Supporting data for Development of a multi-parent population for genetic mapping and allele discovery in six-row barley

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Supporting data for Development of a multi-parent population for genetic mapping and allele discovery in six-row barley

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2019-08-12

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Germplasm collections hold valuable allelic diversity for crop improvement and genetic mapping of complex traits. To gain access to the genetic diversity within the USDA National Small Grain Collection (NSGC), we developed the Barley Recombinant Inbred Diverse Germplasm Population (BRIDG6), a six-row spring barley multi-parent population (MPP) with 88 cultivated accessions ranging from landrace to cultivars crossed to a common parent (Rasmusson). The parents were randomly selected from a core subset of the NSGC that represents the genetic diversity of landrace and breeding accessions. In total, we generated 6,160 F5 recombinant inbred lines (RILs) with an average of 69 and a range of 37-168 RILs per family genotyped with 7,773 SNPs. The number of segregating SNPs per family range from 956 to 6,775, with an average of 3,889 SNPs per family. Using BRIDG6, we detected 23 QTL contributing to flowering time. Five QTL were within five megabase pairs of previously described flowering time genes. For the major QTL detected near HvPpd-H1, a flowering time gene that affects photoperiod, we observed both positive and negative allele effects ranging from +4 to –3 days relative to Rasmusson among the 79 families segregating for the SNP. Haplotype-based analysis of HvPpd-H1 identified private alleles to families of Asian origin conferring both positive and negative effects, providing the first observation of flowering time-related alleles private to Asian accessions. We evaluate several subsampling strategies to determine their effect on the power of QTL detection and found that for flowering time in barley, a sample size larger than 50 families or 3,000 individuals results in the highest QTL detection. This MPP will be useful for uncovering large and small effect QTL for traits of interest and identifying and utilizing valuable alleles from the NSGC for barley improvement.

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https://doi.org/10.1534/genetics.119.302046

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Hemshrot, Alex; Poets, Ana M; Tyagi, Priyanka; Lei, Li; Carter, Corey; Hirsch, Candice N; Li, Lin; Brown-Guedira, Gina; Morrell, Peter L; Muehlbauer, Gary J; Smith, Kevin P. (2019). Supporting data for Development of a multi-parent population for genetic mapping and allele discovery in six-row barley. Retrieved from the Data Repository for the University of Minnesota (DRUM), https://doi.org/10.13020/c5kj-af95.

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Barley_GATK_Calling_NAM_genomewide.raw.snps.indels.vcf.tar.gz
VCF file for 159 landrace and cultivated material genotyped with exome capture sequencing technology. 68 of which correspond to the donor parents in BRIDG6.Genotypes are Homozygous reference (Morex) = 1, Heterozygous = 0, Homozygous alternative = -1. The raw exome capture sequencing data has been submitted in NCBI SRA with the BioProject number of PRJNA473780 and PRJNA524705.
(1023.67 MB)

Barley_NAM_Regionlast26_All.raw.snps.indels.sorted.vcf.tar.gz
Twenty six donor parents in the BRIDG6 genotyped with exome capture sequencing technology. Genotypes are Homozygous reference (Morex) = 1, Heterozygous = 0, Homozygous alternative = -1. The raw exome capture sequencing data has been submitted in NCBI SRA with the BioProject number of PRJNA473780 and PRJNA524705.
(503.25 MB)

NAM_6row_exome_26parents_filter_GQ30_missing75_hmp.txt
HapMap format for SNPs in 26 donor parents genotyped with exome capture data. This file represent SNPs with GQ >30 and missing data <75%. Genotypes are Homozygous reference (Morex) = 1, Heterozygous = 0, Homozygous alternative = -1. This file is derived from "Barley_NAM_Regionlast26_All.raw.snps.indels.sorted.vcf".
(48.88 MB)

NAM_6row_exome_filter_GQ30_missing75_hmp.txt
HapMap format for SNPs in 63 donor parents genotyped with exome capture data. This file represent SNPs with GQ >30 and missing data <75%. Genotypes are Homozygous reference (Morex) = 1, Heterozygous = 0, Homozygous alternative = -1. This file is derived from "Barley_GATK_Calling_NAM_genomewide.raw.snps.indels.vcf".
(153.23 MB)

Barley_GATK_Calling_NAM_genomewide_sampleNames.txt
A list of sample names corresponding to the ID present in the Barley_GATK_Calling_NAM_genomewide.raw.snps.indels.vcf and NAM_6row_exome_filter_GQ30_missing75_hmp.txt files.
(2.76 KB)

genos_GxE.csv
Genotypes for all RILs in the BRIDG6 population. Genotypes are respect to Rasmusson alleles: Rasmusson allele = 2, Heterozygous = 1, Homozygous donor parent = 0.
(78.17 MB)

phenos_GxE.csv
BLUPs and BLUEs for the flowering time data collected for all individuals in the BRIDG6 population.
(335.15 KB)

MNS_July2016_production.vcf.gz
VCF file of all the Parents and RILs genotyped with GBS technology after processing raw GBS sequences using TASSEL pipeline. The raw GBS sequencing data has been submitted in NCBI SRA with the BioProject number of PRJNA488050.
(12.05 GB)

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