Global RNA interactome of Salmonella discovers a 5' UTR sponge for the MicF small RNA that connects membrane permeability to transport capacity.

The envelope of Gram-negative bacteria is a vital barrier that must balance protection and nutrient uptake. Small RNAs are crucial regulators of the envelope composition and function. Here, using RIL-seq to capture the Hfq-mediated RNA-RNA interactome in Salmonella enterica, we discover envelope-related riboregulators, including OppX. We show that OppX acts as an RNA sponge of MicF sRNA, a prototypical porin repressor. OppX originates from the 5' UTR of oppABCDF, encoding the major inner-membrane oligopeptide transporter, and sequesters MicF's seed region to derepress the synthesis of the porin OmpF. Intriguingly, OppX operates as a true sponge, storing MicF in an inactive complex without affecting its levels or stability. Conservation of the opp-OppX-MicF-ompF axis in related bacteria suggests that it serves an important mechanism, adjusting envelope porosity to specific transport capacity. These data also highlight the resource value of this Salmonella RNA interactome, which will aid in unraveling RNA-centric regulation in enteric pathogens.

A network of small RNAs regulates sporulation initiation in Clostridioides difficile.

The obligate anaerobic, enteric pathogen Clostridioides difficile persists in the intestinal tract by forming antibiotic-resistant endospores that contribute to relapsing and recurrent infections. Despite the importance of sporulation for C. difficile pathogenesis, environmental cues and molecular mechanisms that regulate sporulation initiation remain ill-defined. Here, by using RIL-seq to globally capture the Hfq-dependent RNA-RNA interactome, we discovered a network of small RNAs that bind to mRNAs encoding sporulation-related genes. We show that two of these small RNAs, SpoX and SpoY, regulate translation of the master regulator of sporulation, Spo0A, in an opposing manner, which ultimately leads to altered sporulation rates. Infection of antibiotic-treated mice with SpoX and SpoY deletion mutants revealed a global effect on gut colonization and intestinal sporulation. Our work uncovers an elaborate RNA-RNA interactome controlling the physiology and virulence of C. difficile and identifies a complex post-transcriptional layer in the regulation of spore formation in this important human pathogen.

The global RNA-RNA interactome of Klebsiella pneumoniae unveils a small RNA regulator of cell division.

The ubiquitous RNA chaperone Hfq is involved in the regulation of key biological processes in many species across the bacterial kingdom. In the opportunistic human pathogen Klebsiella pneumoniae, deletion of the hfq gene affects the global transcriptome, virulence, and stress resistance; however, the ligands of the major RNA-binding protein in this species have remained elusive. In this study, we have combined transcriptomic, co-immunoprecipitation, and global RNA interactome analyses to compile an inventory of conserved and species-specific RNAs bound by Hfq and to monitor Hfq-mediated RNA-RNA interactions. In addition to dozens of RNA-RNA pairs, our study revealed an Hfq-dependent small regulatory RNA (sRNA), DinR, which is processed from the 3' terminal portion of dinI mRNA. Transcription of dinI is controlled by the master regulator of the SOS response, LexA. As DinR accumulates in K. pneumoniae in response to DNA damage, the sRNA represses translation of the ftsZ transcript by occupation of the ribosome binding site. Ectopic overexpression of DinR causes depletion of ftsZ mRNA and inhibition of cell division, while deletion of dinR antagonizes cell elongation in the presence of DNA damage. Collectively, our work highlights the important role of RNA-based gene regulation in K. pneumoniae and uncovers the central role of DinR in LexA-controlled division inhibition during the SOS response.

Functional allele of a MATE gene selected during domestication modulates seed color in chickpea.

