Cytoplasmic male sterile (CMS) with cytoplasm from Gossypium Trilobum (D8) fails to produce functional pollen. It is useful for commercial hybrid cotton seed production. The restore line of CMS-D8 ...containing Rf.sub.2 gene can restore the fertility of the corresponding sterile line. This study combined the whole genome resequencing bulked segregant analysis (BSA) with high-throughput SNP genotyping to accelerate the physical mapping of Rf.sub.2 locus in CMS-D8 cotton. The fertility of backcross population ((sterile linexrestorer line)xmaintainer line) comprising of 1623 individuals was investigated in the field. The fertile pool (100 plants with fertile phenotypes, F-pool) and the sterile pool (100 plants with sterile phenotypes, S-pool) were constructed for BSA resequencing. The selection of 24 single nucleotide polymorphisms (SNP) through high-throughput genotyping and the development insertion and deletion (InDel) markers were conducted to narrow down the candidate interval. The pentapeptide repeat (PPR) family genes and upregulated genes in restore line in the candidate interval were analysed by qRT-PCR. The fertility investigation results showed that fertile and sterile separation ratio was consistent with 1:1. BSA resequencing technology, high-throughput SNP genotyping, and InDel markers were used to identify Rf.sub.2 locus on candidate interval of 1.48 Mb on chromosome D05. Furthermore, it was quantified in this experiment that InDel markers co-segregated with Rf.sub.2 enhanced the selection of the restorer line. The qRT-PCR analysis revealed PPR family gene Gh_D05G3391 located in candidate interval had significantly lower expression than sterile and maintainer lines. In addition, utilization of anther RNA-Seq data of CMS-D8 identified that the expression level of Gh_D05G3374 encoding NB-ARC domain-containing disease resistance protein in restorer lines was significantly higher than that in sterile and maintainer lines. This study not only enabled us to precisely locate the restore gene Rf.sub.2 but also evaluated the utilization of InDel markers for marker assisted selection in the CMS-D8 Rf.sub.2 cotton breeding line. The results of this study provide an important foundation for further studies on the mapping and cloning of restorer genes.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Over the last decade, two-photon microscopy (TPM) has been the technique of choice for in vivo noninvasive optical brain imaging for neuroscientific study or intra-vital microendoscopic imaging for ...clinical diagnosis or surgical guidance because of its intrinsic capability of optical sectioning for imaging deeply below the tissue surface with sub-cellular resolution. However, most of these research activities and clinical applications are constrained by the bulky size of traditional TMP systems. An attractive solution is to develop miniaturized TPMs, but this is challenged by the difficulty of the integration of dynamically scanning optical and mechanical components into a small space. Fortunately, microelectromechanical systems (MEMS) technology, together with other emerging micro-optics techniques, has offered promising opportunities in enabling miniaturized TPMs. In this paper, the latest advancements in both lateral scan and axial scan techniques and the progress of miniaturized TPM imaging will be reviewed in detail. Miniature TPM probes with lateral 2D scanning mechanisms, including electrostatic, electromagnetic, and electrothermal actuation, are reviewed. Miniature TPM probes with axial scanning mechanisms, such as MEMS microlenses, remote-focus, liquid lenses, and deformable MEMS mirrors, are also reviewed.
Cytoplasmic male sterility (CMS) conferred by the cytoplasm from Gossypium harknessii (D2) is an important system for hybrid seed production in Upland cotton (G. hirsutum). The male sterility of ...CMS-D2 (i.e., A line) can be restored to fertility by a restorer (i.e., R line) carrying the restorer gene Rf1 transferred from the D2 nuclear genome. However, the molecular mechanisms of CMS-D2 and its restoration are poorly understood.
In this study, a genome-wide comparative transcriptome analysis was performed to identify differentially expressed genes (DEGs) in flower buds among the isogenic fertile R line and sterile A line derived from a backcross population (BC
F
) and the recurrent parent, i.e., the maintainer (B line). A total of 1464 DEGs were identified among the three isogenic lines, and the Rf1-carrying Chr_D05 and its homeologous Chr_A05 had more DEGs than other chromosomes. The results of GO and KEGG enrichment analysis showed differences in circadian rhythm between the fertile and sterile lines. Eleven DEGs were selected for validation using qRT-PCR, confirming the accuracy of the RNA-seq results.
Through genome-wide comparative transcriptome analysis, the differential expression profiles of CMS-D2 and its maintainer and restorer lines in Upland cotton were identified. Our results provide an important foundation for further studies into the molecular mechanisms of the interactions between the restorer gene Rf1 and the CMS-D2 cytoplasm.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Utilization of heterosis has greatly improved the productivity of many crops worldwide. Understanding the potential molecular mechanism about how hybridization produces superior yield in upland ...cotton is critical for efficient breeding programs.
