A first insight into peach [Prunus persica (L.) Batsch] SNP variability
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Publication date
2012-06-10ISSN
1614-2942
Abstract
Three factors may have reduced the diversity at
both individual gene and whole genome levels in cultivated
peach: its self-compatible mating system, the narrow genetic
basis of most commercial cultivars, and the recent strong
selection towards agronomically interesting traits. Previous
diversity analyses with markers such as simple sequence
repeats (SSRs) have revealed low levels of genetic variability. Here, we sequenced 23 genome-wide distributed DNA
fragments in 47 occidental peach varieties, also observing
reduced variability levels. On average, there was one single
nucleotide polymorphism (SNP) every 598 bp and one indel
every 4,189 bp. As expected, variability was higher in noncoding than in coding regions (one SNP every 390 noncoding bp versus one in 1,850 bp in coding DNA). In
general, SNPs were observed at relatively high frequency,
mean minor allele frequency00.225, meaning that a large
proportion of the SNPs discovered by sequencing similar
germplasm will be useful for other purposes, such as association mapping. The average heterozygosity of the varieties
was 0.28, with a low correlation between SSR and SNP
heterozygosity. The whole sequence of two candidate genes,
a pectate lyase 1 candidate for fruit firmness (CGPAA2668)
and a sucrose synthase 1 candidate for sugar content
(CGPPB6189), in the 47 varieties revealed that they both
may have suffered a process of balancing selection.
Document Type
Article
Document version
Published version
Language
English
Subject (CDU)
633 - Field crops and their production
Pages
11
Publisher
Springer
Is part of
Tree Genetics and Genomes
Citation
Aranzana, María José, Eudald Illa, Werner Howad, and Pere Arús. 2012. “A First Insight Into Peach [Prunus Persica (L.) Batsch] SNP Variability.” Tree Genetics & Genomes 8 (6): 1359–1369. doi:10.1007/s11295-012-0523-6.
Grant agreement number
MICINN/Programa Nacional de Proyectos de Investigación Fundamental/AGL2009-07305/ES/Evaluacion E Introgresion De Nuevas Fuentes De Variabilidad Genetica En Germoplasma De Melocotonero Europeo Y Norte-Americano/AGR
MEC/Programa nacional de medios de transporte/CSD2007-00036/ES/Centro de Genómica Básica y de orientación Agroalimentaria/
MEC/Programa nacional de medios de transporte/CSD2007-00036/ES/Centro de Genómica Básica y de orientación Agroalimentaria/
Program
Genòmica i Biotecnologia
This item appears in the following Collection(s)
- ARTICLES CIENTÍFICS [2651]
Except where otherwise noted, this item's license is described as http://creativecommons.org/licenses/by/4.0/