Seed color is one of the key target traits of domestication and artificial selection in chickpeas due to its implications on consumer preference and market value. The complex seed color trait has been well dissected in several crop species; however, the genetic mechanism underlying seed color variation in chickpea remains poorly understood. Here, we employed an integrated genomics strategy involving QTL mapping, high-density mapping, map-based cloning, association analysis, and molecular haplotyping in an inter-specific RIL mapping population, association panel, wild accessions, and introgression lines (ILs) of Cicer gene pool. This delineated a MATE gene, CaMATE23, encoding a Transparent Testa (TT) and its natural allele (8-bp insertion) and haplotype underlying a major QTL governing seed color on chickpea chromosome 4. Signatures of selective sweep and a strong purifying selection reflected that CaMATE23, especially its 8-bp insertion natural allelic variant, underwent selection during chickpea domestication. Functional investigations revealed that the 8-bp insertion containing the third cis-regulatory RY-motif element in the CaMATE23 promoter is critical for enhanced binding of CaFUSCA3 transcription factor, a key regulator of seed development and flavonoid biosynthesis, thereby affecting CaMATE23 expression and proanthocyanidin (PA) accumulation in the seed coat to impart varied seed color in chickpea. Consequently, overexpression of CaMATE23 in Arabidopsis tt12 mutant partially restored the seed color phenotype to brown pigmentation, ascertaining its functional role in PA accumulation in the seed coat. These findings shed new light on the seed color regulation and evolutionary history, and highlight the transcriptional regulation of CaMATE23 by CaFUSCA3 in modulating seed color in chickpea. The functionally relevant InDel variation, natural allele, and haplotype from CaMATE23 are vital for translational genomic research, including marker-assisted breeding, for developing chickpea cultivars with desirable seed color that appeal to consumers and meet global market demand.

Identification of candidate genes for Fusarium head blight resistance from QTLs using RIL population in wheat.

Fusarium head blight (FHB) stands out as one of the most devastating wheat diseases and leads to significantly grain yield losses and quality reductions in epidemic years. Exploring quantitative trait loci (QTL) for FHB resistance is a critical step for developing new FHB-resistant varieties. We previously constructed a genetic map of unigenes (UG-Map) according to the physical positions using a set of recombinant-inbred lines (RILs) derived from the cross of 'TN18 × LM6' (TL-RILs). Here, the number of diseased spikelets (NDS) and relative disease index (RDI) for FHB resistance were investigated under four environments using TL-RILs, which were distributed across 13 chromosomes. A number of 36 candidate genes for NDS and RDI from of 19 stable QTLs were identified. The average number of candidate genes per QTL was 1.89, with 14 (73.7%), two (10.5%), and three (15.8%) QTLs including one, two, and 3-10 candidate genes, respectively. Among the 24 candidate genes annotated in the reference genome RefSeq v1.1, the homologous genes of seven candidate genes, including TraesCS4B02G227300 for QNds/Rdi-4BL-4553, TraesCS5B02G303200, TraesCS5B02G303300, TraesCS5B02G303700, TraesCS5B02G303800 and TraesCS5B02G304000 for QNds/Rdi-5BL-9509, and TraesCS7A02G568400 for QNds/Rdi-7AL-14499, were previously reported to be related to FHB resistance in wheat, barely or Brachypodium distachyon. These genes should be closely associated with FHB resistance in wheat. In addition, the homologous genes of five genes, including TraesCS1A02G037600LC for QNds-1AS-2225, TraesCS1D02G017800 and TraesCS1D02G017900 for QNds-1DS-527, TraesCS1D02G018000 for QRdi-1DS-575, and TraesCS4B02G227400 for QNds/Rdi-4BL-4553, were involved in plant defense responses against pathogens. These genes should be likely associated with FHB resistance in wheat.

Identification of qGL4.1 and qGL4.2, two closely linked QTL controlling grain length in rice.

Grain size is an important appearance quality trait in rice, which also affects grain yield. In this study, a recombinant inbred line (RIL) population derived from a cross between indica variety 9311 and japonica variety Cypress was constructed. And 181 out of 600 RILs were sequenced, and a high-density genetic map containing 2842 bin markers was constructed, with a total map length of 1500.6 cM. A total of 10 quantitative trait loci (QTL) related to grain length (GL), grain width (GW), grain length-to-width ratio (LWR), and 1000-grain weight (TGW) were detected under two environments. The genetic effect of qGL4, a minor QTL for GL and TGW, was validated using three heterogeneous inbred family (HIF) segregation populations. It was further dissected into two closed linked QTL, qGL4.1 and qGL4.2. By progeny testing, qGL4.1 and qGL4.2 were successfully delimited to intervals of 1304-kb and 423-kb, respectively. Our results lay the foundation for the map-based cloning of qGL4.1 and qGL4.2 and provide new gene resources for the improvement of grain yield and quality in rice. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-024-01447-y.

Mapping of a Major-Effect Quantitative Trait Locus for Seed Dormancy in Wheat.

