Impact of a tree improvement program on the genetic diversity of sugi (Cryptomeria japonica D Don) plantations

Iwasaki, Hirohide; Uchiyama, Kentaro; Kimura, Megumi; Saito, Yoko; Hakamata, Tetsuji; Ide, Yuji

doi:10.1016/j.foreco.2019.06.023

Cited by 6 publications

(5 citation statements)

References 37 publications

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“…The genetic diversity of the progeny trial corresponded to that of a naturally regenerated stand in Picea sitchensis and Picea abies [35,36]. In addition, the genetic diversity of a plantation with seed orchard crops was not affected by a tree improvement program in Cryptomeria japonica [37].…”

Section: Discussionmentioning

confidence: 98%

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Pedigree Reconstruction and Spatial Analysis for Genetic Testing and Selection In A Larix Kaempferi (Lamb.) Carrière Plantation

kyungmi

Kim

Kang

2021

Preprint

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Background: Larix kaempferi is one of the major timber species in Northeast Asia. Demand for the reforestation of the species is rising in South Korea due to an increase in large timber production and utilization. However, progeny trials for the species have not been explored, making it challenging to foster advanced generations of tree improvement. In the present study, genetic testing and selection for diameter growth were conducted using pedigree reconstruction and phenotypic spatial distribution analysis in a plantation of L. kaempferi. The aim of the present study was to select the superior larch individuals using the pedigree reconstruction and phenotypic spatial distribution to substitute progeny trials. The plantation of seed orchard crops was established in 1990 and one-hundred and eighty-eight trees were selected as the study material. Genetic variation was investigated first to validate its adequacy as breeding material. Genetic testing was carried out using a model considering pedigree information and spatial autoregression of the phenotypes. The major environmental effects on growth were assessed to understand the site characteristics where the breeding materials were located.Results: The expected heterozygosity of the mother trees and offspring were 0.672 and 0.681 presenting the corresponding level of genetic variation between two groups. The pedigree reconstruction using maternity analysis assigned one to six progenies to ninety-two candidate mothers. The accuracy of genetic testing was exceedingly increased with the animal model considering AR1⊗AR1 structure compared to the animal model only. The estimated genetic variance of the former was 9.086 whereas that of the latter was 4.9E-5. The predicted breeding values of the offspring were ranged from -5.937 to 5.655 and the estimated heritability of diameter growth was 0.344. Shifts in the effects of the factors were detected using geographically weighted regression analysis, which provided information on the post-sectioning of the plantation. Conclusions: The genetic testing approach based on pedigree reconstruction and phenotypic spatial distribution analysis was considered a useful analytical scheme that could replace or supplement progeny trials. Subdivision of the plantation as blocks of the progeny testing was accomplished a posteriori based on the changes of the environmental effects.

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Section: Discussionmentioning

confidence: 98%

“…Studying the change in the genetic variation using seed orchard crops is necessary to detect and preclude decline in genetic diversity with increased inbreeding [35,36,37]. Similar levels of genetic diversity in seed orchards and their crops are frequently reported, dispelling concern over narrowed genetic base in tree improvement programs.…”

Section: Discussionmentioning

confidence: 99%

Pedigree Reconstruction and Spatial Analysis for Genetic Testing and Selection In A Larix Kaempferi (Lamb.) Carrière Plantation

kyungmi

Kim

Kang

2021

Preprint

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show abstract

“…Studying the change in the genetic variation using seed orchard crops is necessary to detect and preclude decline in genetic diversity with increased inbreeding [ 35 – 37 ]. Similar levels of genetic diversity in seed orchards and their crops are frequently reported, dispelling concern over narrowed genetic base in tree improvement programs.…”

Section: Discussionmentioning

confidence: 99%

“…The genetic diversity of the progeny trial corresponded to that of a naturally regenerated stand in Picea sitchensis and Picea abies [ 35 , 36 ]. In addition, the genetic diversity of a plantation with seed orchard crops was not affected by a tree improvement program in Cryptomeria japonica [ 37 ].…”

Section: Discussionmentioning

confidence: 99%

Pedigree reconstruction and spatial analysis for genetic testing and selection in a Larix kaempferi (Lamb.) Carrière plantation

