Development of a multiparent population for genetic mapping and allele discovery in six-row barley

Abstract

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 landraces 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 that were 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, both positive and negative allele effects were observed 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 power for 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.