The excavation and utilization of dormancy loci in breeding are effective endeavors for enhancing the resistance to pre-harvest sprouting (PHS) of wheat varieties. CH1539 is a wheat breeding line with high-level seed dormancy. To clarify the dormant loci carried by CH1539 and obtain linked molecular markers, in this study, a recombinant inbred line (RIL) population derived from the cross of weak dormant SY95-71 and strong dormant CH1539 was genotyped using the Wheat17K single-nucleotide polymorphism (SNP) array, and a high-density genetic map covering 21 chromosomes and consisting of 2437 SNP markers was constructed. Then, the germination percentage (GP) and germination index (GI) of the seeds from each RIL were estimated. Two QTLs for GP on chromosomes 5A and 6B, and four QTLs for GI on chromosomes 5A, 6B, 6D and 7A were identified. Among them, the QTL on chromosomes 6B controlling both GP and GI, temporarily named QGp/Gi.sxau-6B, is a major QTL for seed dormancy with the maximum phenotypic variance explained of 17.66~34.11%. One PCR-based diagnostic marker Ger6B-3 for QGp/Gi.sxau-6B was developed, and the genetic effect of QGp/Gi.sxau-6B on the RIL population and a set of wheat germplasm comprising 97 accessions was successfully confirmed. QGp/Gi.sxau-6B located in the 28.7~30.9 Mbp physical position is different from all the known dormancy loci on chromosomes 6B, and within the interval, there are 30 high-confidence annotated genes. Our results revealed a novel QTL QGp/Gi.sxau-6B whose CH1539 allele had a strong and broad effect on seed dormancy, which will be useful in further PHS-resistant wheat breeding.

Widespread and transgenerational retrotransposon activation in inter- and intraspecies recombinant inbred populations of Lotus japonicus.

Transposable elements (TEs) constitute a large proportion of genomes of multicellular eukaryotes, including flowering plants. TEs are normally maintained in a silenced state and their transpositions rarely occur. Hybridization between distant species has been regarded as a 'shock' that stimulates genome reorganization, including TE mobilization. However, whether crosses between genetically close parents that result in viable and fertile offspring can induce TE transpositions has remained unclear. Here, we investigated the activation of long terminal repeat (LTR) retrotransposons in three Lotus japonicus recombinant inbred line (RIL) populations. We found that at least six LTR retrotransposon families were activated and transposed in 78% of the RILs investigated. LORE1a, one of the transposed LTR retrotransposons, showed transgenerational epigenetic activation, indicating the long-term effects of epigenetic instability induced by hybridization. Our study highlights TE activation as an unexpectedly common event in plant reproduction.

Exploiting docetaxel-induced tumor cell necrosis with tumor targeted delivery of IL-12.

There is strong evidence that chemotherapy can induce tumor necrosis which can be exploited for the targeted delivery of immuno-oncology agents into the tumor microenvironment (TME). We hypothesized that docetaxel, a chemotherapeutic agent that induces necrosis, in combination with the bifunctional molecule NHS-IL-12 (M9241), which delivers recombinant IL-12 through specific targeting of necrotic regions in the tumor, would provide a significant antitumor benefit in the poorly inflamed murine tumor model, EMT6 (breast), and in the moderately immune-infiltrated tumor model, MC38 (colorectal). Docetaxel, as monotherapy or in combination with NHS-IL-12, promoted tumor necrosis, leading to the improved accumulation and retention of NHS-IL-12 in the TME. Significant antitumor activity and prolonged survival were observed in cohorts receiving docetaxel and NHS-IL-12 combination therapy in both the MC38 and EMT6 murine models. The therapeutic effects were associated with increased tumor infiltrating lymphocytes and were dependent on CD8+ T cells. Transcriptomics of the TME of mice receiving the combination therapy revealed the upregulation of genes involving crosstalk between innate and adaptive immunity factors, as well as the downregulation of signatures of myeloid cells. In addition, docetaxel and NHS-IL-12 combination therapy effectively controlled tumor growth of PD-L1 wild-type and PD-L1 knockout MC38 in vivo, implying this combination could be applied in immune checkpoint refractory tumors, and/or tumors regardless of PD-L1 status. The data presented herein provide the rationale for the design of clinical studies employing this combination or similar combinations of agents.

Enhanced expression and solubility of main protease (Mpro) of SARS-CoV-2 from E. coli.

