Integrated meta-analysis and transcriptomics pinpoint genomic loci and novel candidate genes associated with submergence tolerance in rice.

BACKGROUND: Due to rising costs, water shortages, and labour shortages, farmers across the globe now prefer a direct seeding approach. However, submergence stress remains a major bottleneck limiting the success of this approach in rice cultivation. The merger of accumulated rice genetic resources provides an opportunity to detect key genomic loci and candidate genes that influence the flooding tolerance of rice. RESULTS: In the present study, a whole-genome meta-analysis was conducted on 120 quantitative trait loci (QTL) obtained from 16 independent QTL studies reported from 2004 to 2023. These QTL were confined to 18 meta-QTL (MQTL), and ten MQTL were successfully validated by independent genome-wide association studies from diverse natural populations. The mean confidence interval (CI) of the identified MQTL was 3.44 times narrower than the mean CI of the initial QTL. Moreover, four core MQTL loci with genetic distance less than 2 cM were obtained. By combining differentially expressed genes (DEG) from two transcriptome datasets with 858 candidate genes identified in the core MQTL regions, we found 38 common differentially expressed candidate genes (DECGs). In silico expression analysis of these DECGs led to the identification of 21 genes with high expression in embryo and coleoptile under submerged conditions. These DECGs encode proteins with known functions involved in submergence tolerance including WRKY, F-box, zinc fingers, glycosyltransferase, protein kinase, cytochrome P450, PP2C, hypoxia-responsive family, and DUF domain. By haplotype analysis, the 21 DECGs demonstrated distinct genetic differentiation and substantial genetic distance mainly between indica and japonica subspecies. Further, the MQTL7.1 was successfully validated using flanked marker S2329 on a set of genotypes with phenotypic variation. CONCLUSION: This study provides a new perspective on understanding the genetic basis of submergence tolerance in rice. The identified MQTL and novel candidate genes lay the foundation for marker-assisted breeding/engineering of flooding-tolerant cultivars conducive to direct seeding.

Identification and Genetic Dissection of Resistance to Red Crown Rot Disease in a Diverse Soybean Germplasm Population.

Red crown rot (RCR) disease caused by Calonectria ilicicola negatively impacts soybean yield and quality. Unfortunately, the knowledge of the genetic architecture of RCR resistance in soybeans is limited. In this study, 299 diverse soybean accessions were used to explore their genetic diversity and resistance to RCR, and to mine for candidate genes via emergence rate (ER), survival rate (SR), and disease severity (DS) by a multi-locus random-SNP-effect mixed linear model of GWAS. All accessions had brown necrotic lesions on the primary root, with five genotypes identified as resistant. Nine single-nucleotide polymorphism (SNP) markers were detected to underlie RCR response (ER, SR, and DS). Two SNPs colocalized with at least two traits to form a haplotype block which possessed nine genes. Based on their annotation and the qRT-PCR, three genes, namely Glyma.08G074600, Glyma.08G074700, and Glyma.12G043600, are suggested to modulate soybean resistance to RCR. The findings from this study could serve as the foundation for breeding RCR-tolerant soybean varieties, and the candidate genes could be validated to deepen our understanding of soybean response to RCR.

DArTseq-based SNP markers reveal high genetic diversity among early generation fall armyworm tolerant maize inbred lines.

Diversity analysis using molecular markers serves as a powerful tool in unravelling the intricacies of inclusivity within various populations and is an initial step in the assessment of populations and the development of inbred lines for host plant resistance in maize. This study was conducted to assess the genetic diversity and population structure of 242 newly developed S3 inbred lines using 3,305 single nucleotide polymorphism (SNP) markers and to also assess the level of homozygosity achieved in each of the inbred lines. A total of 1,184 SNP markers were found highly informative, with a mean polymorphic information content (PIC) of 0.23. Gene diversity was high among the inbred lines, ranging from 0.04 to 0.50, with an average of 0.27. The residual heterozygosity of the 242 S3 inbred lines averaged 8.8%, indicating moderately low heterozygosity levels among the inbred lines. Eighty-four percent of the 58,322 pairwise kinship coefficients among the inbred lines were near zero (0.00-0.05), with only 0.3% of them above 0.50. These results revealed that many of the inbred lines were distantly related, but none were redundant, suggesting each inbred line had a unique genetic makeup with great potential to provide novel alleles for maize improvement. The admixture-based structure analysis, principal coordinate analysis, and neighbour-joining clustering were concordant in dividing the 242 inbred lines into three subgroups based on the pedigree and selection history of the inbred lines. These findings could guide the effective use of the newly developed inbred lines and their evaluation in quantitative genetics and molecular studies to identify candidate lines for breeding locally adapted fall armyworm tolerant varieties in Ghana and other countries in West and Central Africa.

