Genome-wide association study identifies key quantitative trait loci (QTL) for fruit morphometric traits in avocado (Persea spp.)
Abstract Background Avocado, a fruit crop renowned for its high nutritional value, has seen a steadily increasing market demand. However, breeding efforts for avocados have lagged those for other commercial fruits due to limited genomic research and germplasm resources. To address this shortfall, a...
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2024-11-01
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| Online Access: | https://doi.org/10.1186/s12864-024-11043-1 |
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| author | Jin Li Shamseldeen Eltaher Barbie Freeman Sukhwinder Singh Gul Shad Ali |
| author_facet | Jin Li Shamseldeen Eltaher Barbie Freeman Sukhwinder Singh Gul Shad Ali |
| author_sort | Jin Li |
| collection | DOAJ |
| description | Abstract Background Avocado, a fruit crop renowned for its high nutritional value, has seen a steadily increasing market demand. However, breeding efforts for avocados have lagged those for other commercial fruits due to limited genomic research and germplasm resources. To address this shortfall, a genome-wide association study was conducted on 122 avocado accessions from the United States Department of Agriculture (USDA) Agricultural Research Service (ARS) Subtropical Horticultural Research Station (SHRS) germplasm collection. The study aimed to identify genetic markers and regions associated with various morphometric traits in avocado fruits, including fruit weight, length, width, diameter, seed weight, seed length, seed width, fruit seed ratio (FSR), and fruit shape index (FSI). Results Leveraging 4,226 high-quality single nucleotide polymorphism (SNP) markers obtained from genotyping arrays, fifteen markers were identified with strong associations with these traits, utilizing Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) and Fixed and random model Circulating Probability Unification (FarmCPU) models. Gene annotation analyses within a 200-kb window in the vicinity of significant SNPs revealed several genes associated with various metabolic pathways suggesting that some of them likely determine these fruit quality traits, which needs to be verified and validated. Our results, which were conducted at one location, provide directions for conducting future studies using high-resolution genotyping and long-term multi-year and multi-location trait evaluations for precisely identifying the causal SNP(s) and genes associated with these traits. Conclusions These markers reported in this manuscript provide valuable tools for applying marker-assisted selection (MAS) in avocado breeding programs aimed at enhancing fruit quality and value. |
| format | Article |
| id | doaj-art-11d69cff0a154ece9cc1bf51dd31d25c |
| institution | Kabale University |
| issn | 1471-2164 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj-art-11d69cff0a154ece9cc1bf51dd31d25c2024-12-15T12:06:45ZengBMCBMC Genomics1471-21642024-11-0125111810.1186/s12864-024-11043-1Genome-wide association study identifies key quantitative trait loci (QTL) for fruit morphometric traits in avocado (Persea spp.)Jin Li0Shamseldeen Eltaher1Barbie Freeman2Sukhwinder Singh3Gul Shad Ali4United States Department of Agriculture, Agricultural Research Service, Subtropical Horticulture Research StationUnited States Department of Agriculture, Agricultural Research Service, Subtropical Horticulture Research StationUnited States Department of Agriculture, Agricultural Research Service, Subtropical Horticulture Research StationUnited States Department of Agriculture, Agricultural Research Service, Subtropical Horticulture Research StationUnited States Department of Agriculture, Agricultural Research Service, Subtropical Horticulture Research StationAbstract Background Avocado, a fruit crop renowned for its high nutritional value, has seen a steadily increasing market demand. However, breeding efforts for avocados have lagged those for other commercial fruits due to limited genomic research and germplasm resources. To address this shortfall, a genome-wide association study was conducted on 122 avocado accessions from the United States Department of Agriculture (USDA) Agricultural Research Service (ARS) Subtropical Horticultural Research Station (SHRS) germplasm collection. The study aimed to identify genetic markers and regions associated with various morphometric traits in avocado fruits, including fruit weight, length, width, diameter, seed weight, seed length, seed width, fruit seed ratio (FSR), and fruit shape index (FSI). Results Leveraging 4,226 high-quality single nucleotide polymorphism (SNP) markers obtained from genotyping arrays, fifteen markers were identified with strong associations with these traits, utilizing Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) and Fixed and random model Circulating Probability Unification (FarmCPU) models. Gene annotation analyses within a 200-kb window in the vicinity of significant SNPs revealed several genes associated with various metabolic pathways suggesting that some of them likely determine these fruit quality traits, which needs to be verified and validated. Our results, which were conducted at one location, provide directions for conducting future studies using high-resolution genotyping and long-term multi-year and multi-location trait evaluations for precisely identifying the causal SNP(s) and genes associated with these traits. Conclusions These markers reported in this manuscript provide valuable tools for applying marker-assisted selection (MAS) in avocado breeding programs aimed at enhancing fruit quality and value.https://doi.org/10.1186/s12864-024-11043-1AvocadoFruit morphometric traitsPhenotypic variationChip-based genotypingGenetic diversityPopulation structure |
| spellingShingle | Jin Li Shamseldeen Eltaher Barbie Freeman Sukhwinder Singh Gul Shad Ali Genome-wide association study identifies key quantitative trait loci (QTL) for fruit morphometric traits in avocado (Persea spp.) BMC Genomics Avocado Fruit morphometric traits Phenotypic variation Chip-based genotyping Genetic diversity Population structure |
| title | Genome-wide association study identifies key quantitative trait loci (QTL) for fruit morphometric traits in avocado (Persea spp.) |
| title_full | Genome-wide association study identifies key quantitative trait loci (QTL) for fruit morphometric traits in avocado (Persea spp.) |
| title_fullStr | Genome-wide association study identifies key quantitative trait loci (QTL) for fruit morphometric traits in avocado (Persea spp.) |
| title_full_unstemmed | Genome-wide association study identifies key quantitative trait loci (QTL) for fruit morphometric traits in avocado (Persea spp.) |
| title_short | Genome-wide association study identifies key quantitative trait loci (QTL) for fruit morphometric traits in avocado (Persea spp.) |
| title_sort | genome wide association study identifies key quantitative trait loci qtl for fruit morphometric traits in avocado persea spp |
| topic | Avocado Fruit morphometric traits Phenotypic variation Chip-based genotyping Genetic diversity Population structure |
| url | https://doi.org/10.1186/s12864-024-11043-1 |
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