The main protease (Mpro) of SARS-CoV-2 is a essential enzyme that facilitates viral transcription and replication. Furthermore, the conservation of Mpro across different variants and its non-overlapping nature with human proteases make it an appealing target for therapeutic interventions against SARS-CoV-2. Multiple inhibitors specifically target Mpro to mitigate the infection caused by SARS-CoV-2. In the current study, successful cloning and expression of SARS-CoV-2 Mpro were achieved using two E. coli hosts, namely BL21-DE3 and BL21-DE3-RIL. By optimizing the conditions for induction, the expression of Mpro in the soluble fraction of E. coli was improved. Subsequently, Mpro was purified using affinity chromatography, yielding significantly higher quantities from the BL21-DE3-RIL strain compared to the BL21-DE3 strain, with the former producing nearly twice as much as the latter. The purified Mpro was further characterized by mass spectrometry, fluorescence spectroscopy and circular dichroism (CD). Through fluorescence quenching studies, it was discovered that both GC376 and chitosan, which are inhibitors of Mpro, induced structural changes in the purified Mpro protein. This indicates that the protein retained its functional activity even after being expressed in a bacterial host. Further, FRET-based assay highlighted that the enzymatic activity of Mpro was significantly reduced in presence of both GC376 and chitosan. Consequently, the utilization of optimal conditions and the BL21-DE3-RIL bacterial host facilitates the cost-effective production of Mpro on a large scale, enabling high yields. This production approach can be applied for the screening of potent therapeutic drugs, making it a valuable resource for drug development endeavors.

A Critical Review of the Enhanced Recovery of Rare Earth Elements from Phosphogypsum.

The increasing demand for rare earth elements (REEs), especially from new and innovative technology, has strained their supply, which makes the exploration of new REE sources necessary, for example, the recovery of REEs from phsophogypsum (PG). PG is a byproduct during the wet production of phosphoric acid, which is an attractive secondary resource for REEs due to a large amount of REEs locked in them. In most cases, REEs contained in PG are mainly encapsulated in the gypsum crystal, leading to a low leaching efficiency. Therefore, it is particularly important to use various methods to enhance the leaching of REEs from PG. In this review, we summarized and classified various enhanced leaching methods for the recovery of REEs from PG, and the advantages and disadvantages of different methods were compared. A joint method of recrystallization and RIL may be a promising enhanced leaching approach for the recovery of REEs from PG. Recrystallization could achieve both the complete REE release and simultaneous preparation of industrial materials with high value added, such as high-strength α-hemihydrate gypsum by phase transformation of PG, and the RIL technology could adsorb the releasing REEs and realize their efficient extraction. Such a combination appears to show significant advantages because of high REE recovery, as well as high value-added product preparation at low cost.

Fine mapping of qTGW2b and qGL9, two minor QTL conferring grain size and weight in rice.

Rice grain size is a key determinant of both grain yield and quality. In this study, we conducted QTL mapping on grain size using a recombinant inbred line (RIL) population derived from a cross between japonica variety Beilu130 (BL130) and indica variety Jin23B (J23B). A total of twenty-two QTL related to grain length (GL), grain width (GW), grain length-to-width ratio (LWR), grain thickness (GT), and thousand grain weight (TGW) were detected under two environments, and 14 of them were repeatedly detected. Two minor QTL, qTGW2b and qGL9, were validated and further delimited to regions of 631 kb and 272 kb, respectively. Parental sequence comparison of genes expressed in inflorescence in corresponding candidate regions identified frameshifts in the exons of LOC_Os02g38690 and LOC_Os02g38780, both of which encode protein phosphatase 2C-containing protein, and LOC_Os09g29930, which encodes a BIM2 protein. Scanning electron microscopy (SEM) analysis revealed that the increase of cell size rather than cell number caused the differences in grain size between NILs of qTGW2b and qGL9. Quantitative RT-PCR analysis showed that the expression levels of EXPA4, EXPA5, EXPA6, EXPB3, EXPB4, and EXPB7 were significantly different in both qTGW2b NILs and qGL9 NILs. Our results lay the foundation for the cloning of qTGW2b and qGL9, and provide genetic materials for the improvement of rice yield and quality. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-022-01328-2.

Identification of hub genes through co-expression network of major QTLs of fiber length and strength traits in multiple RIL populations of cotton.

