Evolutionary analysis of six chloroplast genomes from three Persea americana ecological races: Insights into sequence divergences and phylogenetic relationships

Ge, Yu; Dong, Xiangshu; Wu, Bin; Wang, Nan; Chen, Di; Chen, Haihong; Zou, Minghong; Xu, Zining; Tan, Lin; Zhan, Rulin

doi:10.1371/journal.pone.0221827

Cited by 19 publications

(19 citation statements)

References 59 publications

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“…), which is a member of the family Lauraceae of the order Laurales, is one of the most economically important subtropical/tropical fruit crops worldwide [1][2][3]. Avocado is a highly diverse species with local variations that have resulted in various ecological races [4]. Additionally, it is native to Meso-America, but the 'subtropical' ecotypes (Guatemalan and Mexican) are currently widely grown in countries and regions with warm-to-cool subtropical and Mediterranean climates.…”

Section: Introductionmentioning

confidence: 99%

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Molecular Markers and a Quality Trait Evaluation for Assessing the Genetic Diversity of Avocado Landraces from China

Liu

Zhan

et al. 2020

Agriculture

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Avocado is an economically important crop that is widely cultivated in the tropical and subtropical regions of China. However, there is a lack of sufficient information regarding the racial origins and genetic diversification of native avocado germplasm. On the basis of a race-specific kompetitive allele-specific PCR genotyping analysis, the 56 avocado accessions examined in this study were classified as complex hybrids, namely Guatemalan × Mexican × West Indian hybrids. The genetic relationships among the avocado accessions were assessed based on a quality trait evaluation and molecular characterization. The total flavonoid content was relatively useful for differentiating between native avocado accessions. A cluster analysis as well as principal component and coordinate analyses of quality traits and molecular characteristics differentiated the avocado accessions, but not according to geographical origins. Thus, the artificial flow of avocado germplasm or seed exchanges among farmers within specific regions may have contributed to the similar genetic backgrounds of avocado germplasm from different collections.

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Section: Introductionmentioning

confidence: 99%

“…Number of observed alleles, 2 effective number of alleles,3 observed heterozygosity,4 expected heterozygosity, and5 Shannon's information index.…”

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confidence: 99%

Molecular Markers and a Quality Trait Evaluation for Assessing the Genetic Diversity of Avocado Landraces from China

Liu

Zhan

et al. 2020

Agriculture

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“…With the increased application of high-throughput sequencing technology, the number of characterized chloroplast genomes of angiosperms is increasing rapidly 55 . In this study, we found that the two newly sequenced Gleditsia species have similar quadripartite structure and gene contents to the published chloroplast genomes of other members of the Caesalpinioideae sub-family 15 , 56 – 58 .…”

Section: Discussionmentioning

confidence: 99%

“…Compared to traditional methods, DNA barcoding can be applied to accurately identify G. sinensi s and its adulterant, G. japonica . DNA barcodes refer to relatively short fragments of DNA with substantial genetic variation, which can be standardized, easily amplified, and representative 55 . DNA degradation frequently occurs during the production of natural medicine, which can decrease the efficiency of PCR 29 .…”

Section: Discussionmentioning

confidence: 99%

The complete chloroplast genome of Gleditsia sinensis and Gleditsia japonica: genome organization, comparative analysis, and development of taxon specific DNA mini-barcodes

Tan

Gao

Jiang

et al. 2020

Sci Rep

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Chloroplast genomes have been widely considered an informative and valuable resource for molecular marker development and phylogenetic reconstruction in plant species. This study evaluated the complete chloroplast genomes of the traditional Chinese medicine Gleditsia sinensis and G. japonica, an adulterant of the former. The complete chloroplast genomes of G. sinensis and G. japonica were found to be of sizes 163,175 bp and 162,391 bp, respectively. A total of 111 genes were identified in each chloroplast genome, including 77 coding sequences, 30 tRNA, and 4 rRNA genes. Comparative analysis demonstrated that the chloroplast genomes of these two species were highly conserved in genome size, GC contents, and gene organization. Additionally, nucleotide diversity analysis of the two chloroplast genomes revealed that the two short regions of ycf1b were highly diverse, and could be treated as mini-barcode candidate regions. The mini-barcode of primers ZJ818F-1038R was proven to precisely discriminate between these two species and reflect their biomass ratio accurately. Overall, the findings of our study will shed light on the genetic evolution and guide species identification of G. sinensis and G. japonica.

