A high-density SNP genotyping array for Brassica napus and its ancestral diploid species based on optimised selection of single-locus markers in the allotetraploid genome
Wayne E. Clarke,Erin E. Higgins,Joerg Plieske,Ralf Wieseke,Christine Sidebottom,Yogendra Khedikar,Jacqueline Batley,Dave Edwards,Jinling Meng,Ruiyuan Li,Cindy Lawley,Jérôme Pauquet,Benjamin Laga,Wing Cheung,Federico L. Iniguez-Luy,Emmanuelle Dyrszka,Stephen Rae,Benjamin Stich,Rod J. Snowdon,Andrew G. Sharpe,Martin W. Ganal,Isobel A. P. Parkin +21 more
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TLDR
A high-density single nucleotide polymorphism (SNP) Illumina Infinium array, containing 52,157 markers, was developed for the allotetraploid Brassica napus, a valuable tool for genetic fine mapping and genome-wide association studies in B. napus and its progenitor genomes.Abstract:
Key message
TheBrassica napusIllumina array provides genome-wide markers linked to the available genome sequence, a significant tool for genetic analyses of the allotetraploidB. napusand its progenitor diploid genomes.read more
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Past and Future Use of Wild Relatives in Crop Breeding
Hannes Dempewolf,Gregory J. Baute,Justin E. Anderson,Benjamin Kilian,Chelsea Smith,Luigi Guarino +5 more
TL;DR: The role that CWR play in modern crop breeding is documented, including their past and current use, advanced breeding methods and technologies that promise to facilitate the continued use, and what constraints continue to hinder increased use of CWR in breeding.
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Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives
Awais Rasheed,Yuanfeng Hao,Xianchun Xia,Awais Khan,Yunbi Xu,Yunbi Xu,Rajeev K. Varshney,Zhonghu He,Zhonghu He +8 more
TL;DR: It is proposed that future practical breeding platforms should adopt automated genotyping technologies, either array or sequencing based, target functional polymorphisms underpinning economic traits, and provide desirable prediction accuracy for quantitative traits, with universal applications under wide genetic backgrounds in crops.
Journal ArticleDOI
Development and Evaluation of a Barley 50k iSelect SNP Array.
Micha Bayer,Paulo Rapazote-Flores,Martin W. Ganal,Pete E. Hedley,Malcolm Macaulay,Jörg Plieske,Luke Ramsay,Joanne Russell,Paul Shaw,William T. B. Thomas,Robbie Waugh +10 more
TL;DR: To test the utility of the 50k chip for genetic mapping, a segregating population derived from a Golden Promise × Morex cross was genotyped and mapped over 14,000 SNPs to genetic positions which showed a near exact correspondence to their known physical positions.
Journal ArticleDOI
Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus
Bhavna Hurgobin,Bhavna Hurgobin,Agnieszka A. Golicz,Philipp E. Bayer,Chon-Kit Kenneth Chan,Soodeh Tirnaz,Aria Dolatabadian,Sarah Schiessl,Birgit Samans,Juan D. Montenegro,Isobel A. P. Parkin,J. Chris Pires,Boulos Chalhoub,Graham J.W. King,Rod J. Snowdon,Jacqueline Batley,David Edwards +16 more
TL;DR: There is an association between HEs and PAV events, particularly in recent Brassica napus synthetic accessions, and these represent a novel source of genetic diversity, which can be captured for the improvement of this important crop species.
Journal ArticleDOI
Designing Future Crops: Genomics-Assisted Breeding Comes of Age
Rajeev K. Varshney,Rajeev K. Varshney,Abhishek Bohra,Jianming Yu,Andreas Graner,Qifa Zhang,Mark E. Sorrells +6 more
TL;DR: In this article, a suite of new approaches that fast-track targeted manipulation of allelic variation for creating novel diversity and facilitate their rapid and efficient incorporation in crop improvement programs is presented.
References
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TL;DR: A computer package, called MAPMAKER, designed specifically for the construction of linkage maps in a number of organisms, including the human and several plants, and it is outlined the mapping strategies that have been used.