Comparative Morpho-Physiological, Biochemical, and Gene Expressional Analyses Uncover Mechanisms of Waterlogging Tolerance in Two Soybean Introgression Lines.

Waterlogging is one of the key abiotic factors that severely impedes the growth and productivity of soybeans on a global scale. To develop soybean cultivars that are tolerant to waterlogging, it is a prerequisite to unravel the mechanisms governing soybean responses to waterlogging. Hence, we explored the morphological, physiological, biochemical, and transcriptional changes in two contrasting soybean introgression lines, A192 (waterlogging tolerant, WT) and A186 (waterlogging sensitive, WS), under waterlogging. In comparison to the WT line, waterlogging drastically decreased the root length (RL), shoot length (ShL), root fresh weight (RFW), shoot fresh weight (ShFW), root dry weight (RDW), and shoot dry weight (ShDW) of the WS line. Similarly, waterlogging inhibited soybean plant growth by suppressing the plant's photosynthetic capacity, enhancing oxidative damage from reactive oxygen species, and decreasing the chlorophyll content in the WS line but not in the WT line. To counteract the oxidative damage and lipid peroxidation, the WT line exhibited increased activity of antioxidant enzymes such as peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT), as well as higher levels of proline content than the WS line. In addition, the expression of antioxidant enzyme genes (POD1, POD2, FeSOD, Cu/ZnSOD, CAT1, and CAT2) and ethylene-related genes (such as ACO1, ACO2, ACS1, and ACS2) were found to be up-regulated in WT line under waterlogging stress conditions. In contrast, these genes showed a down-regulation in their expression levels in the stressed WS line. The integration of morpho-physiological, biochemical, and gene expression analyses provide a comprehensive understanding of the responses of WT and WS lines to waterlogging conditions. These findings would be beneficial for the future development of soybean cultivars that can withstand waterlogging.

Exploring the role of FBXL fbxl gene family in Soybean: Implications for plant height and seed size regulation.

F-box proteins constitute a significant family in eukaryotes and, as a component of the Skp1p-cullin-F-box complex, are considered critical for cellular protein degradation and other biological processes in plants. Despite their importance, the functions of F-box proteins, particularly those with C-terminal leucine-rich repeat (LRR) domains, remain largely unknown in plants. Therefore, the present study conducted genome-wide identification and in silico characterization of F-BOX proteins with C-terminal LRR domains in soybean (Glycine max L.) (GmFBXLs). A total of 45 GmFBXLs were identified. The phylogenetic analysis showed that GmFBXLs could be subdivided into ten subgroups and exhibited a close relationship with those from Arabidopsis thaliana, Cicer aretineum, and Medicago trunculata. It was observed that most cis-regulatory elements in the promoter regions of GmFBXLs are involved in hormone signalling, stress responses, and developmental stages. In silico transcriptome data illustrated diverse expression patterns of the identified GmFBXLs across various tissues, such as shoot apical meristem, flower, green pods, leaves, nodules, and roots. Overexpressing (OE) GmFBXL12 in Tianlong No.1 cultivar resulted in a significant difference in seed size, number of pods, and number of seeds per plant, indicated a potential increase in yield compared to wild type. This study offers valuable perspectives into the role of FBXLs in soybean, serving as a foundation for future research. Additionally, the identified OE lines represent valuable genetic resources for enhancing seed-related traits in soybean.

Molecular and genetic insights into secondary metabolic regulation underlying insect-pest resistance in legumes.

