A chickpea genetic variation map based on the sequencing of 3,366 genomes
暂无分享,去创建一个
M. S. Pithia | Huanming Yang | Jian Wang | J. Bennetzen | W. Cowling | H. Nguyen | A. Rathore | R. Varshney | Guangyi Fan | Xin Liu | Xun Xu | D. Edwards | B. Hayes | Y. Vigouroux | K. Siddique | E. V. von Wettberg | E. Lyons | T. Mohapatra | D. Chattopadhyay | D. Jarquín | S. Chaturvedi | Réka Howard | Shuai Sun | Xiao Du | H. Upadhyaya | S. Datta | J. Crossa | C. Ben | L. Gentzbittel | G. P. Dixit | Shiv Kumar | B. Tar’an | V. Singh | Anne-Céline Thuillet | L. Hickey | H. Kudapa | Aamir W. Khan | Vanika Garg | M. Thudi | A. Chitikineni | P. Cubry | A. Deokar | K. Voss-Fels | M. Yasin | P. Sinha | R. Punna | C. Bharadwaj | A. Hamwieh | Yue Wang | V. Valluri | M. Singh | Aleena Francis | Prasad Bajaj | N. P. Singh | Manish Roorkiwal | Servejeet Singh | K. R. Soren | V. Singh | Xin Liu | Xin Liu
[1] D. I. Givens,et al. Millets Can Have a Major Impact on Improving Iron Status, Hemoglobin Level, and in Reducing Iron Deficiency Anemia–A Systematic Review and Meta-Analysis , 2021, Frontiers in Nutrition.
[2] S. Anitha,et al. Assessing Millets and Sorghum Consumption Behavior in Urban India: A Large-Scale Survey , 2021, Frontiers in Sustainable Food Systems.
[3] M. Zhang,et al. Pan-Genome of Wild and Cultivated Soybeans , 2020, Cell.
[4] R. Varshney,et al. Superior haplotypes for haplotype‐based breeding for drought tolerance in pigeonpea (Cajanus cajan L.) , 2020, Plant biotechnology journal.
[5] S. Mirarab,et al. Sequence Analysis , 2020, Encyclopedia of Bioinformatics and Computational Biology.
[6] Travis A. Parker,et al. Pod indehiscence is a domestication and aridity resilience trait in common bean. , 2019, The New phytologist.
[7] B. Hayes,et al. Breeding improves wheat productivity under contrasting agrochemical input levels , 2019, Nature Plants.
[8] P. Marjoram,et al. WhoGEM: an admixture-based prediction machine accurately predicts quantitative functional traits in plants , 2019, Genome Biology.
[9] Jun Wang,et al. Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits , 2019, Nature Genetics.
[10] Brook T. Moyers,et al. Sunflower pan-genome analysis shows that hybridization altered gene content and disease resistance , 2018, Nature Plants.
[11] Matthias Lange,et al. Genebank genomics highlights the diversity of a global barley collection , 2018, Nature Genetics.
[12] Chi Zhang,et al. PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files , 2018, Bioinform..
[13] Kenneth L. McNally,et al. Genomic variation in 3,010 diverse accessions of Asian cultivated rice , 2018, Nature.
[14] Peter J. Bradbury,et al. Dysregulation of expression correlates with rare-allele burden and fitness loss in maize , 2018, Nature.
[15] Qun Xu,et al. Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice , 2018, Nature Genetics.
[16] Mauricio O. Carneiro,et al. Scaling accurate genetic variant discovery to tens of thousands of samples , 2017, bioRxiv.
[17] Sudhir Kumar,et al. TimeTree: A Resource for Timelines, Timetrees, and Divergence Times. , 2017, Molecular biology and evolution.
[18] E. Buckler,et al. Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation , 2017, Nature Genetics.
[19] Cristobal Uauy,et al. Genomic innovation for crop improvement , 2017, Nature.
[20] Yun S. Song,et al. Robust and scalable inference of population history from hundreds of unphased whole genomes , 2016, Nature Genetics.
[21] Jun Wang,et al. Recent breeding programs enhanced genetic diversity in both desi and kabuli varieties of chickpea (Cicer arietinum L.) , 2016, Scientific Reports.
