Development and validation of functional markers from Dw1 and Dw2 loci to accurately predict apple rootstock dwarfing ability

Abstract Background: ‘M9’ is a widely used apple dwarfing rootstock due to the outstanding effects on both precocity and vigorous control. Two quantitative trait loci (QTLs), Dw1 and Dw2 , for the dwarfing effect were previously mapped on ‘M9’, but the genetic variations that underpin the dwarfing ability have not been elucidated to date. Result: By using ‘Red Fuji’ trees grafted on 1123 hybrids from ‘ M alus baccata ’ × ‘M9’, the intervals of Dw1 and Dw2 were narrowed down. MdLBD3 and MdARF6 were predicted as potential candidate genes from Dw1 , while MdG3OX3 was a possible candidate gene from Dw2 . An 11 bp deletion at -339 bp upstream of the transcription start site (TSS) of MdLBD3 generated a new cis-element binding site with MdWRKY2 and caused increased expression of MdLBD3 . Coincidently, a ten bp deletion at -278 bp upstream of the TSS of MdG3OX3 created an additional binding site of MdABI5 , leading to higher expression of MdG3OX3 . At -954 bp of the MdARF6 promoter, a 14 bp insertion destroyed the binding ability by MdABI5 and reduced MdARF6 expression. The genotype effects of these insertion and deletions as diagnostic markers on dwarfing traits (tree height, trunk diameter, and canopy width) were estimated in 108 F1 hybrids. The genomic predicted genetic values (GEGV) were calculated by adding up the genotype effects of the three markers and the population mean phenotype. The GEGV of the dwarfing traits exhibited high correlation coefficients of 0.93, 0.94, and 0.93 in terms of tree height, trunk diameter, and canopy width for the observed phenotype values, respectively. The predictability of GEGV was validated in 64 Malus accessions. Conclusion : The development of the three functional markers, Ld/Li, Ad/Ai, and Gd/Gi, ensures the accurate genomic assisted prediction of dwarfing ability in apple rootstock breeding. The data also suggested that ABA, auxin, GA, and zeatin signals may be involved in the regulation of apple rootstock dwarfing mechanism.

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Development and validation of functional markers from Dw1 and Dw2 loci to assistant predict apple rootstock dwarfing ability

10.21203/rs.2.24669/v4 ◽

2021 ◽

Author(s):

Feng Yang ◽

Fei Shen ◽

Zhi Liu ◽

Mingli He ◽

Yi Wang ◽

...

Keyword(s):

Transcription Factor ◽

Binding Site ◽

Tree Height ◽

F1 Hybrids ◽

Functional Markers ◽

Potential Candidate ◽

Apple Rootstock ◽

Trunk Diameter ◽

Domain 3 ◽

Genotype Effects

Abstract Background: ‘M9’ is a widely used apple dwarfing rootstock due to the outstanding effects on both precocity and vigorous control. Two quantitative trait loci (QTLs), Dw1 and Dw2, for the dwarfing effect were previously mapped on ‘M9’, but the genetic variations that underpin the dwarfing ability have not been elucidated to date. Result: By using ‘Red Fuji’(Malus × domestica Borkh.) trees grafted on 1123 hybrids from ‘Malus baccata Borkh.’ × ‘M9’, the intervals of Dw1 and Dw2 were narrowed down. MdLBD3 (Md Lateral organ boundaries domain 3)and MdARF6 (Md Auxin response factor 6) were predicted as potential candidate genes from Dw1, while MdG3OX3 (Md Gibberellin 3-beta-dioxygenase 3) was a possible candidate gene from Dw2. An 11 bp deletion at -339 bp upstream of the transcription start site (TSS) of MdLBD3 generated a new cis-element binding site with MdWRKY2 (Md WRKY transcription factor 2)and caused increased expression of MdLBD3. Coincidently, a ten bp deletion at -278 bp upstream of the TSS of MdG3OX3 created an additional binding site of MdABI5 (Md Abscisic acid insensitive 5), leading to higher expression of MdG3OX3. At -954 bp of the MdARF6 promoter, a 14 bp insertion destroyed the binding ability by MdGAMYB (Md transcription factor GAMYB)and reduced MdARF6 expression. The genotype effects of these insertion and deletions as diagnostic markers on dwarfing traits (tree height, trunk diameter, and canopy width) were estimated in 108 F1 hybrids. The genomic predicted genetic values (GEGV) were calculated by adding up the genotype effects of the three markers and the population mean phenotype. The GEGV of the dwarfing traits exhibited high correlation coefficients of 0.93, 0.94, and 0.93 in terms of tree height, trunk diameter, and canopy width for the observed phenotype values, respectively. The predictability of GEGV was validated in 64 Malus accessions. Conclusion: The development of the three functional markers, Ld/Li, Ad/Ai, and Gd/Gi, ensures the genomic assisted prediction of dwarfing ability in apple rootstock breeding. The data also suggested that hormone (ABA, Auxin, GA, and zeatin signals) is one of the regulation pathways in controlling apple rootstock dwarfing mechanisms.

