Additional file 8: of Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci

Kim TA (5967353)
Ngan Giang KHONG (5967356)
Thi HA (5967359)
Dieu Thu NGUYEN (5967362)
Duc Chung MAI (5967365)
Thi Giang HOANG (5967368)
Thi Phuong Nhung PHUNG (5967371)
Isabelle BOURRIE (5967374)
Brigitte COURTOIS (5967377)
Thi Thu Hoai TRAN (5967380)
Bach Yen DINH (5967383)
Tuan LA (5967386)
Nang DO (5967389)
Michel LEBRUN (5967392)
Pascal GANTET (5967395)
Stefan JOUANNIC (5967398)

November 2018

Table S3. Detailed information of the conserved GWAS sites over the two years (2014 and 2015). QTL_1...

Additional file 10: of Comparative whole genome re-sequencing analysis in upland New Rice for Africa: insights into the breeding history and respective genome compositions

Naoki Yamamoto (200072)
Richard Garcia (729646)
Tomohiro Suzuki (436582)
Celymar Solis (5225453)
Yuichi Tada (5225456)
Ramaiah Venuprasad (5225459)
Ajay Kohli (3411152)

May 2018

Figure S3. Graphical representation of allelic patterns in the two fucosyltransferase. Substitution ...

Additional file 2: of Development of Three Sets of High-Throughput Genotyped Rice Chromosome Segment Substitution Lines and QTL Mapping for Eleven Traits

Bin Zhang (64682)
Lianguang Shang (831676)
Banpu Ruan (830060)
Anpeng Zhang (6691766)
Shenglong Yang (6691769)
Hongzhen Jiang (3977132)
Chaolei Liu (6648314)
Kai Hong (514257)
Hai Lin (163369)
Zhenyu Gao (830064)
Jiang Hu (169367)
Dali Zeng (830062)
Longbiao Guo (666334)
Qian Qian (45749)

May 2019

Table S1. Eleven traits of Nipponbare, PA64s and 9311 observed in Shengzhen (SZ) and Hangzhou (HZ). ...

Additional file 9: of Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci

Xiukun Li (4783458)
Lian Wu (166932)
Jiahong Wang (407742)
Jian Sun (27858)
Xiuhong Xia (4783461)
Xin Geng (571200)
Xuhong Wang (4783464)
Zhengjin Xu (4783467)
Quan Xu (554774)

September 2018

Figure S4. Sequence comparison of PHYB, SD1, DTH8, SDG708, and GW5 between SN265 and R99. (PDF 47Â k...

Additional file 1: of Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci

Xiukun Li (4783458)
Lian Wu (166932)
Jiahong Wang (407742)
Jian Sun (27858)
Xiuhong Xia (4783461)
Xin Geng (571200)
Xuhong Wang (4783464)
Zhengjin Xu (4783467)
Quan Xu (554774)

September 2018

Figure S1. Graphic representation of the genotypes of 151 RILs that were identified using a sliding ...

Additional file 13: of Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci

Xiukun Li (4783458)
Lian Wu (166932)
Jiahong Wang (407742)
Jian Sun (27858)
Xiuhong Xia (4783461)
Xin Geng (571200)
Xuhong Wang (4783464)
Zhengjin Xu (4783467)
Quan Xu (554774)

September 2018

Table S6. The QTL analysis for 15 agronomic traits in the three areas. (XLSX 12Â kb

Additional file 12: of Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci

Xiukun Li (4783458)
Lian Wu (166932)
Jiahong Wang (407742)
Jian Sun (27858)
Xiuhong Xia (4783461)
Xin Geng (571200)
Xuhong Wang (4783464)
Zhengjin Xu (4783467)
Quan Xu (554774)

September 2018

Figure S7. The influence of ecological conditions and genetic background on gene function. The upper...

Additional file 2: of Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci

Xiukun Li (4783458)
Lian Wu (166932)
Jiahong Wang (407742)
Jian Sun (27858)
Xiuhong Xia (4783461)
Xin Geng (571200)
Xuhong Wang (4783464)
Zhengjin Xu (4783467)
Quan Xu (554774)

September 2018

Figure S2. Collinearity between the bin map derived from the RIL population and the reference genome...

