Insights into the responses of Akabare chili landraces to drought, heat, and their combined stress during pre-flowering and fruiting stages.

Drought, heat, and their combined stress have increasingly become common phenomena in horticulture, significantly reducing chili production worldwide. The current study aimed to phenotype Akabare chili landraces (Capsicum spp.) in climate chambers subjected to drought and heat treatments during their early generative stage, focusing on PSII efficacy (Fv/Fm), net photosynthetic rate (P N), stomatal conductance (g s), leaf cooling, and biomass production. Six landraces were examined under heat and control conditions at 40/32 °C for 4 days and at 30/22 °C under drought and control conditions followed by a 5-day recovery under control conditions (30/22 °C, irrigated). Two landraces with higher (>0.77) and two with lower (<0.763) Fv/Fm during the stress treatments were later evaluated in the field under 55-day-long drought stress at the fruiting stage. In both treatments, stress-tolerant landraces maintained high Fv/Fm, P N, and better leaf cooling leading to improved biomass compared to the sensitive landraces. Agro-morpho-physiological responses of the tolerant and sensitive landraces during the early generative stage echoed those during the fruiting stage in the field. A climate chamber experiment revealed a 13.9 % decrease in total biomass under heat stress, a further 21.5 % reduction under drought stress, and a substantial 38.7 % decline under combine stress. In field conditions, drought stress reduced total biomass by 28.1 % and total fruit dry weight by 26.2 %. Tolerant landraces showed higher Fv/Fm, demonstrated better wilting scores, displayed a higher chlorophyll content index (CCI), and accumulated more biomass. This study validated lab-based results through field trials and identified two landraces, C44 and DKT77, as potential stress-tolerant genotypes. It recommends Fv/Fm, P N, and CCI as physiological markers for the early detection of stress tolerance.

Genotype selection identified elite lines through quantitative trait loci mapping of agronomically important traits in wheat.

Wheat is one of the most important staple foods in the world. Genetic characterization of wheat agronomically important traits is crucial for yield improvement through molecular breeding. In this study, a recombinant inbred line (RIL) population was developed by crossing a local adapted high yield variety Jimai 22 (JM22) with an external variety Cunmai no.1 (CM1). A high-density genetic map containing 7,359 single nucleotide polymorphism (SNP) markers was constructed. Quantitative trait loci (QTL) mapping identified 61 QTL for eight yield-related traits under six environments (years). Among them, 17 QTL affecting spike number per plant, grain number per spike and thousand grain weight showed high predictability for theoretical yield per plant (TYP), of which, 12 QTL alleles positively contributed to TYP. Nine promising candidate genes for seven of the 12 QTL were identified including three known wheat genes and six rice orthologs. Four elite lines with TYP increased by 5.6%-15.2% were identified through genotype selection which carried 7-9 favorable alleles from JM22 and 2-3 favorable alleles from CM1 of the 12 QTL. Moreover, the linked SNPs of the 12 QTL were converted to high-throughput kompetitive allele-specific PCR (KASP) markers and validated in the population. The mapped QTL, identified promising candidate genes, developed elite lines and KASP markers are highly valuable in future genotype selection to improve wheat yield. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-024-01496-3.

Triple gene mutations boost amylose and resistant starch content in rice: insights from sbe2b/sbe1/OE-Wxa mutants.

Previous studies have modified rice's resistant starch (RS) content by mutating single and double genes. These mutations include knocking out or reducing the expression of sbe1 or sbe2b genes, as well as overexpressing Wxa . However, the impact of triple mutant sbe2b/sbe1/OE-Wxa on RS contents remained unknown. Here, we constructed a double mutant with sbe2b/RNAi-sbe1, based on IR36ae with sbe2b, and a triple mutant with sbe2b/RNAi-sbe1/OE-Wxa , based on the double mutant. The results showed that the amylose and RS contents gradually increased with an increase in the number of mutated genes. The triple mutant exhibited the highest amylose and RS contents, with 41.92% and 4.63%, respectively, which were 2- and 5-fold higher than those of the wild type, which had 22.19% and 0.86%, respectively. All three mutants altered chain length and starch composition compared to the wild type. However, there was minimal difference observed among the mutants. The Wxa gene contributed to the improvement of 1000-grain weight and seed-setting rate, in addition to the highest amylose and RS contents. Thus, our study offers valuable insight for breeding rice cultivars with a higher RS content and yields.

