Nucleotide sequence polymorphism in the RFL-PPR genes of potato

Anisimova, I. N.; Alpatieva, N. V.; Karabitsina, Yulia I; Гавриленко, Т. А.

doi:10.1007/s12041-019-1130-1

Cited by 10 publications

(6 citation statements)

References 38 publications

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“…RFL is almost ubiquitous in plant genomes even when the plant appears to have no relationship to CMS, such as poplar (a dioecious plant species) [63,[65][66][67]. RFL copy number in a genome varies among plant species (sometimes close to 40 copies) [68]. RFL copies tend to cluster with each other in several chromosomal regions, but the location of the cluster is less preserved even between closely related species.…”

Section: Evolution Of Ppr Rfsmentioning

confidence: 99%

What Does the Molecular Genetics of Different Types of Restorer-of-Fertility Genes Imply?

Kubo

Arakawa

Honma

et al. 2020

Plants

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Cytoplasmic male sterility (CMS) is a widely used trait for hybrid seed production. Although male sterility is caused by S cytoplasm (male-sterility inducing mitochondria), the action of S cytoplasm is suppressed by restorer-of-fertility (Rf), a nuclear gene. Hence, the genetics of Rf has attained particular interest among plant breeders. The genetic model posits Rf diversity in which an Rf specifically suppresses the cognate S cytoplasm. Molecular analysis of Rf loci in plants has identified various genes; however, pentatricopeptide repeat (PPR) protein (a specific type of RNA-binding protein) is so prominent as the Rf-gene product that Rfs have been categorized into two classes, PPR and non-PPR. In contrast, several shared features between PPR- and some non-PPR Rfs are apparent, suggesting the possibility of another grouping. Our present focus is to group Rfs by molecular genetic classes other than the presence of PPRs. We propose three categories that define partially overlapping groups of Rfs: association with post-transcriptional regulation of mitochondrial gene expression, resistance gene-like copy number variation at the locus, and lack of a direct link to S-orf (a mitochondrial ORF associated with CMS). These groups appear to reflect their own evolutionary background and their mechanism of conferring S cytoplasm specificity.

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Section: Evolution Of Ppr Rfsmentioning

confidence: 99%

What Does the Molecular Genetics of Different Types of Restorer-of-Fertility Genes Imply?

Kubo

Arakawa

Honma

et al. 2020

Plants

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“…At the same time, R. Ortiz et al (1993Ortiz et al ( , 2009 failed to detect the Rt or Ms genes among the samples with D-type cytoplasm. Recently, using the methods of comparative genomics, homologs of RFL-PPR genes were identified in potato and their structural polymorphism was studied (Anisimova et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Cytoplasmic genetic diversity of potato varieties bred in Russia and FSU countries

et al. 2019

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Male sterility in potato is little studied since traditional breeding is based on the vegetative reproduction of highly heterozygous tetraploid varieties. The rapid development of hybrid diploid breeding contributes to growing interest in studying the male sterility of this important crop. In this work, a set of 6 cytoplasmic markers was employed to describe cytoplasmic genetic diversity of 185 potato cultivars bred in Russia and FSU countries. Three cytoplasm types were identified, T (40.0 %), D (50.8 %) and W/γ (8.7 %), which according to literature are associated with male sterility. With a single exception (0.5 %), cytoplasm types characteristic of male fertile forms (A, P) were not found in the subset of 185 cultivars. A comparison of these results with previously published data suggested expanding the subset to up to 277 cultivars, all developed in Russia or FSU countries; however, the resulting differentiation into three cytoplasm types (T, D and W/γ) was nearly the same. Fertility phenotyping helped identify both male-sterile and male-fertile genotypes within the three groups of varieties with T-, D-and W/γ-type cytoplasm. Fifteen genotypes differing in cytoplasm type and male sterility/fertility traits were selected for direct sequencing of 8 mtDNA loci. Fragments of the nad2, nad7, cox2, atp6 and CcmFc genes were identical in all 15 selected genotypes. The polymorphism, detected in the rps3, atp9 and CcmFc loci, was not associated with male sterility. Two SNPs in the nad1/ atp6 and nad2 loci differentiated 7 genotypes with W/γ-type cytoplasm into five genotypes with tetrad sterility, and two with fertile pollen. The results of an NGS analysis confirmed the association of these SNPs with tetrad sterility in a larger set of 28 genotypes of different origin, all with W/γ-type cytoplasm. A heteroplasmy state was observed both in male-sterile and in male-fertile genotypes.