Insect pests pose a major threat to agricultural production, resulting in significant economic losses for countries. A high infestation of insects in any given area can severely reduce crop yield and quality. This review examines the existing resources for managing insect pests and highlights alternative eco-friendly techniques to enhance insect pest resistance in legumes. Recently, the application of plant secondary metabolites has gained popularity in controlling insect attacks. Plant secondary metabolites encompass a wide range of compounds such as alkaloids, flavonoids, and terpenoids, which are often synthesized through intricate biosynthetic pathways. Classical methods of metabolic engineering involve manipulating key enzymes and regulatory genes to enhance or redirect the production of secondary metabolites in plants. Additionally, the role of genetic approaches, such as quantitative trait loci mapping, genome-wide association (GWAS) mapping, and metabolome-based GWAS in insect pest management is discussed, also, the role of precision breeding, such as genome editing technologies and RNA interference for identifying pest resistance and manipulating the genome to develop insect-resistant cultivars are explored, highlighting the positive contribution of plant secondary metabolites engineering-based resistance against insect pests. It is suggested that by understanding the genes responsible for beneficial metabolite compositions, future research might hold immense potential to shed more light on the molecular regulation of secondary metabolite biosynthesis, leading to advancements in insect-resistant traits in crop plants. In the future, the utilization of metabolic engineering and biotechnological methods may serve as an alternative means of producing biologically active, economically valuable, and medically significant compounds found in plant secondary metabolites, thereby addressing the challenge of limited availability.

k-mer-Based Genome-Wide Association Studies in Plants: Advances, Challenges, and Perspectives.

Genome-wide association studies (GWAS) have allowed the discovery of marker-trait associations in crops over recent decades. However, their power is hampered by a number of limitations, with the key one among them being an overreliance on single-nucleotide polymorphisms (SNPs) as molecular markers. Indeed, SNPs represent only one type of genetic variation and are usually derived from alignment to a single genome assembly that may be poorly representative of the population under study. To overcome this, k-mer-based GWAS approaches have recently been developed. k-mer-based GWAS provide a universal way to assess variation due to SNPs, insertions/deletions, and structural variations without having to specifically detect and genotype these variants. In addition, k-mer-based analyses can be used in species that lack a reference genome. However, the use of k-mers for GWAS presents challenges such as data size and complexity, lack of standard tools, and potential detection of false associations. Nevertheless, efforts are being made to overcome these challenges and a general analysis workflow has started to emerge. We identify the priorities for k-mer-based GWAS in years to come, notably in the development of user-friendly programs for their analysis and approaches for linking significant k-mers to sequence variation.

miRNAs for crop improvement.

Climate change significantly impacts crop production by inducing several abiotic and biotic stresses. The increasing world population, and their food and industrial demands require focused efforts to improve crop plants to ensure sustainable food production. Among various modern biotechnological tools, microRNAs (miRNAs) are one of the fascinating tools available for crop improvement. miRNAs belong to a class of small non-coding RNAs playing crucial roles in numerous biological processes. miRNAs regulate gene expression by post-transcriptional target mRNA degradation or by translation repression. Plant miRNAs have essential roles in plant development and various biotic and abiotic stress tolerance. In this review, we provide propelling evidence from previous studies conducted around miRNAs and provide a one-stop review of progress made for breeding stress-smart future crop plants. Specifically, we provide a summary of reported miRNAs and their target genes for improvement of plant growth and development, and abiotic and biotic stress tolerance. We also highlight miRNA-mediated engineering for crop improvement and sequence-based technologies available for the identification of miRNAs associated with stress tolerance and plant developmental events.

Widely untargeted metabolomic profiling unearths metabolites and pathways involved in leaf senescence and N remobilization in spring-cultivated wheat under different N regimes.

Progression of leaf senescence consists of both degenerative and nutrient recycling processes in crops including wheat. However, the levels of metabolites in flag leaves in spring-cultivated wheat, as well as biosynthetic pathways involved under different nitrogen fertilization regimes, are largely unknown. Therefore, the present study employed a widely untargeted metabolomic profiling strategy to identify metabolites and biosynthetic pathways that could be used in a wheat improvement program aimed at manipulating the rate and onset of senescence by handling spring wheat (Dingxi 38) flag leaves sampled from no-, low-, and high-nitrogen (N) conditions (designated Groups 1, 2, and 3, respectively) across three sampling times: anthesis, grain filling, and end grain filling stages. Through ultrahigh-performance liquid chromatography-tandem mass spectrometry, a total of 826 metabolites comprising 107 flavonoids, 51 phenol lipids, 37 fatty acyls, 37 organooxygen compounds, 31 steroids and steroid derivatives, 18 phenols, and several unknown compounds were detected. Upon the application of the stringent screening criteria for differentially accumulated metabolites (DAMs), 28 and 23 metabolites were differentially accumulated in Group 1_vs_Group 2 and Group 1_vs_Group 3, respectively. From these, 1-O-Caffeoylglucose, Rhoifolin, Eurycomalactone;Ingenol, 4-Methoxyphenyl beta-D-glucopyranoside, and Baldrinal were detected as core conserved DAMs among the three groups with all accumulated higher in Group 1 than in the other two groups. Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that tropane, piperidine, and pyridine alkaloid biosynthesis; acarbose and validamycin biosynthesis; lysine degradation; and biosynthesis of alkaloids derived from ornithine, lysine, and nicotinic acid pathways were the most significantly (p < 0.05) enriched in Group 1_vs_Group 2, while flavone and flavonol as well as anthocyanins biosynthetic pathways were the most significantly (p < 0.05) enriched in Group 1_vs_Group 3. The results from this study provide a foundation for the manipulation of the onset and rate of leaf senescence and N remobilization in wheat.

