Multiple Agronomic Traits Research Articles

EARLY FLOWERING3-1 represses Grain number, plant height, and heading date7 to promote ABC1 REPRESSOR1 and regulate nitrogen uptake in rice.

The extensive use of nitrogen fertilizer boosts rice (Oryza sativa) production but also harms ecosystems. Therefore, enhancing crop nitrogen use efficiency is crucial. Here, we performed map-based cloning and identified the EARLY FLOWERING3 (ELF3) like protein-encoding gene OsELF3-1, which confers enhanced nitrogen uptake in rice. OsELF3-1 forms a ternary complex (OsEC) with OsELF4s and OsLUX, the putative orthologs of ELF4 and LUX ARRHYTHMO (LUX) in Arabidopsis (Arabidopsis thaliana), respectively. OsEC directly binds to the promoter of Grain number, plant height, and heading date7 (Ghd7) and represses its expression. Ghd7 encodes a transcription factor that has major effects on multiple agronomic traits. Ghd7 is also a transcriptional repressor and directly suppresses the expression of ABC1 REPRESSOR1 (ARE1), a negative regulator of nitrogen use efficiency. Therefore, targeting the OsEC-Ghd7-ARE1 module offers an approach to enhance nitrogen uptake, presenting promising avenues for sustainable agriculture.

Exploring Genetic Diversity within aus Rice Germplasm: Insights into the Variations in Agro-morphological Traits

The aus (Oryza sativa L.) varietal group comprises of aus, boro, ashina and rayada seasonal and/or field ecotypes, and exhibits unique stress tolerance traits, making it valuable for rice breeding. Despite its importance, the agro-morphological diversity and genetic control of yield traits in aus rice remain poorly understood. To address this knowledge gap, we investigated the genetic structure of 181 aus accessions using 399,115 SNP markers and evaluated them for 11 morpho-agronomic traits. Through genome-wide association studies (GWAS), we aimed to identify key loci controlling yield and plant architectural traits.Our population genetic analysis unveiled six subpopulations with strong geographical patterns. Subpopulation-specific differences were observed in most phenotypic traits. Principal component analysis (PCA) of agronomic traits showed that principal component 1 (PC1) was primarily associated with panicle traits, plant height, and heading date, while PC2 and PC3 were linked to primary grain yield traits. GWAS using PC1 identified OsSAC1 on Chromosome 7 as a significant gene influencing multiple agronomic traits. PC2-based GWAS highlighted the importance of OsGLT1 and OsPUP4/ Big Grain 3 in determining grain yield. Haplotype analysis of these genes in the 3,000 Rice Genome Panel revealed distinct genetic variations in aus rice.In summary, this study offers valuable insights into the genetic structure and phenotypic diversity of aus rice accessions. We have identified significant loci associated with essential agronomic traits, with GLT1, PUP4, and SAC1 genes emerging as key players in yield determination.

Cotton pedigree genome reveals restriction of cultivar-driven strategy in cotton breeding

BackgroundMany elite genes have been identified from the available cotton genomic data, providing various genetic resources for gene-driven breeding. However, backbone cultivar-driven breeding is the most widely applied strategy. Revealing the genetic basis of cultivar-driven strategy’s restriction is crucial for transition of cotton breeding strategy.ResultCRI12 is a backbone cultivar in cultivar-driven breeding. Here we sequence the pedigree of CRI12 using Nanopore long-read sequencing. We construct a graphical pedigree genome using the high-quality CRI12 genome and 13,138 structural variations within 20 different pedigree members. We find that low hereditary stability of elite segments in backbone cultivars is a drawback of cultivar-driven strategy. We also identify 623 functional segments in CRI12 for multiple agronomic traits in presence and absence variation-based genome-wide association study on three cohorts. We demonstrate that 25 deleterious segments are responsible for the geographical divergence of cotton in pathogen resistance. We also characterize an elite pathogen-resistant gene (GhKHCP) utilized in modern cotton breeding. In addition, we identify 386 pedigree fingerprint segments by comparing the segments of the CRI12 pedigree with those of a large cotton population.ConclusionWe characterize the genetic patterns of functional segments in the pedigree of CRI12 using graphical genome method, revealing restrictions of cultivar-driven strategies in cotton breeding. These findings provide theoretical support for transitioning from cultivar-driven to gene-driven strategy in cotton breeding.

