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[学术文献 ] Pyramiding effects of favorable haplotypes of loci on major fiber yield and quality traits in Upland Cotton (Gossypium hirsutum L.) 进入全文
INDUSTRIAL CROPS AND PRODUCTS
Enhancing both fiber yield and quality is crucial in cotton breeding programs. Typically, a negative correlation exists between fiber yield and quality, and the strategy to decouple this relationship remains obscure. In this study, we generated three multi-parent intercross populations, encompassing 2,852 F2:3 lines, which represent fiber yield potential (FY), fiber quality potential (FQ), and a combination of both potentials (FYQ), derived from sixteen diverse Upland cotton cultivars. We utilized twenty-four kompetitive allele specific PCR (KASP) molecular markers, based on previously identified loci associated with fiber quality (FL5/FS1, FL3/FS2, and FL2) and fiber yield (BW1, BW2, and LP1), for genotyping purposes. The pyramiding of favorable haplotypes from three fiber quality-associated loci resulted in an increase exceeding 10 % in fiber length (FL5+FL3+FL2+LP1) and in an increase exceeding 17 % in fiber strength (FL5+FL3+FL2). Notably, our findings suggest that the combination of FL3+FL2+BW1+LP1 alleles has the potential to disrupt the negative correlation between fiber yield and quality. Lines harboring these alleles simultaneously exhibited an elevated lint percentage (LP), as well as enhanced fiber length and quality. This study offers robust molecular markers for the efficient selection of superior progeny with desired phenotypes in the early stages of cotton breeding. Furthermore, the allelic combination that concurrently improves fiber quality and yield sheds light on for further exploration the molecular basis of breaking unfavorable linkages in crop breeding.
[学术文献 ] Transcriptome analysis reveals potential of down-regulated genes in cotton fiber improvement 进入全文
INDUSTRIAL CROPS AND PRODUCTS
Cotton fiber serves as the predominant source material for operations within the textile industry, and enhancements in fiber quality are likely to yield substantial economic benefits. Nonetheless, the efforts of the cotton genomics community have been predominantly concentrated on up-regulated genes that transcriptionally contribute to fiber quality, revealing a limited pool of genetic resources for the application of gene knock-out technology. To expand the genetic resources available for knock-out strategies in cotton molecular breeding, we assembled two accessions characterized by divergent fiber lengths for comparative transcriptome analysis. Transcriptional abundance analysis identified 1604 up-regulated and 1059 down-regulated genes during the course of fiber development. We further identified the gene regulatory network of the down-regulated genes through weighted gene co-expression network analysis (WGCNA) and selected 17 genes as the final downregulated gene pannel by simulating genomic selection based on a previous cotton cohort. An array of these genes had transcription regulation enriched to sugar metabolism. Our preliminary experiments, where GhUXS5 was overexpressed in Arabidopsis thaliana, significantly inhibited both trichome formation and root elongation. This suggests it may also inhibit cotton fiber elongation. Our approach provided new genetic resources for discovering fiber quality related genes. GhUXS5 and the other 16 down-regulated genes could be used as the potential target genes for genetic engineering of cotton fiber improvement induced by gene knock-out technology.
[学术文献 ] Insights into genetic diversity and functional significance of the bHLH genes in cotton fiber development 进入全文
INDUSTRIAL CROPS AND PRODUCTS
This study investigated the identification and distribution of single nucleotide polymorphisms (SNPs) within basic Helix-Loop-Helix (bHLH) transcription factors (TFs) across diverse cotton (Gossypium hirsutum) accessions, including wild, landrace, and improved varieties. Comprehensive genomic analyses revealed substantial SNP diversity in wild cotton, distinct from that observed in landraces and improved accessions. Comparative analysis showed notable variations in SNP abundance and impact levels across different accessions, with missense SNPs being prevalent. Nucleotide substitution patterns highlighted the dominance of G>A and A>G substitutions. Population genetic analyses unveiled significant genetic diversity within wild accessions and distinct clustering between wild and improved accessions. Temporal expression profiling of bHLH genes during cotton fiber development demonstrated dynamic expression patterns, emphasizing their roles in fiber initiation, elongation, and cellulose biosynthesis. Moreover, association analysis identified SNPs significantly associated within bHLH genes, particularly GhbHLH149, with fiber quality traits, indicating their potential functional significance. Population genetic analyses further revealed evidence of positive selection on GhbHLH149 during cotton improvement. This study provides a comprehensive understanding of SNP diversity, gene expression dynamics, and genetic selection in bHLH genes, offering valuable insights for future cotton breeding efforts aimed at improving fiber quality traits in cotton.