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Development and validation of functional markers from Dw1 and Dw2 loci to accurately predict apple rootstock dwarfing ability

10.21203/rs.2.24669/v3 ◽

2020 ◽

Author(s):

Feng Yang ◽

Fei Shen ◽

Zhi Liu ◽

Mingli He ◽

Yi Wang ◽

...

Keyword(s):

Transcription Factor ◽

Binding Site ◽

Tree Height ◽

F1 Hybrids ◽

Functional Markers ◽

Potential Candidate ◽

Apple Rootstock ◽

Trunk Diameter ◽

Domain 3 ◽

Genotype Effects

Abstract Background: ‘M9’ is a widely used apple dwarfing rootstock due to the outstanding effects on both precocity and vigorous control. Two quantitative trait loci (QTLs), Dw1 and Dw2, for the dwarfing effect were previously mapped on ‘M9’, but the genetic variations that underpin the dwarfing ability have not been elucidated to date. Result: By using ‘Red Fuji’ trees grafted on 1123 hybrids from ‘Malus baccata’ × ‘M9’, the intervals of Dw1 and Dw2 were narrowed down. MdLBD3 (Md Lateral organ boundaries domain 3)and MdARF6 (Md Auxin response factor 6) were predicted as potential candidate genes from Dw1, while MdG3OX3 (Md Gibberellin 3-beta-dioxygenase 3) was a possible candidate gene from Dw2. An 11 bp deletion at -339 bp upstream of the transcription start site (TSS) of MdLBD3 generated a new cis-element binding site with MdWRKY2 (Md WRKY transcription factor 2)and caused increased expression of MdLBD3. Coincidently, a ten bp deletion at -278 bp upstream of the TSS of MdG3OX3 created an additional binding site of MdABI5 (Md Abscisic acid insensitive 5), leading to higher expression of MdG3OX3. At -954 bp of the MdARF6 promoter, a 14 bp insertion destroyed the binding ability by MdGAMYB (Md transcription factor GAMYB)and reduced MdARF6 expression. The genotype effects of these insertion and deletions as diagnostic markers on dwarfing traits (tree height, trunk diameter, and canopy width) were estimated in 108 F1 hybrids. The genomic predicted genetic values (GEGV) were calculated by adding up the genotype effects of the three markers and the population mean phenotype. The GEGV of the dwarfing traits exhibited high correlation coefficients of 0.93, 0.94, and 0.93 in terms of tree height, trunk diameter, and canopy width for the observed phenotype values, respectively. The predictability of GEGV was validated in 64 Malus accessions. Conclusion: The development of the three functional markers, Ld/Li, Ad/Ai, and Gd/Gi, ensures the accurate genomic assisted prediction of dwarfing ability in apple rootstock breeding. The data also suggested that ABA, auxin, GA, and zeatin signals may be involved in the regulation of apple rootstock dwarfing mechanism.

