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[学术文献 ] Population-wide DNA methylation polymorphisms at single-nucleotide resolution in 207 cotton accessions reveal epigenomic contributions to complex traits 进入全文
CELL RESEARCH
DNA methylation plays multiple regulatory roles in crop development. However, the relationships of methylation polymorphisms with genetic polymorphisms, gene expression, and phenotypic variation in natural crop populations remain largely unknown. Here, we surveyed high-quality methylomes, transcriptomes, and genomes obtained from the 20-days-post-anthesis (DPA) cotton fibers of 207 accessions and extended the classical framework of population genetics to epigenetics. Over 287 million single methylation polymorphisms (SMPs) were identified, 100 times more than the number of single nucleotide polymorphisms (SNPs). These SMPs were significantly enriched in intragenic regions while depleted in transposable elements. Association analysis further identified a total of 5,426,782 cis-methylation quantitative trait loci (cis-meQTLs), 5078 cis-expression quantitative trait methylation (cis-eQTMs), and 9157 expression quantitative trait loci (eQTLs). Notably, 36.39% of cis-eQTM genes were not associated with genetic variation, indicating that a large number of SMPs associated with gene expression variation are independent of SNPs. In addition, out of the 1715 epigenetic loci associated with yield and fiber quality traits, only 36 (2.10%) were shared with genome-wide association study (GWAS) loci. The construction of multi-omics regulatory networks revealed 43 cis-eQTM genes potentially involved in fiber development, which cannot be identified by GWAS alone. Among these genes, the role of one encoding CBL-interacting protein kinase 10 in fiber length regulation was successfully validated through gene editing. Taken together, our findings prove that DNA methylation data can serve as an additional resource for breeding purposes and can offer opportunities to enhance and expedite the crop improvement process.
[学术文献 ] Genetic manipulation of the genes for clonal seeds results in sterility in cotton 进入全文
BMC PLANT BIOLOGY
Background Heterosis is a common phenomenon in plants and has been extensively applied in crop breeding. However, the superior traits in the hybrids can only be maintained in the first generation but segregate in the following generations. Maintaining heterosis in generations has been challenging but highly desirable in crop breeding. Recent study showed that maternally produced diploid seeds could be achieved in rice by knocking out three meiosis related genes, namely REC8, PAIR1, OSD1 to create MiMe in combination with egg cell specific expression of BBM transcription factor, a technology called clonal seeds. Interestingly, there has been very limited reports indicating the feasibility of this approach in other crops. Results In this study, we aimed to test whether clonal seeds could be created in cotton. We identified the homologs of the three meiosis related genes in cotton and used the multiplex CRISPR/Cas9 gene editing system to simultaneously knock out these three genes in both A and D sub-genomes. More than 50 transgenic cotton plants were generated, and fragment analysis indicated that multiple gene knockouts occurred in the transgenic plants. However, all the transgenic plants were sterile apparently due to the lack of pollen. Pollination of the flowers of the transgenic plants using the wild type pollens could not generate seeds, an indication of defects in the formation of female sexual cells in the transgenic plants. In addition, we generated transgenic cotton plants expressing the cotton BBM gene driven by the Arabidopsis egg cell specific promoter pDD45. Two transgenic plants were obtained, and both showed severely reduced fertility. Conclusions Overall, our results indicate that knockout of the clonal seeds related genes in cotton causes sterility and how to manipulate genes to create clonal seeds in cotton requires further research.
[学术文献 ] Insights into the genetic divergence in Asiatic cotton (Gossypium arboreum L.) germplasm for fibre-quality traits 进入全文
PLANT GENETIC RESOURCES-CHARACTERIZATION AND UTILIZATION
Asiatic cotton (Gossypium arboreum L.) has evolved in the Indian subcontinent and is known for its adaptability to low-input management conditions. In the present study, 300 diverse G. arboreum lines, including 100 Nandyal arboreum breeding lines (NAB), 132 Arboreum germplasm collections (AGC) and 68 long-linted arboreum genotypes (LLA), were evaluated for fibre quality to assess the diversity among them and to identify promising genotypes with desirable fibre traits. Significant variations were observed among the genotypes for the studied fibre-quality traits. Principal component analysis showed that the traits micronaire (Mic) and elongation percentage (E%) followed by upper half mean length (UHML) and bundle tenacity (tenacity) were the most significant contributors to variation. Cluster analysis based on the Euclidian distance method showed 16 clusters among 300 G. arboreum genotypes. The genotypes in cluster 4 have desirable UHML, tenacity and UI (uniformity index) traits, and cluster 12 has Mic and E% traits. Furthermore, the number of genotypes with desirable fibre-quality traits was found to be higher in the AGC group than in the LLA and NAB groups. The trait tenacity followed by the UHML showed relatively higher Shannon-Weiner diversity index values across different genotypic groups. Based on the superior performance, the genotypes PA 847, PA 809, PA 837, PA 863, NDLA 3147-2, NDLA 2974 and NDLA 3081 were found to be having desirable fibre traits. The identified promising genotypes are valuable genetic resources for improving fibre quality in G. arboreum cotton.