Integrated metabolome and transcriptome analyses provide insight into the effect of red and blue LEDs on the quality of sweet potato leaves.

Red and blue light-emitting diodes (LEDs) affect the quality of sweet potato leaves and their nutritional profile. Vines cultivated under blue LEDs had higher soluble protein contents, total phenolic compounds, flavonoids, and total antioxidant activity. Conversely, chlorophyll, soluble sugar, protein, and vitamin C contents were higher in leaves grown under red LEDs. Red and blue light increased the accumulation of 77 and 18 metabolites, respectively. Alpha-linoleic and linolenic acid metabolism were the most significantly enriched pathways based on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. A total of 615 genes were differentially expressed between sweet potato leaves exposed to red and blue LEDs. Among these, 510 differentially expressed genes were upregulated in leaves grown under blue light compared with those grown under red light, while the remaining 105 genes were expressed at higher levels in the latter than in the former. Among the KEGG enrichment pathways, blue light significantly induced anthocyanin and carotenoid biosynthesis structural genes. This study provides a scientific reference basis for using light to alter metabolites to improve the quality of edible sweet potato leaves.

Comparative Transcriptome Profiling Reveals Potential Candidate Genes, Transcription Factors, and Biosynthetic Pathways for Phosphite Response in Potato (Solanum tuberosum L.).

The study was conducted with C31 and C80 genotypes of the potato (Solanum tuberosum L.), which are tolerant and susceptible to phosphite (Phi, H2PO3), respectively. To decipher the molecular mechanisms underlying tolerance and susceptibility to Phi in the potato, RNA sequencing was used to study the global transcriptional patterns of the two genotypes. Media were prepared with 0.25 and 0.50 mM Phi, No-phosphorus (P), and 1.25 mM (phosphate, Pi as control). The values of fragments per kilobase of exon per million mapped fragments of the samples were also subjected to a principal component analysis, grouping the biological replicates of each sample. Using stringent criteria, a minimum of 819 differential (DEGs) were detected in both C80-Phi-0.25_vs_C80-Phi-0.50 (comprising 517 upregulated and 302 downregulated) and C80-Phi-0.50_vs_C80-Phi-0.25 (comprising 302 upregulated and 517 downregulated) and a maximum of 5214 DEGs in both C31-Con_vs_C31-Phi-0.25 (comprising 1947 upregulated and 3267 downregulated) and C31-Phi-0.25_vs_C31-Con (comprising 3267 upregulated and 1947 downregulated). DEGs related to the ribosome, plant hormone signal transduction, photosynthesis, and plant-pathogen interaction performed important functions under Phi stress, as shown by the Kyoto Encyclopedia of Genes and Genomes annotation. The expressions of transcription factors increased significantly in C31 compared with C80. For example, the expressions of Soltu.DM.01G047240, Soltu.DM.08G015900, Soltu.DM.06G012130, and Soltu.DM.08G012710 increased under P deficiency conditions (Phi-0.25, Phi-0.50, and No-P) relative to the control (P sufficiency) in C31. This study adds to the growing body of transcriptome data on Phi stress and provides important clues to the Phi tolerance response of the C31 genotype.

COVID-19 vaccines uptake: Public knowledge, awareness, perception and acceptance among adult Africans.

