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ARS Home » Plains Area » Fort Collins, Colorado » Center for Agricultural Resources Research » Agricultural Genetic Resources Preservation Research » Research » Publications at this Location » Publication #379422

Research Project: Efficient and Effective Preservation and Management of Plant and Microbial Genetic Resource Collections

Location: Agricultural Genetic Resources Preservation Research

Title: Cataloging microhaplotype diversity at cyst-nematode resistance gene Hs1pro-1 in pools of wild Patellifolia spp

item Reeves, Patrick
item FENWICK, ANN - US Department Of Agriculture (USDA)
item PANELLA, LEE - Retired ARS Employee
item FRESE, LOTHAR - Julius Kuhn Institute
item Richards, Christopher

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 9/24/2020
Publication Date: N/A
Citation: N/A

Interpretive Summary: n/a

Technical Abstract: Wild germplasm accessions hold the raw material for crop improvement. Identifying which accessions hold agronomically valuable alleles, and extracting those alleles, is complex because wild accessions are genetically heterogeneous. Using pool-seq, we characterized microhaplotype diversity at Hs1pro-1, a sugar beet cyst-nematode resistance locus, in Patellifolia spp., where the gene originated. Microhaplotypes, short spans of DNA defined by two or more adjacent SNPs, were identified using phased short read sequence data. Microhaplotype loci have more alleles than SNPs thus have greater predictive power for linkage and diversity analyses. We sequenced 6 DNA pools containing an average of 24 individual genomes to a mean depth of 42X. The minimum tiling path across 4185 bp covering Hs1pro-1 and its 5' cis-regulatory sequence contained 1122 microhaplotype loci with an average length of 3.6±2.1(±1 sd) bp. The coding region contained 236 allelic variants with an average of 4.3±1.6 alleles per locus; 307 variants were found in the regulatory regions (4.3±1.7 alleles/locus). Most microhaplotype loci were short, most variation was caused by indels rather than SNPs, and most variants were shared across the six accessions. The major allele differed between accessions at a minority of loci. Identification of wild germplasm accessions with unique microhaplotypes could expedite breeding for new resistance phenotypes. The procedure outlined here can be used to catalog naturally-occurring microhaplotype variants at any locus of interest.