Abstract
BackgroundInbreeding in seed orchards is expected to increase with the advancement of breeding cycles, which results in the delivery of crops with suboptimal genetic gain, reduced genetic diversity, and lower seed set. Here, a genetic distance-dependent method for clonal spatial deployment in seed orchards was developed and demonstrated, which reduced the inbreeding levels. The method’s main evaluation parameter of inbreeding is the genetic distance among individuals and the deployment method used an improved adaptive parallel genetic algorithm (IAPGA) based on Python language. Using inbreeding-prone Chinese Mongolian pine breeding population material originating from a single natural population, the proposed method was compared to a traditional orchard design and a distance-based design; namely, complete randomized block (RCB) and optimum neighborhood (ONA) designs, respectively.ResultsWith the advancement of selective breeding cycles, group separation among orchard related individuals is expected to increase. Based on the genetic distance among individuals, the IAPGA design was superior in significantly reducing the inbreeding level as compared to the two existing designs, confirming its suitability to advanced-generation orchards where relatedness among parents is common. In the 1st, 2nd, and mixed generations clonal deployment schemes, the IAPGA design produced lower inbreeding with 87.22%, 81.49%, and 87.23% of RCB, and 92.78%, 91.30%, and 91.67% of ONA designs, respectively.ConclusionsThe IAPGA clonal deployment proposed in this study has the obvious advantage of controlling inbreeding, and it is expected to be used in clonal deployment in seed orchards on a large-scale. Further studies are needed to focus on the actual states of pollen dispersal and mating in seed orchards, and more assumptions should be taken into account for the optimized deployment method.
Highlights
Inbreeding in seed orchards is expected to increase with the advancement of breeding cycles, which results in the delivery of crops with suboptimal genetic gain, reduced genetic diversity, and lower seed set
The similarity of parents in the orchards increased with the advancement of breeding cycles With the advancement of selective breeding cycles, group separation (Dendrogram) among seed orchard individuals is expected to increase
This is clearly demonstrated by the genetic distance between individuals in the three seed orchards (1st, 1.5, and 2ndgenerations) (Fig. 1)
Summary
Inbreeding in seed orchards is expected to increase with the advancement of breeding cycles, which results in the delivery of crops with suboptimal genetic gain, reduced genetic diversity, and lower seed set. Extensive studies have been conducted to assess the mating system and pollination dynamics in seed orchards (El-Kassaby and Ritland 1986a, 1986b; ElKassaby et al 1988; El-Kassaby et al 1989; El-Kassaby and Davidson 1991; Song et al 2018); the extent of inbreeding is difficult to determine, as it is a function of the relatedness among the members of parental population. In upgraded (1.5-Gen) or advanced (2nd-Gen) generations and rolling-front orchards (Borralho et al 1998), the level of inbreeding becomes more complex and is mainly determined by the pedigree of orchard population (e.g., as several individuals with various degree of relatedness are often selected and included), in addition to selfing, multiple inbreeding forms are expected (e.g., selfing, sibmating, parent-offspring, etc.) (El-Kassaby, 2000a, b)
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