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“…Previous genetic characterizations providing tangential signals of horticultural races have used targeted genes (Chen et al, 2009), cpDNA (Ge et al, 2019), SSR (Alcaraz and Hormaza, 2007;Ferrer-Pereira et al, 2017;Boza et al, 2018;Sánchez-González et al, 2020) and SNP markers (Kuhn et al, 2019c;Rubinstein et al, 2019;Talavera et al, 2019), in some cases using gene-bank accessions, like from the Venezuelan germplasm bank (INIA-CENIAP) (Ferrer-Pereira et al, 2017), the National Germplasm Repository (SHRS ARS USDA) in Miami (Kuhn et al, 2019a;Kuhn et al, 2019b), and the Spanish germplasm bank (Talavera et al, 2019). Despite some of these analyses captured all three races (Talavera et al, 2019), others exhibited mixed and inconclusive population structure (Cañas-Gutiérrez et al, 2015;Cañas-Gutiérrez et al, 2019;Cañas-Gutierrez et al, 2019).…”

Section: N R E V I E Wmentioning

confidence: 99%

Inheritance of Rootstock Effects in Avocado (Persea americanaMill.) cv. Hass

Reyes-Herrera

Muñoz-Baena

Velásquez-Zapata

et al. 2020

Preprint

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Grafting is typically utilized to merge adapted seedling rootstocks with highly productive clonal scions. This process implies the interaction of multiple genomes to produce a unique tree phenotype. Yet, the interconnection of both genotypes obscures individual contributions to phenotypic variation (i.e. rootstock-mediated heritability), hampering tree breeding. Therefore, our goal was to quantify the inheritance of seedling rootstock effects on scion traits using avocado (Persea americana Mill.) cv. Hass as model fruit tree. We characterized 240 rootstocks from 8 avocado cv. Hass orchards in three regions of the province of Antioquia, in the northwest Andes of Colombia, using 13 microsatellite markers (simple sequence repeats – SSRs). Parallel to this, we recorded 20 phenotypic traits (including morphological, eco-physiological, and fruit yield and quality traits) in the scions for three years (2015–2017). Relatedness among rootstocks was inferred through the genetic markers and inputted in a ‘genetic prediction’ model in order to calculate narrow-sense heritabilities (h2) on scion traits. We used three different randomization tests to highlight traits with consistently significant heritability estimates. This strategy allowed us to capture five traits with significant heritability values that ranged from 0.33 to 0.45 and model fits (R2) that oscillated between 0.58 and 0.74 across orchards. The results showed significance in the rootstock effects for four complex harvest and quality traits (i.e. total number of fruits, number of fruits with exportation quality, and number of fruits discarded because of low weight or thrips damage), while the only morphological trait that had a significant heritability value was overall trunk height (an emergent property of the rootstock-scion interaction). These findings suggest the inheritance of rootstock effects, beyond root phenotype, on a surprisingly wide spectrum of scion traits in ‘Hass’ avocado. They also reinforce the utility of SSR markers for relatedness reconstruction and genetic prediction of complex traits. This research is, up to date, the most cohesive evidence of narrow-sense inheritance of rootstock effects in a tropical fruit tree crop. Ultimately, our work reinforces the importance of considering the rootstock-scion interaction to broaden the genetic basis of fruit tree breeding programs, while enhancing our understanding of the consequences of grafting.

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Evolutionary analysis of six chloroplast genomes from three Persea americana ecological races: Insights into sequence divergences and phylogenetic relationships

Cited by 19 publications

References 59 publications

Molecular Markers and a Quality Trait Evaluation for Assessing the Genetic Diversity of Avocado Landraces from China

Molecular Markers and a Quality Trait Evaluation for Assessing the Genetic Diversity of Avocado Landraces from China

The complete chloroplast genome of Gleditsia sinensis and Gleditsia japonica: genome organization, comparative analysis, and development of taxon specific DNA mini-barcodes

Inheritance of Rootstock Effects in Avocado (Persea americanaMill.) cv. Hass

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