Additional file 5: of Enhancement of Glen Moy x Latham raspberry linkage map using GbS to further understand control of developmental processes leading to fruit ripening

Additional file 10: of Discrimination of candidate subgenome-specific loci by linkage map construction with an S1 population of octoploid strawberry (Fragaria × ananassa)

Soichiro Nagano (4023485)
Kenta Shirasawa (586327)
Hideki Hirakawa (103059)
Fumi Maeda (4023488)
Masami Ishikawa (4023482)
Sachiko Isobe (621484)

May 2017

Number of commonly mapped SNPs among the ‘Reikou’ linkage map and the two previously published linka...

Additional file 4: of Comparative RNA-Seq profiling of berry development between table grape ‘Kyoho’ and its early-ripening mutant ’Fengzao’

Da-Long Guo (3512159)
Fei-Fei Xi (3512162)
Yi-He Yu (3512156)
Xiao-Yu Zhang (738362)
Guo-Hai Zhang (1637623)
Gan-Yuan Zhong (433794)

October 2016

Expression clusters, annotation, and functional categories and distribution of 20,804 genes expresse...

Additional file 1: of Downregulation of RdDM during strawberry fruit ripening

Jingfei Cheng (845454)
Qingfeng Niu (6050822)
Bo Zhang (6559)
Kunsong Chen (105081)
Ruihua Yang (6050831)
Jian-Kang Zhu (23700)
Yijing Zhang (210060)
Zhaobo Lang (3477668)

December 2018

Table S1. Mapping statistics of bisulfite sequencing, RNA sequencing, and small-RNA sequencing. (XLS...

Additional file 4: of Enhancement of Glen Moy x Latham raspberry linkage map using GbS to further understand control of developmental processes leading to fruit ripening

Christine Hackett (210445)
Linda Milne (5636048)
Kay Smith (5636051)
Pete Hedley (4641694)
Jenny Morris (255155)
Craig Simpson (5636054)
Katharine Preedy (5636057)
Julie Graham (2079406)

August 2018

Table S1. Genome scaffolds within 2Â cM of most significant marker containing genes with a potential...

Additional file 3: of Enhancement of Glen Moy x Latham raspberry linkage map using GbS to further understand control of developmental processes leading to fruit ripening

Christine Hackett (210445)
Linda Milne (5636048)
Kay Smith (5636051)
Pete Hedley (4641694)
Jenny Morris (255155)
Craig Simpson (5636054)
Katharine Preedy (5636057)
Julie Graham (2079406)

August 2018

Figure S1. QTL profiles from simulated data. S1(a)-(c) map a QTL simulated on 67Â cM on the map of r...

Additional file 2: of Enhancement of Glen Moy x Latham raspberry linkage map using GbS to further understand control of developmental processes leading to fruit ripening

Christine Hackett (210445)
Linda Milne (5636048)
Kay Smith (5636051)
Pete Hedley (4641694)
Jenny Morris (255155)
Craig Simpson (5636054)
Katharine Preedy (5636057)
Julie Graham (2079406)

August 2018

Appendix B. Fitting a hidden Markov model (HMM) to obtain QTL genotype probabilities from marker dat...

Enhancement of Glen Moy x Latham raspberry linkage map using GbS to further understand control of developmental processes leading to fruit ripening

Christine A. Hackett
Linda Milne
Kay Smith
Pete Hedley
Jenny Morris
Craig G. Simpson
Katharine Preedy
Julie Graham

August 2018

Abstract Background The changing climate is altering timing of key fruit ripening processes and incr...

Additional file 2: of Downregulation of RdDM during strawberry fruit ripening

Jingfei Cheng (845454)
Qingfeng Niu (6050822)
Bo Zhang (6559)
Kunsong Chen (105081)
Ruihua Yang (6050831)
Jian-Kang Zhu (23700)
Yijing Zhang (210060)
Zhaobo Lang (3477668)

December 2018

Figure S1. The strawberry methylomes. Figure S2 Methylomes of fruits at different stages. Figure S3 ...

