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Phylogeographic Diversity and Population Structure of Carica Papaya L. Revealed Through Nuclear Microsatellites

Abu Sayeed Md. Hasibuzzaman
Department of Genetics and Plant Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh

A. K. M. Aminul Islam
Department of Genetics and Plant Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh

· Md. Giashuddin Miah
Department of Agroforestry and Environment, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh

Mehfuz Hasan
Department of Genetics and Plant Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh

Abstract/ Executive Summary:

It is crucial to analyze the population structure and genetic diversity of the samples to be studied before a breeding program can be launched. Thirty-one genotypes of papaya germplasm from Spain, Brazil, Ecuador, China, Taiwan, India, and several locations in Bangladesh were genotyped using ten polymorphic simple sequence repeat markers to investigate their molecular diversity as well as their genetic relatedness. The highest numbers of alleles, gene diversity and polymorphic information content were seen in the P3K1024CC and P6K900CC markers. This result confrms the suitability of these markers in the assay of the genetic diversity of papaya genotypes. The model-based population structure and the distance-based assessment categorized the genotypes into six diferent subcategories. The analysis of molecular variance revealed that 11% of the entire genetic diversity was due to diferences among the populations, while 89% was a result of diferences within the population. The FST value of 0.136 showed a high level of genetic diversity among the groups alongside a negative FIS (−0.232) and FIT (−0.065). The diverse material revealed by our research expands the current papaya genetic resources, which can be used efectively in genomic studies in papaya improvement programs as well as in germplasm conservation studies.

Keywords: Allelic frequency · Dispersion analysis · Dissimilarity matrix · Fixation indices · Germplasm

Location:

Start Date:

End Date:

Program Area: Conservation and Biodiversity

Commodity: Papaya

Objectives:

We aim to determine the genetic diversity and population structure of papaya germplasm sampled from different locations across the world. This can be used effectively in genomic studies in papaya improvement programs as well as in germplasm conservation studies.

Methodology:

Plant materials – Thirty-one samples of papaya were taken from India, China, Spain, Ecuador, Brazil, Bangladesh, and Taiwan for this research (Table S1). DNA extraction of the collected germplasm – An adjusted CTAB approach (Allen et al. 2006) was used for DNA isolation of the sampled germplasm. In this study, two grams of fresh leaf samples collected from 15-day-old seedlings of each genotype were used. A spectrophotometer was used to quantify the extracted DNA, while the DNAs were run on 0.8% agarose gel to determine their quality. The dilution of the DNA samples was performed using Tris–EDTA, and the working concentration of the DNA was set as 50 ng μL−1. PCR condition and gel electrophoresis – The genotypic analysis of the papaya was performed with ten polymorphic SSR markers. PCR amplifcation was done within a 25 μL reaction mixture which was made up of 25 mM MgCl2, 10× PCR bufer, 10 pmol each of forward and reverse primer, 50 ng template DNA, 0.3 units of Taq DNA polymerase, and 2.5 mM dNTPs. The PCR reactions, which were performed in a Bio-Rad Thermal Cycler, include: initial denaturation at 95 °C followed by 35 cycles of 95 °C for 45 s, annealing at 54–59 °C (Table S2) for 45 s, and extension at 72 °C for 1 min. The last extension was made to operate at 72 °C for 5 min. The PCR products were separated using a 3.5% metaphor agarose gel (Huda et al. 2019). Statistical analyses – The data computation for the allele frequency and allele number, gene diversity, and polymorphic information content (PIC) was performed by the use of Power Marker 3.23 software (Liu and Muse 2005). The estimation of genotypic distance was done for all the samples, while the genotypic relation and clustering pattern were shown in an unweighted neighbor-joining (NJ) tree by DARwin 5.0.158 software (Perrier and Jacquemoud-Collet 2010). The analysis of the molecular variance (AMOVA) was conducted with the use of GenAlEx 6.5 (Peakall and Smouse 2006). The analysis of Wright’s F statistics was performed with the same software. STRUCTURE 2.3.3 software (Pritchard et al. 2000) was used for the assessment of the population structure of all sampled genotypes. A triple replication run was done for each K in which the value of K fell between 1 and 10. By using the Monte Carlo chain replicates of 100,000, the burn-in period for every run was 100,000 steps. A web-based program called Structure Harvester (http://taylor0.biology.ucla.edu/structure Harvester/) was used for the determination of the fnal population. MeV 4.9 software (Howe et al. 2011) was used for the production of the graphic representation of the dissimilarity matrix, while the dissimilarity matrix and the 3D dispersion analysis were conducted with the use of Genes software (Cruz 2013). Sigma Plot 12.0 software (Chaturvedi et al. 2015) was used for the construction of the 3D scatter plot.

Source of Information: Brazilian Journal of Botany

Article Link (Online Journal): https://doi.org/10.1007/s40415-020-00594-8

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Achievement/Findings:

An analysis of the diversity pattern of papaya genotypes obtained from different nations across the world was performed in this study. Several statistical methods used in this study showed that a series of variations are present among the studied 31 genotypes. Additionally, this study found that the variable materials used can serve as a fundamental source for the establishment of a mapping population and the choice of parental lines within any hybrid breeding program.

Knowledge Management: Journal