# Wheat genomics of immunity using Kinnex™ Full-length RNAs

INRAE Genomics 2025
June 19th 2025 – Clermont-Ferrand
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hexaploid
sub-genomes
homeologs
haplotypes...

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1A

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1B

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1D

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Courtot (ANR DefiWheat, P. Sourdille)

HiFi 24x REVIO, Gentyane, 2024

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© Marie Unvericht
Zymoseptoria tritici
fungal disease = STB

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Stb6 (Saintenac et al. 2018)

Stb16q (Saintenac et al. 2021)

Stb15 (Hafeez et al. 2025)

A

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B

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D

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Receptor-like kinase = RLK
Chinese Spring:

* ~5800 kinases

* ~2800 RL-kinases (RLKdb Yin et al. 2024)

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❖ Cloning Stb10

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Stb10: Nogal

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Steuernagel et al. Nature Biotech 2016
MutRenSeq
❖ Cloning Stb10

1st run Kinnex™ full-length RNAs at Gentyane, July 2024

1 SMRT Cell: 15 samples multiplexed

o Stb10: Nogal 11 mutants

o Stb19: Lorikeet

o Stb9: Cadenza

113 Gb

15 kb avg

98 % full array reads

58 M fl-mRNAs

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<table><thead><tr><th></th><th></th><th></th><th>#fl-mRNAs</th><th>length (avg)</th></tr></thead><tbody><tr><td>1</td><td>M0001</td><td>bc01</td><td>Cadenza</td><td>4516702</td><td>1659</td></tr><tr><td>2</td><td>M0001</td><td>bc02</td><td>Nogal-129</td><td>3164483</td><td>1804</td></tr><tr><td>3</td><td>M0001</td><td>bc03</td><td>Nogal-275</td><td>3662279</td><td>1789</td></tr><tr><td>4</td><td>M0001</td><td>bc04</td><td>Nogal-89</td><td>2929048</td><td>1805</td></tr><tr><td>5</td><td>M0001</td><td>bc05</td><td>Nogal-250</td><td>3486030</td><td>1906</td></tr><tr><td>6</td><td>M0001</td><td>bc06</td><td>Nogal-19</td><td>3729299</td><td>1760</td></tr><tr><td>7</td><td>M0001</td><td>bc07</td><td>Lorikeet (mock)</td><td>3484013</td><td>1732</td></tr><tr><td>8</td><td>M0001</td><td>bc08</td><td>Nogal-390</td><td>3845439</td><td>1758</td></tr><tr><td>9</td><td>M0002</td><td>bc01</td><td>Nogal-232</td><td>5403499</td><td>1687</td></tr><tr><td>10</td><td>M0002</td><td>bc02</td><td>Cad207</td><td>5143402</td><td>1711</td></tr><tr><td>11</td><td>M0002</td><td>bc03</td><td>Nogal-204</td><td>3468409</td><td>1681</td></tr><tr><td>12</td><td>M0002</td><td>bc04</td><td>Nogal-294</td><td>1284508</td><td>1857</td></tr><tr><td>13</td><td>M0002</td><td>bc05</td><td>Nogal-377</td><td>3473015</td><td>1716</td></tr><tr><td>14</td><td>M0002</td><td>bc06</td><td>Lorikeet</td><td>4104113</td><td>1882</td></tr><tr><td>15</td><td>M0002</td><td>bc07</td><td>Nogal-211</td><td>4985884</td><td>1654</td></tr></tbody></table>
## ❖ Cloning Stb10

reads mapped: 96%

```
for mutantId in ${mutantIds[@]}; do
  sample=${samples[$mutantId]}
  prefix=${basename ${sample%.fastq.gz)}
bams[$mutantId]=${isoseqOutDir}/isoseq_${mutantId}.vs_${refacc}.bam
  sbatch -p $partition -c $cpu --mem=$mem --wrap "
    pbmm2 align --preset ISOSEQ \
    --sample ${mutantId} \
    --rg "@RG	ID:${prefix}	SM:${prefix}" \
    --min-id-perc 98 \
    --sort \
    --bam-index CSI \
    -j $cpu \
    ${refseq} \
    ${sample} \
    ${bams[$mutantId]}"
done
```