Journal ArticleDOI
The genome of the mesopolyploid crop species Brassica rapa
Xiaowu Wang,Hanzhong Wang,Jun Wang,Jun Wang,Jun Wang,Rifei Sun,Jian Wu,Shengyi Liu,Yinqi Bai,Jeong-Hwan Mun,Ian Bancroft,Feng Cheng,Sanwen Huang,Xixiang Li,Wei Hua,Junyi Wang,Xiyin Wang,Xiyin Wang,Michael Freeling,J. Chris Pires,Andrew H. Paterson,Boulos Chalhoub,Bo Wang,Alice Hayward,Alice Hayward,Andrew G. Sharpe,Beom-Seok Park,Bernd Weisshaar,Binghang Liu,Bo Li,Bo Liu,Chaobo Tong,Chi Song,Chris Duran,Chris Duran,Chunfang Peng,Geng Chunyu,Chushin Koh,Chuyu Lin,David Edwards,David Edwards,Desheng Mu,Di Shen,Eleni Soumpourou,Fei Li,Fiona Fraser,Gavin C. Conant,Gilles Lassalle,Graham J.W. King,Guusje Bonnema,Haibao Tang,Haiping Wang,Harry Belcram,Heling Zhou,Hideki Hirakawa,Hiroshi Abe,Hui Guo,Hui Wang,Huizhe Jin,Isobel A. P. Parkin,Jacqueline Batley,Jacqueline Batley,Jeong-Sun Kim,Jérémy Just,Jianwen Li,Jiaohui Xu,Jie Deng,Jin A Kim,Jingping Li,Jingyin Yu,Jinling Meng,Jinpeng Wang,Jiumeng Min,Julie Poulain,Katsunori Hatakeyama,Kui Wu,Li Wang,Lu Fang,Martin Trick,Matthew G. Links,Meixia Zhao,Mina Jin,Nirala Ramchiary,Nizar Drou,Paul J. Berkman,Paul J. Berkman,Qingle Cai,Quanfei Huang,Ruiqiang Li,Satoshi Tabata,Shifeng Cheng,Shu Zhang,Shujiang Zhang,Shunmou Huang,Shusei Sato,Silong Sun,Soo-Jin Kwon,Su-Ryun Choi,Tae-Ho Lee,Wei Fan,Xiang Zhao,Xu Tan,Xun Xu,Yan Wang,Yang Qiu,Ye Yin,Yingrui Li,Yongchen Du,Yongcui Liao,Yong Pyo Lim,Yoshihiro Narusaka,Yupeng Wang,Zhenyi Wang,Zhenyu Li,Zhiwen Wang,Zhiyong Xiong,Zhonghua Zhang +116 more
TL;DR: The annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage, and used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution.
Journal ArticleDOI
Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome
Boulos Chalhoub,Shengyi Liu,Isobel A. P. Parkin,Haibao Tang,Haibao Tang,Xiyin Wang,Julien Chiquet,Harry Belcram,Chaobo Tong,Birgit Samans,Margot Correa,Corinne Da Silva,Jérémy Just,Cyril Falentin,Chu Shin Koh,Isabelle Le Clainche,Maria Bernard,Pascal Bento,Benjamin Noel,Karine Labadie,Adriana Alberti,Mathieu Charles,Dominique Arnaud,Hui Guo,Christian Daviaud,Salman Alamery,Kamel Jabbari,Kamel Jabbari,Meixia Zhao,Patrick P. Edger,Houda Chelaifa,David C. Tack,Gilles Lassalle,Imen Mestiri,Nicolas Schnel,Marie-Christine Le Paslier,Guangyi Fan,Victor Renault,Philippe E. Bayer,Agnieszka A. Golicz,Sahana Manoli,Tae-Ho Lee,Vinh Ha Dinh Thi,Smahane Chalabi,Qiong Hu,Chuchuan Fan,Reece Tollenaere,Yunhai Lu,Christophe Battail,Jinxiong Shen,Christine Sidebottom,Xinfa Wang,Aurélie Canaguier,Aurélie Chauveau,Aurélie Bérard,G. Deniot,Mei Guan,Zhongsong Liu,Fengming Sun,Yong Pyo Lim,Eric Lyons,Christopher D. Town,Ian Bancroft,Xiaowu Wang,Jinling Meng,Jianxin Ma,J. Chris Pires,Graham J.W. King,Dominique Brunel,Régine Delourme,Michel Renard,Jean-Marc Aury,Keith L. Adams,Jacqueline Batley,Jacqueline Batley,Rod J. Snowdon,Jörg Tost,David Edwards,David Edwards,Yongming Zhou,Wei Hua,Andrew G. Sharpe,Andrew H. Paterson,Chunyun Guan,Patrick Wincker,Patrick Wincker,Patrick Wincker +86 more
TL;DR: The polyploid genome of Brassica napus, which originated from a recent combination of two distinct genomes approximately 7500 years ago and gave rise to the crops of rape oilseed, is sequenced.
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