Abstract
Distinctness, uniformity, and stability (DUS) test is the legal requirement in crop breeding to grant the intellectual property right for new varieties by evaluating their morphological characteristics across environments. On the other hand, molecular markers accurately identify genetic variations and validate the purity of the cultivars. Therefore, genomic DUS can improve the efficiency of traditional DUS testing. In this study, 112 Egyptian fenugreek genotypes were grown in Egypt at two locations: Wadi El-Natrun (Wadi), El-Beheira Governorate, with salty and sandy soil, and Giza, Giza governorate, with loamy clay soil. Twelve traits were measured, of which four showed a high correlation above 0.94 over the two locations. We observed significant genotype-by-location interactions (GxL) for seed yield, as it was superior in Wadi, with few overlapping genotypes with Giza. We attribute this superiority in Wadi to the maternal habitat, as most genotypes grew in governorates with newly reclaimed salty and sandy soil. As a first step toward genomic DUS, we performed an association study, and out of 38,142 SNPs, we identified 39 SNPs demonstrating conditional neutrality and four showing pleiotropic effects. Forty additional SNPs overlapped between both locations, each showing a similar impact on the associated trait. Our findings highlight the importance of GxL in validating the effect of each SNP to make better decisions about its suitability in the marker-assisted breeding program and demonstrate its potential use in registering new plant varieties.
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Claims 9
Claim · model-written summary
Four of twelve measured traits correlated above 0.94 across the two locations.
- Taxon
- fenugreek
Trigonella foenum-graecumt0 - Outcome
- high correlatione0
- Value
- above 0.94e0
- Setting
- two locationse0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Twelve traits were measured, of which four showed a high correlation above 0.94 over the two locations”
t0“fenugreek”
Claim · model-written summary
Seed yield showed significant genotype by location interaction.
- Taxon
- fenugreekTrigonella foenum-graecumt0
- Outcome
- seed yielde0
- Setting
- locatione0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“significant genotype-by-location interactions (GxL) for seed yield”
t0“fenugreek”
Claim · model-written summary
Seed yield was superior at Wadi relative to Giza.
- Taxon
- fenugreekTrigonella foenum-graecumt0
- Outcome
- seed yielde0
- Direction
- superiore0
- Comparator
- Gizae0
- Setting
- Wadie0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“seed yield, as it was superior in Wadi, with few overlapping genotypes with Giza”
t0“fenugreek”
Claim · model-written summary
Few genotypes overlapped between Wadi and Giza for seed yield.
- Taxon
- fenugreekTrigonella foenum-graecumt0
- Outcome
- few overlapping genotypese0
- Setting
- Gizae0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“with few overlapping genotypes with Giza”
t0“fenugreek”
Claim · model-written summary
The authors attribute the Wadi yield advantage to the maternal habitat of most genotypes.
- Taxon
- fenugreekTrigonella foenum-graecumt0
- Outcome
- superiority in Wadie0
- Qualifier
- maternal habitate0
- Setting
- Wadie0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“We attribute this superiority in Wadi to the maternal habitat, as most genotypes grew in governorates with newly reclaimed salty and sandy soil”
t0“fenugreek”
Claim · model-written summary
Thirty-nine SNPs showed conditional neutrality in the association study.
- Taxon
- fenugreekTrigonella foenum-graecumt0
- Gene
- SNPse0
- Outcome
- SNPs demonstrating conditional neutralitye0
- Value
- 39 SNPse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“we identified 39 SNPs demonstrating conditional neutrality”
t0“fenugreek”
Claim · model-written summary
Four SNPs showed pleiotropic effects.
- Taxon
- fenugreekTrigonella foenum-graecumt0
- Outcome
- pleiotropic effectse0
- Value
- foure0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“four showing pleiotropic effects”
t0“fenugreek”
Claim · model-written summary
Forty additional SNPs overlapped between both locations and had similar effects on their associated traits.
- Taxon
- fenugreekTrigonella foenum-graecumt0
- Outcome
- SNPs overlapped between both locationse0
- Value
- Fortye0
- Qualifier
- similar impact on the associated traite0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Forty additional SNPs overlapped between both locations, each showing a similar impact on the associated trait”
t0“fenugreek”
Claim · model-written summary
The authors recommend accounting for genotype by location interaction when validating SNPs for marker assisted breeding.
- Taxon
- fenugreekTrigonella foenum-graecumt0
- Outcome
- validating the effect of each SNPe0
- Qualifier
- marker-assisted breeding programe0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“importance of GxL in validating the effect of each SNP to make better decisions about its suitability in the marker-assisted breeding program”
t0“fenugreek”