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## ❖ Cloning Stb10

### TPMs

<table><thead><tr><th>wt</th><th colspan="14">Mutants</th></tr></thead><tbody><tr><td>TraesCS1A03G0000200.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0000400.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0000600.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0000800.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0001000.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0001200.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0001300.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0001400.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0001500.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0001700.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0001800.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0002100.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0002200.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0002400.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0002800.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0002900.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0003200.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0004000.1</td><td>28</td><td>1</td><td>2</td><td>0</td><td>1</td><td>1</td><td>1</td><td>2</td><td>1</td><td>2</td><td>2</td><td>3</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0004200.1</td><td>139</td><td>103</td><td>143</td><td>121</td><td>152</td><td>105</td><td>126</td><td>131</td><td>2</td><td>174</td><td>128</td><td>125</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0004300.1</td><td>0</td><td>1</td><td>1</td><td>1</td><td>2</td><td>1</td><td>1</td><td>2</td><td>2</td><td>0</td><td>2</td><td>3</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0004400.1</td><td>5</td><td>2</td><td>2</td><td>3</td><td>8</td><td>4</td><td>5</td><td>4</td><td>2</td><td>4</td><td>5</td><td>4</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0004500.1</td><td>12</td><td>5</td><td>2</td><td>1</td><td>2</td><td>1</td><td>1</td><td>3</td><td>2</td><td>0</td><td>5</td><td>3</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0004900.1</td><td>18</td><td>35</td><td>45</td><td>30</td><td>58</td><td>36</td><td>39</td><td>38</td><td>38</td><td>44</td><td>30</td><td>30</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0005000.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0005200.1</td><td>12</td><td>6</td><td>7</td><td>6</td><td>15</td><td>5</td><td>6</td><td>5</td><td>5</td><td>4</td><td>7</td><td>6</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0005600.1</td><td>44</td><td>12</td><td>13</td><td>10</td><td>17</td><td>13</td><td>12</td><td>12</td><td>9</td><td>20</td><td>11</td><td>11</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0006700.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0007600.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0007700.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0007800.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0007900.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0013100.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0013200.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0013400.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0013600.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0013800.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0013900.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0014300.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0014400.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0014500.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0014600.1</td><td>28</td><td>8</td><td>6</td><td>5</td><td>8</td><td>9</td><td>5</td><td>4</td><td>2</td><td>5</td><td>5</td><td>5</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0014800.1</td><td>2</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0014900.1</td><td>2</td><td>0</td><td>0</td><td>1</td><td>0</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0015100.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0015200.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0015300.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0015500.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0015600.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0015700.1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0016000.1</td><td>19</td><td>4</td><td>6</td><td>5</td><td>7</td><td>6</td><td>2</td><td>4</td><td>4</td><td>6</td><td>5</td><td>3</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0016200.1</td><td>0</td><td>1</td><td>0</td><td>1</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0016300.1</td><td>25</td><td>11</td><td>18</td><td>24</td><td>12</td><td>12</td><td>10</td><td>11</td><td>18</td><td>11</td><td>12</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0016400.1</td><td>6</td><td>4</td><td>8</td><td>4</td><td>9</td><td>3</td><td>6</td><td>10</td><td>12</td><td>5</td><td>11</td><td>13</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0016500.1</td><td>11</td><td>2</td><td>5</td><td>0</td><td>3</td><td>3</td><td>1</td><td>1</td><td>5</td><td>2</td><td>3</td><td>0</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0016700.1</td><td>8</td><td>2</td><td>3</td><td>0</td><td>4</td><td>1</td><td>2</td><td>1</td><td>1</td><td>3</td><td>0</td><td>2</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0017100.1</td><td>8</td><td>2</td><td>3</td><td>0</td><td>3</td><td>1</td><td>2</td><td>1</td><td>1</td><td>3</td><td>1</td><td>2</td><td>0</td><td>0</td></tr><tr><td>TraesCS1A03G0017200.1</td><td>8</td><td>2</td><td>3</td><td>0</td><td>3</td><td>1</td><td>2</td><td>1</td><td>1</td><td>3</td><td>0</td><td>2</td><td>0</td><td>0</td></tr></tbody></table>

```
for mrnaId in $(echo "$bed" | cut -f4 | sort -u); do
    subbed=$(echo "$bed" | egrep -w $mrnaId | sort -k2,2n)
    strand=$(echo "$subbed" | cut -f6 | sort -u)
    declare -a out=()
    for sample in ${samples[@]}; do
        bam=${bams[$sample]}
        k=$(echo "$subbed" | samtools bedcov -c /dev/stdin $bam | \
            cut -f8 | sort -rn | head -1)
        tmn=$(echo $k ${nbReads[$sample]} | \
            awk -v FS=" ' '{printf "%.0f", $1/$2*1000000}')
        out=$( $tmn )
    done
    echo $mrnaId ${out[@]} | tr -s ' ' '\t'
    done
```

```
for sample in ${samples[@]}; do
    bam=${bams[$sample]}
    isoseq collapse ${bam} ${bam}.gff
    done
```

```
for sample in ${samples[@]}; do
    k=$( \
        bedtools intersect -s -sorted -wa \
        -a <( cat ${gffGenes[$idx{$ref}]} ) \
        | egrep -v '^#' | awk '$3=="gene"' | sort -k1,1 -k4,4n ) \
        -b <( cat ${gffs[$sample]} | egrep -v '^[^#]' \
        | awk '$3=="transcript"' | sort -k1,1 -k4,4n ) \
        | sort -u | wc -l )
    echo -e $sample\\t"$k
    done
```