The construction of a maize-teosinte introgression population and quantitative trait loci analysis of their 21 agronomic traits.

Teosinte is a progenitor species of maize (Zea mays ssp. mays) that retains a significant reservoir of genetic resources unaltered via the domestication process. To harness and explore the genetic reservoirs inherent in teosinte, we used the cultivated publicly inbred line H95 and wild species PI566673 (Zea mays ssp. mexicana) to develop a set of introgression lines (ILs), including 366 BC2F5 lines. Using these lines, 12481 high-quality polymorphic homozygous single nucleotide polymorphisms were converted into 2358 bin markers based on Genotyping by Target Sequencing technology. The homozygous introgression ratio in the ILs was approximately 12.1 % and the heterozygous introgression ratio was approximately 5.7 %. Based on the population phenotypic data across 21 important agronomic traits collected in Sanya and Beijing, 185 and 156 quantitative trait loci (QTLs) were detected in Sanya and Beijing, respectively, with 64 stable QTLs detected in both locations. We detected 12 QTL clusters spanning 10 chromosomes consisting of diverse QTLs related to yield traits such as grain size and weight. In addition, we identified useful materials in the ILs for further gene cloning of related variations. For example, some heterogeneous inbred families with superior genetic purity, shorter target heterozygotes, and some ILs exhibit clear morphological variation associated with plant growth, development, and domestication, manifesting traits such as white stalks, sharp seeds, and cob shattering. In conclusion, our results provide a robust foundation for delving into the genetic reservoirs of teosinte, presenting a wealth of genetic resources and offering insight into the genetic architecture underlying maize agronomic traits.

Genome-Wide Association Analysis of Yield-Related Traits and Candidate Genes in Vegetable Soybean.

Owing to the rising demand for vegetable soybean products, there is an increasing need for high-yield soybean varieties. However, the complex correlation patterns among quantitative traits with genetic architecture pose a challenge for improving vegetable soybean through breeding. Herein, a genome-wide association study (GWAS) was applied to 6 yield-related traits in 188 vegetable soybean accessions. Using a BLINK model, a total of 116 single nucleotide polymorphisms (SNPs) were identified for plant height, pod length, pod number, pod thickness, pod width, and fresh pod weight. Furthermore, a total of 220 genes were found in the 200 kb upstream and downstream regions of significant SNPs, including 11 genes encoding functional proteins. Among them, four candidate genes, Glyma.13G109100, Glyma.03G183200, Glyma.09G102200, and Glyma.09G102300 were analyzed for significant haplotype variations and to be in LD block, which encode MYB-related transcription factor, auxin-responsive protein, F-box protein, and CYP450, respectively. The relative expression of candidate genes in V030 and V071 vegetable soybean (for the plant height, pod number, and fresh pod weight of V030 were lower than those of the V071 strains) was significantly different, and these genes could be involved in plant growth and development via various pathways. Altogether, we identified four candidate genes for pod yield and plant height from vegetable soybean germplasm. This study provides insights into the genomic basis for improving soybean and crucial genomic resources that can facilitate genome-assisted high-yielding vegetable soybean breeding.

CRISPR enables sustainable cereal production for a greener future.

The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system has become the most important tool for targeted genome editing in many plant and animal species over the past decade. The CRISPR/Cas9 technology has also sparked a flood of applications and technical advancements in genome editing in the key cereal crops, including rice, wheat, maize, and barley. Here, we review advanced uses of CRISPR/Cas9 and derived systems in genome editing of cereal crops to enhance a variety of agronomically important features. We also highlight new technological advances for delivering preassembled Cas9-gRNA ribonucleoprotein (RNP)-editing systems, multiplex editing, gain-of-function strategies, the use of artificial intelligence (AI)-based tools, and combining CRISPR with novel speed breeding (SB) and vernalization strategies.