Efficient and versatile multiplex prime editing in hexaploid wheat

Prime editing is limited by low efficiency in plants. Here, we develop an upgraded engineered plant prime editor in hexaploid wheat, ePPEplus, by introducing a V223A substitution into reverse transcriptase in the ePPEmax* architecture. ePPEplus enhances the efficiency by an average 33.0-fold and 6.4-fold compared to the original PPE and ePPE, respectively. Importantly, a robust multiplex prime editing platform is established for simultaneous editing of four to ten genes in protoplasts and up to eight genes in regenerated wheat plants at frequencies up to 74.5%, thus expanding the applicability of prime editors for stacking of multiple agronomic traits.

Serine protease NAL1 exerts pleiotropic functions through degradation of TOPLESS-related corepressor in rice.

NARROW LEAF 1 (NAL1) is a breeding-valuable pleiotropic gene that affects multiple agronomic traits in rice, although the molecular mechanism is largely unclear. Here, we report that NAL1 is a serine protease and displays a novel hexameric structure consisting of two ATP-mediated doughnut-shaped trimeric complexes. Moreover, we identified TOPLESS-related corepressor OsTPR2 involved in multiple growth and development processes as the substrate of NAL1. We found that NAL1 degraded OsTPR2, thus modulating the expression of downstream genes related to hormone signalling pathways, eventually achieving its pleiotropic physiological function. An elite allele, NAL1A, which may have originated from wild rice, could increase grain yield. Furthermore, the NAL1 homologues in different crops have a similar pleiotropic function to NAL1. Our study uncovers a NAL1-OsTPR2 regulatory module and provides gene resources for the design of high-yield crops.

QTL analysis of important agronomic traits and metabolites in foxtail millet (Setaria italica) by RIL population and widely targeted metabolome.

As a bridge between genome and phenotype, metabolome is closely related to plant growth and development. However, the research on the combination of genome, metabolome and multiple agronomic traits in foxtail millet (Setaria italica) is insufficient. Here, based on the linkage analysis of 3,452 metabolites via with high-quality genetic linkage maps, we detected a total of 1,049 metabolic quantitative trait loci (mQTLs) distributed in 11 hotspots, and 28 metabolite-related candidate genes were mined from 14 mQTLs. In addition, 136 single-environment phenotypic QTL (pQTLs) related to 63 phenotypes were identified by linkage analysis, and there were 12 hotspots on these pQTLs. We futher dissected 39 candidate genes related to agronomic traits through metabolite-phenotype correlation and gene function analysis, including Sd1 semidwarf gene, which can affect plant height by regulating GA synthesis. Combined correlation network and QTL analysis, we found that flavonoid-lignin pathway maybe closely related to plant architecture and yield in foxtail millet. For example, the correlation coefficient between apigenin 7-rutinoside and stem diameter reached 0.98, and they were co-located at 41.33-44.15 Mb of chromosome 5, further gene function analysis revealed that 5 flavonoid pathway genes, as well as Sd1, were located in this interval . Therefore, the correlation and co-localization between flavonoid-lignins and plant architecture may be due to the close linkage of their regulatory genes in millet. Besides, we also found that a combination of genomic and metabolomic for BLUP analysis can better predict plant agronomic traits than genomic or metabolomic data, independently. In conclusion, the combined analysis of mQTL and pQTL in millet have linked genetic, metabolic and agronomic traits, and is of great significance for metabolite-related molecular assisted breeding.

Development of 12 sets of chromosome segment substitution lines that enhance allele mining in Asian cultivated rice.

Many agronomic traits that are important in rice breeding are controlled by multiple genes. The extensive time and effort devoted so far to identifying and selecting such genes are still not enough to target multiple agronomic traits in practical breeding in Japan because of a lack of suitable plant materials in which to efficiently detect and validate beneficial alleles from diverse genetic resources. To facilitate the comprehensive analysis of genetic variation in agronomic traits among Asian cultivated rice, we developed 12 sets of chromosome segment substitution lines (CSSLs) with the japonica background, 11 of them in the same genetic background, using donors representing the genetic diversity of Asian cultivated rice. Using these materials, we overviewed the chromosomal locations of 1079 putative QTLs for seven agronomic traits and their allelic distribution in Asian cultivated rice through multiple linear regression analysis. The CSSLs will allow the effects of putative QTLs in the highly homogeneous japonica background to be validated.

