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Open AccessArticle

High-Density SNP-Based Association Mapping of Seed Traits in Fenugreek Reveals Homology with Clover

1
Department of Agronomy, Faculty of Agriculture, Cairo University, Giza 12613, Egypt
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Department of Biology, Faculty of Applied Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia
3
Research Laboratories Centre, Faculty of Applied Science, Umm Al-Qura University, Makkah 21955, Saudi Arabia
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Environmental Studies and Research Unit, Cairo University, Giza 12613, Egypt
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Agricultural Genetic Engineering Research Institute (AGERI), ARC, Giza 12915, Egypt
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Genomics and Bioinformatics Service Texas A&M AgriLife Research, Amarillo College Station, Amarillo, TX 77845, USA
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Plant Biotechnology Department, National Research Center, Giza 12622, Egypt
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Plant Physiology, University of Amsterdam, Swammerdam Institute for Life Sciences Amsterdam, 1098 XH Amsterdam, The Netherlands
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School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading RG6 6AR, UK
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Department of Genetics, Faculty of Agriculture, Cairo University, Giza 12613, Egypt
*
Author to whom correspondence should be addressed.
Present address: Eurac research—Institute for Mummy Studies, 39100 Bolzano, Italy.
Present address: Rijk Zwaan, 2678 KX De Lier, The Netherlands.
Genes 2020, 11(8), 893; https://doi.org/10.3390/genes11080893
Received: 5 July 2020 / Revised: 28 July 2020 / Accepted: 2 August 2020 / Published: 5 August 2020
(This article belongs to the Special Issue Food Legume Genomics)
Fenugreek as a self-pollinated plant is ideal for genome-wide association mapping where traits can be marked by their association with natural mutations. However, fenugreek is poorly investigated at the genomic level due to the lack of information regarding its genome. To fill this gap, we genotyped a collection of 112 genotypes with 153,881 SNPs using double digest restriction site-associated DNA sequencing. We used 38,142 polymorphic SNPs to prove the suitability of the population for association mapping. One significant SNP was associated with both seed length and seed width, and another SNP was associated with seed color. Due to the lack of a comprehensive genetic map, it is neither possible to align the newly developed markers to chromosomes nor to predict the underlying genes. Therefore, systematic targeting of those markers to homologous genomes of other legumes can overcome those problems. A BLAST search using the genomic fenugreek sequence flanking the identified SNPs showed high homology with several members of the Trifolieae tribe indicating the potential of translational approaches to improving our understanding of the fenugreek genome. Using such a comprehensively-genotyped fenugreek population is the first step towards identifying genes underlying complex traits and to underpin fenugreek marker-assisted breeding programs. View Full-Text
Keywords: fenugreek; population structure; ddRAD-sequencing; SNP markers; association mapping; homology fenugreek; population structure; ddRAD-sequencing; SNP markers; association mapping; homology
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Abd El-Wahab, M.M.H.; Aljabri, M.; Sarhan, M.S.; Osman, G.; Wang, S.; Mabrouk, M.; El-Shabrawi, H.M.; Gabr, A.M.M.; Abd El-Haliem, A.M.; O'Sullivan, D.M.; El-Soda, M. High-Density SNP-Based Association Mapping of Seed Traits in Fenugreek Reveals Homology with Clover. Genes 2020, 11, 893.

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