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1. Genomic Outcomes of Haploid Induction Crosses in Potato ( Solanum tuberosum L.)

   https://doi.org/10.1534/genetics.119.302843  

   Amundson, Kirk R; Ordoñez, Benny; Santayana, Monica; Tan, Ek Han; Henry, Isabelle M; Mihovilovich, Elisa; Bonierbale, Merideth; Comai, Luca (February 2020, Genetics)

   null (Ed.)

   Abstract The challenges of breeding autotetraploid potato (Solanum tuberosum) have motivated the development of alternative breeding strategies. A common approach is to obtain uniparental dihaploids from a tetraploid of interest through pollination with S. tuberosum Andigenum Group (formerly S. phureja) cultivars. The mechanism underlying haploid formation of these crosses is unclear, and questions regarding the frequency of paternal DNA transmission remain. Previous reports have described aneuploid and euploid progeny that, in some cases, displayed genetic markers from the haploid inducer (HI). Here, we surveyed a population of 167 presumed dihaploids for large-scale structural variation that would underlie chromosomal addition from the HI, and for small-scale introgression of genetic markers. In 19 progeny, we detected 10 of the 12 possible trisomies and, in all cases, demonstrated the noninducer parent origin of the additional chromosome. Deep sequencing indicated that occasional, short-tract signals appearing to be of HI origin were better explained as technical artifacts. Leveraging recurring copy number variation patterns, we documented subchromosomal dosage variation indicating segregation of polymorphic maternal haplotypes. Collectively, 52% of the assayed chromosomal loci were classified as dosage variable. Our findings help elucidate the genomic consequences of potato haploid induction and suggest that most potato dihaploids will be free of residual pollinator DNA. 

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2. Rare instances of haploid inducer DNA in potato dihaploids and ploidy-dependent genome instability

   https://doi.org/10.1093/plcell/koab100  

   Amundson, Kirk R; Ordoñez, Benny; Santayana, Monica; Nganga, Mwaura Livingstone; Henry, Isabelle M; Bonierbale, Merideth; Khan, Awais; Tan, Ek Han; Comai, Luca (April 2021, The Plant Cell)

   null (Ed.)

   Abstract In cultivated tetraploid potato (Solanum tuberosum), reduction to diploidy (dihaploidy) allows for hybridization to diploids and introgression breeding and may facilitate the production of inbreds. Pollination with haploid inducers yields maternal dihaploids, as well as triploid and tetraploid hybrids. Dihaploids may result from parthenogenesis, entailing the development of embryos from unfertilized eggs, or genome elimination, entailing missegregation and the loss of paternal chromosomes. A sign of genome elimination is the occasional persistence of haploid inducer DNA in some dihaploids. We characterized the genomes of 919 putative dihaploids and 134 hybrids produced by pollinating tetraploid clones with three haploid inducers: IVP35, IVP101, and PL-4. Whole-chromosome or segmental aneuploidy was observed in 76 dihaploids, with karyotypes ranging from 2n=2x-1=23 to 2n=2x+3=27. Of the additional chromosomes in 74 aneuploids, 66 were from the non-inducer parent and 8 from the inducer parent. Overall, we detected full or partial chromosomes from the haploid inducer parent in 0.87% of the dihaploids, irrespective of parental genotypes. Chromosomal breaks commonly affected the paternal genome in the dihaploid and tetraploid progeny, but not in the triploid progeny, correlating instability to sperm ploidy and to haploid induction. The residual haploid inducer DNA discovered in the progeny is consistent with genome elimination as the mechanism of haploid induction. 

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3. Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato

   https://doi.org/10.1101/845818  

   Petek, Marko; Zagorščak, Maja; Ramšak, Živa; Sanders, Sheri; Tomaž, Špela; Tseng, Elizabeth; Zouine, Mohamed; Coll, Anna; Gruden, Kristina (July 2020, Scientific data)

   Although the reference genome of Solanum tuberosum Group Phureja double-monoploid (DM) clone is available, knowledge on the genetic diversity of the highly heterozygous tetraploid Group Tuberosum, representing most cultivated varieties, remains largely unexplored. This lack of knowledge hinders further progress in potato research. In conducted investigation, we first merged and manually curated the two existing partially-overlapping DM genome-based gene models, creating a union of genes in Phureja scaffold. Next, we compiled available and newly generated RNA-Seq datasets (cca. 1.5 billion reads) for three tetraploid potato genotypes (cultivar Désirée, cultivar Rywal, and breeding clone PW363) with diverse breeding pedigrees. Short-read transcriptomes were assembled using several de novo assemblers under different settings to test for optimal outcome. For cultivar Rywal, PacBio Iso-Seq full-length transcriptome sequencing was also performed. EvidentialGene redundancy-reducing pipeline complemented with in-house developed scripts was employed to produce accurate and complete cultivar-specific transcriptomes, as well as to attain the pan-transcriptome. The generated transcriptomes and pan-transcriptome represent a valuable resource for potato gene variability exploration, high-throughput omics analyses, and breeding programmes. 

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4. Durum wheat mutants with enhanced disease resistance to stripe rust show differential responses to other fungal diseases

   https://doi.org/10.1007/s11032-025-01576-y  

   Lunde, China; Seong, Kyungyong; Kumar, Rakesh; Deatker, Andrew; Chhabra, Bhavit; Wang, Meinan; Kaur, Shivreet; Raats, Dina; Schudoma, Christian; Schultink, Alex; et al (June 2025, Molecular Breeding)

   Abstract Introducing and characterizing variation through mutagenesis plus functional genomics can accelerate resistance breeding as well as our understanding of crop plant immunity. To reveal new germplasm resources for fungal disease resistance breeding in elite durum wheat, we challenged the diverse alleles in a sequenced and cataloged ethyl methanesulfonate mutagenized population of elite tetraploid wheatTriticum turgidumsubsp.durumcv ‘Kronos’ with stripe rust. We screened 2,000 mutant lines and identified sixteen enhanced disease resistance (EDR) lines with persistent resistance to stripe rust over four years of field testing. To find broad-spectrum resistance, we challenged these lines with other major biotrophic and necrotrophic pathogens, including those causing Septoria tritici blotch, tan spot, Fusarium head blight and leaf rust. Enhanced resistance to multiple fungi was found in 13 of 16 EDR lines. Five EDR lines showed spontaneous lesion formation in the absence of pathogens, providing new mutant resources to study plant stress response in the absence of the confounding effects of pathogen infection. We mapped exome capture sequencing data of the EDR lines to a recently released long-read Kronos genome to aid in the identification of causal mutations. We located an EDR resistance locus to an 175 Mb interval on chromosome 1B. Importantly, these phenotypically characterized EDR lines are newly described durum germplasm coupled with improved functional genomics resources that are readily available for both wheat fungal resistance breeding and basic plant immunity research. 

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5. Unlikely heroes on the long and winding road to potato inbreeding

   https://doi.org/10.1007/s42994-023-00109-5  

   Comai, Luca (July 2023, aBIOTECH)

   Sanwen Huang, William Lucas (Ed.)

   Abstract Conversion of potato from a tetraploid, heterozygous, vegetatively propagated crop to a diploid F1 hybrid, propagated via botanical seed, would constitute a considerable advance for global agriculture, but faces multiple challenges. One such challenge is the difficulty in inbreeding potato, which involves purging deleterious alleles from its genome. This commentary discusses possible reasons for this difficulty and highlights a recent sequence-based effort to classify SNP variation, in potato germplasm, according to its deleterious potential. Tools and strategies connected to this database may facilitate development of F1 hybrids. 

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