INTRODUCTION: The willingness of Africa's population to patronise the COVID-19 vaccines is critical to the efficiency of national immunisation programmes. This study surveys the views of adult African inhabitants toward vaccination and the possibility of participating or not participating in governments' efforts to get citizens vaccinated. METHOD: A cross-sectional online survey of adult Africans was undertaken from December 2020 to March 2021. Responses were anonymised. The Pearson Chi-square test was performed to determine whether or not there were any variations in knowledge, awareness, perception and acceptance of the COVID-19 vaccines among the participants. Binomial logistic regression was used to evaluate the factors associated with willingness to accept the COVID-19 vaccines and participate in immunisation programmes. RESULTS: The results indicate that COVID-19 vaccines are more likely to be used by adult Africans over the age of 18 who are largely technologically savvy (55 percent) if the vaccine is made broadly available. A total of 33 percent of those who responded said they were unlikely to receive the vaccine, with another 15 percent stating they were undecided. Aside from that, we found that vaccine hesitancy was closely associated with socio-demographic characteristics such as age, gender, education and source of information. We also found that there were widespread conspiracies and myths about the COVID-19 vaccines. CONCLUSION: More than one-third of African adults who participated in the survey indicated they would not receive the COVID-19 vaccine, with majority of them expressing skepticisms about the vaccine's efficacy. It is possible that many of the people who would not be vaccinated would have an impact on the implementation of a COVID-19 immunisation programme that is meant for all of society. Majority of the respondents were unwilling to pay for the COVID-19 vaccines when made available. An awareness campaign should be focused on promoting the benefits of vaccination at the individual and population levels, as well as on taking preemptive actions to debunk misconceptions about the vaccines before they become further widespread.

Synergy of Dietary Quercetin and Vitamin E Improves Cecal Microbiota and Its Metabolite Profile in Aged Breeder Hens.

In the present study, the synergistic effects of quercetin (Q) and vitamin E (E) on cecal microbiota composition and function, as well as the microbial metabolic profile in aged breeder hens were investigated. A total of 400 (65 weeks old) Tianfu breeder hens were randomly allotted to four experimental groups (four replicates per group). The birds were fed diets containing quercetin at 0.4 g/kg, vitamin E (0.2 g/kg), quercetin and vitamin E (QE; 0.4 g/kg and 0.2 g/kg), and a basal diet for a period of 10 wks. After the 10 week experimental period, the cecal contents of 8 aged breeder hens per group were sampled aseptically and subjected to high-throughput 16S rRNA gene sequencing and untargeted metabolomic analysis. The results showed that the relative abundances of phyla Bacteroidota, Firmicutes, and Actinobacteriota were the most prominent among all the dietary groups. Compared to the control group, the relative abundance of the families Bifidobacteriaceae, Lachnospiraceae, Tannerellaceae, Mathonobacteriaceae, Barnesiellaceae, and Prevotellaceae were enriched in the QE group; and Bacteroidaceae, Desulfovibrionaceae, Peptotostretococcaceae, and Fusobacteriaceae were enriched in the Q group, whereas those of Lactobacillaceae, Veillonellaceae, Ruminococcaceae, Akkermansiaceae, and Rikenellaceae were enriched in the E group compared to the control group. Untargeted metabolomics analyses revealed that Q, E, and QE modified the abundance of several metabolites in prominent pathways including ubiquinone and other terpenoid-quinone biosynthesis, regulation of actin cytoskeleton, insulin secretion, pancreatic secretion, nicotine addiction, and metabolism of xenobiotics by cytochrome P450. Furthermore, key cecal microbiota, significantly correlated with important metabolites, for example, (S)-equol positively correlated with Alistipes and Chlamydia in E_vs_C, and negatively correlated with Olsenella, Paraprevotella, and Mucispirillum but, a contrary trend was observed with Parabacteroides in QE_vs_C. This study establishes that the synergy of quercetin and vitamin E alters the cecal microbial composition and metabolite profile in aged breeder hens, which lays a foundation for chicken improvement programs.

Combining Ability and Heterotic Patterns of Tropical Early-Maturing Maize Inbred Lines under Individual and Combined Heat and Drought Environments.