Additional file 9: of MicroRNA profiling analysis of developing berries for âKyohoâ and its early-ripening mutant during berry ripening

Da-Long Guo (3512159)
Qiong Li (346270)
Wen-Qing Lv (5983820)
Guo-Hai Zhang (1637623)
Yi-He Yu (3512156)

November 2018

Figure S4. KEGG analysis of the 20 most enriched pathways. The coloring of the q-values indicates th...

Additional file 5: of Downregulation of RdDM during strawberry fruit ripening

Jingfei Cheng (845454)
Qingfeng Niu (6050822)
Bo Zhang (6559)
Kunsong Chen (105081)
Ruihua Yang (6050831)
Jian-Kang Zhu (23700)
Yijing Zhang (210060)
Zhaobo Lang (3477668)

December 2018

Table S4. Genomic coordinates of 370,630 24-nt siRNA clusters in strawberry fruits. (XLSX 7562 kb

Additional file 9: of Discrimination of candidate subgenome-specific loci by linkage map construction with an S1 population of octoploid strawberry (Fragaria × ananassa)

Soichiro Nagano (4023485)
Kenta Shirasawa (586327)
Hideki Hirakawa (103059)
Fumi Maeda (4023488)
Masami Ishikawa (4023482)
Sachiko Isobe (621484)

May 2017

Number of haploSNPs on the linkage groups of the ‘Reikou’ map. The green, gray, yellow, and blue bar...

Mapping and expression of genes associated with raspberry fruit ripening and softening

Simpson, Craig G.
Cullen, Danny W.
Hackett, Christine A.
Smith, Kay
Hallett, Paul D.
McNicol, Jim
Woodhead, Mary
Graham, Julie

March 2017

KEY MESSAGE: QTL mapping identifies a range of underlying and unrelated genes with apparent roles in...

Mapping and expression of genes associated with raspberry fruit ripening and softening

Simpson, Craig G.
Cullen, Danny W.
Hackett, Christine A.
Smith, Kay
Hallett, Paul D.
McNicol, Jim
Woodhead, Mary
Graham, Julie

March 2017

KEY MESSAGE: QTL mapping identifies a range of underlying and unrelated genes with apparent roles in...

Mapping and expression of genes associated with raspberry fruit ripening and softening

Simpson, Craig G.
Cullen, Danny W.
Hackett, Christine A.
Smith, Kay
Hallett, Paul D.
McNicol, Jim
Woodhead, Mary
Graham, Julie

March 2017

KEY MESSAGE: QTL mapping identifies a range of underlying and unrelated genes with apparent roles in...

Additional file 4: of Downregulation of RdDM during strawberry fruit ripening

Jingfei Cheng (845454)
Qingfeng Niu (6050822)
Bo Zhang (6559)
Kunsong Chen (105081)
Ruihua Yang (6050831)
Jian-Kang Zhu (23700)
Yijing Zhang (210060)
Zhaobo Lang (3477668)

December 2018

Table S3. Expression of genes involved in DNA methylation and demethylation during ripening process....

Additional file 10: of Discrimination of candidate subgenome-specific loci by linkage map construction with an S1 population of octoploid strawberry (Fragaria × ananassa)

Soichiro Nagano (4023485)
Kenta Shirasawa (586327)
Hideki Hirakawa (103059)
Fumi Maeda (4023488)
Masami Ishikawa (4023482)
Sachiko Isobe (621484)

May 2017

Number of commonly mapped SNPs among the ‘Reikou’ linkage map and the two previously published linka...

Additional file 4: of Comparative RNA-Seq profiling of berry development between table grape ‘Kyoho’ and its early-ripening mutant ’Fengzao’

Da-Long Guo (3512159)
Fei-Fei Xi (3512162)
Yi-He Yu (3512156)
Xiao-Yu Zhang (738362)
Guo-Hai Zhang (1637623)
Gan-Yuan Zhong (433794)

October 2016

Expression clusters, annotation, and functional categories and distribution of 20,804 genes expresse...

