Genomic and evolutionary relationships among wild and cultivated blueberry species

Byron R Manzanero; Krishnanand P Kulkarni; Nicholi Vorsa; Umesh K Reddy; Purushothaman Natarajan; Sathya Elavarthi; Massimo Iorizzo; Kalpalatha Melmaiee

doi:10.1186/s12870-023-04124-y

Genomic and evolutionary relationships among wild and cultivated blueberry species

BMC Plant Biol. 2023 Mar 6;23(1):126. doi: 10.1186/s12870-023-04124-y.

Authors

Byron R Manzanero^#¹, Krishnanand P Kulkarni^#¹, Nicholi Vorsa^{2

3}, Umesh K Reddy⁴, Purushothaman Natarajan⁴, Sathya Elavarthi¹, Massimo Iorizzo⁵, Kalpalatha Melmaiee⁶

Affiliations

¹ Department of Agriculture and Natural Resources, Delaware State University, Dover, DE, 19901, USA.
² Department of Plant Biology, Rutgers University, New Brunswick, NJ, 08901, USA.
³ Philip E. Marucci Center for Blueberry and Cranberry Research and Extension, Chatsworth, NJ, 08019, USA.
⁴ Department of Biology, West Virginia State University, Institute, WV, 25112, USA.
⁵ Department of Horticultural Science and Plants for Human Health Institute, NC State University, Kannapolis, NC, 28081, USA.
⁶ Department of Agriculture and Natural Resources, Delaware State University, Dover, DE, 19901, USA. kmelmaiee@desu.edu.

^# Contributed equally.

Abstract

Background: Blueberries (Vaccinium section Cyanococcus) are an economically important fruit crop in the United States. Understanding genetic structure and relationships in blueberries is essential to advance the genetic improvement of horticulturally important traits. In the present study, we investigated the genomic and evolutionary relationships in 195 blueberry accessions from five species (comprising 33 V. corymbosum, 14 V. boreale, 81 V. darrowii, 29 V. myrsinites, and 38 V. tenellum) using single nucleotide polymorphisms (SNPs) mined from genotyping-by-sequencing (GBS) data.

Results: GBS generated ~ 751 million raw reads, of which 79.7% were mapped to the reference genome V. corymbosum cv. Draper v1.0. After filtering (read depth > 3, minor allele frequency > 0.05, and call rate > 0.9), 60,518 SNPs were identified and used in further analyses. The 195 blueberry accessions formed three major clusters on the principal component (PC) analysis plot, in which the first two PCs accounted for 29.2% of the total genetic variance. Nucleotide diversity (π) was highest for V. tenellum and V. boreale (0.023 each), and lowest for V. darrowii (0.012). Using TreeMix analysis, we identified four migration events and deciphered gene flow among the selected species. In addition, we detected a strong V. boreale lineage in cultivated blueberry species. Pairwise SweeD analysis identified a wide sweep (encompassing 32 genes) as a strong signature of domestication on the scaffold VaccDscaff 12. From this region, five genes encoded topoisomerases, six genes encoded CAP-gly domain linker (which regulates the dynamics of the microtubule cytoskeleton), and three genes coded for GSL8 (involved in the synthesis of the cell wall component callose). One of the genes, augustus_masked-VaccDscaff12-processed-gene-172.10, is a homolog of Arabidopsis AT2G25010 and encodes the protein MAINTENANCE OF MERISTEMS-like involved in root and shoot growth. Additional genomic stratification by admixture analysis identified genetic lineages and species boundaries in blueberry accessions. The results from this study indicate that V. boreale is a genetically distant outgroup, while V. darrowii, V. myrsinites, and V. tenellum are closely related.

Conclusion: Our study provides new insights into the evolution and genetic architecture of cultivated blueberries.

Keywords: Admixture analysis; Blueberry; Domestication; Genotyping-by-sequencing; Principal component analysis; Single nucleotide polymorphisms.

MeSH terms

Arabidopsis*
Blueberry Plants*
Cell Wall
Genomics
Pseudogenes

Abstract

MeSH terms

Grants and funding