Improving grain yield prediction through fusion of multi-temporal spectral features and agronomic trait parameters derived from UAV imagery.

Rapid and accurate prediction of crop yield is particularly important for ensuring national and regional food security and guiding the formulation of agricultural and rural development plans. Due to unmanned aerial vehicles' ultra-high spatial resolution, low cost, and flexibility, they are widely used in field-scale crop yield prediction. Most current studies used the spectral features of crops, especially vegetation or color indices, to predict crop yield. Agronomic trait parameters have gradually attracted the attention of researchers for use in the yield prediction in recent years. In this study, the advantages of multispectral and RGB images were comprehensively used and combined with crop spectral features and agronomic trait parameters (i.e., canopy height, coverage, and volume) to predict the crop yield, and the effects of agronomic trait parameters on yield prediction were investigated. The results showed that compared with the yield prediction using spectral features, the addition of agronomic trait parameters effectively improved the yield prediction accuracy. The best feature combination was the canopy height (CH), fractional vegetation cover (FVC), normalized difference red-edge index (NDVI_RE), and enhanced vegetation index (EVI). The yield prediction error was 8.34%, with an R2 of 0.95. The prediction accuracies were notably greater in the stages of jointing, booting, heading, and early grain-filling compared to later stages of growth, with the heading stage displaying the highest accuracy in yield prediction. The prediction results based on the features of multiple growth stages were better than those based on a single stage. The yield prediction across different cultivars was weaker than that of the same cultivar. Nevertheless, the combination of agronomic trait parameters and spectral indices improved the prediction among cultivars to some extent.

Plant trait relationships are maintained within a major crop species: lack of artificial selection signal and potential for improved agronomic performance.

The exploration of phenotypic spaces of large sets of plant species has considerably increased our understanding of diversification processes in the plant kingdom. Nevertheless, such advances have predominantly relied on interspecific comparisons that hold several limitations. Here, we grew in the field a unique set of 179 inbred lines of durum wheat, Triticum turgidum spp. durum, characterized by variable degrees of artificial selection. We measured aboveground and belowground traits as well as agronomic traits to explore the functional and agronomic trait spaces and to investigate trait-to-agronomic performance relationships. We showed that the wheat functional trait space shared commonalities with global cross-species spaces previously described, with two main axes of variation: a root foraging axis and a slow-fast trade-off axis. Moreover, we detected a clear signature of artificial selection on the variation of agronomic traits, unlike functional traits. Interestingly, we identified alternative phenotypic combinations that can optimize crop performance. Our work brings insightful knowledge about the structure of phenotypic spaces of domesticated plants and the maintenance of phenotypic trade-offs in response to artificial selection, with implications for trade-off-free and multi-criteria selection in plant breeding.

Quality and Agronomic Trait Analyses of Pyramids Composed of Wheat Genes NGli-D2, Sec-1s and 1Dx5+1Dy10.

