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Cultivated Cotton Genomes Reveal Crop Trait-Related Structural Variants

NEW YORK – A team led by investigators at the Hebei Agricultural University and the Novogene Bioinformatics Institute in China has come up with high-quality genome assemblies for two cultivated cotton species, uncovering trait-related structural variants that were subsequently assessed in nearly 1,100 more cotton accessions.

Using Pacific Biosciences long-read sequencing, Illumina paired-end sequencing, 10x Genomics mapping, and Hi-C chromatin interaction profiling, the researchers put together high-quality reference genomes for Gossypium hirsutum from a NDM8 cultivar, which is often grown in China's Yellow River Valley, and for G. barbadense accession Pima90, which is used as a source for molecular breeding.

"To improve the fibers and disease resistance of G. hirsutum, a proposed approach is to transfer superior related traits from G. barbadense into G. hirsutum," the authors explained in a paper published in Nature Genetics on Monday, noting that past studies have not spelled out the full suite of genomic differences between the species.

Within the 2.3 gigabase NDM8 genome and the 2.2 gigabase genome for the Pima90 accession, the team tracked down 80,124 and 79,613 predicted protein-coding genes, respectively. With linkage disequilibrium data and other clues, they found more than 900 genes with potential ties to cotton fiber quality or yield, and 60 genes that appeared to coincide with resistance to verticillium wilt fungal disease.

By resequencing another 1,081 cotton accessions, meanwhile, they described more than 1,400 newly identified genes from the G. hirsutum genome that were conserved across hundreds of cotton accessions and narrowed in on nearly 450 structural variants with apparent ties to agriculturally relevant cotton traits.

"Analyzing the two genomes and resequences showed that large-scale genomic variations occurred during breeding, providing resources for cotton crop improvement," the authors reported.

While the A-subgenome of the cotton cultivars tended to be marked by a preponderance of relatively large inversions, the researchers noted, selected trait-related structural variants often turned up more frequently in the smaller D-subgenome, hinting that there may have been more pronounced selection pressure on the Gossypium D-subgenome during cotton domestication and trait selection process.

Moreover, the authors reported, "density of insertions and deletions across each chromosome showed the strongest bias near the telomeres, similar to what has been reported in the human genome. These will enhance the genomic resources for cotton improvement and provide insight into species formation and variety development."

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