Genetic diversity, population structure, and clonal verification in South African avocado cultivars using single nucleotide polymorphism (SNP) markers

Wienk, Raven; Mostert‐O’Neill, Marja M.; Abeysekara, Nilwala S.; Manosalva, Patricia; Freeman, Barbie; Berg, Noëlani van den

doi:10.1007/s11295-022-01573-8

Cited by 4 publications

(3 citation statements)

References 47 publications

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“…This suggests that different analysis methods can yield distinct results. This phenomenon has been observed in other species as well (Wienk et al, 2022;Osundare et al, 2023), possibly attributed to either lower levels of population differentiation or the presence of complex genetic structures. In addition, the Mantel analysis results indicated a moderate correlation between the molecular matrix and the geographic matrix, with a Mantel test value of only 0.09 in this study.…”

Section: Genetic Relationship Analysis Of Three Populationmentioning

confidence: 54%

“…A dataset consisting of 12,745 SNPs was employed for analysis. In comparison to recent studies on other tree species, such as avocado (384 SNPs) (Wienk et al, 2022) and palm (1038 SNPs) (Jara-Arancio et al, 2022), a larger number of filtered SNPs was used in this study, despite their original datasets containing millions or even billions of SNP loci. Thus, differences in analysis results between populations can be attributed to different filtering parameters applied to SNPs.…”

Section: Genetic Relationship Analysis Of Three Populationmentioning

confidence: 99%

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Population structure and genetic diversity in Eucalyptus pellita based on SNP markers

Wang,

Lan,

Wang

et al. 2023

Front. Plant Sci.

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Eucalyptus pellita has the characteristics of rapid growth and high resistance. However, there is little research on molecular breeding of E. pellita, which is essential to shortening breeding life and selecting quality varieties. Therefore, a crucial step before selective breeding can be carried out to increase the wood quality of E. pellita is identifying genetic diversity and population structure using single nucleotide polymorphism (SNP) markers. In this study, the genetic diversity of 1st generation 196 E. pellita families from 23 geographically defined was assessed using 1,677,732 SNP markers identified by whole genome resequencing. SNP annotation showed that the ratio of non-synonymous to synonymous coding mutations was 0.83. Principal component analysis (PCA), phylogenetic tree, and population structure analysis permitted the families to be categorized into three groups, one of which (G2) contains most of the Indonesian (IDN) and Papua New Guinea (PNG) families. Genetic relationship analysis showed that IDN was closely related to PNG. Genetic diversity analysis showed that He, PIC, I, and H mean values were 0.2502, 0.2027, 0.3815, and 0.2680, respectively. PCA analysis classified various provenances in QLD into two categories (G1 and G3). The genetic diversity of G3 was higher than that of G2. The results of genetic differentiation (Fst) showed that PNG region was divided into two groups (PNG1 and PNG2), the Fst (0.172) between QLD and PNG2 region was higher than QLD and PNG1, and the Fst (0.024) between IDN and PNG1 is smaller than IDN and PNG2. A Mantel test revealed a positive correlation between the genetic and geographic distance of E. pellita. This study has a certain reference value for genetic identification, germplasm preservation, and breeding of E. pellita. Also, it provides a basis for subsequent association analysis to explore excellent alleles and introduction.

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Section: Genetic Relationship Analysis Of Three Populationmentioning

confidence: 54%

Section: Genetic Relationship Analysis Of Three Populationmentioning

confidence: 99%

Population structure and genetic diversity in Eucalyptus pellita based on SNP markers

Wang,

Lan,

Wang

et al. 2023

Front. Plant Sci.

