Pear genetics: Recent advances, new prospects, and a roadmap for the future

Li, Jiaming; Zhang, Mingyue; Li, Xiaolong; Khan, Awais; Kumar, Satish; Allan, Andrew C.; Lin‐Wang, Kui; Espley, Richard V.; Wang, Caihong; Wang, Runze; Xue, Cheng; Yao, Gai-Fang; Qin, Mengfan; Sun, Manyi; Tegtmeier, Richard; Liu, Hainan; Wei, Weilin; Ming, Meiling; Zhang, Shaoling; Zhao, Kunkun; Song, Bobo; Ni, Jiangping; An, Jianping; Korban, Schuyler S.; Wu, Jun

doi:10.1093/hr/uhab040

Cited by 23 publications

(10 citation statements)

References 232 publications

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“…However, this assembly was also not phased, lacking information on allelic variants. Genomes are currently available for 5 of 26 Pyrus species in the Genome Database for Rosaceae (GDR; https://www.rosaceae.org/organism/26137 ) and for only a few of the thousands of recognized cultivars ( Li et al . 2022 ).…”

Section: Introductionmentioning

confidence: 99%

A chromosome-scale assembly for ‘d’Anjou’ pear

Yocca,

Akinyuwa,

Bailey

et al. 2024

G3: Genes, Genomes, Genetics

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Cultivated pear consists of several Pyrus species with P. communis (European pear) representing a large fraction of worldwide production. As a relatively recently domesticated crop and perennial tree, pear can benefit from genome-assisted breeding. Additionally, comparative genomics within Rosaceae promises greater understanding of evolution within this economically important family. Here, we generate a fully-phased chromosome-scale genome assembly of P. communis ‘d’Anjou’. Using PacBio HiFi and Dovetail Omni-C reads, the genome is resolved into the expected 17 chromosomes, with each haplotype totalling nearly 540 Megabases and a contig N50 of nearly 14 Mb. Both haplotypes are highly syntenic to each other, and to the Malus domestica ‘Honeycrisp’ apple genome. Nearly 45,000 genes were annotated in each haplotype, over 90% of which have direct RNA-seq expression evidence. We detect signatures of the known whole-genome duplication shared between apple and pear, and we estimate 57% of d’Anjou genes are retained in duplicate derived from this event. This genome highlights the value of generating phased diploid assemblies for recovering the full allelic complement in highly heterozygous crop species.

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Section: Introductionmentioning

confidence: 99%

A chromosome-scale assembly for ‘d’Anjou’ pear

Yocca,

Akinyuwa,

Bailey

et al. 2024

G3: Genes, Genomes, Genetics

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“…Compared to wild pears, the fruits of cultivated pears display significant changes in many morphological characteristics, including fruit size, sugar content, and stone cell content. In addition, early ripening, dwarf stature, and good disease resistance are also important targets in pear breeding programs [20]. A comparative analysis between wild pears and cultivated pears can provide insight into the evolution of critical phenotypic changes.…”

Section: Introductionmentioning

confidence: 99%

Increased DNA methylation contributes to the early ripening of pear fruits during domestication and improvement

Song,

Yu,

et al. 2024

Genome Biol

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Background DNA methylation is an essential epigenetic modification. However, its contribution to trait changes and diversity in the domestication of perennial fruit trees remains unknown. Results Here, we investigate the variation in DNA methylation during pear domestication and improvement using whole-genome bisulfite sequencing in 41 pear accessions. Contrary to the significant decrease during rice domestication, we detect a global increase in DNA methylation during pear domestication and improvement. We find this specific increase in pear is significantly correlated with the downregulation of Demeter-like1 (DML1, encoding DNA demethylase) due to human selection. We identify a total of 5591 differentially methylated regions (DMRs). Methylation in the CG and CHG contexts undergoes co-evolution during pear domestication and improvement. DMRs have higher genetic diversity than selection sweep regions, especially in the introns. Approximately 97% of DMRs are not associated with any SNPs, and these DMRs are associated with starch and sucrose metabolism and phenylpropanoid biosynthesis. We also perform correlation analysis between DNA methylation and gene expression. We find genes close to the hypermethylated DMRs that are significantly associated with fruit ripening. We further verify the function of a hyper-DMR-associated gene, CAMTA2, and demonstrate that overexpression of CAMTA2 in tomato and pear callus inhibits fruit ripening. Conclusions Our study describes a specific pattern of DNA methylation in the domestication and improvement of a perennial pear tree and suggests that increased DNA methylation plays an essential role in the early ripening of pear fruits.