The present study demonstrated a de novo correlation among fiber quality genes in multiple RIL populations including sGK9708 × 0-153, LMY22 × LY343 and Lumianyan28 × Xinluzao24. The current study was conducted to identify the major common QTLs including fiber length and strength, and to identify the co-expression networks of fiber length and strength QTLs harbored genes to target the hub genes. The RNA-seq data of sGK9708 × 0-153 population highlighted 50 and 48 candidate genes of fiber length and fiber strength QTLs. A total of 29 and 21 hub genes were identified in fiber length and strength co-expression network modules. The absolute values of correlation coefficient close to 1 resulted highly positive correlation among hub genes. Results also suggested that the gene correlation significantly influence the gene expression at different fiber development stages. These results might provide useful reference for further experiments in multiple RIL populations and suggest potential candidate genes for functional studies in cotton.

Identification of Quantitative Trait Locus and Candidate Genes for Drought Tolerance in a Soybean Recombinant Inbred Line Population.

With global warming and regional decreases in precipitation, drought has become a problem worldwide. As the number of arid regions in the world is increasing, drought has become a major factor leading to significant crop yield reductions and food crises. Soybean is a crop that is relatively sensitive to drought. It is also a crop that requires more water during growth and development. The aim of this study was to identify the quantitative trait locus (QTL) that affects drought tolerance in soybean by using a recombinant inbred line (RIL) population from a cross between the drought-tolerant cultivar 'Jindou21' and the drought-sensitive cultivar 'Zhongdou33'. Nine agronomic and physiological traits were identified under drought and well-watered conditions. Genetic maps were constructed with 923,420 polymorphic single nucleotide polymorphism (SNP) markers distributed on 20 chromosomes at an average genetic distance of 0.57 centimorgan (cM) between markers. A total of five QTLs with a logarithm of odds (LOD) value of 4.035-8.681 were identified on five chromosomes. Under well-watered conditions and drought-stress conditions, one QTL related to the main stem node number was located on chromosome 16, accounting for 17.177% of the phenotypic variation. Nine candidate genes for drought resistance were screened from this QTL, namely Glyma.16G036700, Glyma.16G036400, Glyma.16G036600, Glyma.16G036800, Glyma.13G312700, Glyma.13G312800, Glyma.16G042900, Glyma.16G043200, and Glyma.15G100700. These genes were annotated as NAC transport factor, GATA transport factor, and BTB/POZ-MATH proteins. This result can be used for molecular marker-assisted selection and provide a reference for breeding for drought tolerance in soybean.

Genetic mapping and QTL analysis for peanut smut resistance.

BACKGROUND: Peanut smut is a disease caused by the fungus Thecaphora frezii Carranza & Lindquist to which most commercial cultivars in South America are highly susceptible. It is responsible for severely decreased yield and no effective chemical treatment is available to date. However, smut resistance has been identified in wild Arachis species and further transferred to peanut elite cultivars. To identify the genome regions conferring smut resistance within a tetraploid genetic background, this study evaluated a RIL population {susceptible Arachis hypogaea subsp. hypogaea (JS17304-7-B) × resistant synthetic amphidiploid (JS1806) [A. correntina (K 11905) × A. cardenasii (KSSc 36015)] × A. batizocoi (K 9484)4×} segregating for the trait. RESULTS: A SNP based genetic map arranged into 21 linkage groups belonging to the 20 peanut chromosomes was constructed with 1819 markers, spanning a genetic distance of 2531.81 cM. Two consistent quantitative trait loci (QTLs) were identified qSmIA08 and qSmIA02/B02, located on chromosome A08 and A02/B02, respectively. The QTL qSmIA08 at 15.20 cM/5.03 Mbp explained 17.53% of the phenotypic variance, while qSmIA02/B02 at 4.0 cM/3.56 Mbp explained 9.06% of the phenotypic variance. The combined genotypic effects of both QTLs reduced smut incidence by 57% and were stable over the 3 years of evaluation. The genome regions containing the QTLs are rich in genes encoding proteins involved in plant defense, providing new insights into the genetic architecture of peanut smut resistance. CONCLUSIONS: A major QTL and a minor QTL identified in this study provide new insights into the genetic architecture of peanut smut resistance that may aid in breeding new varieties resistant to peanut smut.

Genomic regions and candidate genes linked with Phytophthora capsici root rot resistance in chile pepper (Capsicum annuum L.).

