Additional file 14: of Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits

Additional file 1: of Genome-wide nucleotide patterns and potential mechanisms of genome divergence following domestication in maize and soybean

Jinyu Wang (381467)
Xianran Li (6485)
Kyung Kim (31555)
Michael Scanlon (791403)
Scott Jackson (183074)
Nathan Springer (56696)
Jianming Yu (102511)

April 2019

Figure S1. Diagram of SNP filtering process. Figure S2. Frequency of SNP substitution types. Figure ...

Additional file 7: of Genome-wide association study discovered favorable single nucleotide polymorphisms and candidate genes associated with ramet number in ramie (Boehmeria nivea L.)

Kunmei Chen (5135393)
Mingbao Luan (397329)
Heping Xiong (5135387)
Ping Chen (89712)
Jikang Chen (5135381)
Gang Gao (5135390)
Kunyong Huang (6080612)
Aiguo Zhu (3327450)
Chunming Yu (5135384)

December 2018

Results of polymerase chain reaction (PCR) amplification using specific primers of significant singl...

Additional file 4: of Genome-wide association analysis of stalk biomass and anatomical traits in maize

Mona Mazaheri (3995609)
Marlies Heckwolf (3995618)
Brieanne Vaillancourt (108028)
Joseph Gage (3879919)
Brett Burdo (6286337)
Sven Heckwolf (6286340)
Kerrie Barry (276529)
Anna Lipzen (194340)
Camila Ribeiro (6286343)
Thomas Kono (448008)
Heidi Kaeppler (3995606)
Edgar Spalding (3879922)
Candice Hirsch (6286346)
C. Robin Buell (108039)
Natalia Leon (3995600)
Shawn Kaeppler (524084)

February 2019

LD plots of genomic regions containing significant SNPs and adjacent candidate genes. Significant SN...

Additional file 3: of Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits

G. Ramakrishna (2482021)
Parampreet Kaur (699310)
Deepti Nigam (5269685)
Pavan Chaduvula (5494748)
Sangita Yadav (5494745)
Akshay Talukdar (3454961)
Nagendra Singh (359528)
Kishor Gaikwad (3799879)

July 2018

Identification of total SNPs in G. soja with respect to reference genome. (XLSX 19576Â kb

Additional file 4: of Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits

G. Ramakrishna (2482021)
Parampreet Kaur (699310)
Deepti Nigam (5269685)
Pavan Chaduvula (5494748)
Sangita Yadav (5494745)
Akshay Talukdar (3454961)
Nagendra Singh (359528)
Kishor Gaikwad (3799879)

July 2018

Identification of total InDels in G. soja with respect to reference genome. (CSV 97568Â kb

Additional file 5: of Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits

G. Ramakrishna (2482021)
Parampreet Kaur (699310)
Deepti Nigam (5269685)
Pavan Chaduvula (5494748)
Sangita Yadav (5494745)
Akshay Talukdar (3454961)
Nagendra Singh (359528)
Kishor Gaikwad (3799879)

July 2018

Functional classification of non-synonymous SNPs and InDels into diverse pathways. (XLS 636Â kb

Additional file 1: of Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits

G. Ramakrishna (2482021)
Parampreet Kaur (699310)
Deepti Nigam (5269685)
Pavan Chaduvula (5494748)
Sangita Yadav (5494745)
Akshay Talukdar (3454961)
Nagendra Singh (359528)
Kishor Gaikwad (3799879)

July 2018

Table S1. Statistics of Assembly generated from Illumina HiSeq1000 sequencing data. (DOC 29Â kb

Additional file 9: of Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits

G. Ramakrishna (2482021)
Parampreet Kaur (699310)
Deepti Nigam (5269685)
Pavan Chaduvula (5494748)
Sangita Yadav (5494745)
Akshay Talukdar (3454961)
Nagendra Singh (359528)
Kishor Gaikwad (3799879)

July 2018

Functional annotation of 205 interacting patterns as identified for 7 selected genes. (XLS 184Â kb

Additional file 8: of Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits

G. Ramakrishna (2482021)
Parampreet Kaur (699310)
Deepti Nigam (5269685)
Pavan Chaduvula (5494748)
Sangita Yadav (5494745)
Akshay Talukdar (3454961)
Nagendra Singh (359528)
Kishor Gaikwad (3799879)

July 2018

Figure S3. GO annotation of 205 interacting partners of 7 selected genes into cellular compartments....