Due to rising living standards, it is important to improve wheat's quality traits by adjusting its storage protein genes. The introduction or locus deletion of high molecular weight subunits could provide new options for improving wheat quality and food safety. In this study, digenic and trigenic wheat lines were identified, in which the 1Dx5+1Dy10 subunit, and NGli-D2 and Sec-1s genes were successfully polymerized to determine the role of gene pyramiding in wheat quality. In addition, the effects of ω-rye alkaloids during 1BL/1RS translocation on quality were eliminated by introducing and utilizing 1Dx5+1Dy10 subunits through gene pyramiding. Additionally, the content of alcohol-soluble proteins was reduced, the Glu/Gli ratio was increased and high-quality wheat lines were obtained. The sedimentation values and mixograph parameters of the gene pyramids under different genetic backgrounds were significantly increased. Among all the pyramids, the trigenic lines in Zhengmai 7698, which was the genetic background, had the highest sedimentation value. The mixograph parameters of the midline peak time (MPT), midline peak value (MPV), midline peak width (MPW), curve tail value (CTV), curve tail width (CTW), midline value at 8 min (MTxV), midline width at 8 min (MTxW) and midline integral at 8 min (MTxI) of the gene pyramids were markedly enhanced, especially in the trigenic lines. Therefore, the pyramiding processes of the 1Dx5+1Dy10, Sec-1S and NGli-D2 genes improved dough elasticity. The overall protein composition of the modified gene pyramids was better than that of the wild type. The Glu/Gli ratios of the type I digenic line and trigenic lines containing the NGli-D2 locus were higher than that of the type II digenic line without the NGli-D2 locus. The trigenic lines with Hengguan 35 as the genetic background had the highest Glu/Gli ratio among the specimens. The unextractable polymeric protein (UPP%) and Glu/Gli ratios of the type II digenic line and trigenic lines were significantly higher than those of the wild type. The UPP% of the type II digenic line was higher than that of the trigenic lines, while the Glu/Gli ratio was slightly lower than that of the trigenic lines. In addition, the celiac disease (CD) epitopes' level of the gene pyramids significantly decreased. The strategy and information reported in this study could be very useful for improving wheat processing quality and reducing wheat CD epitopes.

Bioengineering of Soybean Oil and Its Impact on Agronomic Traits.

Soybean is a major oil crop and is also a dominant source of nutritional protein. The 20% seed oil content (SOC) of soybean is much lower than that in most oil crops and the fatty acid composition of its native oil cannot meet the specifications for some applications in the food and industrial sectors. Considerable effort has been expended on soybean bioengineering to tailor fatty acid profiles and improve SOC. Although significant advancements have been made, such as the creation of high-oleic acid soybean oil and high-SOC soybean, those genetic modifications have some negative impacts on soybean production, for instance, impaired germination or low protein content. In this review, we focus on recent advances in the bioengineering of soybean oil and its effects on agronomic traits.

Effects of Basal Selenium Fertilizer Application on Agronomic Traits, Yield, Quality, and Se Content of Dryland Maize.

To explore the efficiency of selenium (Se) fertilizer application in dryland maize, we tested five Se fertilizer application treatments: 0 g ha-1 (Se0), 75 g ha-1 (Se1), 150 g ha-1 (Se2), 225 g ha-1 (Se3), and 300 g ha-1 (Se4). Compared with Se0, Se2 increased the leaf area, chlorophyll content, internode length, plant height, and ear height by 7.95%, 3.20%, 13.19%, 1.89%, and 7.98%, respectively. Se2 and Se3 significantly affected the stem internode diameter, cortex thickness, and cellulose content, which were positively correlated with lodging resistance. Compared with Se0, Se3 promoted the contents of soluble sugar, crude protein, crude fat, and starch in grains, which increased by 9.48%, 6.59%, 1.56%, and 4.82%, respectively. It implies that maize grain application of Se significantly improves their Se content. Se1 did not observably influence the growth of maize, and the promoting effect of Se4 on maize decreased. The lodging resistance of maize as analyzed by Pearson correlation analysis correlated with the application of Se fertilizer. It proved that higher yield, grain quality, grain Se content, and lodging resistance of stems were concerned with Se fertilizer application in the range of 150-225 g ha-1. The results provide useful information for Se fertilizer treatment in dryland maize.

Increasing the Grain Yield and Grain Protein Content of Common Wheat (Triticum aestivum) by Introducing Missense Mutations in the Q Gene.

Grain yield (GY) and grain protein content (GPC) are important traits for wheat breeding and production; however, they are usually negatively correlated. The Q gene is the most important domestication gene in cultivated wheat because it influences many traits, including GY and GPC. Allelic variations in the Q gene may positively affect both GY and GPC. Accordingly, we characterized two new Q alleles (Qs1 and Qc1-N8) obtained through ethyl methanesulfonate-induced mutagenesis. Compared with the wild-type Q allele, Qs1 contains a missense mutation in the sequence encoding the first AP2 domain, whereas Qc1-N8 has two missense mutations: one in the sequence encoding the second AP2 domain and the other in the microRNA172-binding site. The Qs1 allele did not significantly affect GPC or other processing quality parameters, but it adversely affected GY by decreasing the thousand kernel weight and grain number per spike. In contrast, Qc1-N8 positively affected GPC and GY by increasing the thousand kernel weight and grain number per spike. Thus, we generated novel germplasm relevant for wheat breeding. A specific molecular marker was developed to facilitate the use of the Qc1-N8 allele in breeding. Furthermore, our findings provide useful new information for enhancing cereal crops via non-transgenic approaches.