BACKGROUND: Phytophthora root rot, caused by Phytophthora capsici, is a major disease affecting Capsicum production worldwide. A recombinant inbred line (RIL) population derived from the hybridization between 'Criollo de Morellos-334' (CM-334), a resistant landrace from Mexico, and 'Early Jalapeno', a susceptible cultivar was genotyped using genotyping-by-sequencing (GBS)-derived single nucleotide polymorphism (SNP) markers. A GBS-SNP based genetic linkage map for the RIL population was constructed. Quantitative trait loci (QTL) mapping dissected the genetic architecture of P. capsici resistance and candidate genes linked to resistance for this important disease were identified. RESULTS: Development of a genetic linkage map using 1,973 GBS-derived polymorphic SNP markers identified 12 linkage groups corresponding to the 12 chromosomes of chile pepper, with a total length of 1,277.7 cM and a marker density of 1.5 SNP/cM. The maximum gaps between consecutive SNP markers ranged between 1.9 (LG7) and 13.5 cM (LG5). Collinearity between genetic and physical positions of markers reached a maximum of 0.92 for LG8. QTL mapping identified genomic regions associated with P. capsici resistance in chromosomes P5, P8, and P9 that explained between 19.7 and 30.4% of phenotypic variation for resistance. Additive interactions between QTL in chromosomes P5 and P8 were observed. The role of chromosome P5 as major genomic region containing P. capsici resistance QTL was established. Through candidate gene analysis, biological functions associated with response to pathogen infections, regulation of cyclin-dependent protein serine/threonine kinase activity, and epigenetic mechanisms such as DNA methylation were identified. CONCLUSIONS: Results support the genetic complexity of the P. capsici-Capsicum pathosystem and the possible role of epigenetics in conferring resistance to Phytophthora root rot. Significant genomic regions and candidate genes associated with disease response and gene regulatory activity were identified which allows for a deeper understanding of the genomic landscape of Phytophthora root rot resistance in chile pepper.

Transcriptional signatures modulating shoot apical meristem morphometric and plant architectural traits enhance yield and productivity in chickpea.

Plant height (PH) and plant width (PW), two of the major plant architectural traits determining the yield and productivity of a crop, are defined by diverse morphometric characteristics of the shoot apical meristem (SAM). The identification of potential molecular tags from a single gene that simultaneously modulates these plant/SAM architectural traits is therefore prerequisite to achieve enhanced yield and productivity in crop plants, including chickpea. Large-scale multienvironment phenotyping of the association panel and mapping population have ascertained the efficacy of three vital SAM morphometric trait parameters, SAM width, SAM height and SAM area, as key indicators to unravel the genetic basis of the wide PW and PH trait variations observed in desi chickpea. This study integrated a genome-wide association study (GWAS); quantitative trait locus (QTL)/fine-mapping and map-based cloning with molecular haplotyping; transcript profiling; and protein-DNA interaction assays for the dissection of plant architectural traits in chickpea. These exertions delineated natural alleles and superior haplotypes from a CabHLH121 transcription factor (TF) gene within the major QTL governing PW, PH and SAM morphometric traits. A genome-wide protein-DNA interaction assay assured the direct binding of a known stem cell master regulator, CaWUS, to the WOX-homeodomain TF binding sites of a CabHLH121 gene and its constituted haplotypes. The differential expression of CaWUS and transcriptional regulation of its target CabHLH121 gene/haplotypes were apparent, suggesting their collective role in altering SAM morphometric characteristics and plant architectural traits in the contrasting near isogenic lines (NILs). The NILs introgressed with a superior haplotype of a CabHLH121 exhibited optimal PW and desirable PH as well as enhanced yield and productivity without compromising any component of agronomic performance. These molecular signatures of the CabHLH121 TF gene have the potential to regulate both PW and PH traits through the modulation of proliferation, differentiation and maintenance of the meristematic stem cell population in the SAM; therefore, these signatures will be useful in the translational genomic study of chickpea genetic enhancement. The restructured cultivars with desirable PH (semidwarf) and PW will ensure maximal planting density in a specified cultivable field area, thereby enhancing the overall yield and productivity of chickpea. This can essentially facilitate the achievement of better remunerative outputs by farmers with rational land use, therefore ensuring global food security in the present scenario of an increasing population density and shrinking per capita land area.