Additional file 6: of Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits

G. Ramakrishna (2482021)
Parampreet Kaur (699310)
Deepti Nigam (5269685)
Pavan Chaduvula (5494748)
Sangita Yadav (5494745)
Akshay Talukdar (3454961)
Nagendra Singh (359528)
Kishor Gaikwad (3799879)

July 2018

Figure S1. GO annotation of 205 interacting partners of 7 selected genes into biological processes. ...

Additional file 7: of Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits

G. Ramakrishna (2482021)
Parampreet Kaur (699310)
Deepti Nigam (5269685)
Pavan Chaduvula (5494748)
Sangita Yadav (5494745)
Akshay Talukdar (3454961)
Nagendra Singh (359528)
Kishor Gaikwad (3799879)

July 2018

Figure S2. GO annotation of 205 interacting partners of 7 selected genes into molecular functions. (...

Additional file 12: of Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits

G. Ramakrishna (2482021)
Parampreet Kaur (699310)
Deepti Nigam (5269685)
Pavan Chaduvula (5494748)
Sangita Yadav (5494745)
Akshay Talukdar (3454961)
Nagendra Singh (359528)
Kishor Gaikwad (3799879)

July 2018

Table S2. Statistics of E3 Ubiquitin ligase protein structural predictions in G. max and G. soja (TM...

Additional file 11: of Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits

G. Ramakrishna (2482021)
Parampreet Kaur (699310)
Deepti Nigam (5269685)
Pavan Chaduvula (5494748)
Sangita Yadav (5494745)
Akshay Talukdar (3454961)
Nagendra Singh (359528)
Kishor Gaikwad (3799879)

July 2018

Figure S5. Pairwise alignment (a) of protein sequence of E3 Ubiquitin ligase from G. max and G. soja...

Additional file 3: of Genome-wide association study of four yield-related traits at the R6 stage in soybean

Xiangnan Li (3459992)
Xiaoli Zhang (135098)
Longming Zhu (5882234)
Yuanpeng Bu (5023004)
Xinfang Wang (747604)
Xing Zhang (11943)
Yang Zhou (65942)
Xiaoting Wang (206653)
Na Guo (198794)
Lijuan Qiu (651900)
Jinming Zhao (349674)
Han Xing (227847)

March 2019

Table S3. Summary of the polymorphic markers on the 20 chromosomes of Glycine max. (XLSX 10 kb

Additional file 3: of A genome-wide association study of seed composition traits in wild soybean (Glycine soja)

Larry Leamy (3620168)
Hengyou Zhang (3620171)
Changbao Li (3620174)
Charles Chen (121346)
Bao-Hua Song (3309945)

January 2017

Genome-wide average LD decay estimated for the wild soybean sample. The LD decay is measured in r2 v...

Additional file 1: of Genome-wide nucleotide patterns and potential mechanisms of genome divergence following domestication in maize and soybean

Jinyu Wang (381467)
Xianran Li (6485)
Kyung Kim (31555)
Michael Scanlon (791403)
Scott Jackson (183074)
Nathan Springer (56696)
Jianming Yu (102511)

April 2019

Figure S1. Diagram of SNP filtering process. Figure S2. Frequency of SNP substitution types. Figure ...

Additional file 7: of Genome-wide association study discovered favorable single nucleotide polymorphisms and candidate genes associated with ramet number in ramie (Boehmeria nivea L.)

Kunmei Chen (5135393)
Mingbao Luan (397329)
Heping Xiong (5135387)
Ping Chen (89712)
Jikang Chen (5135381)
Gang Gao (5135390)
Kunyong Huang (6080612)
Aiguo Zhu (3327450)
Chunming Yu (5135384)

December 2018

Results of polymerase chain reaction (PCR) amplification using specific primers of significant singl...

