Genome sequencing of adapted diploid potato clones

Achakkagari, Sai Reddy; Kyriakidou, Maria; Gardner, Kyle M.; Koeyer, David De; Jong, H. De; Strömvik, Martina V.; Tai, Helen H.

doi:10.3389/fpls.2022.954933

Cited by 8 publications

(7 citation statements)

References 64 publications

(97 reference statements)

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“…This allowed us to evaluate the diversity and characteristics of CNV in Russian potato cultivars and to compare them with those of South American landraces genomes. The data were in agreement with previous results of potato CNV analysis [ 11 , 17 , 18 , 19 , 20 , 39 ]. The number of deletions is greater than the number of duplications in most of the accessions we studied (except for South American accessions of “bitter” cultivated species CUR and JUZ), including all cultivars from Russia.…”

Section: Discussionsupporting

confidence: 92%

“…At the same time, the number of genes that underwent deletion is generally less than the number of duplicated genes (except South American diploid Andean landraces of STN, PHU, GON2, and GON1). This was also observed for South American landraces in [ 17 ], in the analysis of potato somatic hybrid, parents and progeny [ 19 ], diploid potato clones [ 20 ], and one of three potato cultivars of the Ural selection [ 39 ].…”

Section: Discussionmentioning

confidence: 59%

“…Recently, genomic sequences for six accessions of cultivated potato polyploid species were assembled, three of which were tetraploid landraces belonging to the Andigenum group and to the Chilotanum group and two of them were sequenced only by short reads [ 16 ]. Nucleotide and structural variations were analyzed by short-read sequencing in various potato species and landraces from South America [ 17 ], elite tetraploid cultivars [ 18 ], potato somatic hybrid, its parents and progeny [ 19 ], diploid potato clones [ 20 ]. These data made it possible to estimate such structural characteristics of the potato genomes as the set of protein-coding genes [ 16 , 19 ], characterize their functions [ 16 ], estimate copy number variations, single nucleotide, and small insertion–deletion polymorphisms [ 17 , 18 , 19 , 20 ].…”

Section: Introductionmentioning

confidence: 99%

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Analysis of Genome Structure and Its Variations in Potato Cultivars Grown in Russia

Karetnikov

Vasiliev

Toshchakov

et al. 2023

IJMS

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Solanum tuberosum L. (common potato) is one of the most important crops produced almost all over the world. Genomic sequences of potato opens the way for studying the molecular variations related to diversification. We performed a reconstruction of genomic sequences for 15 tetraploid potato cultivars grown in Russia using short reads. Protein-coding genes were identified; conserved and variable parts of pan-genome and the repertoire of the NBS-LRR genes were characterized. For comparison, we used additional genomic sequences for twelve South American potato accessions, performed analysis of genetic diversity, and identified the copy number variations (CNVs) in two these groups of potato. Genomes of Russian potato cultivars were more homogeneous by CNV characteristics and have smaller maximum deletion size in comparison with South American ones. Genes with different CNV occurrences in two these groups of potato accessions were identified. We revealed genes of immune/abiotic stress response, transport and five genes related to tuberization and photoperiod control among them. Four genes related to tuberization and photoperiod were investigated in potatoes previously (phytochrome A among them). A novel gene, homologous to the poly(ADP-ribose) glycohydrolase (PARG) of Arabidopsis, was identified that may be involved in circadian rhythm control and contribute to the acclimatization processes of Russian potato cultivars.

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Section: Discussionsupporting

confidence: 92%

Section: Discussionmentioning

confidence: 59%

Section: Introductionmentioning

confidence: 99%

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Analysis of Genome Structure and Its Variations in Potato Cultivars Grown in Russia

Karetnikov

Vasiliev

Toshchakov

et al. 2023

IJMS

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“…Low depth sequencing of potato varieties and wild species aligned against the DM reference was used to assess genome diversity, copy number variation (CNVs), introgressions, and selective sweeps 11 – 13 . Since then, the genomes of additional potato clones, diploid as well as tetraploid, have been sequenced and de novo assembled 14 – 20 .…”

Section: Background and Summarymentioning

confidence: 99%

The phased Solanum okadae genome and Petota pangenome analysis of 23 other potato wild relatives and hybrids

