Identification of Founding Accessions and Patterns of Relatedness and Inbreeding Derived from Historical Pedigree Data in a Red Clover Germplasm Collection in New Zealand

Abstract

Pedigree maps are useful for germplasm exploration and identification of genetic bottlenecks. The primary objective of this study was to construct pedigree maps for red clover (Trifolium pratense L.) accessions held in the Margot Forde Germplasm Centre (MFGC) in Palmerston North, New Zealand. Pedigree data from accessions introduced into the MFGC between 1934 and 2016 were used. Data were filtered for accessions with breeding activity. A total of 30 founding accessions was identified, of which 25 were categorized as “New Zealand Broad,” two as “English Broad,” another two as “English Giant Hybrid,” and one as “Cotswold Broad.” The first synthetic form was identified from parents derived from English Broad and English Giant Hybrid. Influencing founder accessions were also identified. A relationship between introductions, relatedness, and geographic origin was found. The inbreeding and kinship coefficients were estimated across the population. The largest number of traced generations was eight. A total of 1742 accessions was used in the estimation of relatedness coefficients, with mean relatedness of 0.005. Overall mean inbreeding was 0.56%. Among the accessions with nonzero inbreeding coefficients, inbreeding was 10.68%. A sharp increase in inbreeding was found in the 1990s. Although inbreeding remained stable in the last three decades, a relationship between inbreeding and new introductions into the collection was found (r = 0.62). We conclude red clover diversity has been successfully maintained at MFGC during the past 80 yr. However, risk in loss of diversity is present unless germplasm exploration techniques, such as pedigree analysis, and novel breeding patterns are undertaken.