Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication

X Sun, C Jiao, H Schwaninger, CT Chao, Y Ma… - Nature …, 2020 - nature.com
Domestication of the apple was mainly driven by interspecific hybridization. In the present
study, we report the haplotype-resolved genomes of the cultivated apple (Malus domestica …

[HTML][HTML] Advances in genomics and genome editing for breeding next generation of fruit and nut crops

S Savadi, S Mangalassery, MS Sandesh - Genomics, 2021 - Elsevier
Fruit tree crops are an essential part of the food production systems and are key to achieve
food and nutrition security. Genetic improvement of fruit trees by conventional breeding has …

RosBREED: bridging the chasm between discovery and application to enable DNA-informed breeding in rosaceous crops

AF Iezzoni, J McFerson, J Luby, K Gasic… - Horticulture …, 2020 - academic.oup.com
The Rosaceae crop family (including almond, apple, apricot, blackberry, peach, pear, plum,
raspberry, rose, strawberry, sweet cherry, and sour cherry) provides vital contributions to …

Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar

H Sun, WB Jiao, K Krause, JA Campoy, M Goel… - Nature …, 2022 - nature.com
Potato is the most widely produced tuber crop worldwide. However, reconstructing the four
haplotypes of its autotetraploid genome remained an unsolved challenge. Here, we report …

High-quality genome assembly of'Cuiguan'pear (Pyrus pyrifolia) as a reference genome for identifying regulatory genes and epigenetic modifications responsible for …

Y Gao, Q Yang, X Yan, X Wu, F Yang, J Li… - Horticulture …, 2021 - academic.oup.com
Dormancy-associated MADS-box (DAM) genes serve as crucial regulators of the
endodormancy cycle in rosaceous plants. Although pear DAM genes have been identified …

Near-gapless and haplotype-resolved apple genomes provide insights into the genetic basis of rootstock-induced dwarfing

W Li, C Chu, H Li, H Zhang, H Sun, S Wang, Z Wang… - Nature Genetics, 2024 - nature.com
Dwarfing rootstocks have transformed the production of cultivated apples; however, the
genetic basis of rootstock-induced dwarfing remains largely unclear. We have assembled …

New strategies to overcome present CRISPR/Cas9 limitations in apple and pear: efficient dechimerization and base editing

J Malabarba, E Chevreau, N Dousset, F Veillet… - International journal of …, 2020 - mdpi.com
Despite recent progress, the application of CRISPR/Cas9 in perennial plants still has many
obstacles to overcome. Our previous results with CRISPR/Cas9 in apple and pear indicated …

Transposon insertions regulate genome‐wide allele‐specific expression and underpin flower colour variations in apple (Malus spp.)

Y Tian, A Thrimawithana, T Ding, J Guo… - Plant Biotechnology …, 2022 - Wiley Online Library
Allele‐specific expression (ASE) can lead to phenotypic diversity and evolution. However,
the mechanisms regulating ASE are not well understood, particularly in woody perennial …

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

Q Li, X Qiao, L Li, C Gu, H Yin, K Qi, Z Xie, S Yang… - Plant …, 2024 - cell.com
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 …

High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome

A Marrano, M Britton, PA Zaini, AV Zimin… - …, 2020 - academic.oup.com
Background The release of the first reference genome of walnut (Juglans regia L.) enabled
many achievements in the characterization of walnut genetic and functional variation …