GWAS identifies a polyembryony locus in mango: development of KASP and PACE markers for marker-assisted breeding
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, resultin...
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Frontiers Media S.A.
2025-01-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2025.1508027/full |
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| author | Gul Shad Ali Shamseldeen Eltaher Shamseldeen Eltaher Jin Li Barbie Freeman Sukhwinder Singh |
| author_facet | Gul Shad Ali Shamseldeen Eltaher Shamseldeen Eltaher Jin Li Barbie Freeman Sukhwinder Singh |
| author_sort | Gul Shad Ali |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-d9a98a8c275c4825865b610550e7d59c |
| institution | Kabale University |
| issn | 1664-462X |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj-art-d9a98a8c275c4825865b610550e7d59c2025-01-29T06:46:02ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2025-01-011610.3389/fpls.2025.15080271508027GWAS identifies a polyembryony locus in mango: development of KASP and PACE markers for marker-assisted breedingGul Shad Ali0Shamseldeen Eltaher1Shamseldeen Eltaher2Jin Li3Barbie Freeman4Sukhwinder Singh5Subtropical Horticulture Research Station (SHRS), United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Miami, FL, United StatesSubtropical Horticulture Research Station (SHRS), United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Miami, FL, United StatesDepartment of Plant Biotechnology, Genetic Engineering and Biotechnology Research Institute (GEBRI), University of Sadat City (USC), Sadat City, EgyptSubtropical Horticulture Research Station (SHRS), United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Miami, FL, United StatesSubtropical Horticulture Research Station (SHRS), United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Miami, FL, United StatesSubtropical Horticulture Research Station (SHRS), United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Miami, FL, United StatesApomixis 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.https://www.frontiersin.org/articles/10.3389/fpls.2025.1508027/fullGWASMASKASPPACEmangopolyembryonic mango |
| spellingShingle | Gul Shad Ali Shamseldeen Eltaher Shamseldeen Eltaher Jin Li Barbie Freeman Sukhwinder Singh GWAS identifies a polyembryony locus in mango: development of KASP and PACE markers for marker-assisted breeding Frontiers in Plant Science GWAS MAS KASP PACE mango polyembryonic mango |
| title | GWAS identifies a polyembryony locus in mango: development of KASP and PACE markers for marker-assisted breeding |
| title_full | GWAS identifies a polyembryony locus in mango: development of KASP and PACE markers for marker-assisted breeding |
| title_fullStr | GWAS identifies a polyembryony locus in mango: development of KASP and PACE markers for marker-assisted breeding |
| title_full_unstemmed | GWAS identifies a polyembryony locus in mango: development of KASP and PACE markers for marker-assisted breeding |
| title_short | GWAS identifies a polyembryony locus in mango: development of KASP and PACE markers for marker-assisted breeding |
| title_sort | gwas identifies a polyembryony locus in mango development of kasp and pace markers for marker assisted breeding |
| topic | GWAS MAS KASP PACE mango polyembryonic mango |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2025.1508027/full |
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