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Genomics-assisted prediction of salt and alkali tolerances and functional marker development in apple rootstocks

10.21203/rs.3.rs-17008/v3 ◽

2020 ◽

Author(s):

Jing Liu ◽

Fei Shen ◽

Yao Xiao ◽

Hongcheng Fang ◽

Changpeng Qiu ◽

...

Keyword(s):

Prediction Models ◽

Allelic Variation ◽

Bulked Segregant Analysis ◽

Functional Markers ◽

Alkaline Stress ◽

Alkali Stress ◽

Apple Rootstock ◽

Apple Rootstocks ◽

Alkali Tolerance ◽

Genotype Effects

Abstract Background: Saline, alkaline, and saline-alkaline stress severely affect plant growth and development. The tolerance of plants to these stressors has long been important breeding objectives, especially for woody perennials like apple. The aims of this study were to identify quantitative trait loci (QTLs) and to develop genomics-assisted prediction models for salt, alkali, and salt-alkali tolerance in apple rootstock. Results: A total of 3,258 hybrids derived from the apple rootstock cultivars ‘Baleng Crab’ (Malus robusta Rehd., tolerant) × ‘M9’ (M. pumila Mill., sensitive) were used to identify 17, 13, and two QTLs for injury indices of salt, alkali, and salt–alkali stress via bulked segregant analysis. The genotype effects of single nucleotide polymorphism (SNP) markers designed on candidate genes in each QTL interval were estimated. The genomic predicted value of an individual hybrid was calculated by adding the sum of all marker genotype effects to the mean phenotype value of the population. The prediction accuracy was 0.6569, 0.6695, and 0.5834 for injury indices of salt, alkali, and salt–alkali stress, respectively. SNP182G on MdRGLG3, which changes a leucine to an arginine at the vWFA-domain, conferred tolerance to salt, alkali, and salt-alkali stress. SNP761A on MdKCAB, affecting the Kv_beta domain that cooperated with the linked allelic variation SNP11, contributed to salt, alkali, and salt–alkali tolerance in apple rootstock. Conclusions: The genomics-assisted prediction models can potentially be used in breeding saline, alkaline, and saline-alkaline tolerant apple rootstocks. The QTLs and the functional markers may provide insight for future studies into the genetic variation of plant abiotic stress tolerance.

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Genomics-assisted prediction of salt and alkali tolerances and functional marker development in apple rootstocks

10.21203/rs.3.rs-17008/v5 ◽

2020 ◽

Author(s):

Jing Liu ◽

Fei Shen ◽

Yao Xiao ◽

Hongcheng Fang ◽

Changpeng Qiu ◽

...

Keyword(s):

Prediction Models ◽

Allelic Variation ◽

Bulked Segregant Analysis ◽

Functional Markers ◽

Alkaline Stress ◽

Alkali Stress ◽

Apple Rootstock ◽

Apple Rootstocks ◽

Alkali Tolerance ◽

Genotype Effects

Abstract Background: Saline, alkaline, and saline-alkaline stress severely affect plant growth and development. The tolerance of plants to these stressors has long been important breeding objectives, especially for woody perennials like apple. The aims of this study were to identify quantitative trait loci (QTLs) and to develop genomics-assisted prediction models for salt, alkali, and salt-alkali tolerance in apple rootstock. Results: A total of 3,258 hybrids derived from the apple rootstock cultivars ‘Baleng Crab’ (Malus robusta Rehd., tolerant) × ‘M9’ (M. pumila Mill., sensitive) were used to identify 17, 13, and two QTLs for injury indices of salt, alkali, and salt–alkali stress via bulked segregant analysis. The genotype effects of single nucleotide polymorphism (SNP) markers designed on candidate genes in each QTL interval were estimated. The genomic predicted value of an individual hybrid was calculated by adding the sum of all marker genotype effects to the mean phenotype value of the population. The prediction accuracy was 0.6569, 0.6695, and 0.5834 for injury indices of salt, alkali, and salt–alkali stress, respectively. SNP182G on MdRGLG3, which changes a leucine to an arginine at the vWFA-domain, conferred tolerance to salt, alkali, and salt-alkali stress. SNP761A on MdKCAB, affecting the Kv_beta domain that cooperated with the linked allelic variation SNP11, contributed to salt, alkali, and salt–alkali tolerance in apple rootstock. Conclusions: The genomics-assisted prediction models can potentially be used in breeding saline, alkaline, and saline-alkaline tolerant apple rootstocks. The QTLs and the functional markers may provide insight for future studies into the genetic variation of plant abiotic stress tolerance.