Additional file 10: of Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci

Xiukun Li (4783458)
Lian Wu (166932)
Jiahong Wang (407742)
Jian Sun (27858)
Xiuhong Xia (4783461)
Xin Geng (571200)
Xuhong Wang (4783464)
Zhengjin Xu (4783467)
Quan Xu (554774)

September 2018

Figure S5. Candidate gene prediction of grain shape regulate locus on chromosome 12. (PDF 23Â kb

Additional file 11: of Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci

Xiukun Li (4783458)
Lian Wu (166932)
Jiahong Wang (407742)
Jian Sun (27858)
Xiuhong Xia (4783461)
Xin Geng (571200)
Xuhong Wang (4783464)
Zhengjin Xu (4783467)
Quan Xu (554774)

September 2018

Figure S6. The effects of DTH8, SDG708, and PHYB in different areas: a, the heading date of the diff...

Additional file7: of Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci

Xiukun Li (4783458)
Lian Wu (166932)
Jiahong Wang (407742)
Jian Sun (27858)
Xiuhong Xia (4783461)
Xin Geng (571200)
Xuhong Wang (4783464)
Zhengjin Xu (4783467)
Quan Xu (554774)

September 2018

Table S5. The yield components and quality traits of japonica, intermediate type and indica-type pla...

Additional file 14: of Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci

Xiukun Li (4783458)
Lian Wu (166932)
Jiahong Wang (407742)
Jian Sun (27858)
Xiuhong Xia (4783461)
Xin Geng (571200)
Xuhong Wang (4783464)
Zhengjin Xu (4783467)
Quan Xu (554774)

September 2018

Figure S8. The heading time of RILs in the three areas: a, the heading data of RILs and the day leng...

Additional file 7: of QTL mapping and candidate gene analysis of peduncle vascular bundle related traits in rice by genome-wide association study

Laiyuan Zhai (4917016)
Tianqing Zheng (635384)
Xinyu Wang (341591)
Yun Wang (32846)
Kai Chen (129938)
Shu Wang (180520)
Jianlong Xu (841260)
Zhikang Li (416310)

March 2018

Figure S5. Comparisons of heading date, grain number per panicle and plant height among different ha...

Additional file 6: of Development of Three Sets of High-Throughput Genotyped Rice Chromosome Segment Substitution Lines and QTL Mapping for Eleven Traits

Bin Zhang (64682)
Lianguang Shang (831676)
Banpu Ruan (830060)
Anpeng Zhang (6691766)
Shenglong Yang (6691769)
Hongzhen Jiang (3977132)
Chaolei Liu (6648314)
Kai Hong (514257)
Hai Lin (163369)
Zhenyu Gao (830064)
Jiang Hu (169367)
Dali Zeng (830062)
Longbiao Guo (666334)
Qian Qian (45749)

May 2019

Figure S4. Quantitative real-time RT-PCR analysis and Sequence variations of predicted genes. A-C.RN...

Additional file 4: of Development of Three Sets of High-Throughput Genotyped Rice Chromosome Segment Substitution Lines and QTL Mapping for Eleven Traits

Bin Zhang (64682)
Lianguang Shang (831676)
Banpu Ruan (830060)
Anpeng Zhang (6691766)
Shenglong Yang (6691769)
Hongzhen Jiang (3977132)
Chaolei Liu (6648314)
Kai Hong (514257)
Hai Lin (163369)
Zhenyu Gao (830064)
Jiang Hu (169367)
Dali Zeng (830062)
Longbiao Guo (666334)
Qian Qian (45749)

May 2019

Figure S2. Sequence difference and phenotypic variations on four reported genes. A. Difference sites...

Additional File 8:

Kim TA (5967353)
Ngan Giang KHONG (5967356)
Thi HA (5967359)
Dieu Thu NGUYEN (5967362)
Duc Chung MAI (5967365)
Thi Giang HOANG (5967368)
Thi Phuong Nhung PHUNG (5967371)
Isabelle BOURRIE (5967374)
Brigitte COURTOIS (5967377)
Thi Thu Hoai TRAN (5967380)
Bach Yen DINH (5967383)
Tuan LA (5967386)
Nang DO (5967389)
Michel LEBRUN (5967392)
Pascal GANTET (5967395)
Stefan JOUANNIC (5967398)

November 2018

Table S3. Detailed information of the conserved GWAS sites over the two years (2014 and 2015). QTL_1...

Additional file 10: of Comparative whole genome re-sequencing analysis in upland New Rice for Africa: insights into the breeding history and respective genome compositions

Naoki Yamamoto (200072)
Richard Garcia (729646)
Tomohiro Suzuki (436582)
Celymar Solis (5225453)
Yuichi Tada (5225456)
Ramaiah Venuprasad (5225459)
Ajay Kohli (3411152)

May 2018

Figure S3. Graphical representation of allelic patterns in the two fucosyltransferase. Substitution ...