Mapping quantitative trait loci associated with stem-related traits in maize (Zea mays L.).

KEY MESSAGE: Mapping QTL for stem-related traits using RIL population with ultra-high density bin map can better dissect pleiotropic QTL controlling stem architecture that can provide valuable information for maize genetic improvement. The maize stem is one of the most important parts of the plant and is also a component of many agronomic traits in maize. This study aimed to advance our understanding of the genetic mechanisms underlying maize stem traits. A recombinant inbred line (RIL) population derived from a cross between Ye478 and Qi319 was used to identify quantitative trait loci (QTL) controlling stem height (SH), ear height (EH), stem node number (SN), ear node (EN), and stem diameter (SD), and two derived traits (ear height coefficient (EHc) and ear node coefficient (ENc)). Using an available ultra-high density bin map, 46 putative QTL for these traits were detected on chromosomes 1, 3, 4, 5, 6, 7, 8, and 10. Individual QTL explained 3.5-17.7% of the phenotypic variance in different environments. Two QTL for SH, three for EH, two for EHc, one for SN, one for EN, and one for SD were detected in more than one environment. QTL with pleiotropic effects or multiple linked QTL were also identified on chromosomes 1, 3, 4, 6, 8, and 10, which are potential target regions for fine-mapping and marker-assisted selection in maize breeding programs. Further, we discussed segregation of bin markers (mk1630 and mk4452) associated with EHc QTL in the RIL population. We had identified two putative WRKY DNA-binding domain proteins, AC209050.3_FG003 and GRMZM5G851490, and a putative auxin response factor, GRMZM2G437460, which might be involved in regulating plant growth and development, as candidate genes for the control of stem architecture.

New sequencing methodologies reveal interplay between multiple RNA-binding proteins and their RNAs.

It is now established that base-pairing regulatory RNAs are key players in post-transcriptional regulatory networks where they affect the translation and/or stability of their target RNAs. In many cases, the base-pairing between two RNAs is facilitated by an RNA-binding protein (RBP) that serves as an RNA chaperone. Recent advances in sequencing methods have revealed the RNA populations bound by the RBPs, yielding insights valuable into regulatory networks. Further analyses of these networks can improve our understanding of the roles played by RBPs in the regulation of gene expression by regulatory RNAs, especially when multiple RBPs are involved. For example, using an RNA sequencing-based methodology that captures RNA-RNA pairs on RBP, an interplay between two RBPs in bacteria that compete on the same RNA-RNA pair was revealed. In this case, one protein promotes negative regulation of the target RNA, while the second protein can block this regulation. In this mini-review, I outline the exciting future directions that can be taken to deepen our understanding of the roles played by RBPs in post-transcriptional regulation, and discuss how the different sequencing methods can assist in deciphering the relationships among RBPs, and between the RBPs and the RNAs they bind. Having a more detailed picture of the RBPs-RNAs network will elucidate how bacteria can have nuanced control of gene expression, critical for survival in the varied environments in which bacteria live.

Identification of quantitative trait loci for kernel-related traits and the heterosis for these traits in maize (Zea mays L.).

Heterosis has been extensively applied for many traits during maize breeding, but there has been relatively little attention paid to the heterosis for kernel size. In this study, we evaluated a population of 301 recombinant inbred lines derived from a cross between 08-641 and YE478, as well as 298 hybrids from an immortalized F2 (IF2) population to detect quantitative trait loci (QTLs) for six kernel-related traits and the mid-parent heterosis (MPH) for these traits. A total of 100 QTLs, six pairs of loci with epistatic interactions, and five significant QTL × environment interactions were identified in both mapping populations. Seven QTLs accounted for over 10% of the phenotypic variation. Only four QTLs affected both the trait means and the MPH, suggesting the genetic mechanisms for kernel-related traits and the heterosis for kernel size are not completely independent. Moreover, more than half of the QTLs for each trait in the IF2 population exhibited dominance, implying that dominance is more important than other genetic effects for the heterosis for kernel-related traits. Additionally, 20 QTL clusters comprising 46 QTLs were detected across ten chromosomes. Specific chromosomal regions (bins 2.03, 6.04-6.05, and 9.01-9.02) exhibited pleiotropy and congruency across diverse heterotic patterns in previous studies. These results may provide additional insights into the genetic basis for the MPH for kernel-related traits.