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“…Presently, 22 species of pear with 5000 accessions have been reported. These five species are majorly cultivated for fruit production, including Pyrus bretschneideri, P. pyrifolia, P. communis, P. ussuriensis, and P. sinkiangensis (Li et al, 2022). Most cultivated pears have a diploid genome (2n = 34) that is extremely heterozygous and has several repeating sequences (Chen et al, 2023).…”

Section: Introductionmentioning

confidence: 99%

Comparative genomic profiling of transport inhibitor Response1/Auxin signaling F-box (TIR1/AFB) genes in eight Pyrus genomes revealed the intraspecies diversity and stress responsiveness patterns

Yang,

Yu,

Gao

et al. 2024

Front. Genet.

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In the genomics of plants and the phytoecosystem, Pyrus (pear) is among the most nutritious fruits and contains fiber that has great health benefits to humans. It is mostly cultivated in temperate regions and is one of the most cultivated pome fruits globally. Pears are highly subjected to biotic and abiotic stresses that affect their yield. TIR1/AFB proteins act as auxin co-receptors during the signaling of nuclear auxins and play a primary role in development-related regulatory processes and responses to biotic and abiotic stresses. However, this gene family and its members have not been explored in Pyrus genomes, and understanding these genes will help obtain useful insights into stress tolerance and ultimately help maintain a high yield of pears. This study reports a pangenome-wide investigation of TIR1/AFB genes from eight Pyrus genomes: Cuiguan (Pyrus pyrifolia), Shanxi Duli (P. betulifolia), Zhongai 1 [(P. ussuriensis × communis) × spp.], Nijisseiki (P. pyrifolia), Yunhong No.1 (P. pyrifolia), d’Anjou (P. communis), Bartlett v2.0 (P. communis), and Dangshansuli v.1.1 (P. bretschneideri). These genes were randomly distributed on 17 chromosomes in each genome. Based on phylogenetics, the identified TIR1/AFB genes were divided into six groups. Their gene structure and motif pattern showed the intraspecific structural conservation as well as evolutionary patterns of Pyrus TIR1/AFBs. The expansion of this gene family in Pyrus is mainly caused by segmental duplication; however, a few genes showed tandem duplication. Moreover, positive and negative selection pressure equally directed the gene’s duplication process. The GO and PPI analysis showed that Pyrus TIR1/AFB genes are associated with abiotic stress- and development-related signaling pathways. The promoter regions of Pyrus TIR1/AFB genes were enriched in hormone-, light-, development-, and stress-related cis elements. Furthermore, publicly available RNA-seq data analysis showed that DaTIR1/AFBs have varied levels of expression in various tissues and developmental stages, fruit hardening disease conditions, and drought stress conditions. This indicated that DaTIR1/AFB genes might play critical roles in response to biotic and abiotic stresses. The DaTIR1/AFBs have similar protein structures, which show that they are involved in the same function. Hence, this study will broaden our knowledge of the TIR1/AFB gene family in Pyrus, elucidating their contribution to conferring resistance against various environmental stresses, and will also provide valuable insights for future researchers.

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Pear genetics: Recent advances, new prospects, and a roadmap for the future

Cited by 23 publications

References 232 publications

A chromosome-scale assembly for ‘d’Anjou’ pear

A chromosome-scale assembly for ‘d’Anjou’ pear

Increased DNA methylation contributes to the early ripening of pear fruits during domestication and improvement

Comparative genomic profiling of transport inhibitor Response1/Auxin signaling F-box (TIR1/AFB) genes in eight Pyrus genomes revealed the intraspecies diversity and stress responsiveness patterns

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