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Genomics-assisted prediction of salt and alkali tolerances and functional marker development in apple rootstocks.

10.21203/rs.3.rs-17008/v2 ◽

2020 ◽

Author(s):

Jing Liu ◽

Fei Shen ◽

Yao Xiao ◽

Hongcheng Fang ◽

Changpeng Qiu ◽

...

Keyword(s):

Prediction Models ◽

Allelic Variation ◽

Bulked Segregant Analysis ◽

Functional Markers ◽

Alkaline Stress ◽

Alkali Stress ◽

Apple Rootstock ◽

Apple Rootstocks ◽

Alkali Tolerance ◽

Genotype Effects

Abstract Background: Saline, alkaline, and saline-alkaline stress severely affect plant growth and development. The tolerance of plants to these stressors has long been important breeding objectives, especially for woody perennials like apple. The aims of this study were to identify quantitative trait loci (QTLs) and to develop genomics-assisted prediction models for salt, alkali, and salt-alkali tolerance in apple rootstock. Results: A total of 3,258 hybrids derived from the apple rootstock cultivars ‘Baleng Crab’ ( Malus robusta Rehd., tolerant) × ‘M9’ ( M. pumila Mill., sensitive) were used to identify 17, 13, and two QTLs for injury indices of salt, alkali, and salt–alkali stress via bulked segregant analysis. The genotype effects of single nucleotide polymorphism (SNP) markers designed on candidate genes in each QTL interval were estimated. The genomic predicted value of an individual hybrid was calculated by adding the sum of all marker genotype effects to the mean phenotype value of the population. The prediction accuracy was 0.6569, 0.6695, and 0.5834 for injury indices of salt, alkali, and salt–alkali stress, respectively. SNP182G on MdRGLG3 , which changes a leucine to an arginine at the vWFA-domain, conferred tolerance to salt, alkali, and salt-alkali stress. SNP761A on MdKCAB , affecting the Kv_beta domain that cooperated with the linked allelic variation SNP11, contributed to salt, alkali, and salt–alkali tolerance in apple rootstock. Conclusions: The genomics-assisted prediction models can potentially be used in breeding saline, alkaline, and saline-alkaline tolerant apple rootstocks. The QTLs and the functional markers may provide insight for future studies into the genetic variation of plant abiotic stress tolerance.

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Genomics-assisted prediction of salt and alkali tolerances and functional marker development in apple rootstocks

10.21203/rs.3.rs-17008/v4 ◽

2020 ◽

Author(s):

Jing Liu ◽

Fei Shen ◽

Yao Xiao ◽

Hongcheng Fang ◽

Changpeng Qiu ◽

...

