Genome-Wide SNP Markers Based on SLAF-Seq Uncover Breeding Traces in Rapeseed (Brassica napus L.)

Frontiers in Plant Science
Qinghong ZhouYingjin Huang

Abstract

Single Nucleotide Polymorphisms (SNPs) are the most abundant and richest form of genomic polymorphism, and hence make highly favorable markers for genetic map construction and genome-wide association studies. In this study, a total of 300 rapeseed accessions (278 representative of Chinese germplasm, plus 22 outgroup accessions of different origins and ecotypes) were collected and sequenced using Specific-Locus Amplified Fragment Sequencing (SLAF-seq) technology, obtaining 660.25M reads with an average sequencing depth of 6.27 × and a mean Q30 of 85.96%. Based on the 238,711 polymorphic SLAF tags a total of 1,197,282 SNPs were discovered, and a subset of 201,817 SNPs with minor allele frequency >0.05 and integrity >0.8 were selected. Of these, 30,877 were designated SNP "hotspots," and 41 SNP-rich genomic regions could be delineated, with 100 genes associated with plant resistance, vernalization response, and signal transduction detected in these regions. Subsequent analysis of genetic diversity, linkage disequilibrium (LD), and population structure in the 300 accessions was carried out based on the 201,817 SNPs. Nine subpopulations were observed based on the population structure analysis. Hierarchical clustering and principal c...Continue Reading

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Citations

Dec 14, 2017·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Qinghong ZhouYingjin Huang
Feb 1, 2020·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Hao WangDengfeng Hong
Jan 20, 2021·Molecular Genetics and Genomics : MGG·Ghulam Mustafa WassanHaohua He
Jun 11, 2021·Physiology and Molecular Biology of Plants : an International Journal of Functional Plant Biology·Jian Gao, Xiao-Li Ning
Jul 1, 2021·Ecology and Evolution·Yan ZhangZhibin Zhang

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Methods Mentioned

BETA
genotyping
PCR
PCA
environmental stress

Software Mentioned

GATK
Burrows alignment tool ( BWA )
HAPLOVIEW
BLAT
PLINK
Admixture
SPAGeDi
BLAST
MEGA5
index

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