Cytoplasmic diversity in potato breeding: case study from the International Potato Center

Mihovilovich, E.; Sanetomo, Rena; Hosaka, Kazuyoshi; Ordoñez, Benny; Aponte, Mariela; Bonierbale, Merideth

doi:10.1007/s11032-015-0326-1

Cited by 27 publications

(30 citation statements)

References 34 publications

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“…According to the results of phenotyping performed in the framework of this research, each of the three groups of domestic cultivars with the Т, D and W/γ cytoplasm types contained not only malesterile, but also highly fertile genotypes. Male fertility in the Т-type cytoplasm holders is explained in publications by the presence of a dominant allele of the Rt gene (a male fertility restorer gene) and, for a number of interspecies combinations, by the homozygosity (ms/ms) for the recessive allele of the Ms gene (male sterility gene) (Iwanaga et al, 1991;Ortiz et al, 1993;Mihovilovich et al, 2015). Among the varieties with T-type cytoplasm there are many efficient pollinators that have served as male parents in the development of many domestic cultivars, such as 'Avrora', 'Dina', 'Zarevo', 'Kameraz', 'Priyekulskiy ranniy', 'Smena' and 'Shurminskiy 2' (see the Table and Supplement 1).…”

Section: Discussionmentioning

confidence: 99%

“…In view of this, the T-type is often referred to as the 'cultivated' or Chilean. The А-and Р-types of cytoplasm are characteristic of male-fertile diploid and tetraploid indigenous Andean cultivars, while the W/α and W/β types of many wild potato species (Hosaka, Sanetomo, 2012;Mihovilovich et al, 2015). The D-type of cytoplasm is typical for S. demissum and the cultivars developed with its involvement (as a maternal progenitor), and has been found among the accessions of wild allohexaploid and allotetraploid Mexican potato species (Hosaka, Sanetomo, 2012, 2014.…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

et al. 2019

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“…For these reasons, the frequencies of D- and W/γ-type cytoplasm in Japanese potato germplasm are still lower compared to European potatoes. In contrast, the frequencies of D- and W-type cytoplasm were also much higher (38 % and 11 %, respectively, [60]) in the breeding program of the International Potato Center (CIP = Centro International de la Papa), because CIP aims to deliver pest- and disease-resistant varieties for developing countries where chemical control is not practical.…”

Section: Discussionmentioning

confidence: 99%

Cytoplasmic genome types of European potatoes and their effects on complex agronomic traits

Sanetomo

Gebhardt

2015

BMC Plant Biol

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BackgroundVarious wild species germplasm has been used in European potato breeding since the first introduction of potato (Solanum tuberosum L.) to Europe. As the plant cytoplasmic genome including chloroplast and mitochondrial genomes is transmitted only through the maternal parent, cytoplasmic markers are useful tools in breeding programs to determine cytoplasmic genome types and to trace maternal ancestors. The potato cytoplasmic genome can be distinguished into six distinct types (M, P, A, W, T, and D). Male sterility was found in genotypes with S. demissum-derived D-type cytoplasm and S. stoloniferum-derived W/γ-type cytoplasm. These wild species were frequently used to incorporate superior pathogen resistance genes. As a result, the percentage of these two types is increasing unintentionally in the European germplasm pool. Other than cytoplasmic male sterility, little is known about effects of the cytoplasmic genome on complex agronomic traits in potato.ResultThe cytoplasm types of 1,217 European potato cultivars and breeding clones were determined with type specific DNA markers. Most frequent were T- (59.4 %), D- (27.4 %), and W- (12.2 %) type cytoplasm, while A- (0.7 %) and M-type cytoplasm (0.3 %) was rare and P-type cytoplasm was absent. When comparing varieties with breeding clones, the former showed a relatively higher frequency of T-type and lower frequency of D- and W-type cytoplasm. Correlation analysis of cytoplasm types and agronomic data showed that W/γ-type cytoplasm was correlated with increased tuber starch content and later plant maturity. Correlation with quantitative resistance to late blight was observed for D-type and M-type cytoplasm. Both cytoplasm types had a positive effect on resistance.ConclusionThis study revealed and quantified the cytoplasmic diversity in the European potato germplasm pool. Knowledge of cytoplasm type is important for maintaining genetic diversity and managing the male sterility problem in breeding programs. This is the first comprehensive study to show correlations of distinct cytoplasmic genomes with complex agronomic traits in potato. Correlations particularly with tuber starch content and resistance to late blight provided new knowledge on cytoplasmic effects on these important traits, which can be exploited for genetic improvement of potato.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0545-y) contains supplementary material, which is available to authorized users.

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“…T/β is the most extended cytoplasm type in potato cultivars all over the world except in German cultivars, due to the fact that S. demissum and S. stoloniferum were broadly used in German breeding programs for their resistance to late blight and potato virus Y, respectively. Knowledge of the cytoplasm types is necessary to prevent the cytoplasmic invasion of male sterile types, which severely limits the selection of male parents in breeding programs (Hosaka and Sanetomo, 2012;Mihovilovich et al, 2015;Anisimova and Gabrilenko, 2017). Sanetomo and Gebhardt (2015) estimated the correlation of cytoplasmic genomes with complex agronomic traits using 1,217 cultivars and breeding clones of 6 different populations.…”

Section: Potatomentioning

confidence: 99%

Test of Interaction in the Analysis of Molecular Variance

Bruno

Videla

Balzarini

2019

BAG

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The genomic diversity, expressed in the differences between molecular haplotypes of a group of individuals, can be divided into components of variability between and within some factor of classification of the individuals. For such variance partitioning, molecular analysis of variance (AMOVA) is used, which is constructed from the multivariate distances between pairs of haplotypes. The classical AMOVA allows the evaluation of the statistical significance of two or more hierarchical factors and consequently there is no interaction test between factors. However, there are situations where the factors that classify individuals are crossed rather than nested, that is, all the levels of a factor are represented in each level of the other one. This paper proposes a statistical test to evaluate the interaction between crossed factors in a Non-Hierarchical AMOVA. The null hypothesis of interaction establishes that the molecular differences between individuals of different levels of a factor are the same for all the levels of the other factor that classifies them. The proposed analysis of interaction in a Non-Hierarchical AMOVA includes: calculation of the distance matrix and partition of it into blocks, subsequent calculation of residuals and analysis of non-parametric variance on the residuals. Its implementation is illustrated in simulated and real scenarios. The results suggest that the proposed interaction test for the Non-Hierarchical AMOVA presents high power. Key words: genetic variability, non-parametric methods, distances matrix, AMOVA.

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Cytoplasmic diversity in potato breeding: case study from the International Potato Center

Cited by 27 publications

References 34 publications

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

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

Cytoplasmic genome types of European potatoes and their effects on complex agronomic traits

Test of Interaction in the Analysis of Molecular Variance

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