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

Abstract

Pedigrees provide suitable input for tracking breeding crosses and monitor plants and animal populations. Pedigree analysis is an essential tool to visualize and describe population structure and genetic diversity. Pasture plant breeding relies on a range of strategies from closed system recurrent selection using elite cultivars to diversity‐focused programs using ecotypes and wild germplasm as parents. There is currently no published pedigree analysis of white clover (Trifolium repens L.), despite over a century of breeding efforts in New Zealand. A pedigree map was constructed for white clover germplasm stored in the Margot Forde Germplasm Centre located in Palmerston North, New Zealand. Inbreeding and kinship coefficients and the effective number of founders through time were estimated to assess genetic relatedness in the reference population. A total of 15,265 accessions were included in the map. The maximum number of traced generations was 15, and the mean completeness of parentage for the reference population was 72%. The mean number of offspring was 5.14. The origin of founding and introduced accessions was assessed. The effective number of founders was 175.68 or 17.5% of the total number of reference founders. Founding accessions and influencing ancestors were identified. One of the earliest parental accessions identified was ‘North Canterbury Type I’ from 1941. Relatedness was determined using the k coefficient, with k = 1 as complete relatedness. The overall mean relatedness was k = 0.002. Overall mean inbreeding level was 0.39%. Relatedness and inbreeding coefficients revealed distinct germplasm pools formed across time that are of interest to pre‐breeding efforts.

Pedigree analysis of pre-breeding efforts in Trifolium spp. germplasm in New Zealand

“…The results from the Trifolium species in this study are comparable to the results by [29,30], where diversity within the white and red clover accessions at the MFGC were assessed. Overall, the level of variation was high across all of the Trifolium species accessions.…”

“…The high levels of diversity found in the genebank collections reported in white [29] and red clover [30] are positive for future hybridisation programmes. Prebreeding efforts in minor Trifolium species could complement white and red clover breeding [29]. showed that the country of origin of accessions has influence on the population structure.…”

“…This was due to the software package not having an option for handling the pedigree data with both biparental crosses and polycrosses. Further, polycrosses do not fit the allele frequency expectations of biparental crosses and could therefore skew estimates of relatedness as indicated in Egan et al [29] and Egan et al [30].…”

“…were used in the pedigree analysis, chosen based on the size and completeness of the data available ( Table 2). The methodology used in this study is the same as in Egan et al [29] and Egan et al [30]. In short, accessions have been introduced over a range of decades, from 1950 to 2010.…”

“…Pedigrees are also used alongside molecular studies to increase the accuracy of molecular phylogenetic studies [23]. Pedigree maps can also be used to identify germplasm variation which can be utilised in future prebreeding decisions [29,30]. For this to occur effectively, knowledge of population structure and relatedness coefficients are the first steps [49].…”