High-resolution genetic linkage map of European pear (Pyrus communis) and QTL fine-mapping of vegetative budbreak time

BMC Plant Biology
Gilad GabayMoshe A Flaishman

Abstract

Genomic analysis technologies can promote efficient fruit tree breeding. Genotyping by sequencing (GBS) enables generating efficient data for high-quality genetic map construction and QTL analysis in a relatively accessible way. Furthermore, High-resolution genetic map construction and accurate QTL detection can significantly narrow down the putative candidate genes associated with important plant traits. We genotyped 162 offspring in the F1 'Spadona' x 'Harrow Sweet' pear population using GBS. An additional 21 pear accessions, including the F1 population's parents, from our germplasm collection were subjected to GBS to examine diverse genetic backgrounds that are associated to agriculturally relevant traits and to enhance the power of SNP calling. A standard SNP calling pipeline identified 206,971 SNPs with Asian pear ('Suli') as the reference genome and 148,622 SNPs with the European genome ('Bartlett'). These results enabled constructing a genetic map, after further stringent SNP filtering, consisting of 2036 markers on 17 linkage groups with a length of 1433 cM and an average marker interval of 0.7 cM. We aligned 1030 scaffolds covering a total size of 165.5 Mbp (29%) of the European pear genome to the 17 linkage groups. Fo...Continue Reading

References

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Citations

May 3, 2019·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Javier TelloAgnès Doligez
Jun 4, 2021·Horticulture Research·Qinsong YangYuanwen Teng
Jan 16, 2022·Horticulture Research·Jiaming LiJun Wu

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Methods Mentioned

BETA
MDS
genotyping

Software Mentioned

JMP®
VCFtools
Tassel
MapQTL
GBS
PLINK
GWAF package
R
JoinMap
Archaeopteryx

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