Additional file 2: of Development of Three Sets of High-Throughput Genotyped Rice Chromosome Segment Substitution Lines and QTL Mapping for Eleven Traits

Bin Zhang (64682)
Lianguang Shang (831676)
Banpu Ruan (830060)
Anpeng Zhang (6691766)
Shenglong Yang (6691769)
Hongzhen Jiang (3977132)
Chaolei Liu (6648314)
Kai Hong (514257)
Hai Lin (163369)
Zhenyu Gao (830064)
Jiang Hu (169367)
Dali Zeng (830062)
Longbiao Guo (666334)
Qian Qian (45749)

May 2019

Table S1. Eleven traits of Nipponbare, PA64s and 9311 observed in Shengzhen (SZ) and Hangzhou (HZ). ...

Additional file 9: of Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci

Xiukun Li (4783458)
Lian Wu (166932)
Jiahong Wang (407742)
Jian Sun (27858)
Xiuhong Xia (4783461)
Xin Geng (571200)
Xuhong Wang (4783464)
Zhengjin Xu (4783467)
Quan Xu (554774)

September 2018

Figure S4. Sequence comparison of PHYB, SD1, DTH8, SDG708, and GW5 between SN265 and R99. (PDF 47Â k...

Additional file 1: of Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci

Xiukun Li (4783458)
Lian Wu (166932)
Jiahong Wang (407742)
Jian Sun (27858)
Xiuhong Xia (4783461)
Xin Geng (571200)
Xuhong Wang (4783464)
Zhengjin Xu (4783467)
Quan Xu (554774)

September 2018

Figure S1. Graphic representation of the genotypes of 151 RILs that were identified using a sliding ...

Additional file 13: of Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci

Xiukun Li (4783458)
Lian Wu (166932)
Jiahong Wang (407742)
Jian Sun (27858)
Xiuhong Xia (4783461)
Xin Geng (571200)
Xuhong Wang (4783464)
Zhengjin Xu (4783467)
Quan Xu (554774)

September 2018

Table S6. The QTL analysis for 15 agronomic traits in the three areas. (XLSX 12Â kb

Additional file 12: of Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci

Xiukun Li (4783458)
Lian Wu (166932)
Jiahong Wang (407742)
Jian Sun (27858)
Xiuhong Xia (4783461)
Xin Geng (571200)
Xuhong Wang (4783464)
Zhengjin Xu (4783467)
Quan Xu (554774)

September 2018

Figure S7. The influence of ecological conditions and genetic background on gene function. The upper...

Additional file 2: of Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci

Xiukun Li (4783458)
Lian Wu (166932)
Jiahong Wang (407742)
Jian Sun (27858)
Xiuhong Xia (4783461)
Xin Geng (571200)
Xuhong Wang (4783464)
Zhengjin Xu (4783467)
Quan Xu (554774)

September 2018

Figure S2. Collinearity between the bin map derived from the RIL population and the reference genome...

Additional file 10: of Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci

Xiukun Li (4783458)
Lian Wu (166932)
Jiahong Wang (407742)
Jian Sun (27858)
Xiuhong Xia (4783461)
Xin Geng (571200)
Xuhong Wang (4783464)
Zhengjin Xu (4783467)
Quan Xu (554774)

September 2018

Figure S5. Candidate gene prediction of grain shape regulate locus on chromosome 12. (PDF 23Â kb

Additional file 11: of Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci

Xiukun Li (4783458)
Lian Wu (166932)
Jiahong Wang (407742)
Jian Sun (27858)
Xiuhong Xia (4783461)
Xin Geng (571200)
Xuhong Wang (4783464)
Zhengjin Xu (4783467)
Quan Xu (554774)

September 2018

Figure S6. The effects of DTH8, SDG708, and PHYB in different areas: a, the heading date of the diff...

Additional file7: of Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci

Xiukun Li (4783458)
Lian Wu (166932)
Jiahong Wang (407742)
Jian Sun (27858)
Xiuhong Xia (4783461)
Xin Geng (571200)
Xuhong Wang (4783464)
Zhengjin Xu (4783467)
Quan Xu (554774)

September 2018

Table S5. The yield components and quality traits of japonica, intermediate type and indica-type pla...

