Genetic diversity and structure of the 4th cycle breeding population of Chinese fir (Cunninghamia lanceolata (lamb.) hook)

Abstract

Studying population genetic structure and diversity is crucial for the marker-assisted selection and breeding of coniferous tree species. In this study, using RAD-seq technology, we developed 343,644 high-quality single nucleotide polymorphism (SNP) markers to resolve the genetic diversity and population genetic structure of 233 Chinese fir selected individuals from the 4th cycle breeding program, representing different breeding generations and provenances. The genetic diversity of the 4th cycle breeding population was high with nucleotide diversity (Pi) of 0.003, and Ho and He of 0.215 and 0.233, respectively, indicating that the breeding population has a broad genetic base. The genetic differentiation level between the different breeding generations and different provenances was low (Fst < 0.05), with population structure analysis results dividing the 233 individuals into four subgroups. Each subgroup has a mixed branch with interpenetration and weak population structure, which might be related to breeding rather than provenance, with aggregation from the same source only being in the local branches. Our results provide a reference for further research on the marker-assisted selective breeding of Chinese fir and other coniferous trees.

Efficient genomics-based ‘end-to-end’ selective tree breeding framework

“…During the 1950s, large-scale selective tree breeding programs were initiated worldwide (White et al 2007 ). Despite variation in geography, species, and breeding strategies, most programs followed the recurrent selection, with some reaching their fourth generations (Jing et al 2023 ), yet limited pragmatic changes have been implemented (Cotterill 1986 ). These breeding programs involve thousands of parents and their crosses, and the resulting offspring are evaluated over multiple test sites located within expansive geographic areas known as breeding zones (White et al 2007 ).…”

The Construction of lncRNA/circRNA–miRNA–mRNA Networks Reveals Functional Genes Related to Growth Traits in Schima superba

“…SNPs are one of the latest and most effective allelic variation types that have been widely evaluated in plant species according to population genetic diversity analysis [1]. In addition, the development of target trait-associated allelic variation SNPs identified from the genome and transcriptome is also important work and usually has potential application prospects in tree species breeding [43][44][45][46][47][48]. Except for SNPs distributed across noncoding regions of the genome, SNPs on expressed tags may be closer to related traits.…”

Development of an Advanced-Generation Multi-Objective Breeding Population for the 4th Cycle of Chinese Fir (Cunninghamia lanceolata (Lamb.) Hook.)

“…Marker filtering was performed using Plink v1.9 with the following criteria to keep SNPs: integrity > 0.8, minimum allele frequency ≥0.05, and loci conforming to the Hardy-Weinberg equilibrium. The more detailed description is shown in Jing et al [20].…”

“…After 4 years of observation, 233 unique genotypes with strong flowering and fruiting abilities were selected as the 4th cycle Chinese fir breeding population [18]. 343,644 high-quality single nucleotide polymorphism (SNP) markers have been developed to resolve the genetic diversity and population genetic structure of 233 Chinese fir [20]. In this study, we aimed to use these markers to clarify the genetic diversity and genetic gain of the 4th cycle of the Chinese fir breeding population and construct an advanced-generation structured breeding population.…”