Dataset Information

Genetic Diversity in Diospyros Germplasm in the Western Caucasus Based on SSR and ISSR Polymorphism.

ABSTRACT: Persimmon germplasm in the Western Caucasus represent one of the most northerly collections. In our study, 51 commercial cultivars of D. kaki, 3 accessions of D. virginiana and 57 D. lotus accessions from six geographically distant populations were investigated using 19 microsatellite and 10 inter simple sequence repeat (ISSR) markers. After STRUCTURE analysis, the single accessions of Diospyros were allocated to three genetic clusters. Genetic admixtures in the important genotypes of D. kaki were revealed, whereas D. lotus accessions showed no admixture with other genetic clusters. The correspondence of genetic data and phenotypical traits was estimated in the D. kaki collection. The most frost tolerant genotypes of the collection, such as "Mountain Rogers", "Nikitskaya Bordovaya", "Rossiyanka", "MVG Omarova", "Meader", "Costata", "BBG", and "Jiro", showed a high percentage of genetic admixtures and were grouped close to D. virginiana. Some of these genotypes are known to be interspecific hybrids with D. virginiana. A low level of genetic diversity between the distant D. lotus populations was revealed and it can be speculated that D. lotus was introduced to the Western Caucasus from a single germplasm source. These results are an important basis for the implementation of conservation measures, developing breeding strategies, and improving breeding efficiency.

SUBMITTER: Samarina LS

PROVIDER: S-EPMC8073590 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature

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Genetic Diversity in Diospyros Germplasm in the Western Caucasus Based on SSR and ISSR Polymorphism.

Samarina Lidia S LS Malyarovskaya Valentina I VI Reim Stefanie S Koninskaya Natalia G NG Matskiv Alexandra O AO Tsaturyan Gregory A GA Rakhmangulov Ruslan S RS Shkhalakhova Ruset M RM Shurkina Ekaterina S ES Kulyan Raisa V RV Omarova Zuhra M ZM Omarov Magomed D MD Ryndin Alexey V AV

Biology 20210419 4

Persimmon germplasm in the Western Caucasus represent one of the most northerly collections. In our study, 51 commercial cultivars of D. kaki, 3 accessions of D. virginiana and 57 D. lotus accessions from six geographically distant populations were investigated using 19 microsatellite and 10 inter simple sequence repeat (ISSR) markers. After STRUCTURE analysis, the single accessions of Diospyros were allocated to three genetic clusters. Genetic admixtures in the impor ...[more]

PMID: 33921840

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Project description:BackgroundArctium lappa L. is a medicinal edible homologous plant, commonly known as burdock or bardana, which belongs to the Asteraceae family and is abundant all over the world. Genetic diversity assessment is essential for A. lappa germplasm resource conservation and breeding. The assessment techniques include morphological, biochemical, and DNA marker analysis. However, the limited number of available DNA markers is insufficient to conduct related genetic diversity assessment studies.ResultsIn this study, we conducted RNA sequencing of the A. lappa cultivar 'Yanagikawa Ideal' and developed SSR markers to characterize the genetic diversity and population structure of 56 A. lappa accessions and 8 wild relative accessions. A total of 4,851 simple sequence repeats (SSRs) loci were identified. The proportions of mono-, di- and tri-nucleotide repeat motifs were 30.40%, 21.50% and 33.10%, respectively. We developed and verified the reliability of 28 SSR core primer pairs through electronic polymerase chain reaction (ePCR) and the PCR amplification process. The polymorphism information content (PIC) values of the 28 SSR core primer pairs ranged from 0.246 to 0.848, with 14 pairs of SSR primers displaying high polymorphism (PIC > 0.5). The 28 SSR core primer pairs showed 100% mobility in Arctium tomentosum Miller and 96.43% mobility in Synurus deltoides (Aiton) Nakai, indicating their high versatility. The average Shannon information index (I) was 1.231, and the average observed heterozygosity (Ho) was 0.132, the average expected heterozygosity (He) was 0.564. The 64 accessions were divided into three clusters at a genetic distance of 0.558. AMOVA analysis shows 83% genetic variation within populations and 17% among populations, highlighting implications for conservation and breeding strategies.ConclusionOur study provides 28 newly high-quality SSR markers to enhance genetic resource conservation and breeding programs for A. lappa, as well as to support comparative genomics and cross-species breeding strategies for related species.

Dataset Information

Genetic Diversity in Diospyros Germplasm in the Western Caucasus Based on SSR and ISSR Polymorphism.

Publications

Genetic Diversity in Diospyros Germplasm in the Western Caucasus Based on SSR and ISSR Polymorphism.

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