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“…While hybrids or varieties with S. demissum -derived D-type cytoplasm usually participate in crosses with S. tuberosum as maternal parents due to unilateral incompatibility [ 21 , 74 , 75 , 76 ] or functional pollen sterility [ 29 ]. However, more data are coming about finding efficient pollinators possessing the D-type cytoplasm [ 62 , 72 , 74 , 77 ] that could possibly be explained by the presence of functional alleles of the nuclear restorer genes [ 78 , 79 ]. At the same time, the detection of the R1 gene marker is additional but not direct evidence of introgression from S. demissum because the markers of this gene have no clear phylogenetic signals; their homologous and pseudogenes were found in other potato species [ 80 , 81 , 82 , 83 ].…”

Section: Discussionmentioning

confidence: 99%

“…However, the sources of pollen fertility restorer gene(s) were selected among breeding clones of S. tuberosum exhibiting the typical Chilean cytoplasm [ 74 , 88 , 89 ]. Several genomic fragments belonging to the RFL-PPR (restoration of fertility-like PPR) gene subfamily have been identified in genotypes exhibiting the T-type cytoplasm that might be considered Rf gene candidates in potatoes [ 79 ].…”

Section: Discussionmentioning

confidence: 99%

Comparative Analysis of the Genetic Diversity of Chilean Cultivated Potato Based on a Molecular Study of Authentic Herbarium Specimens and Present-Day Gene Bank Accessions

Гавриленко

Chukhina

Antonova

et al. 2022

Plants

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At the end of the 1920s, Vavilov organized several potato-collecting missions in South and Central America. Vavilov and his colleagues, Juzepczuk and Bukasov, participated in these expeditions and worked on gathered material, designated two centers of potato varietal riches and diversity—the Peru–Bolivia high-mountain center and the southern coast of Chile. The WIR Herbarium holds authentic specimens of many taxa described by Russian taxonomists. Here, a set of 20 plastid DNA-specific markers was applied for 49 authentic herbarium specimens of Solanum tuberosum L. from the WIR Herbarium to analyze the genetic diversity of the landrace population collected by Juzepczuk in 1928 in southern–central Chile. Two plastid DNA types, T and A, and two chlorotypes were identified in herbarium specimens, with a clear predominance (96%) of chlorotype cpT_III. In addition, we analyzed 46 living Chilean accessions from the VIR field potato gene bank that were collected after the appearance of Phytophthora infestans in Chile. These living accessions were differentiated into four chlorotypes. Finding a D-type cytoplasm in living Chilean accessions that possess two new chlorotypes indicates a replacement of native cultivars and introgression from the wild Mexican species S. demissum that was actively used in breeding as a source of race-specific resistance to late blight.

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Nucleotide sequence polymorphism in the RFL-PPR genes of potato

Cited by 10 publications

References 38 publications

What Does the Molecular Genetics of Different Types of Restorer-of-Fertility Genes Imply?

What Does the Molecular Genetics of Different Types of Restorer-of-Fertility Genes Imply?

Cytoplasmic genetic diversity of potato varieties bred in Russia and FSU countries

Comparative Analysis of the Genetic Diversity of Chilean Cultivated Potato Based on a Molecular Study of Authentic Herbarium Specimens and Present-Day Gene Bank Accessions

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