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“…Some studies have utilized 72 SNP markers that have been constructed in the Siberian apricot transcriptome to genotype 70 wild Siberian apricots, and the genetic diversity of the Siberian apricot was statistically analyzed. Seventy-two SNPs were successfully validated and genetically analyzed in the population, but no signi cant chain inequality was found; and these results can help to provide a theoretical basis for the management of germplasm resources [15] . In summary, molecular marker technology can provide a better understanding of the genetic basis of species and provide theoretical support for the development of breeding strategies.…”

Section: Introductionmentioning

confidence: 97%

Studying the evolution of Xinjiang local pear populations using SNP markers

Bi,

Cui,

Fan

et al. 2023

Preprint

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Background To elucidate the genetic basis of local pear varieties in Xinjiang, China, this study was conducted to scan the whole genome of 28 local pear varieties in Xinjiang using single nucleotide polymorphism (SNP) molecular marker technology and analyze their genetic diversity and population structure. Result The pure SNP polymorphic loci obtained through screening were 2,045,692, which basically covered the pear genome. The genetic similarity coefficients between the varieties ranged from 0.3086 to 0.9977; when K = 4, the 28 varieties were divided into four groups, and there was general gene exchange between the populations. The cluster analysis results showed that the 28 varieties were classified into 4 taxa. The PCA results also divided the test material into 4 groups, which deviated from the evolutionary tree. The largest number of populations was found in pears between 2 and 10 million years ago, during which the reproductive development of pears developed rapidly. Conclusions The study showed that SNPs obtained polymorphism information among different pear varieties at the genome-wide level, which can be used for genetic diversity analysis between varieties and provide a reference for future molecular enhancement of pear breeding and systematic conservation of plant genetic resources.

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Pleistocene-dated genomic divergence of avocado trees supports cryptic diversity in the Colombian germplasm

Berdugo-Cely,

Cortés,

López-Hernández

et al. 2023

Tree Genetics & Genomes

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Genomic characterization of ex situ plant collections optimizes the utilization of genetic resources by identifying redundancies among accessions, capturing cryptic variation, establishing reference collections, and ultimately assisting pre-breeding and breeding efforts. Yet, the integration of evolutionary genomic analyses is often lacking when studying the biodiversity of crop gene pools. Such is the case in the avocado, Persea americana Mill., an iconic American fruit tree crop that has seen an unprecedented expansion worldwide because of its nutritional properties. However, given a very restricted number of commercial clones, avocado plantations are becoming more vulnerable to diseases and climate change. Therefore, exploring new sources of evolutionary novelty and genetic diversity beyond the commercial varieties derived from traditional genetic pools in Mexico and Central America is imperative. To fill this gap, we aimed to characterize the genomic diversity of Colombian avocado trees. Specifically, we constructed reduced representation genomic libraries to genotype by sequencing 144 accessions from the Colombian National genebank and 240 materials from local commercial orchards in the Colombian northwest Andes. We merged the resulting reads with available sequences of reference genotypes from known avocado groups (also named as races), Mexican, Guatemalan, and West Indian, to discover 4931 SNPs. We then analyzed the population structure and phylogenetic diversity, and reconstructed evolutionary scenarios, possibly leading to new genetic groups in Colombian germplasm. We detected demographic stratification despite evidence of intergroup gene flow. Besides the classical three avocado groups, we found an exclusive Colombian group with a possible genetic substructure related to the geographical origin (Andean and Caribbean). Phylogenetic and ABC demographic modeling suggested that the Colombian group evolved in the Pleistocene before human agriculture started, and its closest relative from the three recognized races would be the West Indian group. We conclude that northwest South America offers a cryptic source of allelic novelty capable of boosting avocado pre-breeding strategies to select rootstock candidates well adapted to specific eco-geographical regions in Colombia and abroad.

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Genetic diversity, population structure, and clonal verification in South African avocado cultivars using single nucleotide polymorphism (SNP) markers

Cited by 4 publications

References 47 publications

Population structure and genetic diversity in Eucalyptus pellita based on SNP markers

Population structure and genetic diversity in Eucalyptus pellita based on SNP markers

Studying the evolution of Xinjiang local pear populations using SNP markers

Pleistocene-dated genomic divergence of avocado trees supports cryptic diversity in the Colombian germplasm

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