气候变化领域集成服务门户(CCPortal): Four chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding

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DOI	10.1038/s41467-021-24328-w
	Four chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding
	Lovell J.T.; Bentley N.B.; Bhattarai G.; Jenkins J.W.; Sreedasyam A.; Alarcon Y.; Bock C.; Boston L.B.; Carlson J.; Cervantes K.; Clermont K.; Duke S.; Krom N.; Kubenka K.; Mamidi S.; Mattison C.P.; Monteros M.J.; Pisani C.; Plott C.; Rajasekar S.; Rhein H.S.; Rohla C.; Song M.; Hilaire R.S.; Shu S.; Wells L.; Webber J.; Heerema R.J.; Klein P.E.; Conner P.; Wang X.; Grauke L.J.; Grimwood J.; Schmutz J.; Randall J.J.
发表日期	2021
ISSN	2041-1723
卷号	12 期号:1
英文摘要	Genome-enabled biotechnologies have the potential to accelerate breeding efforts in long-lived perennial crop species. Despite the transformative potential of molecular tools in pecan and other outcrossing tree species, highly heterozygous genomes, significant presence–absence gene content variation, and histories of interspecific hybridization have constrained breeding efforts. To overcome these challenges, here, we present diploid genome assemblies and annotations of four outbred pecan genotypes, including a PacBio HiFi chromosome-scale assembly of both haplotypes of the ‘Pawnee’ cultivar. Comparative analysis and pan-genome integration reveal substantial and likely adaptive interspecific genomic introgressions, including an over-retained haplotype introgressed from bitternut hickory into pecan breeding pedigrees. Further, by leveraging our pan-genome presence–absence and functional annotation database among genomes and within the two outbred haplotypes of the ‘Lakota’ genome, we identify candidate genes for pest and pathogen resistance. Combined, these analyses and resources highlight significant progress towards functional and quantitative genomics in highly diverse and outbred crops. © 2021, The Author(s).
语种	英语
scopus关键词	chromosome; genome; hybridization; introgression; outcrossing; perennial plant; plant breeding; tree; article; breeding; chromosome; crop; cultivar; diploidy; genomics; haplotype; introgression; nonhuman; pecan; pedigree; plant defense; quantitative analysis; Carya; disease resistance; genetic variation; genetics; genomics; genotype; phenotype; plant breeding; plant genome; Carya cordiformis; Carya; Chromosomes; Diploidy; Disease Resistance; Genetic Variation; Genome, Plant; Genomics; Genotype; Haplotypes; Phenotype; Plant Breeding
来源期刊	Nature Communications
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/251400
作者单位	Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States; Department of Horticultural Science, Texas A&M University, College Station, TX, United States; Institute of Plant Breeding, Genetics & Genomics, University of Georgia, Athens, GA, United States; Noble Research Institute, Ardmore, OK, United States; USDA Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA, United States; DOE Joint Genome Institute, Berkeley, CA, United States; Department of Entomology, Plant Pathology and Weed Science, New Mexico State University, Las Cruces, NM, United States; USDA-ARS Food Processing and Sensory Quality Research, New Orleans, LA, United States; USDA-ARS Plains Area Administrative Office, College Station, TX, United States; USDA Pecan Breeding and Genetics, College Station, TX, United States; Arizona Genomics Institute, University of Arizona, Tucson, AZ, United States; Department of Computer Science, New Mexico State University, Las Cruces, NM, United States; Plant...
推荐引用方式 GB/T 7714	Lovell J.T.,Bentley N.B.,Bhattarai G.,et al. Four chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding[J],2021,12(1).
APA	Lovell J.T..,Bentley N.B..,Bhattarai G..,Jenkins J.W..,Sreedasyam A..,...&Randall J.J..(2021).Four chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding.Nature Communications,12(1).
MLA	Lovell J.T.,et al."Four chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding".Nature Communications 12.1(2021).