Pan-genome and transcriptome analyses provide insights into genomic variation and differential gene expression profiles related to disease resistance and fatty acid biosynthesis in eastern black walnut (Juglans nigra)  

作　　者：Huijuan Zhou Feng Yan Fan Hao Hang Ye Ming Yue Keith Woeste Peng Zhao Shuoxin Zhang 

机构地区：[1]College of Forestry,Northwest A&F University,Yangling,Shaanxi 712100,China [2]Key Laboratory of Resource Biology and Biotechnology in Western China,Ministry of Education,College of Life Sciences,Northwest University,Xi’an,Shaanxi 710069,China [3]Xi’an Botanical Garden of Shaanxi Province,Xi’an,Shaanxi 710061,China [4]USDA Forest Service Hardwood Tree Improvement and Regeneration Center(HTIRC),Department of Forestry and Natural Resources,Purdue University,715 West State Street,West Lafayette,Indiana,47907,USA

出　　处：《Horticulture Research》2023年第3期250-265,共16页园艺研究（英文）

基　　金：supported by the National Natural Science Foundation of China(32070372,41471038,and 31800372);the Operating Services of Qinling National Forest Ecosystem Research Station financed by Ministry of Science and Technology of China,Natural Science Basis Research Plan in Shaanxi Province of China(2019JQ-641);Shaanxi Academy of Science Research Funding Project(2019 K-06);Science Foundation for Distinguished Young Scholars of Shaanxi Province(2023-JC-JQ-22).

摘　　要：Walnut(Juglans)species are used as nut crops worldwide.Eastern black walnut(EBW,Juglans nigra),a diploid,horticultural important woody species is native to much of eastern North America.Although it is highly valued for its wood and nut,there are few resources for understanding EBW genetics.Here,we present a high-quality genome assembly of J.nigra based on Illumina,Pacbio,and HiC technologies.The genome size was 540.8 Mb,with a scaffold N50 size of 35.1 Mb,and 99.0%of the assembly was anchored to 16 chromosomes.Using this genome as a reference,the resequencing of 74 accessions revealed the effective population size of J.nigra declined during the glacial maximum.A single whole-genome duplication event was identified in the J.nigra genome.Large syntenic blocks among J.nigra,Juglans regia,and Juglans microcarpa predominated,but inversions of more than 600 kb were identified.By comparing the EBW genome with those of J.regia and J.microcarpa,we detected InDel sizes of 34.9 Mb in J.regia and 18.3 Mb in J.microcarpa,respectively.Transcriptomic analysis of differentially expressed genes identified five presumed NBS-LRR(NUCLEOTIDE BINDING SITELEUCINE-RICH REPEAT)genes were upregulated during the development of walnut husks and shells compared to developing embryos.We also identified candidate genes with essential roles in seed oil synthesis,including FAD(FATTY ACID DESATURASE)and OLE(OLEOSIN).Our work advances the understanding of fatty acid bioaccumulation and disease resistance in nut crops,and also provides an essential resource for conducting genomics-enabled breeding in walnut.

关 键 词：CROPS BREEDING black 

分 类 号：S664.1[农业科学—果树学]