Journal ArticleDOI
A high-throughput SNP array in the amphidiploid species Brassica napus shows diversity in resistance genes.
Jessica Dalton-Morgan,Alice Hayward,Salman Alamery,Reece Tollenaere,Annaliese S. Mason,Emma Campbell,Dhwani A. Patel,Michal T. Lorenc,Bin Yi,Yan Long,Jinling Meng,Rosy Raman,Harsh Raman,Cindy Lawley,David Edwards,Jacqueline Batley,Jacqueline Batley +16 more
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TLDR
This study presents an efficient custom SNP assay development pipeline in the complex polyploid Brassica genome and demonstrates the utility of the array for high-throughput genotyping in a number of related Brassica species.Abstract:
Single-nucleotide polymorphisms (SNPs)are molecular markers based on nucleotide variation and can be used for genotyping assays across populations and to track genomic inheritance. SNPs offer a comprehensive genotyping alternative to whole-genome sequencing for both agricultural and research purposes including molecular breeding and diagnostics, genome evolution and genetic diversity analyses, genetic mapping, and trait association studies. Here genomic SNPs were discovered between four cultivars of the important amphidiploid oilseed species Brassica napus and used to develop a B. napus Infinium™ array containing 5,306 SNPs randomly dispersed across the genome. Assay success was high, with >94 % of these producing a reproducible, polymorphic genotype in the 1,070 samples screened. Although the assay was designed to B. napus, successful SNP amplification was achieved in the B. napus progenitor species, Brassica rapa and Brassica oleracea, and to a lesser extent in the related species Brassica nigra. Phylogenetic analysis was consistent with the expected relationships between B. napus individuals. This study presents an efficient custom SNP assay development pipeline in the complex polyploid Brassica genome and demonstrates the utility of the array for high-throughput genotyping in a number of related Brassica species. It also demonstrates the utility of this assay in genotyping resistance genes on chromosome A7, which segregate amongst the 1,070 samples.read more
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Journal ArticleDOI
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
TL;DR: 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.
Journal ArticleDOI
Development of a 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of Gossypium spp.
Amanda M. Hulse-Kemp,Jana Lemm,Joerg Plieske,Hamid Ashrafi,Ramesh Buyyarapu,David D. Fang,James Frelichowski,Marc Giband,Steve Hague,Lori L. Hinze,Kelli J. Kochan,Penny K. Riggs,Jodi A. Scheffler,Joshua A. Udall,Mauricio Ulloa,Shirley S Wang,Qian-Hao Zhu,Sumit K. Bag,Archana Bhardwaj,John J. Burke,Robert L. Byers,Michel Claverie,Michael A. Gore,David B. Harker,S. Islam,Johnie N. Jenkins,Don C. Jones,Jean-Marc Lacape,Danny J. Llewellyn,Richard G. Percy,Alan E. Pepper,Jesse Poland,Krishan Mohan Rai,Samir V. Sawant,Sunil Kumar Singh,Andrew Spriggs,Jen Taylor,Fei Wang,Scott Yourstone,Xiuting Zheng,Cindy Lawley,Martin W. Ganal,Allen Van Deynze,Iain W. Wilson,David M. Stelly +44 more
TL;DR: The produced intraspecific genetic map is the first saturated map that associates into 26 linkage groups corresponding to the number of cotton chromosomes for a cross between two G. hirsutum lines.
Journal ArticleDOI
Tools for Genetic Studies in Experimental Populations of Polyploids.
TL;DR: The tools available to the research community to better understand polyploid inheritance are looked at, including software for assigning marker genotypes, establishing chromosome-scale linkage phase among marker alleles, constructing (short-range) haplotypes, generating linkage maps, performing genome-wide association studies (GWAS) and quantitative trait locus (QTL) analyses, and simulatingpolyploid populations.
Journal ArticleDOI
Development and Applications of a High Throughput Genotyping Tool for Polyploid Crops: Single Nucleotide Polymorphism (SNP) Array.
