Efficient QTL detection of flowering date in a soybean RIL population using the novel restricted two-stage multi-locus GWAS procedure

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
Liyuan PanJunyi Gai

Abstract

Eighty-six R1 QTLs accounting for 89.92% phenotypic variance in a soybean RIL population were identified using RTM-GWAS with SNPLDB marker which performed superior over CIM and MLM-GWAS with BIN/SNPLDB marker. A population (NJRIKY) composed of 427 recombinant inbred lines (RILs) derived from Kefeng-1 × NN1138-2 (MGII × MGV, MG maturity group) was applied for detecting flowering date (R1) quantitative trait locus (QTL) system in soybean. From a low-depth re-sequencing (~ 0.75 ×), 576,874 SNPs were detected and organized into 4737 BINs (recombination breakpoint determinations) and 3683 SNP linkage disequilibrium blocks (SNPLDBs), respectively. Using the association mapping procedures "Restricted Two-stage Multi-locus Genome-wide Association Study" (RTM-GWAS), "Mixed Linear Model Genome-wide Association Study" (MLM-GWAS) and the linkage mapping procedure "Composite Interval Mapping" (CIM), 67, 36 and 10 BIN-QTLs and 86, 14 and 23 SNPLDB-QTLs were detected with their phenotypic variance explained (PVE) 88.70-89.92% (within heritability 98.2%), 146.41-353.62% (overflowing) and 88.29-172.34% (overflowing), respectively. The RTM-GWAS with SNPLDBs which showed to be more efficient and reasonable than the others was used to identify the...Continue Reading

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Citations

Feb 29, 2020·International Journal of Molecular Sciences·Samuel LanFrank M You
Feb 8, 2020·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Mengmeng FuJunyi Gai
Jan 20, 2021·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Shanshan ZhangDeyue Yu
Feb 10, 2021·International Journal of Molecular Sciences·Cheng LiuJunyi Gai
Oct 26, 2021·Frontiers in Plant Science·Jessica DelfiniLeandro Simões Azeredo Gonçalves

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Methods Mentioned

BETA
PCR
genotyping

Software Mentioned

NJRIKY
GWAS
RTM
WinQTL Cartographer
SAS
Sequence Alignment / Map tools ( SAMtools )
LASTZ
BLASTP
Singular Enrichment Analysis ( SEA )
full

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