Roles of microRNAs in abiotic stress response and characteristics regulation of plant.

MicroRNAs (miRNAs) are a class of non-coding endogenous small RNAs (long 20-24 nucleotides) that negatively regulate eukaryotes gene expression at post-transcriptional level via cleavage or/and translational inhibition of targeting mRNA. Based on the diverse roles of miRNA in regulating eukaryotes gene expression, research on the identification of miRNA target genes has been carried out, and a growing body of research has demonstrated that miRNAs act on target genes and are involved in various biological functions of plants. It has an important influence on plant growth and development, morphogenesis, and stress response. Recent case studies indicate that miRNA-mediated regulation pattern may improve agronomic properties and confer abiotic stress resistance of plants, so as to ensure sustainable agricultural production. In this regard, we focus on the recent updates on miRNAs and their targets involved in responding to abiotic stress including low temperature, high temperature, drought, soil salinity, and heavy metals, as well as plant-growing development. In particular, this review highlights the diverse functions of miRNAs on achieving the desirable agronomic traits in important crops. Herein, the main research strategies of miRNAs involved in abiotic stress resistance and crop traits improvement were summarized. Furthermore, the miRNA-related challenges and future perspectives of plants have been discussed. miRNA-based research lays the foundation for exploring miRNA regulatory mechanism, which aims to provide insights into a potential form of crop improvement and stress resistance breeding.

CRISPR/Cas-mediated editing of cis-regulatory elements for crop improvement.

To improve future agricultural production, major technological advances are required to increase crop production and yield. Targeting the coding region of genes via the Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated Protein (CRISPR/Cas) system has been well established and has enabled the rapid generation of transgene-free plants, which can lead to crop improvement. The emergence of the CRISPR/Cas system has also enabled scientists to achieve cis-regulatory element (CRE) editing and, consequently, engineering endogenous critical CREs to modulate the expression of target genes. Recent genome-wide association studies have identified the domestication of natural CRE variants to regulate complex agronomic quantitative traits and have allowed for their engineering via the CRISPR/Cas system. Although engineering plant CREs can be advantageous to drive gene expression, there are still many limitations to its practical application. Here, we review the current progress in CRE editing and propose future strategies to effectively target CREs for transcriptional regulation for crop improvement.

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A pot experiment was conducted at the Shaoyang University test base in May 2020, with Xudou 18 as the research object. We investigated the growth and development as well as the agronomic traits and nutrient content across a gradient of 0 (CK), 5, 10, 20, and 40 g·kg-1 of biochar addition. The results showed that compared with CK, the biochar application significantly affected growth dynamic, plant height, number of effective pods per plant, 100-grain weight, and leaf and stem dry weights of soybean plants, and the contents of protein, crude fat and isoflavone in soybean seeds. At the application rate of 20 g·kg-1, the germination rate of soybean was the highest, the growth period was the shortest, the number of effective pods per plant was the highest, the 100-grain weight was the largest, and the contents of protein, crude fat, and isoflavone were the highest in the seeds. When biochar application reached 40 g·kg-1, the plant height of soybean was the highest with extended vegetative growth and delayed maturity, whereas the effective pods per plant and 100-grain weight was reduced compared to that with 20 g·kg-1 application. In conclusion, the effects of biochar addition on agronomic traits and nutrient content of soybean varied with application amount, with 20 g·kg-1 being the optimal under the test condition.

Linking Autophagy to Potential Agronomic Trait Improvement in Crops.