TL;DR: This review presents a complete overview of SNP array development and applications in polypoid crops, which will benefit the research in molecular breeding and genetics of crops with complex genomes.
Journal ArticleDOI
SNP markers‐based map construction and genome‐wide linkage analysis in Brassica napus
Harsh Raman,Jessica Dalton-Morgan,Simon Diffey,Rosy Raman,Salman Alamery,David Edwards,Jacqueline Batley +6 more
TL;DR: The results suggest that SNP markers will be suitable for various applications such as trait introgression, comparative mapping and high-resolution mapping of loci in B. napus.
References
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Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
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
Genome-wide association studies of 14 agronomic traits in rice landraces
Xuehui Huang,Xinghua Wei,Tao Sang,Qiang Zhao,Qiang Zhao,Qi Feng,Yan Zhao,Canyang Li,Chuanrang Zhu,Tingting Lu,Zhiwu Zhang,Meng Li,Meng Li,Danlin Fan,Yunli Guo,Ahong Wang,Lu Wang,Liuwei Deng,Wenjun Li,Yiqi Lu,Qijun Weng,Kunyan Liu,Tao Huang,Taoying Zhou,Yufeng Jing,Wei Li,Zhang Lin,Edward S. Buckler,Edward S. Buckler,Qian Qian,Qifa Zhang,Jiayang Li,Bin Han,Bin Han +33 more
TL;DR: This study identifies ∼3.6 million SNPs by sequencing 517 rice landraces and constructed a high-density haplotype map of the rice genome using a novel data-imputation method, demonstrating that an approach integrating second-generation genome sequencing and GWAS can be used as a powerful complementary strategy to classical biparental cross-mapping for dissecting complex traits in rice.
Journal ArticleDOI
Accessing genetic variation: genotyping single nucleotide polymorphisms
TL;DR: The hope that single nucleotide polymorphisms will allow genes that underlie complex disease to be identified, together with progress in identifying large sets ofSNPs, are the driving forces behind intense efforts to establish the technology for large-scale analysis of SNPs.
Journal ArticleDOI
The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes
Shengyi Liu,Yumei Liu,Xinhua Yang,Chaobo Tong,David Edwards,Isobel A. P. Parkin,Meixia Zhao,Jianxin Ma,Jingyin Yu,Shunmou Huang,Xiyin Wang,Junyi Wang,Kun Lu,Zhiyuan Fang,Ian Bancroft,Tae-Jin Yang,Qiong Hu,Xinfa Wang,Zhen Yue,Haojie Li,Linfeng Yang,Jian Wu,Qing Zhou,Wanxin Wang,Graham J.W. King,J. Chris Pires,Changxin Lu,Zhangyan Wu,Perumal Sampath,Zhuo Wang,Hui Guo,Shengkai Pan,Limei Yang,Jiumeng Min,Dong Zhang,Dianchuan Jin,Wanshun Li,Harry Belcram,Jinxing Tu,Mei Guan,Cunkou Qi,Dezhi Du,Jiana Li,Liangcai Jiang,Jacqueline Batley,Andrew G. Sharpe,Beom Seok Park,Pradeep Ruperao,Feng Cheng,Nomar Espinosa Waminal,Yin Huang,Caihua Dong,Li Wang,Jingping Li,Zhiyong Hu,Mu Zhuang,Yi Huang,Junyan Huang,Jiaqin Shi,Desheng Mei,Jing Liu,Tae-Ho Lee,Jinpeng Wang,Huizhe Jin,Zaiyun Li,Xun Li,Jiefu Zhang,Lu Xiao,Yongming Zhou,Zhongsong Liu,Xuequn Liu,Rui Qin,Xu Tang,Wenbin Liu,Yupeng Wang,Yangyong Zhang,Jonghoon Lee,Hyun Hee Kim,Xun Xu,Xinming Liang,Wei Hua,Xiaowu Wang,Jun Wang,Boulos Chalhoub,Andrew H. Paterson +84 more
TL;DR: A draft genome sequence of Brassica oleracea is described, comparing it with that of its sister species B. rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks.
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