Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Admixture Analysis Using Genotyping-by-Sequencing Reveals Genetic Relatedness and Parental Lineage Distribution in Highbush Blueberry Genotypes and Cross Derivatives

Version 1 : Received: 21 November 2020 / Approved: 23 November 2020 / Online: 23 November 2020 (09:48:11 CET)

A peer-reviewed article of this Preprint also exists.

Kulkarni, K.P.; Vorsa, N.; Natarajan, P.; Elavarthi, S.; Iorizzo, M.; Reddy, U.K.; Melmaiee, K. Admixture Analysis Using Genotyping-by-Sequencing Reveals Genetic Relatedness and Parental Lineage Distribution in Highbush Blueberry Genotypes and Cross Derivatives. Int. J. Mol. Sci. 2021, 22, 163. Kulkarni, K.P.; Vorsa, N.; Natarajan, P.; Elavarthi, S.; Iorizzo, M.; Reddy, U.K.; Melmaiee, K. Admixture Analysis Using Genotyping-by-Sequencing Reveals Genetic Relatedness and Parental Lineage Distribution in Highbush Blueberry Genotypes and Cross Derivatives. Int. J. Mol. Sci. 2021, 22, 163.

Journal reference: Int. J. Mol. Sci. 2020, 22, 163
DOI: 10.3390/ijms22010163

Abstract

Blueberries (Vaccinium section Cyanococcus) are perennial shrubs widely cultivated for their edible fruits. In this study, we used admixture and genetic relatedness analysis of northern highbush (NHB, V. corymbosum) and southern highbush (SHB, V. darrowii) blueberry genotypes and F2 progenies of the V. corymbosum × V. darrowii cross. Using genotyping-by-sequencing (GBS), we generated ~3.34 billion reads (75 bp). The GBS reads were aligned to the Vaccinium corymbosum cv. Draper v1.0 reference genome sequence, and ~2.8 million reads were successfully mapped. From the alignments, we identified 2,244,039 single nucleotide polymorphisms (SNPs), which were used for principal component, haplotype, and admixture analysis. PCA formed three main groups: 1) NHB cultivars, 2) SHB cultivars, and 3) BNJ16-5 progenies. The overall fixation index (FST) and nucleotide diversity for NHB and SHB, indicated wide genetic differentiation, and haplotype analysis revealed that SHB cultivars are more genetically diverse than NHB cultivars. The admixture analysis identified a mix of various lineages of parental genomic introgression. This study demonstrated the effectiveness of GBS-derived SNP markers in genetic and admixture analyses to reveal genetic relatedness and to examine parental lineages in blueberry, which may be useful for future breeding plans.

Subject Areas

vaccinium; admixture analysis; genotyping-by-sequencing; genetic relatedness; Blueberry germplasm

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