Abstract
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.
Highlights
Fenugreek (Trigonella foenum-graecum L.) is a small-seeded annual dicotyledonous legume that belongs to the family Leguminosae (Fabaceae)
FreeBayes reported >2M raw variations that were further filtered to minimize the calling of false single nucleotide polymorphisms (SNP) due to sequencing error, paralogs, or artifacts from library preparation
The raw variant call file (VCF) was filtered using vcftools v0.1.15 [41] with a minimum quality score of 30, minimum genotype depth set to 3 reads, no more than 0.2% missing data per SNP, and minimum mean depth of coverage (DP)
Summary
Fenugreek (Trigonella foenum-graecum L.) is a small-seeded annual dicotyledonous legume that belongs to the family Leguminosae (Fabaceae). Fenugreek is a famous aromatic spice derived from the dry seeds and green leaves and has been used since ancient times in Roman, Chinese, Indian, and Egyptian history as a human food and herbal medicine. In the modern food industry, it can be used as a supplement for wheat and maize flour in bread making as a source of flavor, color, and to modify the texture of food materials [3,4]. As a self-pollinated plant, selecting single new lines has been proven as a powerful breeding approach for selecting highly heritable quantitative traits such as seed size, and seed color [5,6,7,8]
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