[学术文献 ] Impact of active root zone soil potassium levels on cotton yield and fiber quality under no tillage 进入全文
FRONTIERS IN PLANT SCIENCE
Introduction Potassium deficiency significantly hinders cotton growth and development, adversely affecting yield and fiber quality. Applying potassium fertilizer is a common practice to address potassium deficiency in the soil. However, the effectiveness of potassium fertilizer application depends on the appropriate soil potassium levels in cotton fields.Methods This study used a randomized block design with six different soil potassium levels and conducted experiments across 18 micro-zones in the field. This study aimed to investigate the response of cotton yield and quality to different soil potassium levels, to try to clarify the suitable soil potassium levels for cotton growth, so as to provide practical and effective help for determining the amount of potash fertilizer in the cotton field.Results The results showed that the seedcotton yield was increasing, with the soil potassium level increased under no tillage. There was no significant difference among K4, K5, and K6 on seedcotton yield, which were significantly higher than K1 and K2. As soil potassium levels increased, the proportion of autumn boll and the proportion of outer boll also increased, indicating that higher soil potassium levels support the better growth and development of cotton in the middle and late stages, leading to increased boll sets and higher yields. Additionally, the available potassium content in the 0-40-cm soil layer was significantly correlated with yield and yield parameters but not with fiber quality indices.Discussion It is concluded that K4 treatment could provide sufficient potassium to meet the growth and development needs of cotton. Potassium fertilizer application is recommended when the available potassium content in the 0-40-cm soil layer falls below 122.88 mg kg-1 in the cotton field.
[学术文献 ] Evolutionary comparison of lncRNAs in four cotton species and functional identification of LncR4682-PAS2-KCS19 module in fiber elongation 进入全文
PLANT JOURNAL
Long non-coding RNAs (lncRNAs) play an important role in various biological processes in plants. However, there have been few reports on the evolutionary signatures of lncRNAs in closely related cotton species. The lncRNA transcription patterns in two tetraploid cotton species and their putative diploid ancestors were compared in this paper. By performing deep RNA sequencing, we identified 280 429 lncRNAs from 21 tissues in four cotton species. lncRNA transcription evolves more rapidly than mRNAs, and exhibits more severe turnover phenomenon in diploid species compared to that in tetraploid species. Evolutionarily conserved lncRNAs exhibit higher expression levels, and lower tissue specificity compared with species-specific lncRNAs. Remarkably, tissue expression of homologous lncRNAs in Gossypium hirsutum and G. barbadense exhibited similar patterns, suggesting that these lncRNAs may be functionally conserved and selectively maintained during domestication. An orthologous lncRNA, lncR4682, was identified and validated in fibers of G. hirsutum and G. barbadense with the highest conservatism and expression abundance. Through virus-induced gene silencing in upland cotton, we found that lncR4682 and its target genes GHPAS2 and GHKCS19 positively regulated fiber elongation. In summary, the present study provides a systematic analysis of lncRNAs in four closely related cotton species, extending the understanding of transcriptional conservation of lncRNAs across cotton species. In addition, LncR4682-PAS2-KCS19 contributes to cotton fiber elongation by participating in the biosynthesis of very long-chain fatty acids.
[学术文献 ] Natural variation at the cotton HIC locus increases trichome density and enhances resistance to aphids 进入全文
PLANT JOURNAL
Plant trichomes are an excellent model for studying cell differentiation and development, providing crucial defenses against biotic and abiotic stresses. There is a well-established inverse relationship between trichome density and aphid prevalence, indicating that higher trichome density leads to reduced aphid infestations. Here we present the cloning and characterization of a dominant quantitative trait locus, HIC (hirsute cotton), which significantly enhances cotton trichome density. This enhancement leads to markedly improved resistance against cotton aphids. The HIC encodes an HD-ZIP IV transcriptional activator, crucial for trichome initiation. Overexpression of HIC leads to a substantial increase in trichome density, while knockdown of HIC results in a marked decrease in density, confirming its role in trichome regulation. We identified a variant in the HIC promoter (-810 bp A to C) that increases transcription of HIC and trichome density in hirsute cotton compared with Gossypium hirsutum cultivars with fewer or no trichomes. Interestingly, although the -810 variant in the HIC promoter is the same in G. barbadense and hirsute cotton, the presence of a copia-like retrotransposon insertion in the coding region of HIC in G. barbadense causes premature transcription termination. Further analysis revealed that HIC positively regulates trichome density by directly targeting the EXPANSIN A2 gene, which is involved in cell wall development. Taken together, our results underscore the pivotal function of HIC as a primary regulator during the initial phases of trichome formation, and its prospective utility in enhancing aphid resistance in superior cotton cultivars via selective breeding.
