Microsatellite null alleles affected population genetic analyses: a case study of Maire yew (<i>Taxus chinensis var. mairei</i>)

Wu, Xingtong; Wang, Libao; Zhang, Donglin; Yi, Wen

doi:10.1080/13416979.2019.1634230

Cited by 4 publications

(5 citation statements)

References 33 publications

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“…However, due to the large differences in the populations' sources and sizes, previous genetic diversity studies vary significantly. Additionally, the shortcomings of SSR markers, including the unclarity of homozygosity and heterozygosity and invalid alleles, can lead to misidentification of SSR genotypes [6].…”

Section: Introductionmentioning

confidence: 99%

Employing Genome-Wide SNP Discovery to Characterize the Genetic Diversity in Cinnamomum camphora Using Genotyping by Sequencing

Gong

Yang

et al. 2021

Forests

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Cinnamomum camphora (L.) J.Presl is a representative tree species of evergreen broad-leafed forests in East Asia and has exceptionally high economic, ornamental, and ecological value. However, the excessive exploitation and utilization of C. camphora trees have resulted in the shrinking of wild population sizes and rare germplasm resources. In this study, we characterized 171 C. camphora trees from 39 natural populations distributed throughout the whole of China and one Japanese population. We investigated genetic diversity and population structure using genome-wide single-nucleotide polymorphism (SNP) identified by genotyping by sequencing (GBS) technology. The results showed the genetic diversity of the C. camphora populations from western China > central China > eastern China. Moreover, the Japanese population showed the highest diversity among all populations. The molecular variance analysis showed 92.03% of the genetic variation within populations. The average pairwise FST was 0.099, and gene flow Nm was 2.718, suggesting a low genetic differentiation among populations. Based on the genetic clustering analysis, the 40 C. camphora populations clustered into three major groups: Western China, Central China, and Eastern China + Japan. Eastern China’s population had the closest genetic relationship with the Japanese population, suggesting possible gene exchange between the two adjacent areas. This study furthers our understanding of the genetic diversity and genetic structure of C. camphora in East Asia and provides genetic tools for developing strategies of C. camphora germplasm utilization.

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Section: Introductionmentioning

confidence: 99%

Employing Genome-Wide SNP Discovery to Characterize the Genetic Diversity in Cinnamomum camphora Using Genotyping by Sequencing

Gong

Yang

et al. 2021

Forests

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“…This means that the genotyping of the samples may appear homozygous rather than heterozygous for the null allele. Certainly, underestimation of the heterozygosity parameter, such as Wright’s inbreeding estimates, can arise [ 68 , 69 , 70 ]. For instance, the estimated F is of the oriental fruit moth populations derived from 10 SSR with high NAF was reported to be two to three times higher than the estimation derived from another set of 10 SSR with low NAF [ 71 ].…”

Section: Discussionmentioning

confidence: 99%

“…The presence of null alleles predicates the need to redesign the primers [ 70 ], but that was not feasible in this study. The length of the flanking region of RAD tag-SSR was extremely limited.…”

Section: Discussionmentioning

confidence: 99%

Development of Nuclear DNA Markers for Applications in Genetic Diversity Study of Oil Palm-Pollinating Weevil Populations

Rodzik

Sudirman

Teh³

et al. 2023

Insects

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The oil palm-pollinating weevil (Elaeidobius kamerunicus Faust) was introduced from Cameroon, West Africa, to Malaysia in 1981, and subsequently, to other oil palm-growing countries as well. This study aims to develop a set of robust E. kamerunicus-specific nuclear DNA markers to directly assess the genetic diversity of the weevil populations. A total of 19,148 SNP and 223,200 SSR were discovered from 48 weevils representing three origins (Peninsular Malaysia, Sabah, and Riau) using RAD tag sequencing. Subsequent filtering steps further reduced these to 1000 SNP and 120 SSR. The selected 220 SNP exhibited a polymorphism information content (PIC) of 0.2387 (±0.1280), and 8 SSR had the PIC of 0.5084 (±0.1928). These markers were found to show sufficient polymorphism, making it possible to assign 180 weevils into three major clusters from Ghana, Cameroon, and Southeast Asia (mainly in Malaysia and Indonesia). These DNA markers successfully confirmed the Cameroon origin of the Southeast Asian cluster. However, the presence of null alleles in the SSR markers, due to limited flexibility of the probe design on the short RAD tags, led to an underestimation of heterozygosity within the populations. Hence, the developed SNP markers turned out to be more efficient than the SSR markers in the genetic diversity assessment of the E. kamerunicus populations. The genetic information provides useful insight into developing guidelines for the genetic monitoring and conservation planning of E. kamerunicus.

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“…Many of the markers included in this study have already proved to be prone to NA flaws but, to date, there is no consensus about the appropriate limit of NA to be allowed across loci and geographical samples [73][74][75]. Furthermore, the results obtained with POWSIM confirmed the high-resolution power of the dataset built on both 20 and 14 microsatellite loci when an F ST = 0.005 or higher was considered, leading to the conclusion that no informative loci were excluded from the dataset when using the restricted dataset (14 microsatellite loci) in the analyses of genetic differentiation.…”

Section: Discussionmentioning

confidence: 99%

Matching an Old Marine Paradigm: Limitless Connectivity in a Deep-Water Fish over a Large Distance

Ferrari,

Spiga,

Rodriguez

et al. 2023

Animals

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Investigations of population structuring in wild species are fundamental to complete the bigger picture defining their ecological and biological roles in the marine realm, to estimate their recovery capacity triggered by human disturbance and implement more efficient management strategies for fishery resources. The Blackspot Seabream (Pagellus bogaraveo, Brünnich 1768) is a commercially valuable deep-water fish highly exploited over past decades. Considering its exploitation status, deepening the knowledge of intraspecific variability, genetic diversity, and differentiation using high-performing molecular markers is considered an important step for a more effective stock assessment and fishery management. With one of the largest efforts conceived of and completed by countries overlooking the Atlantic and Mediterranean coasts in recent years, a total of 320 individuals were collected from different fishing grounds in the Mediterranean Sea and Atlantic Ocean and analysed using 29 microsatellite loci. We applied multiple statistical approaches to investigate the species’ connectivity and population structure across most of its described distribution area. Considering the incomplete knowledge regarding the migratory behaviour of adults, here we suggest the importance of egg and larval dispersal in sustaining the observed genetic connectivity on such a large geographical scale.

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Microsatellite null alleles affected population genetic analyses: a case study of Maire yew (Taxus chinensis var. mairei)

Cited by 4 publications

References 33 publications

Employing Genome-Wide SNP Discovery to Characterize the Genetic Diversity in Cinnamomum camphora Using Genotyping by Sequencing

Employing Genome-Wide SNP Discovery to Characterize the Genetic Diversity in Cinnamomum camphora Using Genotyping by Sequencing

Development of Nuclear DNA Markers for Applications in Genetic Diversity Study of Oil Palm-Pollinating Weevil Populations

Matching an Old Marine Paradigm: Limitless Connectivity in a Deep-Water Fish over a Large Distance

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