Dissection of a rapidly evolving wheat resistance gene cluster by long-read genome sequencing accelerated the cloning of Pm69

Li, Yinghui; Wei, Zhen-Zhen; Sela, Hanan; Govta, Liubov; Klymiuk, Valentyna; Roychowdhury, Rajib; Chawla, Harmeet Singh; Ens, Jennifer; Wiebe, Krystalee; Bocharova, Valeria; Ben‐David, Roi; Pawar, Prerna Balkrishna; Zhang, Yuqi; Jaiwar, Samidha; Molnár, István; Doležel, Jaroslav; Coaker, Gitta; Pozniak, Curtis; Fahima, Tzion

doi:10.1016/j.xplc.2023.100646

Cited by 46 publications

(24 citation statements)

References 87 publications

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“…The finding also demonstrates structural variations are major obstacles to gene identification in complex genomes, such as wheat and wild relatives, based on the limited availability of reference and pan-genome sequences. Recently, long-read sequencing technologies have also been used to clone wheat yellow rust resistance gene Yr27 49 and powdery mildew resistance gene Pm69 21 , indicating a powerful tactic for facilitating disease resistance gene cloning in wheat.…”

Section: Discussionmentioning

confidence: 99%

“…To date, eighteen powdery mildew resistance ( Pm ) genes, Pm1a 4 , Pm2 5 , Pm3 6 , Pm4 7 , Pm5e 8 , Pm8 9 , Pm12 10 , Pm13 11 , Pm17 12 , Pm21 13 , 14 , Pm24 15 , Pm38/Yr18/Lr34/Sr57 16 , Pm41 17 , Pm46 / Yr46 / Lr67 / Sr55 18 , Pm57 19 , Pm60 20 , Pm69 21 and WTK4 22 have been cloned in wheat and its wild relatives. Most of them encode coiled coil nucleotide-binding leucine-rich-repeat (NLR) proteins, except for Pm4 , Pm13 , Pm24 , WTK4 , Pm57 , Pm38/Yr18/Lr34/Sr57 , and Pm46 / Yr46 / Lr67 / Sr55 .…”

Section: Introductionmentioning

confidence: 99%

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A membrane associated tandem kinase from wild emmer wheat confers broad-spectrum resistance to powdery mildew

Li,

Zhang,

Xiao

et al. 2024

Nat Commun

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Crop wild relatives offer natural variations of disease resistance for crop improvement. Here, we report the isolation of broad-spectrum powdery mildew resistance gene Pm36, originated from wild emmer wheat, that encodes a tandem kinase with a transmembrane domain (WTK7-TM) through the combination of map-based cloning, PacBio SMRT long-read genome sequencing, mutagenesis, and transformation. Mutagenesis assay reveals that the two kinase domains and the transmembrane domain of WTK7-TM are critical for the powdery mildew resistance function. Consistently, in vitro phosphorylation assay shows that two kinase domains are indispensable for the kinase activity of WTK7-TM. Haplotype analysis uncovers that Pm36 is an orphan gene only present in a few wild emmer wheat, indicating its single ancient origin and potential contribution to the current wheat gene pool. Overall, our findings not only provide a powdery mildew resistance gene with great potential in wheat breeding but also sheds light into the mechanism underlying broad-spectrum resistance.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A membrane associated tandem kinase from wild emmer wheat confers broad-spectrum resistance to powdery mildew

Li,

Zhang,

Xiao

et al. 2024

Nat Commun

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Section: Introductionmentioning

confidence: 99%

“…Although more than 60 official Pm resistance genes ( Pm1 - Pm69 ) have been identified in wheat and its wild relatives 7 , 8 , so far only 16 of these genes have been cloned and characterized. Most of these isolated Pm genes, including Pm3 9 , Pm8 10 , Pm2 11 , Pm21 12 , 13 , Pm60 14 , Pm17 15 , Pm41 16 , Pm5e 17 , Pm1a 18 , MlIW172/MlWE18 19 , Pm12 20 and Pm69 8 , encode NLR immune receptors. Only a few partial resistance genes have been identified, including Pm38/Yr18/Lr34/Sr57 and Pm46/Yr46/Lr67/Sr55 , which encode an ATP-binding cassette (ABC) transporter and a hexose transporter 21 , 22 , respectively.…”