Autophagy is an evolutionarily conserved catabolic process in eukaryotic cells, by which the superfluous or damaged cytoplasmic components can be delivered into vacuoles or lysosomes for degradation and recycling. Two decades of autophagy research in plants uncovers the important roles of autophagy during diverse biological processes, including development, metabolism, and various stress responses. Additionally, molecular machineries contributing to plant autophagy onset and regulation have also gradually come into people's sights. With the advancement of our knowledge of autophagy from model plants, autophagy research has expanded to include crops in recent years, for a better understanding of autophagy engagement in crop biology and its potentials in improving agricultural performance. In this review, we summarize the current research progress of autophagy in crops and discuss the autophagy-related approaches for potential agronomic trait improvement in crop plants.

Exploring transposable element-based markers to identify allelic variations underlying agronomic traits in rice.

Transposable elements (TEs) are a major force in the production of new alleles during domestication; nevertheless, their use in association studies has been limited because of their complexity. We have developed a TE genotyping pipeline (TEmarker) and applied it to whole-genome genome-wide association study (GWAS) data from 176 Oryza sativa subsp. japonica accessions to identify genetic elements associated with specific agronomic traits. TE markers recovered a large proportion (69%) of single-nucleotide polymorphism (SNP)-based GWAS peaks, and these TE peaks retained ca. 25% of the SNPs. The use of TEs in GWASs may reduce false positives associated with linkage disequilibrium (LD) among SNP markers. A genome scan revealed positive selection on TEs associated with agronomic traits. We found several cases of insertion and deletion variants that potentially resulted from the direct action of TEs, including an allele of LOC_Os11g08410 associated with plant height and panicle length traits. Together, these findings reveal the utility of TE markers for connecting genotype to phenotype and suggest a potential role for TEs in influencing phenotypic variations in rice that impact agronomic traits.

Genome-wide identification of quantitative trait loci for morpho-agronomic and yield-related traits in foxtail millet (Setaria italica) across multi-environments.

Foxtail millet (Setaria italica) is an ideal model of genetic system for functional genomics of the Panicoideae crop. Identification of QTL responsible for morpho-agronomic and yield-related traits facilitates dissection of genetic control and breeding in cereal crops. Here, based on a Yugu1 × Longgu7 RIL population and genome-wide resequencing data, an updated linkage map harboring 2297 bin and 74 SSR markers was constructed, spanning 1315.1 cM with an average distance of 0.56 cM between adjacent markers. A total of 221 QTL for 17 morpho-agronomic and yield-related traits explaining 5.5 ~ 36% of phenotypic variation were identified across multi-environments. Of these, 109 QTL were detected in two to nine environments, including the most stable qLMS6.1 harboring a promising candidate gene Seita.6G250500, of which 70 were repeatedly identified in different trials in the same geographic location, suggesting that foxtail millet has more identical genetic modules under the similar ecological environment. One hundred-thirty QTL with overlapping intervals formed 22 QTL clusters. Furthermore, six superior recombinant inbred lines, RIL35, RIL48, RIL77, RIL80, RIL115 and RIL125 with transgressive inheritance and enrichment of favorable alleles in plant height, tiller, panicle morphology and yield related-traits were screened by hierarchical cluster. These identified QTL, QTL clusters and superior lines lay ground for further gene-trait association studies and breeding practice in foxtail millet.

Genetic Control of Seed Phytate Accumulation and the Development of Low-Phytate Crops: A Review and Perspective.

Breeding low phytic acid (lpa) crops is a strategy that has potential to both improve the nutritional quality of food and feed and contribute to the sustainability of agriculture. Here, we review the lipid-independent and -dependent pathways of phytate synthesis and their regulatory mechanisms in plants. We compare the genetic variation of the phytate concentration and distribution in seeds between dicot and monocot species as well as the associated temporal and spatial expression patterns of the genes involved in phytate synthesis and transport. Quantitative trait loci or significant single nucleotide polymorphisms for the seed phytate concentration have been identified in different plant species by linkage and association mapping, and some genes have been cloned from lpa mutants. We summarize the effects of various lpa mutations on important agronomic traits in crop plants and propose SULTR3;3 and SULTR3;4 as optimal target genes for lpa crop breeding.