Abstract
Blueberries (Vaccinium section Cyanococcus) are perennial shrubs widely cultivated for their edible fruits. In this study, we performed admixture and genetic relatedness analysis of northern highbush (NHB, primarily V. corymbosum) and southern highbush (SHB, V. corymbosum introgressed with V. darrowii, V. virgatum, or V. tenellum) blueberry genotypes, and progenies of the BNJ16-5 cross (V. corymbosum × V. darrowii). Using genotyping-by-sequencing (GBS), we generated more than 334 million reads (75 bp). The GBS reads were aligned to the V. 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, 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 (FST) 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.
Highlights
Blueberry is a very high-value crop [3] that can thrive on acidic soils
V. corymbosum cultivars with high chilling requirements (>800 chilling hours measured as accumulated hours of temperature
An average of 2.8 million reads with a tag per sample were successfully mapped to the reference genome, which corresponds to an overall mapping rate of 83% to the genome
Summary
Blueberry is a very high-value crop [3] that can thrive on acidic soils. Consumer demand for blueberries is at an all-time high; its production around the world has quickly increased (http://www.fao.org/faostat, accessed November, 2020) primarily because of its health benefits [4]. There is evidence that V. darrowii is the most ancestral taxon of the Cyanococcus section [21] and V. darrowii may have played a greater role in the evolution of this section as a sole survivor of the extant taxa [14] In this process, today’s cultivars represent a mixture of alleles from four different species. Several studies have used older generation types of molecular markers in highbush blueberry for population structure analysis: random amplification of polymorphic DNA (RAPD), simple sequence repeats [6,19,23,24], expressed sequence tag (EST)-PCR markers [19,25,26], and retrotransposon-based sequence-specific amplification polymorphism markers [27]. Such marker systems have several limitations and are not amenable for highthroughput screening of larger populations
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