[学术文献 ] GhCKX1 is an important genetic target for improving fiber strength in cotton 进入全文
INDUSTRIAL CROPS AND PRODUCTS
Cotton is a widely grown crop to produce natural textile fiber, and improving the fiber strength (FS) is one of the main targets that cotton breeders focus on. The long-term natural selection and domestication have produced abundant germplasm resources of Gossypium hirsutum, and exploring genetic underpinnings underlying these FS innovation in elite collections is crucial. PCAMP is proposed as a most optimized NGS based bulked segregant analysis (NGS-BSA) for the high-resolution identification of markers linked to specific genomic regions through pairwise comparing multiple BSA bulks. In this study, we firstly applied PCAMP to resolved the FS genetic architecture in G. hirsutum cv. CCRI127. As an extension for PCAMP approach, graded bulks were constructed using F-2 segregants with the FS phenotype revalidated by F-2:3 lines, and then, a major QTL was eventually narrowed to 2.47 Mb from 8.14 Mb generated by traditional BSA approaches. Subsequently, through a saturated genetic map constructed in this locus, an novel FS gene, GhCKX1, predicted to produce a cytokinin (CTK) oxidase was isolated. It can negatively modulate the CTK signaling circuit via irreversible degradation of CTKs, resulting in an additional cell wall thickness to xylem tracheary elements in transgenic lines of Arabidopsis thaliana. Thus, the GhCKX1 gene will be an potential genetic target, with which, we can genetically manipulate the secondary wall synthesis in unicellular cotton fibers.
[学术文献 ] Deepening genomic sequences of 1081 Gossypium hirsutum accessions reveals novel SNPs and haplotypes relevant for practical breeding utility 进入全文
GENOMICS
Fiber quality is a major breeding goal in cotton, but phenotypically direct selection is often hindered. In this study, we identified fiber quality and yield related loci using GWAS based on 2.97 million SNPs obtained from 10.65x resequencing data of 1081 accessions. The results showed that 585 novel fiber loci, including two novel stable SNP peaks associated with fiber length on chromosomes At12 and Dt05 and one novel genome regions linked with fiber strength on chromosome Dt12 were identified. Furthermore, by means of gene expression analysis, GhM_A12G0090, GhM_D05G1692, GhM_D12G3135 were identified and GhM_D11G2208 function was identified in Arabidopsis. Additionally, 14 consistent and stable superior haplotypes were identified, and 25 accessions were detected as possessing these 14 superior haplotype in breeding. This study providing fundamental insight relevant to identification of genes associated with fiber quality and yield will enhance future efforts toward improvement of upland cotton.
[学术文献 ] A cotton mitochondrial alternative electron transporter, GhD2HGDH, induces early flowering by modulating GA and photoperiodic pathways 进入全文
PHYSIOLOGIA PLANTARUM
D-2-hydroxyglutarate dehydrogenase (D2HGDH) is a mitochondrial enzyme containing flavin adenine dinucleotide FAD, existing as a dimer, and it facilitates the specific oxidation of D-2HG to 2-oxoglutarate (2-OG), which is a key intermediate in the tricarboxylic acid (TCA) cycle. A Genome-wide expression analysis (GWEA) has indicated an association between GhD2HGDH and flowering time. To further explore the role of GhD2HGDH, we performed a comprehensive investigation encompassing phenotyping, physiology, metabolomics, and transcriptomics in Arabidopsis thaliana plants overexpressing GhD2HGDH. Transcriptomic and qRT-PCR data exhibited heightened expression of GhD2HGDH in upland cotton flowers. Additionally, early-maturing cotton exhibited higher expression of GhD2HGDH across all tissues than delayed-maturing cotton. Subcellular localization confirmed its presence in the mitochondria. Overexpression of GhD2HGDH in Arabidopsis resulted in early flowering. Using virus-induced gene silencing (VIGS), we investigated the impact of GhD2HGDH on flowering in both early- and delayed-maturing cotton plants. Manipulation of GhD2HGDH expression levels led to changes in photosynthetic pigment and gas exchange attributes. GhD2HGDH responded to gibberellin (GA3) hormone treatment, influencing the expression of GA biosynthesis genes and repressing DELLA genes. Protein interaction studies, including yeast two-hybrid, luciferase complementation (LUC), and GST pull-down assays, confirmed the interaction between GhD2HGDH and GhSOX (Sulfite oxidase). The metabolomics analysis demonstrated GhD2HGDH's modulation of the TCA cycle through alterations in various metabolite levels. Transcriptome data revealed that GhD2HGDH overexpression triggers early flowering by modulating the GA3 and photoperiodic pathways of the flowering core factor genes. Taken together, GhD2HGDH positively regulates the network of genes associated with early flowering pathways.