Additional file 4: of Genome-wide association analysis of stalk biomass and anatomical traits in maize

Mona Mazaheri (3995609)
Marlies Heckwolf (3995618)
Brieanne Vaillancourt (108028)
Joseph Gage (3879919)
Brett Burdo (6286337)
Sven Heckwolf (6286340)
Kerrie Barry (276529)
Anna Lipzen (194340)
Camila Ribeiro (6286343)
Thomas Kono (448008)
Heidi Kaeppler (3995606)
Edgar Spalding (3879922)
Candice Hirsch (6286346)
C. Robin Buell (108039)
Natalia Leon (3995600)
Shawn Kaeppler (524084)

February 2019

LD plots of genomic regions containing significant SNPs and adjacent candidate genes. Significant SN...

Additional file 3: of Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits

G. Ramakrishna (2482021)
Parampreet Kaur (699310)
Deepti Nigam (5269685)
Pavan Chaduvula (5494748)
Sangita Yadav (5494745)
Akshay Talukdar (3454961)
Nagendra Singh (359528)
Kishor Gaikwad (3799879)

July 2018

Identification of total SNPs in G. soja with respect to reference genome. (XLSX 19576Â kb

Additional file 4: of Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits

G. Ramakrishna (2482021)
Parampreet Kaur (699310)
Deepti Nigam (5269685)
Pavan Chaduvula (5494748)
Sangita Yadav (5494745)
Akshay Talukdar (3454961)
Nagendra Singh (359528)
Kishor Gaikwad (3799879)

July 2018

Identification of total InDels in G. soja with respect to reference genome. (CSV 97568Â kb

Additional file 5: of Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits

G. Ramakrishna (2482021)
Parampreet Kaur (699310)
Deepti Nigam (5269685)
Pavan Chaduvula (5494748)
Sangita Yadav (5494745)
Akshay Talukdar (3454961)
Nagendra Singh (359528)
Kishor Gaikwad (3799879)

July 2018

Functional classification of non-synonymous SNPs and InDels into diverse pathways. (XLS 636Â kb

Additional file 1: of Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits

G. Ramakrishna (2482021)
Parampreet Kaur (699310)
Deepti Nigam (5269685)
Pavan Chaduvula (5494748)
Sangita Yadav (5494745)
Akshay Talukdar (3454961)
Nagendra Singh (359528)
Kishor Gaikwad (3799879)

July 2018

Table S1. Statistics of Assembly generated from Illumina HiSeq1000 sequencing data. (DOC 29Â kb

Additional file 9: of Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits

G. Ramakrishna (2482021)
Parampreet Kaur (699310)
Deepti Nigam (5269685)
Pavan Chaduvula (5494748)
Sangita Yadav (5494745)
Akshay Talukdar (3454961)
Nagendra Singh (359528)
Kishor Gaikwad (3799879)

July 2018

Functional annotation of 205 interacting patterns as identified for 7 selected genes. (XLS 184Â kb

Additional file 8: of Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits

G. Ramakrishna (2482021)
Parampreet Kaur (699310)
Deepti Nigam (5269685)
Pavan Chaduvula (5494748)
Sangita Yadav (5494745)
Akshay Talukdar (3454961)
Nagendra Singh (359528)
Kishor Gaikwad (3799879)

July 2018

Figure S3. GO annotation of 205 interacting partners of 7 selected genes into cellular compartments....

Additional file 6: of Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits

G. Ramakrishna (2482021)
Parampreet Kaur (699310)
Deepti Nigam (5269685)
Pavan Chaduvula (5494748)
Sangita Yadav (5494745)
Akshay Talukdar (3454961)
Nagendra Singh (359528)
Kishor Gaikwad (3799879)

July 2018

Figure S1. GO annotation of 205 interacting partners of 7 selected genes into biological processes. ...