Keyword(s):

Prediction Models ◽

Allelic Variation ◽

Bulked Segregant Analysis ◽

Functional Markers ◽

Alkaline Stress ◽

Alkali Stress ◽

Apple Rootstock ◽

Apple Rootstocks ◽

Alkali Tolerance ◽

Genotype Effects

Abstract Background: Saline, alkaline, and saline-alkaline stress severely affect plant growth and development. The tolerance of plants to these stressors has long been important breeding objectives, especially for woody perennials like apple. The aims of this study were to identify quantitative trait loci (QTLs) and to develop genomics-assisted prediction models for salt, alkali, and salt-alkali tolerance in apple rootstock. Results: A total of 3,258 hybrids derived from the apple rootstock cultivars ‘Baleng Crab’ (Malus robusta Rehd., tolerant) × ‘M9’ (M. pumila Mill., sensitive) were used to identify 17, 13, and two QTLs for injury indices of salt, alkali, and salt–alkali stress via bulked segregant analysis. The genotype effects of single nucleotide polymorphism (SNP) markers designed on candidate genes in each QTL interval were estimated. The genomic predicted value of an individual hybrid was calculated by adding the sum of all marker genotype effects to the mean phenotype value of the population. The prediction accuracy was 0.6569, 0.6695, and 0.5834 for injury indices of salt, alkali, and salt–alkali stress, respectively. SNP182G on MdRGLG3, which changes a leucine to an arginine at the vWFA-domain, conferred tolerance to salt, alkali, and salt-alkali stress. SNP761A on MdKCAB, affecting the Kv_beta domain that cooperated with the linked allelic variation SNP11, contributed to salt, alkali, and salt–alkali tolerance in apple rootstock. Conclusions: The genomics-assisted prediction models can potentially be used in breeding saline, alkaline, and saline-alkaline tolerant apple rootstocks. The QTLs and the functional markers may provide insight for future studies into the genetic variation of plant abiotic stress tolerance.

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Genomics-assisted prediction of salt and alkali tolerances and functional marker development in apple rootstocks

10.21203/rs.3.rs-17008/v1 ◽

2020 ◽

Author(s):

Jing Liu ◽

Fei Shen ◽

Yao Xiao ◽

Hongcheng Fang ◽

Changpeng Qiu ◽

...

Keyword(s):

Prediction Models ◽

Allelic Variation ◽

Bulked Segregant Analysis ◽

Functional Markers ◽

Alkaline Stress ◽

Alkali Stress ◽

Apple Rootstock ◽

Apple Rootstocks ◽

Alkali Tolerance ◽

Genotype Effects

Abstract Background: Saline, alkaline, and saline-alkaline stress severely affect plant growth and development. The tolerance of plants to these stressors has long been important breeding objectives, especially for woody perennials like apple. The aims of this study were to identify quantitative trait loci (QTLs) and to develop genomics-assisted prediction models for salt, alkali, and salt-alkali tolerance in apple rootstock. Results: A total of 3,258 hybrids derived from the apple rootstock cultivars ‘Baleng Crab’ ( Malus robusta Rehd., tolerant) × ‘M9’ ( M. pumila Mill., sensitive) were used to identify 17, 13, and two QTLs for injury indices of salt, alkali, and salt–alkali stress via bulked segregant analysis. The genotype effects of single nucleotide polymorphism (SNP) markers designed on candidate genes in each QTL interval were estimated. The genomic predicted value of an individual hybrid was calculated by adding the sum of all marker genotype effects to the mean phenotype value of the population. The prediction accuracy was 0.6569, 0.6695, and 0.5834 for injury indices of salt, alkali, and salt–alkali stress, respectively. SNP182G on MdRGLG3 , which changes a leucine to an arginine at the vWFA-domain, conferred tolerance to salt, alkali, and salt-alkali stress. SNP761A on MdKCAB , affecting the Kv_beta domain that cooperated with the linked allelic variation SNP11, contributed to salt, alkali, and salt–alkali tolerance in apple rootstock. Conclusions: The genomics-assisted prediction models can potentially be used in breeding saline, alkaline, and saline-alkaline tolerant apple rootstocks. The QTLs and the functional markers may provide insight for future studies into the genetic variation of plant abiotic stress tolerance.

