Genetic mapping and transcriptomic characterization of a new fuzzless-tufted cottonseed mutant

Abstract

Fiber mutants are unique and valuable resources for understanding the genetic and molecular mechanisms controlling initiation and development of cotton fibers that are extremely elongated single epidermal cells protruding from the seed coat of cottonseeds. In this study, we reported a new fuzzless-tufted cotton mutant (Gossypium hirsutum) and showed that fuzzless-tufted near-isogenic lines (NILs) had similar agronomic traits and a higher ginning efficiency compared to their recurrent parents with normal fuzzy seeds. Genetic analysis revealed that the mutant phenotype is determined by a single incomplete dominant locus, designated N5. The mutation was fine mapped to an approximately 250-kb interval containing 33 annotated genes using a combination of bulked segregant sequencing, SNP chip genotyping, and fine mapping. Comparative transcriptomic analysis using 0–6 days post-anthesis (dpa) ovules from NILs segregating for the phenotypes of fuzzless-tufted (mutant) and normal fuzzy cottonseeds (wild-type) uncovered candidate genes responsible for the mutant phenotype. It also revealed that the flanking region of the N5 locus is enriched with differentially expressed genes (DEGs) between the mutant and wild-type. Several of those DEGs are members of the gene families with demonstrated roles in cell initiation and elongation, such as calcium-dependent protein kinase and expansin. The transcriptome landscape of the mutant was significantly reprogrammed in the 6 dpa ovules and, to a less extent, in the 0 dpa ovules, but not in the 2 and 4 dpa ovules. At both 0 and 6 dpa, the reprogrammed mutant transcriptome was mainly associated with cell wall modifications and transmembrane transportation, while transcription factor activity was significantly altered in the 6 dpa mutant ovules. These results imply a similar molecular basis for initiation of lint and fuzz fibers despite certain differences.

Analysis of meiosis in Pristionchus pacificus reveals plasticity in homolog pairing and synapsis in the nematode lineage

“…Second, the distal regions (‘arms’) show higher recombination rates than the central regions of each chromosome, as in Caenorhabditis ( Barnes et al, 1995 ; Rockman and Kruglyak, 2009 ). This bias was also evident in a map constructed using RNA sequencing data ( Rödelsperger et al, 2017 ) and seems to be a widely conserved feature among Rhabditids and perhaps other nematode clades ( Doyle et al, 2018 ; Gonzalez de la Rosa et al, 2021 ).…”

“…We have previously speculated that unique PC regions may have arisen in holocentric nematodes as part of a meiotic system that promotes karyotype stability ( MacQueen et al, 2005 ; Rog and Dernburg, 2013 ), an idea that seems more viable in light of our indirect evidence for their conservation in Pristionchus . The existence of such a mechanism could potentially account for the preservation of genetic linkage units known as ‘Nigon elements’ over long evolutionary periods, which has been documented through genome sequencing of diverse nematodes ( Foster et al, 2020 ; Gonzalez de la Rosa et al, 2021 ; Tandonnet et al, 2019 ). When inversions arise that suppress local recombination, they can lead to intraspecies reproductive barriers such as toxin/antitoxin systems, and eventually to full speciation.…”

Unravelling population structure heterogeneity within the genome of the malaria vector Anopheles gambiae

“…Big data visualisation and dimensionality-reducing embedding techniques continue to be developed. Successors to t-SNE, such as UMAP [ 74 ] and variational autoencoder neural networks [ 75 ] may further improve the visualization and interpretation of intra-genomic population structure heterogeneity.…”

Proteomic Identification of Bombyx mori Organelles Using the Engineered Ascorbate Peroxidase APEX and Development of Silkworm Organelle Proteome Database (SilkOrganPDB)

“…To find orthologs of silkworm proteins in other insects, we downloaded the genome data of Bombyx mandarina [ 44 ], Manduca sexta [ 45 ], Papilio xuthus [ 46 ], Spodoptera litura [ 47 ], Trichoplusia ni [ 48 ], Tribolium castaneum [ 49 ], Aedes aegypti [ 50 ], D. melanogaster [ 51 ], Apis cerana [ 52 ], and Apis mellifera [ 53 ] from GenBank. All protein sequences were all-to-all aligned using BLASTP [ 41 ] with an E-value cutoff less than 1e−5.…”