[HTML][HTML] Graph pangenomes track genetic variants for crop improvement

A Hameed, P Poznanski, A Nadolska-Orczyk… - International Journal of …, 2022 - mdpi.com
… limited selection of cultivars for many crops such as maize, cotton… In cotton, pangenomics
datasets built from 1961 accessions … of genes (32,569 and 8851) lost during domestication from …

[HTML][HTML] Genomic evolution and insights into agronomic trait innovations of Sesamum species

H Miao, L Wang, L Qu, H Liu, Y Sun, M Le, Q Wang… - Plant …, 2024 - cell.com
… position within eudicots were observed. Pan-genome analysis revealed 9164 core gene
terminal repeat insertion and a sequence deletion in DIR genes of wild Sesamum angustifolium …

The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features

W Qi, YW Lim, A Patrignani, P Schläpfer… - …, 2022 - academic.oup.com
sequencing efforts using different technologies over the past … of genomic selection, genome
editing, and improving genetic … haplotigs can be regions still missing from the present set of …

The intervention of multi-omics approaches for developing abiotic stress resistance in cotton crop under climate change

MKR Khan, A Ditta, B Wang, L Fang, Z Anwar… - … agriculture in the era of …, 2023 - Springer
… integrity of the chloroplast being lost. Consequently, photosystem … In domesticated cotton,
CAT and SOD activities are enhanced by … selection in the upland cotton genotypes, the genetic

The evolution, variation and expression patterns of the Annexin gene family in the maize pan-genome

X Liu, M Zhang, X Zhao, M Shen, R Feng, Q Wei - 2024 - researchsquare.com
selection in certain varieties, while the remaining genes had … ber development, the highly
expressed cotton annexin gene, … , species origin and domestication, and providing valuable …

[HTML][HTML] Fingerprint Finder: Identifying Genomic Fingerprint Sites in Cotton Cohorts for Genetic Analysis and Breeding Advancement

S Liu, H Cheng, Y Zhang, M He, D Zuo, Q Wang, L Lv… - Genes, 2024 - mdpi.com
… With the short-read sequencing of an elite cotton pedigree, … ), missing some critical genomic
features in this cotton pedigree. … unique genes may have suffered extreme selection because …

[HTML][HTML] Genetic and genomic resources for soybean breeding research

J Petereit, JI Marsh, PE Bayer, MF Danilevicz… - Plants, 2022 - mdpi.com
… has been selected for or lost during domestication and breeding, … and 14 domesticated
soybean individuals, sequenced to an … hubs to retrieve genotypic and genetic information across …

[HTML][HTML] Pan-genome analyses of model fungal species

CGP McCarthy, DA Fitzpatrick - Microbial genomics, 2019 - microbiologyresearch.org
… (~98 %) were retrieved as complete gene models in each strain (… gene cluster that confers
arsenic resistance was missing a … Our selection covers fungal species with different genomic …

Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes

F Zhang, H Xue, X Dong, M Li, X Zheng, Z Li… - Genome …, 2022 - genome.cshlp.org
… In this paper, we report a high-quality rice pan-genome … To achieve this, we carefully
selected 105 OS accessions, most … gene families, including 2132 novel gene families missing in …

[HTML][HTML] Resequencing of durian genomes reveals large genetic variations among different cultivars

W Nawae, C Naktang, S Charoensri… - Frontiers in Plant …, 2023 - frontiersin.org
… the protein sequences of all durians with those of cottons (G. … in pathogen response, while
the missing genes in KD and PM … demonstrated genetic variations among the selected durian …