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ORIGINAL RESEARCH article

Front. Plant Sci.
Sec. Functional and Applied Plant Genomics
Volume 16 - 2025 | doi: 10.3389/fpls.2025.1508027

GWAS Identifies a Polyembryony Locus in Mango: Development of KASP and PACE Markers for Marker-Assisted Breeding

Provisionally accepted
Gul Shad Ali Gul Shad Ali *Shamseldeen Eltaher Shamseldeen Eltaher Jin Li Jin Li Sukhwinder Singh Sukhwinder Singh
  • Subtropical Horticulture Research Station, Agricultural Research Service (USDA), Miami, United States

The final, formatted version of the article will be published soon.

    Apomixis is a horticultural trait that enables clonal propagation of hybrids by producing asexual embryos from maternal cells in the ovule without meiosis. Many mango cultivars exhibit apomictic polyembryony, where one embryo develops from zygotic tissues and the rest from nucellar tissues, resulting in seedlings that are genetically identical to the mother tree. In Mangifera indica L. commercially important rootstocks are raised from apomictic seeds, which are then grafted with desired cultivars. Identifying molecular markers for polyembryony and understanding its genetics would facilitate introducing this trait in commercially important cultivars. In this report, genome-wide association studies were conducted on a diversity panel consisting of 42 polyembryonic and 42 monoembryonic M. indica cultivars using high-density single nucleotide polymorphism (SNP) markers. These studies revealed that the polyembryony locus is in a 360-kb region on linkage group 17 of the 'Alphonso' reference genome. This locus contains the MiRWP/MiRKD4 gene, which codes for an RWP-RK domain-containing protein previously implicated in citrus apomixis.Comparative genomic analyses revealed synteny between the citrus and the mango polyembryony loci, suggesting a common evolutionary mechanism for this trait. A total of 29 SNP markers in this locus were significantly associated with polyembryony in M. indica.Five of these markers were developed into convenient genotyping assays using competitive allele-specific PCR chemistry implemented in two different genotyping platforms -Kompetitive Allele-Specific PCR (KASP) and PCR allele competitive extension (PACE).The utility of these assays was validated and demonstrated in diverse germplasm collection and open-pollinated mango breeding populations with known pedigrees and polyembryony phenotypes. These SNP markers, especially those flanking the MiRWP/MiRKD4 gene, provide a valuable tool for mango breeders to select polyembryonic progenies at the seedling stages in mango breeding programs.

    Keywords: GWAS, MAS, KASP, PACE, Mango, Polyembryonic mango, Apomixis

    Received: 08 Oct 2024; Accepted: 09 Jan 2025.

    Copyright: © 2025 Ali, Eltaher, Li and Singh. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Gul Shad Ali, Subtropical Horticulture Research Station, Agricultural Research Service (USDA), Miami, United States

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.