Genetic linkage maps and QTLs associated with fruit skin color and acidity in apple (Malus × domestica)

Oh, Sewon; Ahn, Suji; Han, Hye‐Suk; Kim, Keumsun; Kim, Seon Ae; Kim, Daeil

doi:10.1007/s13580-022-00473-z

Cited by 3 publications

(4 citation statements)

References 41 publications

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“…Sun et al [ 88 ] showed several QTLs in LGs 7, 8, and 15, which are the same LGs as the SSR markers linked to organic acids in the present study. Oh et al [ 90 ] found a fruit acidity-related QTL in the LG13 of the ‘Jonathan’ cultivar, although no significant association was found in the present work.…”

Section: Discussioncontrasting

confidence: 89%

“…Howard et al [ 85 ] found many QTLs in LGs 2, 5, 8, and 9 regarding these agronomical traits. Moreover, Oh et al [ 90 ] found QTLs for the apple skin color in LGs 9, 10, and 13 using the ‘Jonathan’ cultivar. A higher number of significant QTLs related to the basic fruit quality traits were found in previous works [ 84 , 86 , 87 , 89 ].…”

Section: Discussionmentioning

confidence: 99%

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Population Structure and Association Mapping for Agronomical and Biochemical Traits of a Large Spanish Apple Germplasm

Mignard

Forcada

Giménez

et al. 2023

Plants

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A basic knowledge of linkage disequilibrium and population structure is necessary in order to determine the genetic control and identify significant associations with agronomical and phytochemical compounds in apple (Malus × domestica Borkh). In this study, 186 apple accessions (Pop1), representing both Spanish native accessions (94) and non-Spanish cultivars (92) from the EEAD-CSIC apple core collection, were assessed using 23 SSRs markers. Four populations were considered: Pop1, Pop2, Pop3, and Pop4. The initial Pop1 was divided into 150 diploid (Pop2) and 36 triploid accessions (Pop3), while for the inter-chromosomal linkage disequilibrium and the association mapping analysis, 118 phenotype diploid accessions were considered Pop4. Thus, the average number of alleles per locus and observed heterozygosity for the overall sample set (Pop1) were 15.65 and 0.75, respectively. The population structure analysis identified two subpopulations in the diploid accessions (Pop2 and Pop4) and four in the triploids (Pop3). Regarding the Pop4, the population structure with K = 2 subpopulations segregation was in agreement with the UPGMA cluster analysis according to the genetic pairwise distances. Moreover, the accessions seemed to be segregated by their origin (Spanish/non-Spanish) in the clustering analysis. One of the two subpopulations encountered was quite-exclusively formed by non-Spanish accessions (30 out of 33). Furthermore, agronomical and basic fruit quality parameters, antioxidant traits, individual sugars, and organic acids were assessed for the association mapping analysis. A high level of biodiversity was exhibited in the phenotypic characterization of Pop4, and a total of 126 significant associations were found between the 23 SSR markers and the 21 phenotypic traits evaluated. This study also identified many new marker-locus trait associations for the first time, such as in the antioxidant traits or in sugars and organic acids, which may be useful for predictions and for a better understanding of the apple genome.

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Section: Discussioncontrasting

confidence: 89%

Section: Discussionmentioning

confidence: 99%

Population Structure and Association Mapping for Agronomical and Biochemical Traits of a Large Spanish Apple Germplasm

Mignard

Forcada

Giménez

et al. 2023

Plants

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show abstract

“…Even though color is a qualitative trait, subjective scoring may not depict color variations in a population precisely. Studies have reported employing the Color reader for measuring color attributes like L*, a*, and b* for scoring and identification of QTLs for fruit peel color and pulp color in segregating mapping populations ( Oh et al., 2023 ; Srivastav et al., 2023 and Zhang et al., 2019 ). In the present study, leaf and fruit colors were scored using both methods in order to identify the QTL regions with more accuracy.…”

Section: Discussionmentioning

confidence: 99%

“…GBS has become a cost-effective approach for genotyping large numbers of samples, especially the mapping populations that are required for constructing linkage maps. GBS has been employed for constructing genetic linkage maps in several fruit tree species including apple ( Oh et al., 2023 ), Japanese plum ( Battistoni et al., 2022 ), Korean pears ( Han et al., 2019 ), banana ( Sampangi-Ramaiah et al., 2023 ) and in the guava’s closest related species eucalyptus ( Zhu et al., 2023 ). In our study, GBS has been applied for the first time in SNP calling in guava mapping populations which enabled us to identify 119,343 SNPs in both parents and hybrids.…”

Section: Discussionmentioning

confidence: 99%

A high-density linkage map construction in guava (Psidium guajava L.) using genotyping by sequencing and identification of QTLs for leaf, peel, and pulp color in an intervarietal mapping population

Mathiazhagan,

Elangovan,

Chinnaiyan

et al. 2024

Front. Plant Sci.

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Psidium guajava L. is an important fruit crop in the tropical and subtropical regions of the world. The advanced breeding methods are not employed for important commercial traits like peel and pulp color, seed hardiness, fruit size, etc., due to the scarcity of genome-wide molecular markers and high-density linkage maps. In this study, we employed single-nucleotide polymorphism (SNP) markers and identified quantitative trait loci (QTL) regions that are associated with color traits of leaf, peel, and pulp in the guava intervarietal mapping population. The mapping population was developed from the contrasting genotypes of fruit and leaf color. Variations in color among the segregating hybrids were recorded both visually and using a Color reader. A high-density linkage map of guava was constructed using the SNP markers from genotyping by sequencing (GBS) of 150 hybrid individuals of the cross ‘Arka Poorna’ (green) x ‘Purple Local’ (purple). The integrated linkage map consisted of 1426 SNPs mapped on 11 linkage groups (LG), spanning a total distance of around 730 cM with an average of 129.6 markers per LG. Through QTL analysis for color traits, a minor QTL region was identified for visually scored leaf color and peel color on LG1, whereas a major QTL was detected for pulp color in LG4. The Hunter color values (L* and, a*) also had major QTLs with overlapping marker intervals for leaf and peel colors, establishing the association of SNP markers to the trait. The QTLs harbored genes and transcription factors involved in lycopene and anthocyanin pigment biosynthesis. This is the first report of a high-density linkage map based on SNP markers in guava and QTL mapping for color characters in leaf, fruit peel and pulp. The genotyping information generated in this study can aid in genetic engineering and marker-assisted breeding in guava.

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QTL mapping of fruit quality traits in tetraploid kiwiberry (Actinidia arguta)

Wang,

Bourke,

et al. 2024

Horticultural Plant Journal

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Genetic linkage maps and QTLs associated with fruit skin color and acidity in apple (Malus × domestica)

Cited by 3 publications

References 41 publications

Population Structure and Association Mapping for Agronomical and Biochemical Traits of a Large Spanish Apple Germplasm

Population Structure and Association Mapping for Agronomical and Biochemical Traits of a Large Spanish Apple Germplasm

A high-density linkage map construction in guava (Psidium guajava L.) using genotyping by sequencing and identification of QTLs for leaf, peel, and pulp color in an intervarietal mapping population

QTL mapping of fruit quality traits in tetraploid kiwiberry (Actinidia arguta)

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