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4 results for “Shorea macrophylla”
Growth traits of a tropical timber species at Southeast Asia, Shorea macrophylla, and scripts for genome wide association study and genomic prediction
<p><em><span>Shorea macrophylla</span></em><span> is a commercially important tropical tree species grown for timber and oil. It is amenable to plantation forestry due to its fast initial growth. Genomic selection (GS) has been used in tree breeding studies to shorten long breeding cycles but has not previously been applied to <em>S. macrophylla</em>. To build genomic prediction models for GS, leaves and growth trait data were collected from a half-sib progeny population of <em>S. macrophylla</em> in Sari Bumi Kusuma forest concession, central Kalimantan, Indonesia. 18037 SNP markers were identified in two ddRAD-seq libraries. Genomic prediction models based on these SNPs were then generated for breast height and total height in the 7th year from planting (D7 and H7). These traits were chosen because of their relatively high narrow-sense genomic heritability and because seven years was considered long enough to assess initial growth. Genomic prediction models were built using 12 methods with the full set of identified SNPs and subsets of 48, 96, and 192 SNPs selected based on the results of a genome-wide association study (GWAS). The GBLUP and RKHS methods gave the highest predictive ability (PA) for D7 and H7 and showed that D7 has an additive genetic architecture while H7 has an epistatic genetic architecture. LightGBM and CNN1D also achieved high PA for D7 with 48 and 96 selected SNPs, and for H7 with 96 and 192 selected SNPs, showing that gradient boosting decision trees and deep learning can be useful in genomic prediction. For almost all methods and both traits, PA was higher when SNPs were selected based on their GWAS P-values than when using the full set of SNPs. These results suggest that GS with GWAS-based SNP selection could be used in <em>S. macrophylla </em>breeding to improve initial growth and reduce genotyping costs for next generation seedlings.</span></p>
Growth traits of a tropical timber species at Southeast Asia, Shorea macrophylla, and scripts for genome wide association study and genomic prediction
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Data from: Effects of Pleistocene climate change on genetic structure and diversity of Shorea macrophylla in Kalimantan rainforest
The island of Borneo is the diversity center of the Dipterocarpaceae, the most important family of tropical rainforest trees in Southeast Asia. However, changes in land use and climate have affected dipterocarp distributions on the island, raising concerns about the vulnerability (inter alia) of the endemic riparian species Shorea macrophylla. Thus, to aid conservation efforts we have investigated the genetic diversity, structure and demographic history of S. macrophylla. The species' genetic diversity and structure in Kalimantan (part of Indonesia, covering 75% of the island) was explored by examining genotypes of 377 individuals representing 13 populations in three regions (Northeast, Central and West Kalimantan) using 14 newly developed microsatellite loci. Higher genetic diversity was found, at all loci, in samples from Northeast Kalimantan than in samples from the other regions. Moderate genetic differentiation between populations was detected (FST: 0.093). Bayesian clustering, principal coordinate, and neighbor joining tree analysis of the population structure consistently identified two genetically distinct groups, one in the Northeast and the other in the Central and West regions. The higher diversity of the diverged populations in Northeast Kalimantan indicates that the region may have hosted rainforest refugia during the ice age. Accordingly, analysis using DIY ABC software indicated that the Northeast and Central-West Kalimantan groups diverged 194 000 years ago. We conclude that global climate change during the Pleistocene strongly influenced the genetic diversity and structure of S. macrophylla populations in Kalimantan.
Data from: Effects of Pleistocene climate change on genetic structure and diversity of Shorea macrophylla in Kalimantan rainforest
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