Additional file 1: of Downregulation of RdDM during strawberry fruit ripening

Jingfei Cheng (845454)
Qingfeng Niu (6050822)
Bo Zhang (6559)
Kunsong Chen (105081)
Ruihua Yang (6050831)
Jian-Kang Zhu (23700)
Yijing Zhang (210060)
Zhaobo Lang (3477668)

December 2018

Table S1. Mapping statistics of bisulfite sequencing, RNA sequencing, and small-RNA sequencing. (XLS...

Additional file 4: of Enhancement of Glen Moy x Latham raspberry linkage map using GbS to further understand control of developmental processes leading to fruit ripening

Christine Hackett (210445)
Linda Milne (5636048)
Kay Smith (5636051)
Pete Hedley (4641694)
Jenny Morris (255155)
Craig Simpson (5636054)
Katharine Preedy (5636057)
Julie Graham (2079406)

August 2018

Table S1. Genome scaffolds within 2Â cM of most significant marker containing genes with a potential...

Additional file 3: of Enhancement of Glen Moy x Latham raspberry linkage map using GbS to further understand control of developmental processes leading to fruit ripening

Christine Hackett (210445)
Linda Milne (5636048)
Kay Smith (5636051)
Pete Hedley (4641694)
Jenny Morris (255155)
Craig Simpson (5636054)
Katharine Preedy (5636057)
Julie Graham (2079406)

August 2018

Figure S1. QTL profiles from simulated data. S1(a)-(c) map a QTL simulated on 67Â cM on the map of r...

Additional file 2: of Enhancement of Glen Moy x Latham raspberry linkage map using GbS to further understand control of developmental processes leading to fruit ripening

Christine Hackett (210445)
Linda Milne (5636048)
Kay Smith (5636051)
Pete Hedley (4641694)
Jenny Morris (255155)
Craig Simpson (5636054)
Katharine Preedy (5636057)
Julie Graham (2079406)

August 2018

Appendix B. Fitting a hidden Markov model (HMM) to obtain QTL genotype probabilities from marker dat...

Enhancement of Glen Moy x Latham raspberry linkage map using GbS to further understand control of developmental processes leading to fruit ripening

Christine A. Hackett
Linda Milne
Kay Smith
Pete Hedley
Jenny Morris
Craig G. Simpson
Katharine Preedy
Julie Graham

August 2018

Abstract Background The changing climate is altering timing of key fruit ripening processes and incr...

Additional file 2: of Downregulation of RdDM during strawberry fruit ripening

Jingfei Cheng (845454)
Qingfeng Niu (6050822)
Bo Zhang (6559)
Kunsong Chen (105081)
Ruihua Yang (6050831)
Jian-Kang Zhu (23700)
Yijing Zhang (210060)
Zhaobo Lang (3477668)

December 2018

Figure S1. The strawberry methylomes. Figure S2 Methylomes of fruits at different stages. Figure S3 ...

Additional file 9: of MicroRNA profiling analysis of developing berries for âKyohoâ and its early-ripening mutant during berry ripening

Da-Long Guo (3512159)
Qiong Li (346270)
Wen-Qing Lv (5983820)
Guo-Hai Zhang (1637623)
Yi-He Yu (3512156)

November 2018

Figure S4. KEGG analysis of the 20 most enriched pathways. The coloring of the q-values indicates th...