2022

View full text Add to dashboard Cite

Background Larix kaempferi is one of the major timber species in Northeast Asia. Demand for the reforestation of the species is rising in South Korea due to an increase in large timber production and utilization. However, progeny trials for the species have not been explored, making it challenging to foster advanced generations of tree improvement. In the present study, genetic testing and selection for diameter growth were conducted using pedigree reconstruction and phenotypic spatial distribution analysis in a plantation of L. kaempferi. The aim of the present study was to select the superior larch individuals using the pedigree reconstruction and phenotypic spatial distribution to substitute progeny trials. The plantation of seed orchard crops was established in 1990 and one-hundred and eighty-eight trees were selected as the study material. Genetic variation was investigated first to validate its adequacy as breeding material. Genetic testing was carried out using a model considering pedigree information and spatial autoregression of the phenotypes. Results The expected heterozygosity of the mother trees and offspring were 0.672 and 0.681 presenting the corresponding level of genetic variation between two groups. The pedigree reconstruction using maternity analysis assigned one to six progenies to ninety-two candidate mothers. The accuracy of genetic testing was exceedingly increased with the animal model considering AR1 ⊗ AR1 structure compared to the animal model only. The estimated genetic variance of the former was 9.086 whereas that of the latter was 4.9E-5 for DBH. The predicted breeding values of the offspring for DBH were ranged from -5.937 cm to 5.655 cm and the estimated heritability of diameter growth was 0.344. Conclusions The genetic testing approach based on pedigree reconstruction and phenotypic spatial distribution analysis was considered a useful analytical scheme that could replace or supplement progeny trials.

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“…In recent years, high-throughput genotyping technology, relying on single nucleotide polymorphisms (SNPs), has proven to be a reliable methodology to estimate genetic diversity parameters of seedlots in tree breeding programs, including the Shannon Index, expected and observed heterozygosity, inbreeding coefficients, allele frequencies, coancestry (complete seedlot and tree pairs), and genotype-based pedigree reconstruction [17][18][19][20] . In addition, genotyping allows for more precise estimations of heritability and genetic gain compared with using pedigree information alone 13,17,[21][22][23] .…”

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confidence: 99%

SNP-based analysis reveals unexpected features of genetic diversity, parental contributions and pollen contamination in a white spruce breeding program

Galeano

Bousquet

Thomas

2021

Sci Rep

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Accurate monitoring of genetic diversity levels of seedlots and mating patterns of parents from seed orchards are crucial to ensure that tree breeding programs are long-lasting and will deliver anticipated genetic gains. We used SNP genotyping to characterize founder trees, five bulk seed orchard seedlots, and trees from progeny trials to assess pollen contamination and the impact of severe roguing on genetic diversity and parental contributions in a first-generation open-pollinated white spruce clonal seed orchard. After severe roguing (eliminating 65% of the seed orchard trees), we found a slight reduction in the Shannon Index and a slightly negative inbreeding coefficient, but a sharp decrease in effective population size (eightfold) concomitant with sharp increase in coancestry (eightfold). Pedigree reconstruction showed unequal parental contributions across years with pollen contamination levels between 12 and 51% (average 27%) among seedlots, and 7–68% (average 30%) among individual genotypes within a seedlot. These contamination levels were not correlated with estimates obtained using pollen flight traps. Levels of pollen contamination also showed a Pearson’s correlation of 0.92 with wind direction, likely from a pollen source 1 km away from the orchard under study. The achievement of 5% genetic gain in height at rotation through eliminating two-thirds of the orchard thus generated a loss in genetic diversity as determined by the reduction in effective population size. The use of genomic profiles revealed the considerable impact of roguing on genetic diversity, and pedigree reconstruction of full-sib families showed the unanticipated impact of pollen contamination from a previously unconsidered source.

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Impact of a tree improvement program on the genetic diversity of sugi (Cryptomeria japonica D Don) plantations

Cited by 6 publications

References 37 publications

Pedigree Reconstruction and Spatial Analysis for Genetic Testing and Selection In A Larix Kaempferi (Lamb.) Carrière Plantation

Pedigree Reconstruction and Spatial Analysis for Genetic Testing and Selection In A Larix Kaempferi (Lamb.) Carrière Plantation

Pedigree reconstruction and spatial analysis for genetic testing and selection in a Larix kaempferi (Lamb.) Carrière plantation

SNP-based analysis reveals unexpected features of genetic diversity, parental contributions and pollen contamination in a white spruce breeding program

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