Additional file 7: of Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits

G. Ramakrishna (2482021)
Parampreet Kaur (699310)
Deepti Nigam (5269685)
Pavan Chaduvula (5494748)
Sangita Yadav (5494745)
Akshay Talukdar (3454961)
Nagendra Singh (359528)
Kishor Gaikwad (3799879)

July 2018

Figure S2. GO annotation of 205 interacting partners of 7 selected genes into molecular functions. (...

Additional file 12: of Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits

G. Ramakrishna (2482021)
Parampreet Kaur (699310)
Deepti Nigam (5269685)
Pavan Chaduvula (5494748)
Sangita Yadav (5494745)
Akshay Talukdar (3454961)
Nagendra Singh (359528)
Kishor Gaikwad (3799879)

July 2018

Table S2. Statistics of E3 Ubiquitin ligase protein structural predictions in G. max and G. soja (TM...

Additional file 11: of Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits

G. Ramakrishna (2482021)
Parampreet Kaur (699310)
Deepti Nigam (5269685)
Pavan Chaduvula (5494748)
Sangita Yadav (5494745)
Akshay Talukdar (3454961)
Nagendra Singh (359528)
Kishor Gaikwad (3799879)

July 2018

Figure S5. Pairwise alignment (a) of protein sequence of E3 Ubiquitin ligase from G. max and G. soja...

Additional file 3: of Genome-wide association study of four yield-related traits at the R6 stage in soybean

Xiangnan Li (3459992)
Xiaoli Zhang (135098)
Longming Zhu (5882234)
Yuanpeng Bu (5023004)
Xinfang Wang (747604)
Xing Zhang (11943)
Yang Zhou (65942)
Xiaoting Wang (206653)
Na Guo (198794)
Lijuan Qiu (651900)
Jinming Zhao (349674)
Han Xing (227847)

March 2019

Table S3. Summary of the polymorphic markers on the 20 chromosomes of Glycine max. (XLSX 10 kb

Additional file 3: of A genome-wide association study of seed composition traits in wild soybean (Glycine soja)

Larry Leamy (3620168)
Hengyou Zhang (3620171)
Changbao Li (3620174)
Charles Chen (121346)
Bao-Hua Song (3309945)

January 2017

Genome-wide average LD decay estimated for the wild soybean sample. The LD decay is measured in r2 v...

Additional file 1: of Genome-wide nucleotide patterns and potential mechanisms of genome divergence following domestication in maize and soybean

Jinyu Wang (381467)
Xianran Li (6485)
Kyung Kim (31555)
Michael Scanlon (791403)
Scott Jackson (183074)
Nathan Springer (56696)
Jianming Yu (102511)

April 2019

Figure S1. Diagram of SNP filtering process. Figure S2. Frequency of SNP substitution types. Figure ...

Additional file 7: of Genome-wide association study discovered favorable single nucleotide polymorphisms and candidate genes associated with ramet number in ramie (Boehmeria nivea L.)

Kunmei Chen (5135393)
Mingbao Luan (397329)
Heping Xiong (5135387)
Ping Chen (89712)
Jikang Chen (5135381)
Gang Gao (5135390)
Kunyong Huang (6080612)
Aiguo Zhu (3327450)
Chunming Yu (5135384)

December 2018

Results of polymerase chain reaction (PCR) amplification using specific primers of significant singl...

Additional file 4: of Genome-wide association analysis of stalk biomass and anatomical traits in maize

Mona Mazaheri (3995609)
Marlies Heckwolf (3995618)
Brieanne Vaillancourt (108028)
Joseph Gage (3879919)
Brett Burdo (6286337)
Sven Heckwolf (6286340)
Kerrie Barry (276529)
Anna Lipzen (194340)
Camila Ribeiro (6286343)
Thomas Kono (448008)
Heidi Kaeppler (3995606)
Edgar Spalding (3879922)
Candice Hirsch (6286346)
C. Robin Buell (108039)
Natalia Leon (3995600)
Shawn Kaeppler (524084)

February 2019

LD plots of genomic regions containing significant SNPs and adjacent candidate genes. Significant SN...

Additional file 14: of Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits

Abstract

Extracted data

Additional file 14: of Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits

Abstract

Extracted data

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