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

Authors: OFFHOFF, ALEX - University Of Minnesota; POETS, ANA - University Of Minnesota; TYAGI, PRIYANKA - North Carolina State University; LEI, LI - University Of Minnesota; CARTER, COREY - University Of Minnesota; HIRSCH, CANDICE - University Of Minnesota; LI, LIN - University Of Minnesota; Brown-Guedira, Gina; MORRELL, PETER - University Of Minnesota; MUEHLBAUER, GARY - University Of Minnesota; SMITH, KEVIN - University Of Minnesota

Submitted to: Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/16/2019
Publication Date: 10/8/2019
Citation: Offhoff, A., Poets, A.M., Tyagi, P., Lei, L., Carter, C.K., Hirsch, C.N., Li, L., Brown Guedira, G.L., Morrell, P.L., Muehlbauer, G.J., Smith, K.P. 2019. Development of a multi-parent population for genetic mapping and allele discovery in six-row barley. Genetics. 213:595–613.

Interpretive Summary: Collections of plant germplasm 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) by crossing 88 cultivated accessions to the common parent variety 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. DNA of these lines were analyzed to identified 7,773 SNPs with an average of 3,889 SNPs segregating per family. We detected 23 chromosome regions associated with flowering time with five regions found coincident with previously described flowering time genes. A major locus was detected near the flowering time gene, HvPpd-H1, which affects photoperiod. Haplotype-based analysis of HvPpd-H1 identified unique 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 evaluated 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 genes of large and small effect for traits of interest and identifying and utilizing valuable alleles from the NSGC for barley improvement.

Technical 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 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 with an average of 3,889 SNPs segregating per family. We detected 23 QTL associated with flowering time with five QTL found coincident with previously described flowering time genes. A major QTL was detected near the flowering time gene, HvPpd-H1, which affects photoperiod. 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 evaluated 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.