Information on combining ability and heterotic patterns of multiple stress-tolerant inbred lines are fundamental prerequisites for devising appropriate breeding strategies for the development of climate-resilient maize hybrids. In the present study, we evaluated 150 single cross hybrids derived from the North Carolina Design II (NCD II) along with six commercial checks under terminal drought stress (TDS), heat stress (HS), and combined drought and heat stress (CHDS)conditions. The objectives of the study were to: (i) determine the combining ability of the inbred lines and identify the best testers across the stresses; (ii) classify the inbred lines into heterotic groups (HGs) based on the general combining ability of multiple traits (HGCAMT) and sequencing-based diversity array technology (DArTseq) and (iii) assess the performance and stability of the lines in hybrid combinations. The inbred lines showed significantly (p < 0.01 and p < 0.05) positive and negative general combining ability (GCA) and specific combining ability (SCA) effects for grain yield (GY) and most other measured traits. The inbred line TZEI 135 displayed relatively larger positive GCA effects for GY when mated either as male or female and was identified as the best tester. TZEI 135 × TZEI 182 was identified as the best single-cross tester across environments. Results of the assessment of the relative importance of GCA and SCA effects revealed the predominance of additive gene action over the non-additive. Six HGs of inbreds were identified using the HGCAMT and three, based on the DArTseq marker genetic distance method, were the most efficient. The best hybrids in this study significantly out-yielded the best checks by 21, 46, and 70% under CHDS, HS, and TDS, respectively. These hybrids should be extensively tested in on-farm trials for possible commercialization in sub-Saharan Africa.

Identification of superior haplotypes in a diverse natural population for breeding desirable plant height in soybean.

KEY MESSAGE: Plant height of soybean is associated with a haplotype block on chromosome 19, which classified 211 soybean accessions into five distinct groups showing significant differences for the target trait. Genetic variation is pivotal for crop improvement. Natural populations are precious genetic resources. However, efficient strategies for the targeted utilization of these resources for quantitative traits, such as plant height (PH), are scarce. Being an important agronomic trait associated with soybean yield and quality, it is imperative to unravel the genetic mechanisms underlying PH in soybean. Here, a genome-wide association study (GWAS) was performed to identify single nucleotide polymorphisms (SNPs) significantly associated with PH in a natural population of 211 cultivated soybeans, which was genotyped with NJAU 355 K Soy SNP Array and evaluated across six environments. A total of 128 SNPs distributed across 17 chromosomes were found to be significantly associated with PH across six environments and a combined environment. Three significant SNPs were consistently identified in at least three environments on Chr.02 (AX-93958260), Chr.17 (AX-94154834), and Chr.19 (AX-93897200). Genomic regions of ~ 130 kb flanking these three consistent SNPs were considered as stable QTLs, which included 169 genes. Of these, 22 genes (including Dt1) were prioritized and defined as putative candidates controlling PH. The genomic region flanking 12 most significant SNPs was in strong linkage disequilibrium (LD). These SNPs formed a single haplotype block containing five haplotypes for PH, namely Hap-A, Hap-B, Hap-C, Hap-D, and Hap-E. Deployment of such superior haplotypes in breeding programs will enable development of improved soybean varieties with desirable plant height.

CRISPR-Cas9 based stress tolerance: New hope for abiotic stress tolerance in chickpea (Cicer arietinum).

Plants are subjected to biotic and abiotic stresses regularly, which irreparably harm agricultural production. Eco-friendly and sustainable technology to deal with this challenge is to breed abiotic stress tolerant cultivars. To generate crop plants conferring resistance against stresses, conventional breeding was used in the past, but because of the complex heredity of abiotic stress tolerance traits, such techniques remain insufficient in making greater enhancement. Genome-engineering based on CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats-CRISPR associated protein9) has shown enormous potential in developing climate-resilient cultivars. Likewise, the development of chickpea transgenic lines by knockout of 4CL and REV7 genes exhibits drought tolerance which establishes a foundation for future studies in chickpea. In addition, the CRISPR-Cas9 system can boost yield potential under abiotic stress situations by producing non-transgenic plants having the required characteristics. This review article discusses the validation of gene function based on the CRISPR-Cas9 for the development of abiotic stress-tolerant crop plants, emphasizing the chickpea to open the new ventures of generating abiotic stress-tolerant chickpea varieties.

Post-anthesis Relationships Between Nitrogen Isotope Discrimination and Yield of Spring Wheat Under Different Nitrogen Levels.

