Genomic predictions and candidate single nucleotide polymorphisms for growth, form, and wood properties of teak clones

• Published in: Silvae genetica Vol. 73; no. 1; pp. 13 - 23
• Main Authors: Callister, Andrew N., Jiménez-Madrigal, Jose P., Whetten, Ross W., Murillo, Olman
• Format: Journal Article
• Language: English
• Published: Sciendo 01.01.2024
• Subjects: Early selection; Genomic relationship matrix; Genomic Selection; GWAS; RADseq; SNP
• ISSN: 2509-8934; 2509-8934
• DOI: 10.2478/sg-2024-0002

Teak ( ) is a premier hardwood timber, extensively cultivated throughout the tropics. The study aimed to undertake the first genomic selection of teak clones using single nucleotide polymorphism (SNP) markers and evaluate the prospects for prediction of stem volume (VOL), diameter (DBH), form Quality Score (QS), Specific Gravity (SG), and Heartwood Percentage (HW). Thirty-three elite teak clones from a genetic test in northern Costa Rica were genotyped at 10812 SNP loci and aligned to the teak reference genome sequence. The genomic relationship matrix revealed 7 cryptic groups of more highly related clones and within-group kinship values were consistent with full-sib families. Clone values for each of the 5 traits were calculated from 5-year field data for 26 of the geno-typed clones. Genomic prediction models were fitted to clone values using Bayesian Ridge Regression, BayesA, BayesB, BayesC, and Bayes Lasso. Predictive ability (PA) was greatest for DBH (up to 0.66), VOL (up to 0.63), SG (0.58), with 0.42 and 0.40 as the best PA for QS and HW, respectively. GWAS resulted in the discovery of 7 unique SNP markers for volume, 7 for DBH, 4 for QS, and 8 for SG. The small experimental size resulted in relatively large false discovery rates. Teak breeders are well positioned to benefit from the genomic tools and approaches to genotyping teak breeding and deployment populations on a large scale. Significant advantages are expected from widespread integration of genomic technologies into teak breeding systems to allow shortening of the breeding cycle.