Articles
Genotypic characterization of an F1 Japanese plum progeny through genotyping by sequencing (GBS) and preliminary quantitative trait locus (QTL) analysis for important agronomic traits
Article number
1260_10
Pages
49 – 58
Language
English
Abstract
Nowadays, the widespread use of DNA sequencing technologies for single nucleotide polymorphism (SNP) detection is very common for studying genetic diversity, genetic mapping or association mapping analysis.
Genotyping by sequencing (GBS) provides a large quantity of data useful for fine mapping using SNPs from a reference genome, allowing accurate and easy quantitative trait locus (QTL) detection.
The main goal of this research was to apply GBS to map an F1 Japanese plum progeny and to establish the genetic diversity of 11 cultivars.
Genotype 98-99 (female) was crossed with three male parents: Angeleno, September King and September Queen. Paternity Z-test analysis was used, resulting in 161, 62 and 15 seedlings derived from Angeleno, September King and September Queen, respectively.
Tags on a physical map were aligned to peach genome v1, yielding 2,244,856 (42.9%) tags aligned to unique positions and only 190,411 (3.6%) tags aligned to multiple positions.
Moreover, 102,992 (100%) unfiltered SNPs and 42,909 (41.7%) filtered SNPs were obtained from the alignment genome.
Genetic linkage maps for 98-99 × Angeleno were constructed with a total of 955 SNPs, 454 SNPs for 98-99 and 501 SNPs for Angeleno, with a coverage of 673.56 and 643.01 cM, respectively.
Furthermore, a preliminary QTL analysis was performed on 58 seedlings, which allowed the localization of major QTLs for skin color and ripening time traits in linkage groups 3 and 4, respectively.
The occurrence of a skin-color QTL could also indicate a significant component for polyphenolic compounds, which will be monitored in future seasons.
Moreover, another QTL associated with skin chlorophyll degradation (IAD) was also localized in linkage group 3. These preliminary data point to the 98-99 × Angeleno cross as an attractive tool for the study of inheritance of fruit quality and functional compound content in Japanese plum.
Genotyping by sequencing (GBS) provides a large quantity of data useful for fine mapping using SNPs from a reference genome, allowing accurate and easy quantitative trait locus (QTL) detection.
The main goal of this research was to apply GBS to map an F1 Japanese plum progeny and to establish the genetic diversity of 11 cultivars.
Genotype 98-99 (female) was crossed with three male parents: Angeleno, September King and September Queen. Paternity Z-test analysis was used, resulting in 161, 62 and 15 seedlings derived from Angeleno, September King and September Queen, respectively.
Tags on a physical map were aligned to peach genome v1, yielding 2,244,856 (42.9%) tags aligned to unique positions and only 190,411 (3.6%) tags aligned to multiple positions.
Moreover, 102,992 (100%) unfiltered SNPs and 42,909 (41.7%) filtered SNPs were obtained from the alignment genome.
Genetic linkage maps for 98-99 × Angeleno were constructed with a total of 955 SNPs, 454 SNPs for 98-99 and 501 SNPs for Angeleno, with a coverage of 673.56 and 643.01 cM, respectively.
Furthermore, a preliminary QTL analysis was performed on 58 seedlings, which allowed the localization of major QTLs for skin color and ripening time traits in linkage groups 3 and 4, respectively.
The occurrence of a skin-color QTL could also indicate a significant component for polyphenolic compounds, which will be monitored in future seasons.
Moreover, another QTL associated with skin chlorophyll degradation (IAD) was also localized in linkage group 3. These preliminary data point to the 98-99 × Angeleno cross as an attractive tool for the study of inheritance of fruit quality and functional compound content in Japanese plum.
Authors
J. Salazar, I. Pacheco, P. Shinya, D. Ruiz, P. Martínez-Gómez, R. Infante
Keywords
genetic mapping, SNPs, fruit quality, Prunus salicina
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