The integrated genomics of crop domestication and breeding
X Huang, S Huang, B Han, J Li - Cell, 2022 - cell.com
As a major event in human civilization, wild plants were successfully domesticated to be
crops, largely owing to continuing artificial selection. Here, we summarize new discoveries …
crops, largely owing to continuing artificial selection. Here, we summarize new discoveries …
Plant pan-genomics and its applications
J Shi, Z Tian, J Lai, X Huang - Molecular Plant, 2023 - cell.com
Plant genomes are so highly diverse that a substantial proportion of genomic sequences are
not shared among individuals. The variable DNA sequences, along with the conserved core …
not shared among individuals. The variable DNA sequences, along with the conserved core …
Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species
Effective utilization of wild relatives is key to overcoming challenges in genetic improvement
of cultivated tomato, which has a narrow genetic basis; however, current efforts to decipher …
of cultivated tomato, which has a narrow genetic basis; however, current efforts to decipher …
A draft human pangenome reference
Abstract Here the Human Pangenome Reference Consortium presents a first draft of the
human pangenome reference. The pangenome contains 47 phased, diploid assemblies …
human pangenome reference. The pangenome contains 47 phased, diploid assemblies …
A graph-based genome and pan-genome variation of the model plant Setaria
Setaria italica (foxtail millet), a founder crop of East Asian agriculture, is a model plant for C4
photosynthesis and developing approaches to adaptive breeding across multiple climates …
photosynthesis and developing approaches to adaptive breeding across multiple climates …
Building pangenome graphs
Pangenome graphs can represent all variation between multiple reference genomes, but
current approaches to build them exclude complex sequences or are based upon a single …
current approaches to build them exclude complex sequences or are based upon a single …
Pangenome graph construction from genome alignments with Minigraph-Cactus
Pangenome references address biases of reference genomes by storing a representative
set of diverse haplotypes and their alignment, usually as a graph. Alternate alleles …
set of diverse haplotypes and their alignment, usually as a graph. Alternate alleles …
Pangenome analysis reveals genomic variations associated with domestication traits in broomcorn millet
Broomcorn millet (Panicum miliaceum L.) is an orphan crop with the potential to improve
cereal production and quality, and ensure food security. Here we present the genetic …
cereal production and quality, and ensure food security. Here we present the genetic …
Telomere-to-telomere Citrullus super-pangenome provides direction for watermelon breeding
To decipher the genetic diversity within the cucurbit genus Citrullus, we generated telomere-
to-telomere (T2T) assemblies of 27 distinct genotypes, encompassing all seven Citrullus …
to-telomere (T2T) assemblies of 27 distinct genotypes, encompassing all seven Citrullus …
Structural variation (SV)-based pan-genome and GWAS reveal the impacts of SVs on the speciation and diversification of allotetraploid cottons
S Jin, Z Han, Y Hu, Z Si, F Dai, L He, Y Cheng, Y Li… - Molecular Plant, 2023 - cell.com
Structural variations (SVs) have long been described as being involved in the origin,
adaption, and domestication of species. However, the underlying genetic and genomic …
adaption, and domestication of species. However, the underlying genetic and genomic …