Application of High-Throughput Sequencing to Evaluate the Genetic Diversity Among Wild Apple Species Indigenous to Shandong, China, and Introduced Cultivars

Chang, Yuansheng; He, Ping; Wang, Haibo; Li, Huifeng; Wang, Sen; Li, Linguang

doi:10.1007/s11105-019-01138-5

Cited by 3 publications

(3 citation statements)

References 57 publications

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“…SNPs are found throughout the genome, and their distribution can reflect the population's genetic variation. SLAF-seq has been used to analyze several species' genetic diversity and phylogenetic structure (Li et al, 2017;Chang et al, 2019;Qin et al, 2019;Zhang J. et al, 2020a;Fang et al, 2020;Ababaikeri et al, 2021). In addition, mtDNA provides a different perspective of population genetic structure because it is maternally inherited and generally lacks intermolecular recombination (Allendorf, 2017).…”

Section: Introductionmentioning

confidence: 99%

Population genetics analysis of Tolai hares (Lepus tolai) in Xinjiang, China using genome-wide SNPs from SLAF-seq and mitochondrial markers

et al. 2023

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The main topic of population genetics and evolutionary biology is the influence of the ecological environment, geographical isolation, and climatic factors on population structure and history. Here, we estimated the genetic diversity, genetic structure, and population history of two subspecies of Tolai hares (Lepus tolai Pallas, 1778), L. t. lehmanni inhabiting Northern and Northwest Xinjiang and L. t. centrasiaticus inhabiting Central and Eastern Xinjiang using SNP of specific-length amplified fragment sequencing (SLAF-seq) and four mitochondrial DNA (mtDNA). Our results showed a relatively high degree of genetic diversity for Tolai hares, and the diversity of L. t. lehmanni was slightly higher than that of L. t. centrasiaticus, likely due to the more favorable ecological environment, such as woodlands and plains. Phylogenetic analysis from SNP and mtDNA indicated a rough phylogeographical distribution pattern among Tolai hares. Strong differentiation was found between the two subspecies and the two geographical groups in L. t. centrasiaticus, possibly due to the geographical isolation of mountains, basins, and deserts. However, gene flow was also detected between the two subspecies, which might be attributed to the Tianshan Corridor and the strong migration ability of hares. Tolai hare population differentiation occurred at approximately 1.2377 MYA. Population history analysis based on SNP and mtDNA showed that the Tolai hare population has a complex history and L. t. lehmanni was less affected by the glacial event, possibly because its geographic location and terrain conditions weaken the drastic climate fluctuations. In conclusion, our results indicated that the joint effect of ecological environment, geographic events, and climatic factors might play important roles in the evolutionary process of L. t. lehmanni and L. t. centrasiaticus, thus resulting in differentiation, gene exchange, and different population history.

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Section: Introductionmentioning

confidence: 99%

Population genetics analysis of Tolai hares (Lepus tolai) in Xinjiang, China using genome-wide SNPs from SLAF-seq and mitochondrial markers

et al. 2023

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“…Although previous studies have examined the genetic diversity of Malus in Europe [71][72][73] and central Asia 74,75 , with several reports on cultivar 76,77 , studies on Malus in the Korean Peninsula are limited. In this study, we evaluated the genetic diversity and structure of Malus species in the East Asia, using a GBS-based analysis.…”

Section: Discussionmentioning

confidence: 99%

Genetic structure and geneflow of Malus across the Korean Peninsula using genotyping-by-sequencing

Gil

Kim

et al. 2022

Sci Rep

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This study was to understand the genetic structure and diversity of the Korean Malus species. We used genotyping-by-sequencing (GBS) technology to analyze samples of 112 individuals belonging to 18 populations of wild Malus spp. Using GBS, we identified thousands of single nucleotide polymorphisms in the species analyzed. M. baccata and M. toringo, two dominant mainland species of the Korean Peninsula, were distinguishable based on their genetic structure. However, M. toringo collected from Jeju Island exhibited a different genetic profile than that from the mainland. We identified M. cf. micromalus as a hybrid resulting from the Jeju Island M. toringo (pollen donor) and the mainland M. baccata, (pollen recipient). Putative M. mandshurica distributed on the Korean Peninsula showed a high structural and genetic similarity with M. baccata, indicating that it might be an ecotype. Overall, this study contributes to the understanding of the population history and genetic structure of Malus in the Korean Peninsula.

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“…Specific-locus amplified fragment sequencing (SLAF-seq) technology was an efficient method, which was developed by Beijing Biomarker Technologies Corporation ( Sun et al., 2013 ). To date, SLAF-seq has been used successfully to dissect accurately the genetic diversity and population structure for many crops ( Shen et al., 2017 ; Zeng et al., 2017 ; Chang et al., 2019 ). The results of such techniques were further used in plant breeding ( Jones et al., 2013 ; Boeven et al., 2016 ; Wu et al., 2016 ; Zhang et al., 2018 ; Bruce et al., 2019 ; Cui et al., 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Population structure and genetic diversity of mango (Mangifera indica L.) germplasm resources as revealed by single-nucleotide polymorphism markers

Liang,

Pan,

et al. 2024

Front. Plant Sci.

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IntroductionMango is a vital horticultural fruit crop, and breeding is an essential strategy to enhance ongoing sustainability. Knowledge regarding population structure and genetic diversity in mango germplasm is essential for crop improvement.MethodsA set of 284 mango accessions from different regions of the world were subjected to high-throughput sequencing and specific-locus amplified fragment (SLAF) library construction to generate genomic single-nucleotide polymorphism (SNP).ResultsAfter filtering, raw data containing 539.61 M reads were obtained. A total of 505,300 SLAFs were detected, of which, 205,299 were polymorphic. Finally, 29,136 SNPs were employed to dissect the population structure, genetic relationships, and genetic diversity. The 284 mango accessions were divided into two major groups: one group consisted mainly of mango accessions from Australia, the United States, Cuba, India, Caribbean, Israel, Pakistan, Guinea, Burma, China, and Sri Lanka, which belonged to the Indian type (P1); the other group contained mango accessions from the Philippines, Thailand, Indonesia, Vietnam, Cambodia, Malaysia, and Singapore, which belonged to Southeast Asian type (P2). Genetic diversity, principal component analysis (PCA), and population structure analyses revealed distinct accession clusters. Current results indicated that the proposed hybridization occurred widely between P1 and P2.DiscussionMost of the accessions (80.99%) were of mixed ancestry, perhaps including multiple hybridization events and regional selection, which merits further investigation.

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Application of High-Throughput Sequencing to Evaluate the Genetic Diversity Among Wild Apple Species Indigenous to Shandong, China, and Introduced Cultivars

Cited by 3 publications

References 57 publications

Population genetics analysis of Tolai hares (Lepus tolai) in Xinjiang, China using genome-wide SNPs from SLAF-seq and mitochondrial markers

Population genetics analysis of Tolai hares (Lepus tolai) in Xinjiang, China using genome-wide SNPs from SLAF-seq and mitochondrial markers

Genetic structure and geneflow of Malus across the Korean Peninsula using genotyping-by-sequencing

Population structure and genetic diversity of mango (Mangifera indica L.) germplasm resources as revealed by single-nucleotide polymorphism markers

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