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Haplotype-resolved T2T genome assemblies and pangenome graph of pear reveal diverse patterns of allele-specific expression and the genomic basis of fruit quality traits

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Plant Communications 2024年第10期5卷 100-120页

作者： qionghou li Xin Qiao Lanqing li Chao Gu Hao Yin Kaijie Qi Zhihua Xie Sheng Yang Qifeng Zhao Zewen Wang Yuhang Yang Jiahui Pan Hongxiang li Jie Wang Chao Wang Loren H.Rieseberg Shaoling Zhang Shutian Tao National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization Sanya Institute of Nanjing Agricultural UniversityCollege of HorticultureNanjing Agricultural UniversityNanjingJiangsu 210095China Pomology Institute Shanxi Agricultural UniversityTaiguShanxi 030801China Department of Botany and Biodiversity Research Centre University of British ColumbiaVancouverBCCanada

Hybrid crops often exhibit increased yield and greater resilience,yet the genomic mechanism(s)underlying hybrid vigor or heterosis remain unclear,hindering our ability to predict the expression of phenotypic traits in hybrid ***,we generated haplotype-resolved T2T genome assemblies of two pear hybrid varieties,‘Yuluxiang’(YLX)and‘Hongxiangsu’(HXS),which share the same maternal parent but differ in their paternal *** then used these assemblies to explore the genome-scale landscape of allele-specific expression(ASE)and create a pangenome graph for *** was observed for close to 6000 genes in both hybrid cultivars.A subset of ASE genes related to aspects of fruit quality such as sugars,organic acids,and cuticular wax were identified,suggesting their important contributions to ***,Ma1,a gene regulating fruit acidity,is absent in the paternal haplotypes of HXS and YLX.A pangenome graph was built based on our assemblies and seven published pear *** data for 139 cultivated pear genotypes(including 97 genotypes sequenced here)were subsequently aligned to the pangenome graph,revealing numerous structural variant hotspots and selective sweeps during pear diversifica*** predicted,the Ma1 allele was found to be absent in varieties with low organic acid content,and this association was functionally validated by Ma1 overexpression in pear fruit and ***,these results reveal the contributions of ASE to fruit-quality heterosis and provide a robust pangenome reference for high-resolution allele discovery and association mapping.

关键词： pear haplotype-resolved assembly allele-specific expression fruit quality traits pangenome graph

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PbrChiA:a key chitinase of pear in response to Botryosphaeria dothidea infection by interacting with PbrLYK1b2 and down-regulating ROS accumulation

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Horticulture Research 2023年第10期10卷 185-201页

作者： Qiming Chen Huizhen Dong qionghou li Xun Sun Xin Qiao Hao Yin Zhihua Xie Kaijie Qi Xiaosan Huang Shaoling Zhang State Key Laboratory of Crop Genetics and Germplasm Enhancement Centre of Pear Engineering Technology ResearchNanjing Agricultural UniversityNanjing 210095China

Pear ring rot,caused by the pathogenic fungi Botryosphaeria dothidea,seriously affects pear *** the infection-induced reactive oxygen species(ROS)burst of infected plants limits the proliferation of *** during the early infection stage,high ROS levels can also contribute to their growth during the later necrotrophic infection ***,it is important to understand how plants balance ROS levels and resistance to pathogenic *** during the later *** this study,we identified PbrChiA,a glycosyl hydrolases 18(GH18)chitinase-encoding gene with high infection-induced expression,through a comparative transcriptome *** substitution,stable overexpression,and virus induced gene silencing(VIGS)experiments demonstrated that PbrChiA can positively regulate pear resistance as a secreted chitinase to break down *** mycelium in vitro and that overexpression of PbrChiA suppressed infection-induced ROS *** analysis revealed that PbrChiA can bind to the ectodomain of PbrLYK1b2,and this interaction suppressed PbrLYK1b2-mediated chitin-induced ROS ***,we propose that the combination of higher antifungal activity from abundant PbrChiA and lower ROS levels during later necrotrophic infection stage confer resistance of pear against ***.

关键词： infection ChiA resistance

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Unbiased subgenome evolution following a recent whole-genome duplication in pear(Pyrus bretschneideri Rehd.)

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Horticulture Research 2019年第1期6卷 1393-1404页

作者： qionghou li Xin Qiao Hao Yin Yuhang Zhou Huizhen Dong Kaijie Qi Leiting li Shaoling Zhang State Key Laboratory of Crop Genetics and Germplasm Enhancement Centre of Pear Engineering Technology ResearchNanjing Agricultural University210095 NanjingChina

Genome fractionation(also known as diploidization)frequently occurs following paleopolyploidization *** fractionation between subgenomes has been found in some paleo-allopolyploids,while this phenomenon is absent in ***(Pyrus bretschneideri Rehd.)experienced a recent whole-genome duplication(WGD,~30 million years ago);however,the evolutionary fate of the two subgenomes derived from this WGD event is not *** this study,we identified the two paleo-subgenomes in pear using peach(Prunus persica)as an outgroup and investigated differences in the gene loss rate,evolutionary rate,gene expression level,and DNA methylation level between these two *** bias was not found between the two pear subgenomes,which evolved at similar evolutionary *** DNA methylation level of the two subgenomes showed little bias,and we found no expression dominance between the ***,we found that singleton genes and homeologous genes within each subgenome showed divergent evolutionary patterns of selective constraints,expression and epigenetic *** results provide insights into subgenome evolution following paleopolyploidization in pear.

关键词： evolution evolutionary insight

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