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

• Main Authors: Krishnanand P. Kulkarni, Nicholi Vorsa, Purushothaman Natarajan, Sathya Elavarthi, Massimo Iorizzo, Umesh K. Reddy, Kalpalatha Melmaiee
• Format: Article
• Language: English
• Published: MDPI AG 2021-12-01
• Series: International Journal of Molecular Sciences
• Subjects: <i>Vaccinium</i>; admixture analysis; genotyping-by-sequencing; genetic relatedness
• Online Access: https://www.mdpi.com/1422-0067/22/1/163

Blueberries (<i>Vaccinium</i> section <i>Cyanococcus</i>) are perennial shrubs widely cultivated for their edible fruits. In this study, we performed admixture and genetic relatedness analysis of northern highbush (NHB, primarily <i>V. corymbosum</i>) and southern highbush (SHB, <i>V. corymbosum</i> introgressed with <i>V. darrowii, V. virgatum, or V. tenellum</i>) blueberry genotypes, and progenies of the BNJ16-5 cross (<i>V. corymbosum</i> × <i>V. darrowii</i>). Using genotyping-by-sequencing (GBS), we generated more than 334 million reads (75 bp). The GBS reads were aligned to the <i>V. corymbosum</i> 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, which were used for principal component, haplotype, and admixture analysis. Principal component analysis revealed three main groups: (1) NHB cultivars, (2) SHB cultivars, and (3) BNJ16-5 progenies. The overall fixation index (<i>F_ST</i>) and nucleotide diversity for NHB and SHB cultivars indicated wide genetic differentiation, and haplotype analysis revealed that SHB cultivars are more genetically diverse than NHB cultivars. The admixture analysis identified a mixture of various lineages of parental genomic introgression. This study demonstrated the effectiveness of GBS-derived single-nucleotide polymorphism 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.