Kruskal index (l) was 0.37, indicating an extremely strong correlation between MD and NAC genotype. In addition, we determined 15 sequences from 10 cultivars of five Prunus species including peach, almond, apricot, sour cherry, and European plum with E-values ranging from 9e-88 to 2e-74, supporting their homology to PpNAC1. A total of 69 single nucleotide polymorphisms and two insertion/deletions were detected in the coding region of the partial NAC domain sequences with three mutations putatively inducing nonconservative amino acid replacements and a nonsense mutation in specific alleles of early ripening apricot and sour cherry cultivars. The results are discussed with focus on the putative molecular mechanisms of mutations in the NAC genes, crop evolutionary perspectives, and the opportunities for designing cost-efficient markers to predict MD in Prunus breeding programs.

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Section: Introductionsupporting

confidence: 60%

Correspondence between maturity date and molecular variations in a NAC transcription factor of diploid and polyploid Prunus species

Balogh¹,

Halász²,

Szani³

et al. 2018

Turk J Agric For

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“…The gene ppa021959m may be involved in deletion events since it encodes a putative transposase. On the other hand, SR individuals in the F1 population of the cross between BBelbinette^and BNectalady^(Bb × Nl) were identified by Eduardo et al (2015). The Sr gene was located in LG4 on the Bb × Nl genetic map in the same region of the gene ANAC072 and co-located with the CPP15636 and PSR2 markers.…”

Section: Candidate Genes For M Md and Srmentioning

confidence: 99%

Identification of candidate genes associated with mealiness and maturity date in peach [Prunus persica (L.) Batsch] using QTL analysis and deep sequencing

Núñez-Lillo

Cifuentes-Esquivel

Troggio

et al. 2015

Tree Genetics & Genomes

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Artículo de publicación ISIPeach and nectarine quality traits such as flavor, texture, and juiciness are important for consumer acceptance. Maturity date (MD) also plays a role in the fruit-ripening process and is an important factor for marketing fresh fruit. On the other hand, cold storage produces a physiological disorder known as chilling injury where the most important symptom is a lack of juice in the flesh or mealiness (M). In this study, we analyzed an F2 population obtained from a self-pollination of "Venus" nectarine that segregates for MD and M. We built a linkage map with 1,830 SNPs, 7 SSRs and two slow-ripening (SR) morphological markers, spanning 389.2 cM distributed over eight linkage groups (LGs). The SR trait was mapped to LG4 and we compared the whole genome sequences of a SR individual and "Venus" and identified a deletion of 26.6 kb containing ppa008301m (ANAC072) co-localized with the SR trait. Three Quantitative Trait Loci (QTL) for MD were detected; they all co-localize on LG4 between 31.0 and 42.0 cM. Four co-localizing QTLs on LG4 between 33.3 and 40.3 cM were detected for M, explaining 34 % of the phenotypic variation. We identified five and nine candidate genes (CGs) for MD and M from the QTL regions, respectively. Our results suggest that the transcription factors (TFs) ANAC072 and ppa010982m (ERF4) are CGs for both traits. LG4 contains a cluster for genetic factors that possibly regulate MandMD, but functional validation is necessary to unravel the complexity of genetic control responsible for fruit traits.Conicyt-Fondecyt 11121396 Conicyt-FONDEF G13i10005 Corfo-Innova 09PMG-7240 Fondo de Areas Prioritarias Centro de Regulacion del Genoma 15090007 UNAB DI-489-14R CONICYT D-21090737 PFB-1

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“…Many studies have been carried out for QTL identification in Prunus (Zeballos 2012). Nevertheless, many important agronomic traits of Prunus species have not yet been mapped, and only a few are currently being used for marker-assisted selection (including major genes for disease and pest resistance, self-incompatibility, slow ripening, and fruit quality traits such as flesh color, endocarp staining, flesh adherence to stone, non-acid fruit, skin pubescence, skin color, and fruit shape) (Dirlewanger et al 2004;Eduardo et al 2015;Ru et al 2015 and references therein). Important QTLs that control fruit quality traits have been found for total sugar content, organic acid content, fruit weight, acidity, blooming and harvest dates (Dirlewanger et al 1999;Etienne et al 2002;Quilot et al 2004), blooming and ripening dates Dirlewanger et al 2012), chilling injury susceptibility (Cantín et al 2010a), and other traits anchored in the T × E Prunus reference map that have been widely described by Arús et al (2012).…”

Section: Introductionmentioning

confidence: 99%

Mapping QTLs associated with fruit quality traits in peach [Prunus persica (L.) Batsch] using SNP maps

Zeballos

Abidi

Giménez

et al. 2016

Tree Genetics & Genomes

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Zeballos, JL.; Adibi, W.; Giménez Millán, R.; Monforte Gilabert, AJ.; Moreno, MA.; Gogorcena, Y. (2016). Mapping QTLs associated with fruit quality traits in peach Prunus persica (L.) Batsch using SNP maps. Tree Genetics and Genomes. 12(3):1-17. doi:10.1007/s11295-016-0996-9. AbstractFruit quality is an essential criterion used to select new cultivars in peach breeding programs and is determined based on a combination of organoleptic and nutritional traits. The aim of this study was to identify quantitative trait loci (QTLs) for fruit quality traits in an F 1 nectarine population derived from 'Venus' and 'Big Top' cultivars. The progeny were evaluated over 4 years for agronomical and biochemical characteristics, and genotyped using SSR markers and 'IPSC 9K peach SNP array v1'. Two genetic maps were constructed using 411 markers. The 'Venus' map spanned 259 cM on nine linkage groups (LGs) with 104 markers. The 'Big Top' map spanned 464 cM on ten LGs with 122 markers.Single or Multiple QTL models mapping was applied separately for each year and all years combined. A total of 54 QTLs mapped over 12LGs belonged to seven peach chromosomes. Most of the QTLs were consistent over the 4 years of study and were validated with the Multi-year analysis. QTLs for total phenolic, flavonoid, and anthocyanin contents were reported for the first time in peach.LG4 in 'Venus' and LG5 in 'Big Top' showed the highest numbers of QTLs. This work represents the first study in an F 1 nectarine family to identify peach genomic regions that control fruit quality traits using 'IPSC 9K SNP array v1' and provides useful information for marker-assisted breeding to produce peaches with better antioxidant content and healthy attributes.

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Mapping of a major gene for the slow ripening character in peach: co-location with the maturity date gene and development of a candidate gene-based diagnostic marker for its selection

Cited by 51 publications

References 23 publications

Correspondence between maturity date and molecular variations in a NAC transcription factor of diploid and polyploid Prunus species

Correspondence between maturity date and molecular variations in a NAC transcription factor of diploid and polyploid Prunus species

Identification of candidate genes associated with mealiness and maturity date in peach [Prunus persica (L.) Batsch] using QTL analysis and deep sequencing

Mapping QTLs associated with fruit quality traits in peach [Prunus persica (L.) Batsch] using SNP maps

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