Identifying Rare Alleles Affecting Seed Coat and Hilum Color in Soybean (Glycine max) Using Applied Genomics

Kód výsledku v 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>

Výsledek na webu

<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>

Jazyk výsledku

angličtina

Název v původním jazyce

Identifying Rare Alleles Affecting Seed Coat and Hilum Color in Soybean (Glycine max) Using Applied Genomics

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

Identifying Rare Alleles Affecting Seed Coat and Hilum Color in Soybean (Glycine max) Using Applied Genomics

Popis výsledku anglicky

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.

Druh

J_SC - Článek v periodiku v databázi SCOPUS

CEP obor

—

OECD FORD obor

10611 - Plant sciences, botany

Projekt

—

Návaznosti

S - Specificky vyzkum na vysokych skolach

Rok uplatnění

2024

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Legume Science

ISSN

2639-6181

e-ISSN

2639-6181

Svazek periodika

6

Číslo periodika v rámci svazku

4

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

12

Strana od-do

"e70019-1"-"e70019-12"

Kód UT WoS článku

001381808200001

EID výsledku v databázi Scopus

2-s2.0-85212772229