[22] C. K. Chan,et al. The pangenome of an agronomically important crop plant Brassica oleracea , 2016, Nature Communications.
[23] Yan Liang,et al. Neglecting legumes has compromised human health and sustainable food production , 2016, Nature Plants.
[24] Jennifer Geist Rutledge,et al. Feeding the future , 2020, Food and Society.
[25] J. Grimwood,et al. Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity , 2016, Nature Biotechnology.
[26] Evgeny M. Zdobnov,et al. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..
[27] M. Heuertz,et al. Living on the edge: timing of Rand Flora disjunctions congruent with ongoing aridification in Africa , 2015, Front. Genet..
[28] J. Woolliams,et al. Genetic contributions and their optimization. , 2015, Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie.
[29] Carson C Chow,et al. Second-generation PLINK: rising to the challenge of larger and richer datasets , 2014, GigaScience.
[30] Kunihiko Sadakane,et al. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph , 2014, Bioinform..
[31] George Graef,et al. Genotyping by sequencing for genomic prediction in a soybean breeding population , 2014, BMC Genomics.
[32] G. de los Campos,et al. Genome-Wide Regression and Prediction with the BGLR Statistical Package , 2014, Genetics.
[33] Nikolaos S. Alachiotis,et al. SweeD: Likelihood-Based Detection of Selective Sweeps in Thousands of Genomes , 2013, Molecular biology and evolution.
[34] Heng Li. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM , 2013, 1303.3997.
[35] James K. Hane,et al. Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement , 2013, Nature Biotechnology.
[36] Tatiana Popova,et al. Supplementary Methods , 2012, Acta Neuropsychiatrica.
[37] Jeffrey B. Endelman,et al. Ridge Regression and Other Kernels for Genomic Selection with R Package rrBLUP , 2011 .
[38] Alvaro J. González,et al. The Medicago Genome Provides Insight into the Evolution of Rhizobial Symbioses , 2011, Nature.
[39] Kenneth Lange,et al. Enhancements to the ADMIXTURE algorithm for individual ancestry estimation , 2011, BMC Bioinformatics.
[40] B. Kinghorn. An algorithm for efficient constrained mate selection , 2011, Genetics Selection Evolution.
[41] M. DePristo,et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.
[42] Thomas L. Madden,et al. BLAST+: architecture and applications , 2009, BMC Bioinformatics.
[43] R. Wilson,et al. BreakDancer: An algorithm for high resolution mapping of genomic structural variation , 2009, Nature Methods.
[44] Kai Ye,et al. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads , 2009, Bioinform..
[45] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[46] Brad T. Sherman,et al. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists , 2008, Nucleic acids research.
[47] Ziheng Yang. PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.
[48] Alexandros Stamatakis,et al. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models , 2006, Bioinform..
[49] D. Reich,et al. Principal components analysis corrects for stratification in genome-wide association studies , 2006, Nature Genetics.
[50] Adam Godzik,et al. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..
[51] M. Wojciechowski,et al. Evolutionary rates analysis of Leguminosae implicates a rapid diversification of lineages during the tertiary. , 2005, Systematic biology.
[52] P. Caputo,et al. Phylogenetic relationships among annual and perennial species of the genus Cicer as inferred from ITS sequences of nuclear ribosomal DNA , 2005, Biologia Plantarum.
[53] Robert C. Edgar,et al. MUSCLE: a multiple sequence alignment method with reduced time and space complexity , 2004, BMC Bioinformatics.
[54] R. Durbin,et al. GeneWise and Genomewise. , 2004, Genome research.
[55] F. Javadi,et al. Interspecific relationships of the genus Cicer L. (Fabaceae) based on trnT-F sequences , 2004, Theoretical and Applied Genetics.
[56] S. Salzberg,et al. Versatile and open software for comparing large genomes , 2004, Genome Biology.
[57] Wei Qian,et al. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. , 2000, Molecular biology and evolution.
[58] M T Clegg,et al. Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. , 1996, Proceedings of the National Academy of Sciences of the United States of America.
[59] Andy South,et al. rworldmap : a new R package for mapping global data , 2011, R J..
[60] S. Henikoff,et al. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm , 2009, Nature Protocols.