Additional file 14: of Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci

Xiukun Li (4783458)
Lian Wu (166932)
Jiahong Wang (407742)
Jian Sun (27858)
Xiuhong Xia (4783461)
Xin Geng (571200)
Xuhong Wang (4783464)
Zhengjin Xu (4783467)
Quan Xu (554774)

September 2018

Figure S8. The heading time of RILs in the three areas: a, the heading data of RILs and the day leng...

Additional file 7: of QTL mapping and candidate gene analysis of peduncle vascular bundle related traits in rice by genome-wide association study

Laiyuan Zhai (4917016)
Tianqing Zheng (635384)
Xinyu Wang (341591)
Yun Wang (32846)
Kai Chen (129938)
Shu Wang (180520)
Jianlong Xu (841260)
Zhikang Li (416310)

March 2018

Figure S5. Comparisons of heading date, grain number per panicle and plant height among different ha...

Additional file 6: of Development of Three Sets of High-Throughput Genotyped Rice Chromosome Segment Substitution Lines and QTL Mapping for Eleven Traits

Bin Zhang (64682)
Lianguang Shang (831676)
Banpu Ruan (830060)
Anpeng Zhang (6691766)
Shenglong Yang (6691769)
Hongzhen Jiang (3977132)
Chaolei Liu (6648314)
Kai Hong (514257)
Hai Lin (163369)
Zhenyu Gao (830064)
Jiang Hu (169367)
Dali Zeng (830062)
Longbiao Guo (666334)
Qian Qian (45749)

May 2019

Figure S4. Quantitative real-time RT-PCR analysis and Sequence variations of predicted genes. A-C.RN...

Additional file 4: of Development of Three Sets of High-Throughput Genotyped Rice Chromosome Segment Substitution Lines and QTL Mapping for Eleven Traits

Bin Zhang (64682)
Lianguang Shang (831676)
Banpu Ruan (830060)
Anpeng Zhang (6691766)
Shenglong Yang (6691769)
Hongzhen Jiang (3977132)
Chaolei Liu (6648314)
Kai Hong (514257)
Hai Lin (163369)
Zhenyu Gao (830064)
Jiang Hu (169367)
Dali Zeng (830062)
Longbiao Guo (666334)
Qian Qian (45749)

May 2019

Figure S2. Sequence difference and phenotypic variations on four reported genes. A. Difference sites...

Additional File 8:

Kim TA (5967353)
Ngan Giang KHONG (5967356)
Thi HA (5967359)
Dieu Thu NGUYEN (5967362)
Duc Chung MAI (5967365)
Thi Giang HOANG (5967368)
Thi Phuong Nhung PHUNG (5967371)
Isabelle BOURRIE (5967374)
Brigitte COURTOIS (5967377)
Thi Thu Hoai TRAN (5967380)
Bach Yen DINH (5967383)
Tuan LA (5967386)
Nang DO (5967389)
Michel LEBRUN (5967392)
Pascal GANTET (5967395)
Stefan JOUANNIC (5967398)

November 2018

Table S3. Detailed information of the conserved GWAS sites over the two years (2014 and 2015). QTL_1...

Additional file 10: of Comparative whole genome re-sequencing analysis in upland New Rice for Africa: insights into the breeding history and respective genome compositions

Naoki Yamamoto (200072)
Richard Garcia (729646)
Tomohiro Suzuki (436582)
Celymar Solis (5225453)
Yuichi Tada (5225456)
Ramaiah Venuprasad (5225459)
Ajay Kohli (3411152)

May 2018

Figure S3. Graphical representation of allelic patterns in the two fucosyltransferase. Substitution ...

Additional file 2: of Development of Three Sets of High-Throughput Genotyped Rice Chromosome Segment Substitution Lines and QTL Mapping for Eleven Traits

Bin Zhang (64682)
Lianguang Shang (831676)
Banpu Ruan (830060)
Anpeng Zhang (6691766)
Shenglong Yang (6691769)
Hongzhen Jiang (3977132)
Chaolei Liu (6648314)
Kai Hong (514257)
Hai Lin (163369)
Zhenyu Gao (830064)
Jiang Hu (169367)
Dali Zeng (830062)
Longbiao Guo (666334)
Qian Qian (45749)

May 2019

Table S1. Eleven traits of Nipponbare, PA64s and 9311 observed in Shengzhen (SZ) and Hangzhou (HZ). ...

Additional file 8: of Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci

Abstract

Extracted data

Additional file 8: of Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci

Abstract

Extracted data

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