In this study, high, medium, and low hybrids varying in the level of yield heterosis were screened based on field experimentation of different years and locations. Phenotypically, high hybrid produced a mean of 14% more seed cotton yield than its better parent. Whole-genome RNA sequencing of these hybrids and their four inbred parents was performed using different tissues of the squaring stage. Comparative transcriptomic differences in each hybrid parent triad revealed a higher percentage of differentially expressed genes (DEGs) in each tissue. Expression level dominance analysis identified majority of hybrids DEGs were biased towards parent like expressions. An array of DEGs involved in ATP and protein binding, membrane, cell wall, mitochondrion, and protein phosphorylation had more functional annotations in hybrids. Sugar metabolic and plant hormone signal transduction pathways were most enriched in each hybrid. Further, these two pathways had most mapped DEGs on known seed cotton yield QTLs. Integration of transcriptome, QTLs, and gene co-expression network analysis discovered genes Gh_A03G1024, Gh_D08G1440, Gh_A08G2210, Gh_A12G2183, Gh_D07G1312, Gh_D08G1467, Gh_A03G0889, Gh_A08G2199, and Gh_D05G0202 displayed a complex regulatory network of many interconnected genes. qRT-PCR of these DEGs was performed to ensure the accuracy of RNA-Seq data.
Through genome-wide comparative transcriptome analysis, the current study identified nine key genes and pathways associated with biological process of yield heterosis in upland cotton. Our results and data resources provide novel insights and will be useful for dissecting the molecular mechanism of yield heterosis in cotton.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The cytoplasmic male sterility (CMS) system is ideal for exploiting heterosis in crops such as cotton. However, CMS-D2, which is based on
Gossypium harknessii
cytoplasm, is still not widely used for ...cotton production. In this study, we developed an efficient marker-assisted selection method based on insertion/deletion (InDel) markers that can identify restorer lines carrying
Rf1
. Whole-genome resequencing was first completed for restorer N(
Rf1Rf1
) and maintainer N(
rf1rf1
) lines with normal fertile cytoplasm (N). Comparisons with the TM-1 reference genome sequence resulted in the identification of 292,065 and 183,657 InDels for the restorer and maintainer lines, respectively. Most of the InDels in the restorer line were distributed on Chromosome_D05, which carries
Rf1
. Of the 12 InDel markers near the
Rf1
target region that were further validated, four co-dominant markers (i.e., InDel-1891, InDel-3434, InDel-7525, and InDel-9356) co-segregated with
Rf1
, as verified by a segregation analysis in an F
2
population. We subsequently used InDel-1891 to determine the allele status at the
Rf1
locus in a backcross scheme for transferring
Rf1
. In this study, we developed new markers to increase the marker density in the
Rf1
target region, which will be useful for the fine mapping of
Rf1
. The development of convenient and inexpensive co-segregating InDel markers will facilitate the marker-assisted selection of restorer lines carrying
Rf1
.
Heterosis breeding is the most useful method for yield increase around the globe. Heterosis is an intriguing process to develop superior offspring to either parent in the desired character. The ...biomass vigor produced during seedling emergence stage has a direct influence on yield heterosis in plants. Unfortunately, the genetic basis of early biomass vigor in cotton is poorly understood.
Three stable performing F
hybrids varying in yield heterosis named as high, medium and low hybrids with their inbred parents were used in this study. Phenotypically, these hybrids established noticeable biomass heterosis during the early stage of seedling growth in the field. Transcriptome analysis of root and leaf revealed that hybrids showed many differentially expressed genes (DEGs) relative to their parents, while the comparison of inbred parents showed limited number of DEGs indicating similarity in their genetic constitution. Further analysis indicated expression patterns of most DEGs were overdominant in both tissues of hybrids. According to GO results, functions of overdominance genes in leaf were enriched for chloroplast, membrane, and protein binding, whereas functions of overdominance genes in root were enriched for plasma membrane, extracellular region, and responses to stress. We found several genes of circadian rhythm pathway related to LATE ELONGATED HYPOCOTYL (LHY) showed downregulated overdominant expressions in both tissues of hybrids. In addition to circadian rhythm, several leaf genes related to Aux/IAA regulation, and many root genes involved in peroxidase activity also showed overdominant expressions in hybrids. Twelve genes involved in circadian rhythm plant were selected to perform qRT-PCR analysis to confirm the accuracy of RNA-seq results.
Through genome-wide comparative transcriptome analysis, we strongly predict that overdominance at gene expression level plays a pivotal role in early biomass vigor of hybrids. The combinational contribution of circadian rhythm and other metabolic process may control vigorous growth in hybrids. Our result provides an important foundation for dissecting molecular mechanisms of biomass vigor in hybrid cotton.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
As a vital type of noncoding RNAs, circular RNAs (circRNAs) play important roles in plant growth and development and stress response. However, little is known about the biological roles of circRNAs ...in regulating the stability of male fertility restoration for cytoplasmic male sterility (CMS) conditioned by Gossypium harknessii cytoplasm (CMS-D2) cotton under high-temperature (HT) stress.
