Comparative analysis of SNP data and hybrid taxa information by using a classificatory linear mixed model to study the g
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ORIGINAL ARTICLE
Comparative analysis of SNP data and hybrid taxa information by using a classificatory linear mixed model to study the genetic variation and heritability of initial height growth in selected poplar hybrids Francisco Zamudio 1
&
Marco Yañez 2 & Fernando Guerra 3 & Derie Fuentes 4 & Alvaro Gonzalez 4
Received: 2 August 2019 / Revised: 26 March 2020 / Accepted: 7 April 2020 # Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract Advances in genomics increase the possibility of using SNP markers in selecting new parental genotypes for poplar breeding or new poplar varieties for commercial deployment. Here, we use a classificatory linear mixed model and a quantitative genetic approach for the combined analysis of SNP and phenotypic data from poplar hybrids at the beginning of their testing program. The main objective was to compare genetic parameters estimated based on two classification criteria: original (hybrid) taxa and SNP clustering. Height growth measurements obtained in three consecutive years from a poplar trial planted in 2002 in the center of Chile were included. In 2016, DNA was extracted from leaves of the same hybrids and genotyped by sequencing. An increasing number of clusters based on the similarity of SNP information was obtained. Broad sense heritability values observed at all levels of genomic clustering were larger than the only estimate obtained by using the original taxa classification. Thus, the method can help to predict a higher genetic gain in the early selection of poplars, based on initial height growth. The method did not affect the accuracy of the heritability estimation. The systematic increment in the intra-clonal covariance with the clustering level also suggests a highly positive genotype-by-time interaction effect at high levels of SNP clustering, which can also be positive for selection purposes. We concluded that the use of SNP clustering allowed the expression of larger genetic differences among hybrids in initial height growth, regardless of the original hybrid taxa. Keywords SNP . Heritability . Poplar hybrids . Linear mixed models . Cluster analysis
Introduction Poplar hybrids show great growth potential in Mediterranean regions, such as the center part of Chile. To enlarge the reduced genetic diversity that sustained the poplar-based industry in the country, the Poplar Technology Center (PTC) of Talca University imported between 1999 and 2001 more than Communicated by C. Kulheim * Francisco Zamudio [email protected] 1
Centro Tecnologico del Alamo, Poplar Technology Center, Talca University, 1 Poniente, 1141 Talca, Chile
2
Multidisciplinary Scientific Nucleus, Talca University, Talca, Chile
3
Institute of Biological Science, Talca University, Talca, Chile
4
Fraunhofer Chile Research, Santiago, Chile
2500 hybrids, mainly from the former Poplar Molecular Genetic Cooperative (PMGC), the University of Washington Seattle, USA. Hybrids were obtained from crosses of Populus trichocarpa, P. balsamifera, P. deltoides, P. maximowiczii, and
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