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Perspectives and recent progress of genome-wide association studies (GWAS) in fruits

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Abstract

Background

Earlier next-generation sequencing technologies are being vastly used to explore, administer, and investigate the gene space with accurate profiling of nucleotide variations in the germplasm.

Overview and Progress

Recently, novel advancements in high-throughput sequencing technologies allow a genotyping-by-sequencing approach that has opened up new horizons for extensive genotyping exploiting single-nucleotide-polymorphisms (SNPs). This method acts as a bridge to support and minimize a genotype to phenotype gap allowing genetic selection at the genome-wide level, named genomic selection that could facilitate the selection of traits also in the pomology sector. In addition to this, genome-wide genotyping is a prerequisite for genome-wide association studies that have been used successfully to discover the genes, which control polygenic traits including the genetic loci, associated with the trait of interest in fruit crops.

Aims and Prospects

This review article emphasizes the role of genome-wide approaches to unlock and explore the genetic potential along with the detection of SNPs affecting the phenotype of fruit crops and highlights the prospects of genome-wide association studies in fruits.

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Data availability

The data used to support the review of this study is included in the review article.

Abbreviations

QTLs:

Quantitative trait loci

RIL:

Recombinant inbred line

LD:

Linkage disequilibrium

GWAS:

Genome-wide association study

SNP:

Single-nucleotide polymorphism

WGS:

Whole genome sequencing

GS:

Genomic selection

NGS:

Next-generation sequencing

MAS:

Marker-assisted selection

GBS:

Genotyping-by-sequencing

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Acknowledgements

We are grateful to all the contributors for their endless support during the write-up of the manuscript.

Funding

There is no external funding received for the article.

Author information

Authors and Affiliations

  1. Department of Biotechnology, Institute of Natural and Applied Sciences, Çukurova University, 01330, Adana, Turkey

    Ghassan Zahid

  2. Department of Horticulture, Faculty of Agriculture, Çukurova University, 01330, Adana, Turkey

    Yıldız Aka Kaçar & Ayzin Küden

  3. Biotechnology Research and Application Center, Çukurova University, 01330, Adana, Turkey

    Dicle Dönmez

  4. Department of Agriculture, Food and Environment, University of Pisa, 56124, Pisa, Italy

    Tommaso Giordani

Authors
  1. Ghassan Zahid
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  2. Yıldız Aka Kaçar
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  3. Dicle Dönmez
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  4. Ayzin Küden
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  5. Tommaso Giordani
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Contributions

YAK conceived the need for this review and suggested it to GZ who initiated the process and did a good part of the review work.GZ, DD and AK assisted in the write-up, and YK, GZ, and TG prepared the framework for the study. All authors read and approved the final manuscript.

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Correspondence to Ghassan Zahid.

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Zahid, G., Aka Kaçar, Y., Dönmez, D. et al. Perspectives and recent progress of genome-wide association studies (GWAS) in fruits. Mol Biol Rep 49, 5341–5352 (2022). https://doi.org/10.1007/s11033-021-07055-9

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  • DOI: https://doi.org/10.1007/s11033-021-07055-9

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