<table><thead><tr><th></th><th>#ref genes<br>(~100,000)</th><th>#unannotated<br>genes</th></tr></thead><tbody><tr><td>wt</td><td>42603</td><td>14881</td></tr><tr><td>Nog129</td><td>43792</td><td>10390</td></tr><tr><td>Nog275</td><td>45042</td><td>11763</td></tr><tr><td>Nog89</td><td>41808</td><td>9372</td></tr><tr><td>Nog250</td><td>44416</td><td>12490</td></tr><tr><td>Nog19</td><td>42500</td><td>10967</td></tr><tr><td>Nog390</td><td>43914</td><td>11910</td></tr><tr><td>Nog232</td><td>46982</td><td>14302</td></tr><tr><td>Nog204</td><td>43810</td><td>12031</td></tr><tr><td>Nog294</td><td>36266</td><td>7090</td></tr><tr><td>Nog377</td><td>46220</td><td>12136</td></tr><tr><td>Nog211</td><td>47196</td><td>13874</td></tr></tbody><tfoot><tr><td colspan="3">~75%</td></tr><tr><td colspan="3">~25%</td></tr></tfoot></table>
## ❖ Cloning Stb10

### Variants

```
for sample in ${!bams[@]}; do
  echo $sample "..." >&2
  bcf=$dirSnp/${basename ${bams[$sample]}}.bcf"
  bcftools mpileup -d 100 --min-MQ 10 --min-BQ 20 --threads $ncpus \
    --fasta-ref ${fais[$idx[$ref]]} \
    ${bams[$sample]} 2>/dev/null | \
    bcftools call --ploidy 1 --threads $ncpus -mv -Ob -W 2>/dev/null -o
  $bcf
done
```

