Haplotype hitchhiking promotes trait coselection in Brassica napus

Plant Biotechnology Journal
Lunwen QianRod J Snowdon

Abstract

Local haplotype patterns surrounding densely spaced DNA markers with significant trait associations can reveal information on selective sweeps and genome diversity associated with important crop traits. Relationships between haplotype and phenotype diversity, coupled with analysis of gene content in conserved haplotype blocks, can provide insight into coselection for nonrelated traits. We performed genome-wide analysis of haplotypes associated with the important physiological and agronomic traits leaf chlorophyll and seed glucosinolate content, respectively, in the major oilseed crop species Brassica napus. A locus on chromosome A01 showed opposite effects on leaf chlorophyll content and seed glucosinolate content, attributed to strong linkage disequilibrium (LD) between orthologues of the chlorophyll biosynthesis genes EARLY LIGHT-INDUCED PROTEIN and CHLOROPHYLL SYNTHASE, and the glucosinolate synthesis gene ATP SULFURYLASE 1. Another conserved haplotype block, on chromosome A02, contained a number of chlorophyll-related genes in LD with orthologues of the key glucosinolate biosynthesis genes METHYLTHIOALKYMALATE SYNTHASE-LIKE 1 and 3. Multigene haplogroups were found to have a significantly greater contribution to variation f...Continue Reading

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Citations

Feb 22, 2017·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Annaliese S MasonIsobel A P Parkin
Sep 21, 2017·Frontiers in Plant Science·Lunwen QianKai P Voss-Fels
Dec 15, 2018·The Plant Journal : for Cell and Molecular Biology·Armin SchebenDavid Edwards
May 26, 2021·Plant Biotechnology Journal·Dandan HuJun Zou
Nov 6, 2021·Communications Biology·Javaid Akhter BhatRajeev K Varshney

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Methods Mentioned

BETA
genotyping
PCA
dissect

Software Mentioned

r package psych
powermarker
symap
tcs1
r package
SelectionTools
figtree
spss Statistics
r package LDheatmap
hmisc

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