10.5061/DRYAD.Q83BK3JDT
Thomson, Michael
0000-0003-1868-6867
Texas A&M University
Thapa, Ranjita
0000-0001-6116-7611
University of Nebraska–Lincoln
Septiningsih, Endang
Texas A&M University
Genome-wide association mapping to identify genetic loci for cold
tolerance and cold recovery during germination in rice
Dryad
dataset
2019
low temperature stress
cold recovery
germination
Genome-wide association study
QTL
Rice
Texas A&M University
https://ror.org/01f5ytq51
2020-02-25T00:00:00Z
2020-02-25T00:00:00Z
en
https://doi.org/10.3389/fgene.2020.00022
2894226 bytes
2
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
To investigate the genetic architecture underlying cold tolerance during
germination in rice (Oryza sativa), we conducted a genome-wide association
study (GWAS) using a novel diversity panel of 257 rice accessions from
around the world and 5,185 SNP markers from a 7K SNP marker array.
Genotyping was performed using a 7K Illumina iSelect custom-designed array
by following the Infinium HD Array Ultra Protocol. The 7K array, called
the C7AIR, was designed by Dr. Susan McCouch’s Lab at Cornell University
and consists of 7,098 SNPs (Morales et al. 2020, under review). After
genotyping 257 rice accessions with the 7K array (C7AIR), poor-performing
SNP markers (SNPs of call rate <90%; minor allele frequency
<5%; or heterozygosity >20%) were removed from the dataset.
For our study, a subset of 5,185 high-quality SNP markers obtained after
filtering was used to perform the genome-wide association analysis. The
dataset representing the genotype data of 5,185 SNP markers by 257 rice
accessions is presented here.