In this study, RNA-sequencing and bioinformatics analysis were performed on pollen grains of isonuclear alloplasmic near-isogenic restorer lines NH N(Rf
rf
) and SH S(Rf
rf
) with obvious differences in fertility stability under HT stress at two environments. A total of 967 circRNAs were identified, with 250 differentially expressed under HT stress. We confirmed the back-splicing sites of eight selected circRNAs using divergent primers and Sanger sequencing. Tissue-specific expression patterns of five differentially expressed circRNAs (DECs) were also verified by RT-PCR and qRT-PCR. Functional enrichment and metabolic pathway analysis revealed that the parental genes of DECs were significantly enriched in fertility-related biological processes such as pollen tube guidance and cell wall organization, as well as the Pentose and glucuronate interconversions, Steroid biosynthesis, and N-Glycan biosynthesis pathways. Moreover, we also constructed a putative circRNA-mediated competing endogenous RNA (ceRNA) network consisting of 21 DECs, eight predicted circRNA-binding miRNAs, and their corresponding 22 mRNA targets, especially the two ceRNA modules circRNA346-miR159a-MYB33 and circRNA484-miR319e-MYB33, which might play important biological roles in regulating pollen fertility stability of cotton CMS-D2 restorer line under HT stress.
Through systematic analysis of the abundance, characteristics and expression patterns of circRNAs, as well as the potential functions of their parent genes, our findings suggested that circRNAs and their mediated ceRNA networks acted vital biological roles in cotton pollen development, and might be also essential regulators for fertility stability of CMS-D2 restorer line under heat stress. This study will open a new door for further unlocking complex regulatory mechanisms underpinning the fertility restoration stability for CMS-D2 in cotton.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
DNA methylation is an important epigenetic modification involved in multiple biological processes. Altered methylation patterns have been reported to be associated with male sterility in some plants, ...but their role in cotton cytoplasmic male sterility (CMS) remains unclear. Here, integrated methylome and transcriptome analyses were conducted between the CMS-D2 line ZBA and its near-isogenic maintainer line ZB in upland cotton. More methylated cytosine sites (mCs) and higher methylation levels (MLs) were found among the three sequence contexts in ZB compared to ZBA. A total of 4568 differentially methylated regions (DMRs) and 2096 differentially methylated genes (DMGs) were identified. Among the differentially expressed genes (DEGs) associated with DMRs (DMEGs), 396 genes were upregulated and 281 genes were downregulated. A bioinformatics analysis of these DMEGs showed that hyper-DEGs were significantly enriched in the "oxidative phosphorylation" pathway. Further qRT-PCR validation indicated that these hypermethylated genes (encoding the subunits of mitochondrial electron transport chain (ETC) complexes I and V) were all significantly upregulated in ZB. Our biochemical data revealed a higher extent of H
O
production but a lower level of adenosine triphosphate (ATP) synthesis in CMS-D2 line ZBA. On the basis of the above results, we propose that disrupted DNA methylation in ZBA may disrupt the homeostasis of reactive oxygen species (ROS) production and ATP synthesis in mitochondria, triggering a burst of ROS that is transferred to the nucleus to initiate programmed cell death (PCD) prematurely, ultimately leading to microspore abortion. This study illustrates the important role of DNA methylation in cotton CMS.
The objective of this study was to examine the relationship between heterosis and genetic distance in upland cotton (Gossypium hirsutum L.). Heterosis in the different environments was evaluated and ...the relationship between heterosis and genetic distance (GD) was determined based on SSR markers for yield quantitative trait loci (QTL). Yields of seed cotton and lint showed a linear relationship with mid‐parent heterosis (MPH) and better‐parent heterosis (BPH). The variation in heterosis for other traits and their correlation with GD may be due to environmental factors or the effort of QTLs tested in the present study may vary in different environments. The present findings provide a foundation for heterotic grouping of parental lines and breeding of new cotton hybrids with improved seed cotton yield. This study calls for more research with stable QTLs as well as advance molecular marker techniques may be used in predicting yield heterosis in a more precise and reliable manner.
Swept-source optical coherence tomography (SS-OCT), benefiting from its high sensitivity, relatively large penetration depth, and non-contact and non-invasive imaging capability, is ideal for human ...skin imaging. However, limited by the size and performance of the reported optical galvanometer scanners, existing portable/handheld OCT probes are still bulky, which makes continuously handheld imaging difficult. Here, we reported a miniaturized electrothermal-MEMS-based SS-OCT microscope that only weighs about 25 g and has a cylinder with a diameter of 15 mm and a length of 40 mm. This MEMS-based handheld imaging probe can achieve a lateral resolution of 25 μm, a 3D imaging time of 5 s, a penetration depth of up to 3.3 mm, and an effective imaging field of view (FOV) of 3 × 3 mm2. We have carried out both calibration plate and biological tissue imaging experiments to test the imaging performance of this microscope. OCT imaging of leaves, dragonfly, and human skin has been successfully obtained, showing the imaging performance and potential applications of this probe on human skin in the future.
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