Genetic diversity of avocado (Persea americana Mill.) germplasm using pooled sequencing

Rubinstein, Mor; Eshed, Ravit; Rozen, Ada; Zviran, Tali; Kuhn, David N.; Irihimovitch, Vered; Sherman, Amir; Ophir, Ron

doi:10.1186/s12864-019-5672-7

Cited by 31 publications

(20 citation statements)

References 35 publications

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“…Up to now, NGS applied to avocado research has been reduced to transcriptome analyses 26,27 and the development of SNPs to characterize genetic diversity 28–30 . In addition, very recently, a first avocado nuclear genome sequence has been published 31 .…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide SNP discovery and genomic characterization in avocado (Persea americana Mill.)

Talavera

Soorni

Bombarely

et al. 2019

Sci Rep

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Modern crop breeding is based on the use of genetically and phenotypically diverse plant material and, consequently, a proper understanding of population structure and genetic diversity is essential for the effective development of breeding programs. An example is avocado, a woody perennial fruit crop native to Mesoamerica with an increasing popularity worldwide. Despite its commercial success, there are important gaps in the molecular tools available to support on-going avocado breeding programs. In order to fill this gap, in this study, an avocado ‘Hass’ draft assembly was developed and used as reference to study 71 avocado accessions which represent the three traditionally recognized avocado horticultural races or subspecies (Mexican, Guatemalan and West Indian). An average of 5.72 M reads per individual and a total of 7,108 single nucleotide polymorphism (SNP) markers were produced for the 71 accessions analyzed. These molecular markers were used in a study of genetic diversity and population structure. The results broadly separate the accessions studied according to their botanical race in four main groups: Mexican, Guatemalan, West Indian and an additional group of Guatemalan × Mexican hybrids. The high number of SNP markers developed in this study will be a useful genomic resource for the avocado community.

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Section: Introductionmentioning

confidence: 99%

Genome-Wide SNP discovery and genomic characterization in avocado (Persea americana Mill.)

Talavera

Soorni

Bombarely

et al. 2019

Sci Rep

View full text Add to dashboard Cite

show abstract

“…Some genetic markers that have been applied are isozymes [ 16 ], minisatellites [ 17 ], variable number tandem repeats (VNTRs) [ 18 ], randomly amplified polymorphic DNA (RAPD) [ 19 ], and restriction fragment length polymorphisms (RFLP) [ 20 , 21 ]. Others are inter-simple sequence repeats (ISSR) [ 22 ], simple sequence repeat (SSR) [ 15 , 23 , 24 , 25 ], and single nucleotide polymorphisms (SNPs) [ 5 , 26 , 27 ]. Choosing which marker type to employ in a diversity study depends on the study objectives and available financial resources, expertise, and facilities [ 28 ].…”

Section: Introductionmentioning

confidence: 99%

Comparison of Morphological and Genetic Characteristics of Avocados Grown in Tanzania

Juma

Geleta

Hovmalm

et al. 2021

Genes

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Tanzania has been growing avocado for decades. A wide variability of the avocado germplasm has been found, and the crop is largely contributing to the earnings of the farmers, traders, and the government, but its genetic diversity is scantly investigated. With the purpose of comparing morphological and genetic characteristics of this germplasm and uncovering the correlation between them and the geographical location, 226 adult seedling avocado trees were sampled in southwestern Tanzania. Their morphological characters were recorded, and their genetic diversity was evaluated based on 10 microsatellite loci. Discriminant analysis of principal components showed that the germplasm studied consisted of four genetic clusters that had an overall average gene diversity of 0.59 and 15.9% molecular variation among them. Most of the phenotypes were common in at least two clusters. The genetic clusters were also portrayed by multivariate analysis and hierarchical clustering for the molecular data but not for the morphology data. Using the Mantel test, a weak significant correlation was found between the genetic, morphological, and geographical distances, which indicates that the genetic variation present in the material is weakly reflected by the observed phenotypic variation and that both measures of variation varied slightly with the geographical sampling locations.

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“…Either in mutagenized or in natural populations, variants could be quickly identified by bulk sequencing of large numbers of individuals to avoid the costs of sample by sample barcoding and library preparation. Germplasm banks are using pooled sequencing to validate genetic stability of accessions avoiding the cost of individual sequencing of potential clones (see for example Rubinstein et al, 2019 ). Moreover, the same underlying model to perform pooled genotyping might be useful to perform individual genotyping in species with high ploidy such as sugar cane, where genotyping by sequencing is preferred over SNP arrays for variant detection ( Manimekalai et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Accurate, Efficient and User-Friendly Mutation Calling and Sample Identification for TILLING Experiments

2021

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TILLING (Targeting Induced Local Lesions IN Genomes) is a powerful reverse genetics method in plant functional genomics and breeding to identify mutagenized individuals with improved behavior for a trait of interest. Pooled high throughput sequencing (HTS) of the targeted genes allows efficient identification and sample assignment of variants within genes of interest in hundreds of individuals. Although TILLING has been used successfully in different crops and even applied to natural populations, one of the main issues for a successful TILLING experiment is that most currently available bioinformatics tools for variant detection are not designed to identify mutations with low frequencies in pooled samples or to perform sample identification from variants identified in overlapping pools. Our research group maintains the Next Generation Sequencing Experience Platform (NGSEP), an open source solution for analysis of HTS data. In this manuscript, we present three novel components within NGSEP to facilitate the design and analysis of TILLING experiments: a pooled variants detector, a sample identifier from variants detected in overlapping pools and a simulator of TILLING experiments. A new implementation of the NGSEP calling model for variant detection allows accurate detection of low frequency mutations within pools. The samples identifier implements the process to triangulate the mutations called within overlapping pools in order to assign mutations to single individuals whenever possible. Finally, we developed a complete simulator of TILLING experiments to enable benchmarking of different tools and to facilitate the design of experimental alternatives varying the number of pools and individuals per pool. Simulation experiments based on genes from the common bean genome indicate that NGSEP provides similar accuracy and better efficiency than other tools to perform pooled variants detection. To the best of our knowledge, NGSEP is currently the only tool that generates individual assignments of the mutations discovered from the pooled data. We expect that this development will be of great use for different groups implementing TILLING as an alternative for plant breeding and even to research groups performing pooled sequencing for other applications.

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Genetic diversity of avocado (Persea americana Mill.) germplasm using pooled sequencing

Cited by 31 publications

References 35 publications

Genome-Wide SNP discovery and genomic characterization in avocado (Persea americana Mill.)

Genome-Wide SNP discovery and genomic characterization in avocado (Persea americana Mill.)

Comparison of Morphological and Genetic Characteristics of Avocados Grown in Tanzania

Accurate, Efficient and User-Friendly Mutation Calling and Sample Identification for TILLING Experiments

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