Genetic Diversity and Differentiation of Northern Populations of Pedunculate Oak Based on Analysis of New SNP Markers

Деген, Бернд; Yanbaev, Yulai; Ianbaev, Ruslan; Bakhtina, Svetlana; Gabitova, A.A.; Tagirova, Albina

doi:10.1134/s1022795421030054

Cited by 5 publications

(1 citation statement)

References 20 publications

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“…SLAF-seq has the advantages of high throughput, high accuracy, short cycle time and low cost [4]. This technique has been widely used in genetic diversity analysis [5], high-density genetic map construction [6], and germplasm resources identification [7]. At present, it has been widely used to develop high-density molecular labels in plants that include tea plant [8,9], rice [10,11], maize [12,13], barley [14,15], bean [16,17], rape [18,19], peanut [20,21], potato [22], soybean [23,24] and other plants.…”

Section: Introductionmentioning

confidence: 99%

Population Structure Analysis and Genome-Wide Association Study of Tea (Camellia sinensis (L.) Kuntze) Germplasm in Qiannan, China, Based on SLAF-Seq Technology

Zhang¹,

Tian²,

Cen³

et al. 2022

Phyton

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Duyun Maojian tea is a famous tea in China. In this study, the specific-locus amplified fragment (SLAF) sequencing method was used to analyze the population structure and conduct a genome-wide association study (GWAS) of 2 leaf traits of 123 tea plants in Qiannan, China. A total of 462,019 SLAF tags and 11,362,041 single-nucleotide polymorphism (SNP) loci were obtained. The results of phylogenetic tree analysis, cluster analysis, and principal component analysis showed that 123 tea germplasms were clustered into three groups, and the heterozygosity rates for Groups I, II, and II were 0.206, 0.224, and 0.34, respectively. Generally, tea germplasms in a production area are clustered in a group, indicating that tea germplasms in different production areas have certain genetic diversity. The traditional Duyun Maojian tea core production areas, TS and DC-SJ, are clustered into Group I and Group II respectively, while the ZY production area is relatively independent in Group III. Furthermore, based on GWAS analysis, 11 candidate genes related to leaf apex and 7 candidate genes related to leaf shape were obtained. This study clarified the genetic relationship among eight Duyun Maojian tea production areas and obtained candidate genes related to leaf apex and leaf shape development. The results showed that population structure and candidate genes are an effective basis for the breeding of Duyun Maojian tea germplasm.

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Section: Introductionmentioning

confidence: 99%

Population Structure Analysis and Genome-Wide Association Study of Tea (Camellia sinensis (L.) Kuntze) Germplasm in Qiannan, China, Based on SLAF-Seq Technology

Zhang¹,

Tian²,

Cen³

et al. 2022

Phyton

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When does habitat fragmentation lead to changes in populations gene pool of pedunculate oak (Quercus robur L.)?

Деген

Yanbaev

Ianbaev

et al. 2021

Forest Ecology and Management

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Genetic diversity and population structure of pedunculate oaks (Quercus robur) in Wytham Woods

Hung,

Formaggia,

Morley

et al. 2024

Preprint

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Genetic diversity is fundamental for adaptation to changing environments. It is particularly important in forest trees because of their significant role in nature's contribution to people. However, their genetic diversity has been significantly changed by human activities in the past centuries. This paper investigates a focal site, the Wytham Woods, one of the most researched woodlands on Earth, and presents a population genetic study on pedunculate oaks (Quercus robur), a keystone species in the ecosystem. We characterised 210 trees with Genotyping by Sequencing (GbS) and quantified levels of genetic diversity across stands with different histories and management regimes. We detected only a weak population structure within the 218,567 SNPs, such that most genetic variation occurred within but not among stands, which included semi-natural woodland areas and plantations aged between 200 to 50 years ago. We also observed little difference in observed and expected heterozygosity among stand types, but detected some inbreeding in the youngest plantation. We discovered 26,174 SNPs (11.98%) that were highly differentiated and under potential selection. We suggest that the life history traits of oak contribute to their resistance against genetic erosion, which is also observed in beeches, spruces, and pines. Preference for oaks as a timber tree and the tendency to use local seed source might have resulted in the homogeneous population structure. However, tree-to-tree differences may harbour variation in putative adaptive loci. Our study contributes crucial baseline information on for conservation and management of human-modified woodlands, in addition to supporting long-term ecological studies on many other species, which depend on this keystone oak species.

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Genetic Diversity and Differentiation of Northern Populations of Pedunculate Oak Based on Analysis of New SNP Markers

Cited by 5 publications

References 20 publications

Population Structure Analysis and Genome-Wide Association Study of Tea (Camellia sinensis (L.) Kuntze) Germplasm in Qiannan, China, Based on SLAF-Seq Technology

Population Structure Analysis and Genome-Wide Association Study of Tea (Camellia sinensis (L.) Kuntze) Germplasm in Qiannan, China, Based on SLAF-Seq Technology

When does habitat fragmentation lead to changes in populations gene pool of pedunculate oak (Quercus robur L.)?

Genetic diversity and population structure of pedunculate oaks (Quercus robur) in Wytham Woods

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