Additional file 5: of Downregulation of RdDM during strawberry fruit ripening

Jingfei Cheng (845454)
Qingfeng Niu (6050822)
Bo Zhang (6559)
Kunsong Chen (105081)
Ruihua Yang (6050831)
Jian-Kang Zhu (23700)
Yijing Zhang (210060)
Zhaobo Lang (3477668)

December 2018

Table S4. Genomic coordinates of 370,630 24-nt siRNA clusters in strawberry fruits. (XLSX 7562 kb

Additional file 9: of Discrimination of candidate subgenome-specific loci by linkage map construction with an S1 population of octoploid strawberry (Fragaria × ananassa)

Soichiro Nagano (4023485)
Kenta Shirasawa (586327)
Hideki Hirakawa (103059)
Fumi Maeda (4023488)
Masami Ishikawa (4023482)
Sachiko Isobe (621484)

May 2017

Number of haploSNPs on the linkage groups of the ‘Reikou’ map. The green, gray, yellow, and blue bar...

Mapping and expression of genes associated with raspberry fruit ripening and softening

Simpson, Craig G.
Cullen, Danny W.
Hackett, Christine A.
Smith, Kay
Hallett, Paul D.
McNicol, Jim
Woodhead, Mary
Graham, Julie

March 2017

KEY MESSAGE: QTL mapping identifies a range of underlying and unrelated genes with apparent roles in...

Mapping and expression of genes associated with raspberry fruit ripening and softening

Simpson, Craig G.
Cullen, Danny W.
Hackett, Christine A.
Smith, Kay
Hallett, Paul D.
McNicol, Jim
Woodhead, Mary
Graham, Julie

March 2017

KEY MESSAGE: QTL mapping identifies a range of underlying and unrelated genes with apparent roles in...

Mapping and expression of genes associated with raspberry fruit ripening and softening

Simpson, Craig G.
Cullen, Danny W.
Hackett, Christine A.
Smith, Kay
Hallett, Paul D.
McNicol, Jim
Woodhead, Mary
Graham, Julie

March 2017

KEY MESSAGE: QTL mapping identifies a range of underlying and unrelated genes with apparent roles in...

Additional file 4: of Downregulation of RdDM during strawberry fruit ripening

Jingfei Cheng (845454)
Qingfeng Niu (6050822)
Bo Zhang (6559)
Kunsong Chen (105081)
Ruihua Yang (6050831)
Jian-Kang Zhu (23700)
Yijing Zhang (210060)
Zhaobo Lang (3477668)

December 2018

Table S3. Expression of genes involved in DNA methylation and demethylation during ripening process....

Additional file 10: of Discrimination of candidate subgenome-specific loci by linkage map construction with an S1 population of octoploid strawberry (Fragaria × ananassa)

Soichiro Nagano (4023485)
Kenta Shirasawa (586327)
Hideki Hirakawa (103059)
Fumi Maeda (4023488)
Masami Ishikawa (4023482)
Sachiko Isobe (621484)

May 2017

Number of commonly mapped SNPs among the ‘Reikou’ linkage map and the two previously published linka...

Additional file 4: of Comparative RNA-Seq profiling of berry development between table grape ‘Kyoho’ and its early-ripening mutant ’Fengzao’

Da-Long Guo (3512159)
Fei-Fei Xi (3512162)
Yi-He Yu (3512156)
Xiao-Yu Zhang (738362)
Guo-Hai Zhang (1637623)
Gan-Yuan Zhong (433794)

October 2016

Expression clusters, annotation, and functional categories and distribution of 20,804 genes expresse...

Additional file 1: of Downregulation of RdDM during strawberry fruit ripening

Jingfei Cheng (845454)
Qingfeng Niu (6050822)
Bo Zhang (6559)
Kunsong Chen (105081)
Ruihua Yang (6050831)
Jian-Kang Zhu (23700)
Yijing Zhang (210060)
Zhaobo Lang (3477668)

December 2018

Table S1. Mapping statistics of bisulfite sequencing, RNA sequencing, and small-RNA sequencing. (XLS...

Additional file 5: of Enhancement of Glen Moy x Latham raspberry linkage map using GbS to further understand control of developmental processes leading to fruit ripening

Abstract

Extracted data

Additional file 5: of Enhancement of Glen Moy x Latham raspberry linkage map using GbS to further understand control of developmental processes leading to fruit ripening

Abstract

Extracted data

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