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Key message <p>QTL mapping and GWAS detected resistance QTL to <i>Aphanomyces euteiches</i> in faba bean, lentil, and <i>Medicago truncatula</i>. Weak genomic conservation between resistance QTL was identified between these legumes and pea.</p> Abstract <p>Aphanomyces root rot, caused by <i>Aphanomyces euteiches</i>, is a damaging disease affecting various legume species. Quantitative trait loci (QTL) for partial resistance have been mainly identified in pea, and to a lesser extent in lentil and <i>Medicago truncatula</i>. This study aimed to identify novel resistance loci from available lentil and faba bean populations, and examine genomic conservation of resistance QTL across legume host species. QTL mapping in the <i>Pop2</i> faba bean recombinant inbred line (RIL) population and genome-wide association study (GWAS) in the <i>AGILE</i> lentil diversity panel were performed for resistance to <i>A. euteiches</i> under controlled conditions, using genotyping data previously reported. A previous QTL mapping in the <i>LR3 M. truncatula</i> RIL population was updated using 1,536 new SNPs (single-nucleotide polymorphisms). Synteny between resistance QTL to <i>A. euteiches</i> was analyzed based on gene orthology in QTL regions projected onto genomes, using the OrthoLegKB graph database.</p> <p>Four loci, including a major-effect QTL on chromosome 3, <i>Ae-Vf3.1</i>, were associated with resistance in faba bean. In lentil, six minor-effect GWAS-SNPs and two favorable haplotypes at <i>Ae-Lc1.1</i> and <i>Ae-Lc2.1</i> loci were identified. Updated analyses in <i>M. truncatula</i> narrowed to 8&#xa0;Kb the interval of the major-effect locus <i>AER1</i> and revealed three candidate genes. No synteny between major-effect QTL, detected in this study or previously reported in the literature, was identified across grain legume genomes. These results pave the way for translational genomics approaches facilitating resistance gene discovery and for resistance QTL deployment strategies in legume rotations to preserve their durability.</p>

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Comparative genomic analysis of QTL for resistance to Aphanomyces euteiches between pea, lentil, faba bean, and the model species Medicago truncatula

  • 期刊论文

  • 发表日期：

    2025年12月10日

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  • Théo Leprévost,
  • Baptiste Imbert,
  • Clément Lavaud,
  • Gilles Boutet,
  • Henri Miteul,
  • Antoine Leduc,
  • Jonathan Kreplak,
  • Ha-Trang Phung,
  • Grégoire Aubert,
  • Estefania Carrillo-Perdomo,
  • Renan Uhdre,
  • Hatice Sari,
  • Britton Bourland,
  • Carolyn T. Caron,
  • Nadim Tayeh,
  • Yu Ma,
  • Clarice J. Coyne,
  • Akiko Sugio,
  • Marie-Laure Pilet-Nayel

摘要

Key message

QTL mapping and GWAS detected resistance QTL to Aphanomyces euteiches in faba bean, lentil, and Medicago truncatula. Weak genomic conservation between resistance QTL was identified between these legumes and pea.

Abstract

Aphanomyces root rot, caused by Aphanomyces euteiches, is a damaging disease affecting various legume species. Quantitative trait loci (QTL) for partial resistance have been mainly identified in pea, and to a lesser extent in lentil and Medicago truncatula. This study aimed to identify novel resistance loci from available lentil and faba bean populations, and examine genomic conservation of resistance QTL across legume host species. QTL mapping in the Pop2 faba bean recombinant inbred line (RIL) population and genome-wide association study (GWAS) in the AGILE lentil diversity panel were performed for resistance to A. euteiches under controlled conditions, using genotyping data previously reported. A previous QTL mapping in the LR3 M. truncatula RIL population was updated using 1,536 new SNPs (single-nucleotide polymorphisms). Synteny between resistance QTL to A. euteiches was analyzed based on gene orthology in QTL regions projected onto genomes, using the OrthoLegKB graph database.

Four loci, including a major-effect QTL on chromosome 3, Ae-Vf3.1, were associated with resistance in faba bean. In lentil, six minor-effect GWAS-SNPs and two favorable haplotypes at Ae-Lc1.1 and Ae-Lc2.1 loci were identified. Updated analyses in M. truncatula narrowed to 8 Kb the interval of the major-effect locus AER1 and revealed three candidate genes. No synteny between major-effect QTL, detected in this study or previously reported in the literature, was identified across grain legume genomes. These results pave the way for translational genomics approaches facilitating resistance gene discovery and for resistance QTL deployment strategies in legume rotations to preserve their durability.