Construction of the Core Collection of Catalpa fargesii f. duclouxii (Huangxinzimu) Based on Molecular Markers and Phenotypic Traits

Huifen Xue,Bingyang Liu,Xiaochi Yu,Xiyang Zhao,Wenji Zhai,Shen Zhang,Junhui Wang,Nan Lu,Pengyue Fu,Jie Li,Wenjun Ma

doi:10.3390/f12111518

Abstract

To promote the conservation and utilization of Catalpa fargesii f. duclouxii (Huangxinzimu) germplasm resources, a total of 252 accessions were used to construct a preliminary core collection according to phenotypic traits and single nucleotide polymorphism (SNP) markers. In this study, 24 phenotypic traits, namely, 9 quantitative traits and 15 qualitative traits, were investigated. The core collection of C. fargesii f. duclouxii (Huangxinzimu) was constructed to remove redundant samples from the collected materials. First, the phenotypic core collection, with a sample proportion of 30, consisting of 24 clones, was constructed according to two genetic distances (Euclidean distance and Mahalanobis), four system clustering methods (the unweighted pair-group average method, Ward’s method, the complete linkage method, and the single linkage method), and three sampling methods (random sampling, deviation sampling, and preferred sampling). The best construction strategies were selected for further comparison. Three core collections (D2C3S3-30, D2C3S3-50, and D2C3S3-70) were constructed according to the optimal construction strategy at three sampling proportions. The core collection D2C3S3-30 with the best parameters was evaluated by using six parameters: the mean difference percentage (MD), variance difference percentage (VD), periodic rate of range (CR), changeable rate of the coefficient of variation (VR), minimum rate of change (CRMIN), and maximum rate of change (CRMAX). Three core collections (M-30, M-50, and M-70) were constructed by molecular markers, and the optimal core collection M-30 was selected by using five parameters, namely, Ho, He, PIC, MAF, and loci. The combination of D2C3S3-30 and M-30 was used to construct the final core collection DM-45, 45 samples representing the complete range of phenotypic and genetic variability. In this study, phenotypic traits combined with molecular markers were used to construct core collections to effectively capture the entire range of trait variation, effectively representing the original germplasm and providing a basis for the conservation and utilization of C. fargesii f. duclouxii (Huangxinzimu).

Highlights

Core collections have been widely used in the conservation and utilization of germplasm resources, which represents the genetic diversity of original germplasm resources with minimum redundancy [1]
At the sampling size of 30, among the 24 core collections constructed by the combination of 2 genetic distances, 4 clustering methods, and 3 sampling methods, the mean difference percentage (MD) of 22 core collections was less than 20% of the original population, and the CR was more than 80% of the original population, indicating that these 22 core collections could represent the genetic diversity of the original population
The results showed that the higher the minor allele frequency (MAF) and polymorphism information content (PIC) values were, the greater the representativeness and good reproductivity of these single nucleotide polymorphism (SNP) loci, which indicated that the core collection had good representativeness

Summary

Introduction

Core collections have been widely used in the conservation and utilization of germplasm resources, which represents the genetic diversity of original germplasm resources with minimum redundancy [1]. Phenotypic traits are widely used in constructing core collections, such as those of Cynodon dactylon [3], Erythrophleum fordii [2], Populus deltoides [4], Eucalyptus urophylla [5], Prunus armeniac L. Molecular markers have been widely used in the construction of core collections, such as those of Castanea mollissima Blume [11], Prunus persica (L.) [12], soybean [13], P. armeniac L. The use of molecular markers alone in the construction of core collections may result in the loss of the genetic diversity that controls the mutant traits [17]. The use of genotypic or phenotypic information alone for the establishment of core collections may not efficiently capture the entire genetic diversity of species [18]. The combination of phenotypic traits and molecular markers can effectively avoid the loss of important germplasms and increase the accuracy and reliability of core collections [20]

Methods

Results

Discussion

Conclusion