High-Density Linkage Map Construction and QTL Identification in a Diploid Blueberry Mapping Population.

Xinpeng Qi,Elizabeth L Ogden,Lisa J Rowland,Judson Ward,Massimo Iorizzo,Jessica Gilbert,Daniel J Sargent,Hamed Bostan

doi:10.3389/fpls.2021.692628

Abstract

Genotyping by sequencing approaches have been widely applied in major crops and are now being used in horticultural crops like berries and fruit trees. As the original and largest producer of cultivated blueberry, the United States maintains the most diverse blueberry germplasm resources comprised of many species of different ploidy levels. We previously constructed an interspecific mapping population of diploid blueberry by crossing the parent F1#10 (Vaccinium darrowii Fla4B × diploid V. corymbosum W85–20) with the parent W85–23 (diploid V. corymbosum). Employing the Capture-Seq technology developed by RAPiD Genomics, with an emphasis on probes designed in predicted gene regions, 117 F1 progeny, the two parents, and two grandparents of this population were sequenced, yielding 131.7 Gbp clean sequenced reads. A total of 160,535 single nucleotide polymorphisms (SNPs), referenced to 4,522 blueberry genome sequence scaffolds, were identified and subjected to a parent-dependent sliding window approach to further genotype the population. Recombination breakpoints were determined and marker bins were deduced to construct a high density linkage map. Twelve blueberry linkage groups (LGs) consisting of 17,486 SNP markers were obtained, spanning a total genetic distance of 1,539.4 cM. Among 18 horticultural traits phenotyped in this population, quantitative trait loci (QTLs) that were significant over at least 2 years were identified for chilling requirement, cold hardiness, and fruit quality traits of color, scar size, and firmness. Interestingly, in 1 year, a QTL associated with timing of early bloom, full bloom, petal fall, and early green fruit was identified in the same region harboring the major QTL for chilling requirement. In summary, we report here the first high density bin map of a diploid blueberry mapping population and the identification of several horticulturally important QTLs.

Highlights

A total of 160,535 high quality single nucleotide polymorphisms (SNPs), after excluding highly distorted sites by Chi-square test, were obtained. These SNPs were located on 4,522 blueberry scaffolds, which resulted in a SNP density of 4.08 SNPs per 10 Kbp of the reference genome
Identified SNPs were evenly distributed along each blueberry chromosome, which is similar to the distribution pattern of annotated blueberry genes (Supplementary Figure 2)
Parent F1#10 was expected to be heterozygous at more SNP sites than parent W85–23, because F1#10 is an interspecific hybrid derived from crossing a V. darrowii selection (Fla4B) to a diploid V. corymbosum selection (W85–20)

Summary

Introduction

Commercial types of blueberry are native to North America and belong to the Cyanococcus section of the genus Vaccinium in the heath family Ericaceae. The major commercial types in the U.S are cultivars of V. corymbosum L. (tetraploid highbush blueberry) and V. virgatum Ait. V. ashei Reade), and wild, managed stands of V. angustifolium Ait. Highbush blueberry cultivars can be further classified into northern and southern types, depending on their chilling requirements and, the geographical areas where they can be grown. With low chilling requirements, have been developed through the introgression of the low-chilling southern diploid species V. darrowii Camp into the tetraploid V. corymbosum background (Rowland et al, 2014)

Methods

Results

Conclusion