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

10.21203/rs.2.24669/v2 ◽

2020 ◽

Author(s):

Feng Yang ◽

Fei Shen ◽

Zhi Liu ◽

Mingli He ◽

Yi Wang ◽

...

Keyword(s):

Binding Site ◽

Correlation Coefficients ◽

Tree Height ◽

F1 Hybrids ◽

Functional Markers ◽

Potential Candidate ◽

Apple Rootstock ◽

Trunk Diameter ◽

Development And Validation ◽

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 ‘ 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 accurately predict apple rootstock dwarfing ability

10.21203/rs.2.24669/v1 ◽

2020 ◽

Author(s):

Feng Yang ◽

Fei Shen ◽

Zhi Liu ◽

Mingli He ◽

Yi Wang ◽

...

Keyword(s):

Binding Site ◽

Correlation Coefficients ◽

Tree Height ◽

F1 Hybrids ◽

Functional Markers ◽

Apple Rootstock ◽

Trunk Diameter ◽

Cis Element ◽

Development And Validation ◽

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 ‘ M alus baccata ’ × ‘M9’, the intervals of Dw1 and Dw2 were narrowed down. MdLBD3 and MdARF6 were predicted as candidate genes from Dw1 , while MdG3OX3 was a 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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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.

Download Full-text

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.

Download Full-text