Wheat grain yield and nitrogen (N) content are influenced by the amount of N remobilized to the grain, together with pre-anthesis and post-anthesis N uptake. Isotopic techniques in farmed areas may provide insight into the mechanism underlying the N cycle. 15N-labeled urea was applied to microplots within five different fertilized treatments 0 kg ha-1 (N1), 52.5 kg ha-1 (N2), 105 kg ha-1 (N3), 157.5 kg ha-1 (N4), and 210 kg ha-1 (N5) of a long-term field trial (2003-2021) in a rainfed wheat field in the semi-arid loess Plateau, China, to determine post-anthesis N uptake and remobilization into the grain, as well as the variability of 15N enrichment in aboveground parts. Total N uptake was between 7.88 and 29.27 kg ha-1 for straw and 41.85 and 95.27 kg ha-1 for grain. In comparison to N1, N fertilization increased straw and grain N uptake by 73.1 and 56.1%, respectively. Nitrogen use efficiency (NUE) and harvest index were altered by N application rates. The average NUE at maturity was 19.9% in 2020 and 20.01% in 2021; however, it was usually higher under the control and low N conditions. The amount of 15N excess increased as the N rate increased: N5 had the highest 15N excess at the maturity stage in the upper (2.28 ± 0.36%), the middle (1.77 ± 0.28%), and the lower portion (1.68 ± 1.01%). Compared to N1, N fertilization (N2-N5) increased 15N excess in the various shoot portions by 50, 38, and 35% at maturity for upper, middle, and lower portions, respectively. At maturity, the 15N excess remobilized to the grain under N1-N5 was between 5 and 8%. Our findings revealed that N had a significant impact on yield and N isotope discrimination in spring wheat that these two parameters can interact, and that future research on the relationship between yield and N isotope discrimination in spring wheat should take these factors into account.

Detection of QTLs for Plant Height Architecture Traits in Rice (Oryza sativa L.) by Association Mapping and the RSTEP-LRT Method.

Plant height (PH) and its component traits are critical determinants of lodging resistance and strongly influence yield in rice. The genetic architecture of PH and its component traits were mined in two mapping populations. In the natural population composed of 504 accessions, a total of forty simple sequence repeat (SSR) markers associated with PH and its component traits were detected across two environments via association mapping. Allele RM305-210 bp on chromosome 5 for PH had the largest phenotypic effect value (PEV) (-51.42 cm) with a reducing effect. Allele RM3533-220 bp on chromosome 9 for panicle length and allele RM264-120 bp on chromosome 8 for the length of upper first elongated internode (1IN) showed the highest positive PEV. Among the elongated internodes with negative effects being desirable, the allele RM348-130 bp showed the largest PEV (-7.48 cm) for the length of upper second elongated internode. In the chromosome segment substitution line population consisting of 53 lines, a total of nine QTLs were detected across two environments, with the phenotypic variance explained (PVE) ranging 10.07-28.42%. Among the detected QTLs, q1IN-7 explained the largest PVE (28.42%) for the 1IN, with an additive of 5.31 cm. The favorable allele RM257-125 bp on chromosome 9 for the 1IN increasing was detected in both populations. The favorable alleles provided here could be used to shape PH architecture against lodging.

Genome-Wide Association Study Reveals Genetic Architecture and Candidate Genes for Yield and Related Traits under Terminal Drought, Combined Heat and Drought in Tropical Maize Germplasm.

Maize (Zea mays L.) production is constrained by drought and heat stresses. The combination of these two stresses is likely to be more detrimental. To breed for maize cultivars tolerant of these stresses, 162 tropical maize inbred lines were evaluated under combined heat and drought (CHD) and terminal drought (TD) conditions. The mixed linear model was employed for the genome-wide association study using 7834 SNP markers and several phenotypic data including, days to 50% anthesis (AD) and silking (SD), husk cover (HUSKC), and grain yield (GY). In total, 66, 27, and 24 SNPs were associated with the traits evaluated under CHD, TD, and their combined effects, respectively. Of these, four single nucleotide polymorphism (SNP) markers (SNP_161703060 on Chr01, SNP_196800695 on Chr02, SNP_195454836 on Chr05, and SNP_51772182 on Chr07) had pleiotropic effects on both AD and SD under CHD conditions. Four SNPs (SNP_138825271 (Chr03), SNP_244895453 (Chr04), SNP_168561609 (Chr05), and SNP_62970998 (Chr06)) were associated with AD, SD, and HUSKC under TD. Twelve candidate genes containing phytohormone cis-acting regulating elements were implicated in the regulation of plant responses to multiple stress conditions including heat and drought. The SNPs and candidate genes identified in the study will provide invaluable information for breeding climate smart maize varieties under tropical conditions following validation of the SNP markers.