Identifying Rare Alleles Affecting Seed Coat and Hilum Color in Soybean (Glycine max) Using Applied Genomics
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15310%2F24%3A73628420" target="_blank" >RIV/61989592:15310/24:73628420 - isvavai.cz</a>
Result on the web
<a href="https://onlinelibrary.wiley.com/doi/epdf/10.1002/leg3.70019" target="_blank" >https://onlinelibrary.wiley.com/doi/epdf/10.1002/leg3.70019</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1002/leg3.70019" target="_blank" >10.1002/leg3.70019</a>
Alternative languages
Result language
angličtina
Original language name
Identifying Rare Alleles Affecting Seed Coat and Hilum Color in Soybean (Glycine max) Using Applied Genomics
Original language description
Breeding programs are often constrained by the genetic diversity of the parental lines, even though these lines can be a rare source of unique alleles not found elsewhere. Therefore, identifying these rare alleles is crucial for keeping them in the breeding programs while introducing new genetic resources. The growing amount of whole genome sequenced data has made Genome-wide Association Study (GWAS) dominant in investigations to find causal genes for all crops, including legumes. However, GWAS often fails to predict more than one causative mutation (CM) in multiple alleles of a single causal gene. Consequently, multiple alleles complicate breeding when not recognized by a single associated marker, which typically identifies only the most frequent CM and discriminates against the others. In this work, we focus on adopting recent applied genomics methods to identify multiple independent alleles and rare alleles in soybean as a model for other legumes. We predicted, identified, and confirmed a new and extremely rare CM for the loss of black pigmentation in the soybean seed coat and hilum color R gene, the Q25fs. The deletion of eight bases leads to a frameshift, a premature stop codon, and a truncated, nonfunctional protein. Our results also suggest a possibly new gene or an allele of the seed coat color inhibitor I gene. Using a soybean model, we demonstrate how applied genomics methods can accelerate pre-breeding, and additionally, we discuss the potential for adopting these methods for application to other legumes.
Czech name
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Czech description
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Classification
Type
J<sub>SC</sub> - Article in a specialist periodical, which is included in the SCOPUS database
CEP classification
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OECD FORD branch
10611 - Plant sciences, botany
Result continuities
Project
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Continuities
S - Specificky vyzkum na vysokych skolach
Others
Publication year
2024
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Legume Science
ISSN
2639-6181
e-ISSN
2639-6181
Volume of the periodical
6
Issue of the periodical within the volume
4
Country of publishing house
US - UNITED STATES
Number of pages
12
Pages from-to
"e70019-1"-"e70019-12"
UT code for WoS article
001381808200001
EID of the result in the Scopus database
2-s2.0-85212772229