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A protocol for sampling vascular epiphyte richness and abundance

Journal of Tropical Ecology ◽

10.1017/s0266467408005786 ◽

2009 ◽

Vol 25 (2) ◽

pp. 107-121 ◽

Cited By ~ 24

Author(s):

Jan H. D. Wolf ◽

S. Robbert Gradstein ◽

Nalini M. Nadkarni

Keyword(s):

Tree Height ◽

Dry Weight ◽

Mantel Test ◽

Tree Size ◽

Tree Level ◽

Trunk Diameter ◽

Host Trees ◽

Epiphyte Communities ◽

Vascular Epiphyte

Abstract:The sampling of epiphytes is fraught with methodological difficulties. We present a protocol to sample and analyse vascular epiphyte richness and abundance in forests of different structure (SVERA). Epiphyte abundance is estimated as biomass by recording the number of plant components in a range of size cohorts. Epiphyte species biomass is estimated on 35 sample-trees, evenly distributed over six trunk diameter-size cohorts (10 trees with dbh > 30 cm). Tree height, dbh and number of forks (diameter > 5 cm) yield a dimensionless estimate of the size of the tree. Epiphyte dry weight and species richness between forests is compared with ANCOVA that controls for tree size. SChao1 is used as an estimate of the total number of species at the sites. The relative dependence of the distribution of the epiphyte communities on environmental and spatial variables may be assessed using multivariate analysis and Mantel test. In a case study, we compared epiphyte vegetation of six Mexican oak forests and one Colombian oak forest at similar elevation. We found a strongly significant positive correlation between tree size and epiphyte richness or biomass at all sites. In forests with a higher diversity of host trees, more trees must be sampled. Epiphyte biomass at the Colombian site was lower than in any of the Mexican sites; without correction for tree size no significant differences in terms of epiphyte biomass could be detected. The occurrence of spatial dependence, at both the landscape level and at the tree level, shows that the inclusion of spatial descriptors in SVERA is justified.

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Development and Validation of Crosswalks Between FIM® and SCIM III for Voluntary Musculoskeletal Movement Functions

Neurorehabilitation and Neural Repair ◽

10.1177/15459683211033854 ◽

2021 ◽

pp. 154596832110338

Author(s):

Linda A. T. Jones ◽

Chih-Ying Li ◽

David Weitzenkamp ◽

John Steeves ◽

Susie Charlifue ◽

...

Keyword(s):

Spinal Cord ◽

Spinal Cord Injury ◽

Functional Recovery ◽

Systems Of Care ◽

Functional Independence Measure ◽

Correlation Coefficients ◽

Functional Independence ◽

Cord Injury ◽

Parametric Analyses ◽

Development And Validation

Background. In spinal cord injury, there are multiple databases containing information on functional recovery, but data cannot be pooled or compared due to differences in how function is measured. A crosswalk is needed to link or convert scores between instruments. Objectives. To create a crosswalk between the voluntary musculoskeletal movement items in the Functional Independence Measure (FIM®) and the Spinal Cord Independence Measure III (SCIM III) for spinal cord injury. Methods. Retrospective datasets with FIM® and SCIM III on the same people were used to develop (Swiss dataset, n = 662) and validate (US, n = 119, and Canadian datasets, n = 133) the crosswalks. Three different crosswalk methods (expert panel, equipercentile, and Rasch analysis) were employed. We used the correlation between observed scores on FIM® and SCIM III to crosswalked scores as the primary criterion to assess the strength of the crosswalk. Secondary criteria such as score distributions, Cohen’s effect size, point differences, and subgroup invariance were also evaluated. Results. All three methods resulted in strong correlation coefficients, exceeding the primary criterion value of r = .866 (.897–.972). Assessment of secondary criteria suggests the equipercentile and Rasch methods produced the strongest crosswalks. Conclusions. The Rasch FIM®/SCIM III crosswalk is recommended because it is based on co-calibration of linearized measures, allowing for more sophisticated parametric analyses. The crosswalk will allow comparisons of voluntary musculoskeletal functional recovery across international databases using different functional measures, as well as different systems of care and rehabilitation approaches.

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