A Japanese Plum Breeding Core Collection Capturing and Exploiting Genetic Variation

María Osorio, Sebastián Ahumada, Rodrigo Infante, Igor Pacheco, Arnau Fiol () and Paulina Ballesta ()
Additional contact information
María Osorio: BVISA—Nutribreeding, Instituto de Nutrición y Tecnología de Alimentos Dr. Fernando Monckeberg Barros (INTA), Universidad de Chile, El Líbano #5524, Macul 7830490, Chile
Sebastián Ahumada: Departamento de Producción Agrícola, Facultad de Ciencias Agronómicas, Universidad de Chile, Santa Rosa #11315, La Pintana 8820808, Chile
Rodrigo Infante: Departamento de Producción Agrícola, Facultad de Ciencias Agronómicas, Universidad de Chile, Santa Rosa #11315, La Pintana 8820808, Chile
Igor Pacheco: BVISA—Nutribreeding, Instituto de Nutrición y Tecnología de Alimentos Dr. Fernando Monckeberg Barros (INTA), Universidad de Chile, El Líbano #5524, Macul 7830490, Chile
Arnau Fiol: BVISA—Nutribreeding, Instituto de Nutrición y Tecnología de Alimentos Dr. Fernando Monckeberg Barros (INTA), Universidad de Chile, El Líbano #5524, Macul 7830490, Chile
Paulina Ballesta: Núcleo de Investigación en Sustentabilidad Agroambiental (NISUA), Facultad de Medicina Veterinaria y Agronomía, Universidad de las Américas, Manuel Montt #948, Providencia 7500975, Chile

Agriculture, 2025, vol. 15, issue 13, 1-20

Abstract: The optimal exploitation of genetic variability is essential for the success of breeding programs and for identifying quantitative trait loci (QTLs) in genetic association studies. These benefit from populations with a high number of individuals; however, they are expensive since extensive plant maintenance, characterization, and evaluation are required. Core collections offer a practical solution by reducing the number of individuals while representing the original diversity of the population. This study aimed to construct a core collection for Japanese plum to serve as pre-breeding material and enable genetic association studies for traits that are difficult to evaluate. Starting from a population of 1062 individuals genotyped by sequencing, genetic distance and allele coverage metrics were applied to construct several core collections. Genetic parameters and phenotype distribution comparisons allowed for the selection of a core collection of 108 individuals that maximized genetic variability while representative of the original population, confirmed by linkage disequilibrium and population structure analyses. Its usefulness was validated by successfully mapping flowering and maturity dates through marker–trait association. The core collection constructed here will help in the study of fruit quality traits and biotic and abiotic responses, ultimately generating molecular markers to assist the crop’s molecular breeding.

Keywords: Prunus salicina; genetic diversity; population structure; marker–trait association; SNP (search for similar items in EconPapers)
JEL-codes: Q1 Q10 Q11 Q12 Q13 Q14 Q15 Q16 Q17 Q18 (search for similar items in EconPapers)
Date: 2025
References: Add references at CitEc
Citations:

Downloads: (external link)
https://www.mdpi.com/2077-0472/15/13/1369/pdf (application/pdf)
https://www.mdpi.com/2077-0472/15/13/1369/ (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:gam:jagris:v:15:y:2025:i:13:p:1369-:d:1687778

Access Statistics for this article

Agriculture is currently edited by Ms. Leda Xuan

More articles in Agriculture from MDPI
Bibliographic data for series maintained by MDPI Indexing Manager ().