<table><thead><tr><th>ID</th><th>wt</th><th>Nog129</th><th>Nog275</th><th>Nog89</th><th>Nog250</th><th>Nog19</th><th>Nog390</th><th>Nog232</th><th>Nog204</th><th>Nog294</th><th>Nog377</th><th>Nog211</th></tr></thead><tbody><tr><td>TraesCS1A03G0004200.1</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>1159757:G/A</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>TraesCS1A03G0050800.1</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>12360390:G/A</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>TraesCS1A03G0066600.1</td><td>NA</td><td>15304674:C/T</td><td>NA</td><td>15304674:C/T</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>TraesCS1A03G0068200.1</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>15585980:G/A</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>TraesCS1A03G0106500.1</td><td>NA</td><td>NA</td><td>27648781:C/T</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>TraesCS1A03G0126000.1</td><td>NA</td><td>DP:0</td><td>35203097:G/A</td><td>NA</td><td>NA</td><td>DP:0</td><td>NA</td><td>NA</td><td>NA</td><td>DP:0</td><td>DP:0</td><td>NA</td></tr><tr><td>TraesCS1A03G0127500.1</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>35553431:C/T</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>TraesCS1A03G0135600.1</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>38557166:G/A</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>TraesCS1A03G0136200.1</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>38846251:G/A</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>TraesCS1A03G0175300.1</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>56533660:C/T</td><td>NA</td><td>NA</td><td>NA</td><td>56530961:C/T</td><td>NA</td></tr><tr><td>TraesCS1A03G0175400.1</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>56582793:C/T</td><td>NA</td></tr><tr><td>TraesCS1A03G0175800.1</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>56856098:C/T</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>TraesCS1A03G0176200.1</td><td>NA</td><td>NA</td><td>56968943:C/T</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>TraesCS1A03G0180300.1</td><td>NA</td><td>NA</td><td>60255514:C/T</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>TraesCS1A03G0202700.1</td><td>NA</td><td>NA</td><td>70084317:C/T</td><td>DP:0</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>DP:0</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>TraesCS1A03G0211100.1</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>75715850:G/A</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>TraesCS1A03G0213700.1</td><td>NA</td><td>NA</td><td>78384221:C/T</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>TraesCS1A03G0214000.1</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>78847001:T/C</td><td>NA</td><td>78841612:G/A</td><td>NA</td></tr><tr><td>TraesCS1A03G0215400.1</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>79458077:G/A</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>TraesCS1A03G0217700.1</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>81448598:C/T</td></tr><tr><td>TraesCS1A03G0217900.1</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>TraesCS1A03G0218400.1</td><td>NA</td><td>NA</td><td>82521057:C/T</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>TraesCS1A03G0218600.1</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>82627857:C/T</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>TraesCS1A03G0224700.1</td><td>NA</td><td>87634048:C/T</td><td>NA</td><td>87634048:C/T</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>TraesCS1A03G0243600.1</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>98692174:G/A</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>TraesCS1A03G0253200.1</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>102147046:G/A</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>TraesCS1A03G0255000.1</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>103165190:G/A</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>TraesCS1A03G0260600.1</td><td>NA</td><td>NA</td><td>NA</td><td>DP:0</td><td>NA</td><td>DP:0</td><td>108924702:G/A</td><td>NA</td><td>NA</td><td>DP:0</td><td>NA</td><td>NA</td></tr><tr><td>TraesCS1A03G0260900.1</td><td>NA</td><td>NA</td><td>108939785:C/T</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr></tbody></table>

5-9% of genes with EMS mutation(s) in the 11 mutants
❖ Cloning Stb10

<figure><img src="image_27.png" /></figure>

➤ Stb10 gene probably absent from the ref...
<figure><img src="image_28.png" /></figure>

Cloning a newly discovered Stb QTL

1 run Kinnex (May 2025; Gentyane)

1 SMRT Cell: 9 samples

o Fielder

Control

x3 rep

Infected by virulent strain

x3 rep

Infected by avirulent strain

x3 rep

6o M FL-mRNAs

% mapped

<figure><img src="image_29.png" /></figure>
Perspectives

* Rapid cloning of R genes EMS-Kinnex IsoSeq-Bioinfo

* Annotation improvement

* Diversity of Stb genes

* Identification of molecular factors of interactions

* Quantification of Stb isoforms
## ❖ Acknowledgments

### ❖ GDEC

Immunity of Plants
and Multistress

C. Saintenac

M. Unvericht

F. Cambon

O. Soudière

A. Garavito

Gentyane

C. Poncet

V. Gautier

E. Belmonte

V. Pailler

et al.

VégéPole

S. Bernard

et al.

MÉSOCENTRE
Université Clermont Auvergne

Fsv

<figure><img src="image_30.png" /></figure>

I-SITE
CLERMONT AUVERGNE PROJECT
Université Clermont Auvergne

<figure><img src="image_31.png" /></figure>

CIR1 Agroécosystèmes durables

<figure><img src="image_32.png" /></figure>

RÉPUBLIQUE
FRANÇAISE

Liberté
Rgalat
Praterrt

anr

agence nationale
de la recherche

PEPR AgroEcoNum
<figure><img src="image_33.png" /></figure>