Section: Introductionmentioning

confidence: 99%

Wheat powdery mildew resistance gene Pm13 encodes a mixed lineage kinase domain-like protein

Li,

Men,

et al. 2024

Nat Commun

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Wheat powdery mildew is one of the most destructive diseases threatening global wheat production. The wild relatives of wheat constitute rich sources of diversity for powdery mildew resistance. Here, we report the map-based cloning of the powdery mildew resistance gene Pm13 from the wild wheat species Aegilops longissima. Pm13 encodes a mixed lineage kinase domain-like (MLKL) protein that contains an N-terminal-domain of MLKL (MLKL_NTD) domain in its N-terminus and a C-terminal serine/threonine kinase (STK) domain. The resistance function of Pm13 is validated by mutagenesis, gene silencing, transgenic assay, and allelic association analyses. The development of introgression lines with significantly reduced chromosome segments of Ae. longissima encompassing Pm13 enables widespread deployment of this gene into wheat cultivars. The cloning of Pm13 may provide valuable insights into the molecular mechanisms underlying Pm13-mediated powdery mildew resistance and highlight the important roles of kinase fusion proteins (KFPs) in wheat immunity.

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“…This means Eps genes can be characterized and cloned positionally in the same way as photoperiod and vernalization genes can. This validation investigation is the initial step toward detailed mapping, and eventually direct cloning of the genes in hexaploid wheat (Zikhali et al, 2014;Li et al, 2024). Thus, the objectives of the current study were: a) to identify alleles of major genes that underpin earliness per se in wheat, b) to narrow down wheat cultivars having characteristic of early maturity to ensure maximum productivity under projected heat stress environments, and c) to validate the phenotypic effect of genes controlling flowering time and drought tolerance in the historical wheat panel.…”

Section: Introductionmentioning

confidence: 99%

Allelic variation and effects of earliness <i> per se (Eps) </i> genes in wheat cultivars of Pakistan

Iltaf,

Qayyum,

Suleman

et al. 2024

Int. J. Appl. Exp. Biol.

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Optimization of the flowering time in wheat is an important breeding target for its adaptability in target environments. Flowering time is controlled by vernalization, photoperiod, and the relatively poorly characterized earliness per se (Eps) genes. When vernalization and photoperiod criteria are met, Eps genes account for the variance in flowering time. The objective of the study was to decipher the allelic variations for Eps genes in the wheat cultivars of Pakistan and draw their association with agronomic traits. The wheat cultivars released prior to 1965 had an average flowering duration of 82 days, whereas the cultivars released between 1965 and 2000 had an average flowering time of 79 days and 81 days, respectively. Kompetitive allele-specific PCR (KASP) markers were used to genotype all these cultivars for TaElf3-B1, TaElf3-D1, and TaMOT1-D1 genes. For the gene TaElf3-B1, allele Cadenza-type had a frequency of 61.71%. For the gene TaElf3-D1, the proportion of its respective major alleles was recorded, i.e., deletion had a frequency of 72.94%, and Savannah-type was 86.04%. For the gene TaMOT1-D1, the allele Wild-type was found in 55.88% accessions. The gene Elf3-B1 had a significant allelic effect for grain yield (GY), TaElf3-D1 for grain length, and TaMOT1-D1 for GY. Among the wheat cultivars, high percentage (56.89%) of the Savanah-type allele was associated with early flowering. However, the Wild-type alleles (43.1%) were observed to have low allelic frequency, and they were associated with late flowering. This study may allow wheat breeders to make genetic selection of wheat cultivars that are most suited to target environment, ensuring better yield and adaptability.

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Dissection of a rapidly evolving wheat resistance gene cluster by long-read genome sequencing accelerated the cloning of Pm69

Cited by 46 publications

References 87 publications

A membrane associated tandem kinase from wild emmer wheat confers broad-spectrum resistance to powdery mildew

A membrane associated tandem kinase from wild emmer wheat confers broad-spectrum resistance to powdery mildew

Wheat powdery mildew resistance gene Pm13 encodes a mixed lineage kinase domain-like protein

Allelic variation and effects of earliness <i> per se (Eps) </i> genes in wheat cultivars of Pakistan

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