Markers, Maps, and Marker-Assisted Selection

  • Tokurou ShimizuEmail author
  • Yıldız Aka Kacar
  • Mariângela Cristofani-Yaly
  • Maiara Curtolo
  • Marcos Antonio Machado
Part of the Compendium of Plant Genomes book series (CPG)


DNA marker analysis, combined with linkage and quantitative trait locus (QTL) analyses, has drastically changed the scheme of citrus breeding by enabling the marker-assisted selection (MAS) of a promising scion at the early seedling stage. This technique has greatly enhanced breeding efficiency by minimizing the period of trait evaluation at the orchard. It has also provided remarkable achievements for understanding the classification and pedigree of citrus varieties by molecular phylogenetic analysis. In the past decades, valuable DNA markers have been developed from various crosses undertaken for the selection of fruit traits, apomixis, dwarfism and for resistance against pests, stress, or acclimation. Zygotic embryo selection is a basic but important application of MAS for the cross of polyembryonic seed parents. The advent of next-generation sequencing technologies dramatically enhanced the accumulation of genome sequence data. They were used for the development of codominant DNA marker systems (simple sequence repeat: SSR and single nucleotide polymorphism: SNP) that enabled high-throughput genotyping and high-density linkage map construction. Consequently, they also enabled the identification of a gene or genome sequence responsible for a trait by associating the map with the genome sequence. While these advances provided us with the genomic basis for trait selection and the tools to improve breeding, MAS of a complex trait controlled by many genes having a small effect still remained a challenge due to the difficulty in conducting large scale genetic analysis in citrus. Now, two alternative analysis methods based on genome-wide genotype data, genome-wide association study (GWAS) and genomic selection (GS), have become available for identifying QTLs of any trait of interest without the need to cross for predicting the breeding value of offspring. These new methods facilitate the selection of complex traits as well as shed light on the significance of measuring methods, for these methods to become applicable.



The authors thank Emma Tacken, Ph.D., from Edanz Group ( for editing a draft of this manuscript.


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Copyright information

© Springer Nature Switzerland AG 2020

Authors and Affiliations

  • Tokurou Shimizu
    • 1
    Email author
  • Yıldız Aka Kacar
    • 2
  • Mariângela Cristofani-Yaly
    • 3
  • Maiara Curtolo
    • 3
  • Marcos Antonio Machado
    • 3
  1. 1.Citrus Research DivisionInstitute of Fruit Tree and Tea Science, NAROTsukubaJapan
  2. 2.Horticulture Department, Faculty of AgricultureUniversity of ÇukurovaAdanaTurkey
  3. 3.Citrus Center Sylvio Moreira, Agronomic Institute (IAC)CordeirópolisBrazil

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