High-density Linkage Mapping and Identification of Quantitative Trait Loci Associated with Scab Resistance in Pecan
Genetic maps are essential tools for gene positional cloning and marker-assisted breeding. A pecan (Carya illinoinensis) mapping population of 119 F1 trees was developed from a cross of the widely planted cultivars ‘Pawnee’ and ‘Elliott’. Whereas ‘Pawnee’ is susceptible, ‘Elliott’ has long-standing...
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American Society for Horticultural Science (ASHS)
2025-03-01
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| Series: | Journal of the American Society for Horticultural Science |
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| author | Gaurab Bhattarai Shanshan Cao Nolan Bentley Patricia Klein Clive H. Bock Cristina Pisani Patrick J. Conner |
| author_facet | Gaurab Bhattarai Shanshan Cao Nolan Bentley Patricia Klein Clive H. Bock Cristina Pisani Patrick J. Conner |
| author_sort | Gaurab Bhattarai |
| collection | DOAJ |
| description | Genetic maps are essential tools for gene positional cloning and marker-assisted breeding. A pecan (Carya illinoinensis) mapping population of 119 F1 trees was developed from a cross of the widely planted cultivars ‘Pawnee’ and ‘Elliott’. Whereas ‘Pawnee’ is susceptible, ‘Elliott’ has long-standing resistance to pecan scab caused by the fungal pathogen Venturia effusa. Molecular markers were developed using genotyping by sequencing, and linkage maps were constructed for each parent following the two-way pseudo-test-cross strategy used for cross-pollinated species. The ‘Pawnee’ and ‘Elliott’ maps contain 1347 and 1050 single-nucleotide polymorphism markers spanning a genetic distance of 4493 and 3758 centimorgans, respectively. While these map lengths are likely inflated due to genotyping errors, a high level of synteny between genetic and physical distances of the markers in both parental maps was achieved. Scab resistance was evaluated through controlled inoculations in the greenhouse using two scab isolates, and a significant quantitative trait locus (QTL) for scab resistance was identified on chromosome 5 in ‘Elliott’. Candidate gene searches within the 2-logarithm of the odds interval of the scab-resistant QTL identified a number of disease resistance–related genes, including genes encoding wall-associated receptor kinases, cytochrome P450s, leucine-rich repeats receptor–like serine/threonine-protein kinases, a pectinesterase inhibitor, a cellulose synthase, a flavonol synthase, a 4-coumarate–coenzyme A ligase, caffeic acid 3-O-methyltransferase, and a myeloblastosis (MYB) domain transcription factor. |
| format | Article |
| id | doaj-art-7facec2fa6c2479bbbecda73f4fdd09c |
| institution | DOAJ |
| issn | 2327-9788 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | American Society for Horticultural Science (ASHS) |
| record_format | Article |
| series | Journal of the American Society for Horticultural Science |
| spelling | doaj-art-7facec2fa6c2479bbbecda73f4fdd09c2025-08-20T02:46:07ZengAmerican Society for Horticultural Science (ASHS)Journal of the American Society for Horticultural Science2327-97882025-03-011502https://doi.org/10.21273/JASHS05460-24High-density Linkage Mapping and Identification of Quantitative Trait Loci Associated with Scab Resistance in PecanGaurab Bhattarai0Shanshan Cao1Nolan Bentley2Patricia Klein3Clive H. Bock4Cristina Pisani5Patrick J. Conner6US Department of Agriculture, Agricultural Research Service, Southeastern Fruit and Tree Nut Research Station, Byron, GA 31088, USA; and Institute of Plant Breeding, Genetics and Genomics, Department of Horticulture, University of Georgia, Athens, GA 30602, USAInstitute of Plant Breeding, Genetics and Genomics, Department of Horticulture, University of GeorgiaDepartment of Integrative Biology, University of Texas at AustinDepartment of Horticultural Sciences, TX A&M UniversityUS Department of Agriculture, Agricultural Research Service, Southeastern Fruit and Tree Nut Research Station, Byron, GA 31088, USAUS Department of Agriculture, Agricultural Research Service, Southeastern Fruit and Tree Nut Research Station, Byron, GA 31088, USAInstitute of Plant Breeding, Genetics and Genomics, Department of Horticulture, University of GeorgiaGenetic maps are essential tools for gene positional cloning and marker-assisted breeding. A pecan (Carya illinoinensis) mapping population of 119 F1 trees was developed from a cross of the widely planted cultivars ‘Pawnee’ and ‘Elliott’. Whereas ‘Pawnee’ is susceptible, ‘Elliott’ has long-standing resistance to pecan scab caused by the fungal pathogen Venturia effusa. Molecular markers were developed using genotyping by sequencing, and linkage maps were constructed for each parent following the two-way pseudo-test-cross strategy used for cross-pollinated species. The ‘Pawnee’ and ‘Elliott’ maps contain 1347 and 1050 single-nucleotide polymorphism markers spanning a genetic distance of 4493 and 3758 centimorgans, respectively. While these map lengths are likely inflated due to genotyping errors, a high level of synteny between genetic and physical distances of the markers in both parental maps was achieved. Scab resistance was evaluated through controlled inoculations in the greenhouse using two scab isolates, and a significant quantitative trait locus (QTL) for scab resistance was identified on chromosome 5 in ‘Elliott’. Candidate gene searches within the 2-logarithm of the odds interval of the scab-resistant QTL identified a number of disease resistance–related genes, including genes encoding wall-associated receptor kinases, cytochrome P450s, leucine-rich repeats receptor–like serine/threonine-protein kinases, a pectinesterase inhibitor, a cellulose synthase, a flavonol synthase, a 4-coumarate–coenzyme A ligase, caffeic acid 3-O-methyltransferase, and a myeloblastosis (MYB) domain transcription factor.https://journals.ashs.org/jashs/view/journals/jashs/150/2/article-p86.xmlcarya illinoinensisdiseasemapventuria effusa |
| spellingShingle | Gaurab Bhattarai Shanshan Cao Nolan Bentley Patricia Klein Clive H. Bock Cristina Pisani Patrick J. Conner High-density Linkage Mapping and Identification of Quantitative Trait Loci Associated with Scab Resistance in Pecan Journal of the American Society for Horticultural Science carya illinoinensis disease map venturia effusa |
| title | High-density Linkage Mapping and Identification of Quantitative Trait Loci Associated with Scab Resistance in Pecan |
| title_full | High-density Linkage Mapping and Identification of Quantitative Trait Loci Associated with Scab Resistance in Pecan |
| title_fullStr | High-density Linkage Mapping and Identification of Quantitative Trait Loci Associated with Scab Resistance in Pecan |
| title_full_unstemmed | High-density Linkage Mapping and Identification of Quantitative Trait Loci Associated with Scab Resistance in Pecan |
| title_short | High-density Linkage Mapping and Identification of Quantitative Trait Loci Associated with Scab Resistance in Pecan |
| title_sort | high density linkage mapping and identification of quantitative trait loci associated with scab resistance in pecan |
| topic | carya illinoinensis disease map venturia effusa |
| url | https://journals.ashs.org/jashs/view/journals/jashs/150/2/article-p86.xml |
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