Achakkagari,

Bozan,

Camargo-Tavares

et al. 2024

Sci Data

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Potato is an important crop in the genus Solanum section Petota. Potatoes are susceptible to multiple abiotic and biotic stresses and have undergone constant improvement through breeding programs worldwide. Introgression of wild relatives from section Petota with potato is used as a strategy to enhance the diversity of potato germplasm. The current dataset contributes a phased genome assembly for diploid S. okadae, and short read sequences and de novo assemblies for the genomes of 16 additional wild diploid species in section Petota that were noted for stress resistance and were of interest to potato breeders. Genome sequence data for three additional genomes representing polyploid hybrids with cultivated potato, and an additional genome from non-tuberizing S. etuberosum, which is outside of section Petota, were also included. High quality short reads assemblies were achieved with genome sizes ranging from 575 to 795 Mbp and annotations were performed utilizing transcriptome sequence data. Genomes were compared for presence/absence of genes and phylogenetic analyses were carried out using plastome and nuclear sequences.

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“…Furthermore, purifying selection of sexual offspring is limited due to vegetative propagation and long generation time (Mirzaghaderi and Hörandl, 2016;Otto, 2007). Prediction of deleterious mutation based on resequencing data have highlighted the severity of the mutational load in potato and the correlation between the number of deleterious alleles and the overall level of heterozygosity (Achakkagari et al, 2022;Zhang et al, , 2021.…”

Section: Selfing Of Diploids Results In the Loss Of Vigour And Fertilitymentioning

confidence: 99%

Natural variation in potato sexual reproduction facilitates breeding

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The origin and widespread occurrence of Sli based self-compatibility in potato Chapter 3 46 High-density linkage map constructed from a skim sequenced diploid potato population reveals transmission distortion and QTLs for tuber yield and pollen shed Chapter 4 74Desynapsis in potato is caused by StMSH4 mutant alleles and leads to either highly uniform unreduced pollen or sterility Chapter 5 94Identification of two mutant JASON-RELATED genes associated with unreduced pollen production in potato Chapter 6 122 General discussion References 143Summary 167Acknowledgements 171 About the author 179Education statement recognition model (Kubo et al., 2010), the combined action of the SLFs encoded by one S-haplotype results in the recognition and degradation of all S-RNases except of the one encoded by their own haplotype. Hence, self-incompatibility occurs when the Shaplotype of the pollen matches either of the two S-haplotypes of the style. This elegant model also provides an explanation for the phenomenon of competitive interaction that allows tetraploid potatoes to become self-compatible (Olsder and Hermsen, 1976). When tetraploid clones produce diploid heteroallelic pollen that expresses two complementary sets of S-locus F-box proteins (SLFs), all S-RNases are ubiquitinated, which breaks down gametophytic self-incompatibility.Recently, self-compatible diploid potato clones were engineered by a knock-out of the gene encoding for the S-RNase (Enciso-Rodriguez et al., 2019;Ye et al., 2018). Furthermore, a self-compatible diploid clone bearing a naturally weakly expressed S-RNase was recently identified . Other cases of self-compatibility among S. tuberosum dihaploids were reported in earlier studies (De Jong and Rowe, 1971;Olsder and Hermsen, 1976), but the genetic and mechanistic basis of their selfcompatibility remained undetermined prior to this thesis. Despite those alternative options, the most widely used source of self-compatibility is the dominant gene Sli originally identified from a S. chacoense accession and located on chromosome 12 Hanneman, 1998a, 1998b). The causal gene behind Sli was recently shown to encode for a pollen-expressed F-box protein functioning as a general S-RNase inhibitor (Eggers et al., 2021;Ma et al., 2021).

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Genome sequencing of adapted diploid potato clones

Cited by 8 publications

References 64 publications

Analysis of Genome Structure and Its Variations in Potato Cultivars Grown in Russia

Analysis of Genome Structure and Its Variations in Potato Cultivars Grown in Russia

The phased Solanum okadae genome and Petota pangenome analysis of 23 other potato wild relatives and hybrids

Natural variation in potato sexual reproduction facilitates breeding

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