Fast and Cost-Effective Genetic Mapping in Apple Using Next-Generation Sequencing

Publication Overview
TitleFast and Cost-Effective Genetic Mapping in Apple Using Next-Generation Sequencing
AuthorsGardner KM, Brown PJ, Cooke TF, Cann S, Costa F, Bustamante CD, Velasco R, Troggio M, Myles S
TypeJournal Article
Journal NameG3 (Bethesda, Md.)
Year2014
CitationGardner KM, Brown PJ, Cooke TF, Cann S, Costa F, Bustamante CD, Velasco R, Troggio M, Myles S. Fast and Cost-Effective Genetic Mapping in Apple Using Next-Generation Sequencing. G3 (Bethesda, Md.). 2014 Jul 16.

Abstract

Next-generation DNA sequencing (NGS) produces vast amounts of DNA sequence data, but it is not specifically designed to generate data suitable for genetic mapping. Recently developed DNA library preparation methods for NGS have helped solve this problem, however, by combining the use of reduced representation libraries with DNA sample barcoding to generate genome-wide genotype data from a common set of genetic markers across a large number of samples. Here we use such a method, called genotyping-by-sequencing (GBS), to produce a data set for genetic mapping in an F1 population of apples (Malus x domestica) segregating for skin color. We show that GBS produces a relatively large, but extremely sparse, genotype matrix: over 270,000 SNPs were discovered, but most SNPs have too much missing data across samples to be useful for genetic mapping. After filtering for genotype quality and missing data, only 6% of the 85 million DNA sequence reads contributed to useful genotype calls. Despite this limitation, using existing software and a set of simple heuristics, we generated a final genotype matrix containing 3967 SNPs from 89 DNA samples from a single lane of Illumina HiSeq and used it to create a saturated genetic linkage map and to identify a known QTL underlying apple skin color. We therefore demonstrate that GBS is a cost effective method for generating genome-wide SNP data suitable for genetic mapping in a highly diverse and heterozygous agricultural species. We anticipate future improvements to the GBS analysis pipeline presented here that will enhance the utility of next-generation DNA sequence data for the purposes of genetic mapping across diverse species.

Features
This publication contains information about 1,907 features:
Feature NameUniquenameType
6_4217856_421785genetic_marker
6_9193906_919390genetic_marker
6_9409286_940928genetic_marker
6_8159516_815951genetic_marker
6_13713446_1371344genetic_marker
6_44511096_4451109genetic_marker
6_68926556_6892655genetic_marker
6_43105926_4310592genetic_marker
6_43098526_4309852genetic_marker
6_43098786_4309878genetic_marker
6_43098456_4309845genetic_marker
3_193630363_19363036genetic_marker
6_68927456_6892745genetic_marker
6_44511356_4451135genetic_marker
6_49948336_4994833genetic_marker
10_1931953910_19319539genetic_marker
8_283664688_28366468genetic_marker
1_59942891_5994289genetic_marker
14_1449688714_14496887genetic_marker
6_81282576_8128257genetic_marker
6_81291546_8129154genetic_marker
6_92940116_9294011genetic_marker
6_163052276_16305227genetic_marker
15_2335861715_23358617genetic_marker
15_2335856515_23358565genetic_marker

Pages

Projects
This publication contains information about 1 projects:
Project NameDescription
Apple skin color trait-Myles-2014
Featuremaps
This publication contains information about 1 maps:
Map Name
Apple-GDxSS-F1