Genetic control of tolerance to drought stress in soybean

BackgroundDrought stress limits the production of soybean [Glycine max (L.) Merr.], which is the most grown high-value legume crop worldwide. Breeding for drought tolerance is a difficult endeavor and understanding the genetic basis of drought tolerance in soybean is therefore crucial for harnessing the genomic regions involved in the tolerance mechanisms. A genome-wide association study (GWAS) analysis was applied in a soybean germplasm collection (the EUCLEG collection) of 359 accessions relevant for breeding in Europe, to identify genomic regions and candidate genes involved in the response to short duration and long duration drought stress (SDS and LDS respectively) in soybean.ResultsThe phenotypic response to drought was stronger in the long duration drought (LDS) than in the short duration drought (SDS) experiment. Over the four traits considered (canopy wilting, leaf senescence, maximum absolute growth rate and maximum plant height) the variation was in the range of 8.4−25.2% in the SDS, and 14.7−29.7% in the LDS experiments. The GWAS analysis identified a total of 17 and 22 significant marker-trait associations for four traits in the SDS and LDS experiments, respectively. In the genomic regions delimited by these markers we identified a total of 12 and 16 genes with putative functions that are of particular relevance for drought stress responses including stomatal movement, root formation, photosynthesis, ABA signaling, cellular protection and cellular repair mechanisms. Some of these genomic regions co-localized with previously known QTLs for drought tolerance traits including water use efficiency, chlorophyll content and photosynthesis.ConclusionOur results indicate that the mechanism of slow wilting in the SDS might be associated with the characteristics of the root system, whereas in the LDS, slow wilting could be due to low stomatal conductance and transpiration rates enabling a high WUE. Drought-induced leaf senescence was found to be associated to ABA and ROS responses. The QTLs related to WUE contributed to growth rate and canopy height maintenance under drought stress. Co-localization of several previously known QTLs for multiple agronomic traits with the SNPs identified in this study, highlights the importance of the identified genomic regions for the improvement of agronomic performance in addition to drought tolerance in the EUCLEG collection.

CRISPR-induced miRNA156-recognition element mutations in TaSPL13 improve multiple agronomic traits in wheat.

Increase in grain yield is always a major objective of wheat genetic improvement. The SQUAMOSA promoter-binding protein-like (SPL) genes, coding for a small family of diverse plant-specific transcription factors, represent important targets for improving grain yield and other major agronomic traits in rice. The function of the SPL genes in wheat remains to be investigated in this respect. In this study, we identified 56 wheat orthologues of rice SPL genes belonging to 19 homoeologous groups. Like in rice, nine orthologous TaSPL genes harbour the microRNA156 recognition elements (MRE) in their last exons except for TaSPL13, which harbour the MRE in its 3'-untranslated region (3'UTR). We modified the MRE of TaSPL13 using CRISPR-Cas9 and generated 12 mutations in the three homoeologous genes. As expected, the MRE mutations led to an approximately two-fold increase in the TaSPL13 mutant transcripts. The phenotypic evaluation showed that the MRE mutations in TaSPL13 resulted in a decrease in flowering time, tiller number, and plant height, and a concomitantly increase in grain size and number. The results show that the TaSPL13 mutants exhibit a combination of different phenotypes observed in Arabidopsis AtSPL3/4/5 mutants and rice OsSPL13/14/16 mutants and hold great potential in improving wheat yield by simultaneously increasing grain size and number and by refining plant architecture. The novel TaSPL13 mutations generated can be utilized in wheat breeding programmes to improve these agronomic traits.

Ethylene-mediated regulation of coleoptile elongation in rice seedlings.

Rice is an important food crop in the world and the study of its growth and plasticity has a profound influence on sustainable development. Ethylene modulates multiple agronomic traits of rice as well as abiotic and biotic stresses during its lifecycle. It has diverse roles, depending on the organs, developmental stages and environmental conditions. Compared to Arabidopsis (Arabidopsis thaliana), rice ethylene signalling pathway has its own unique features due to its special semiaquatic living environment and distinct plant structure. Ethylene signalling and responses are part of an intricate network in crosstalk with internal and external factors. This review will summarize the current progress in the mechanisms of ethylene-regulated coleoptile growth in rice, with a special focus on ethylene signaling and interaction with other hormones. Insights into these molecular mechanisms may shed light on ethylene biology and should be beneficial for the genetic improvement of rice and other crops.

Rotation of Triticale and Sweet Sorghum Improves Saline-Alkali Soil and Increases Productivity in a Saline Soil

ABSTRACT Soil salinization significantly restricts crop yield, animal foraging, and biomass production for biofuels. Identifying an efficient farming system to mitigate these concerns has become a major research focus. The present study addresses the potential of rotating triticale and sweet sorghum at various planting densities to alleviate soil salt stress, enhance production, improve agronomic characteristics, and boost soil microbial communities in a saline agricultural environment in East China. Several indicators in 2017 and 2018. Results show that triticale and sweet sorghum planting significantly decreased soil salt contents compared to bare land plots. Multiple agronomic traits were measured for each planting density. For triticale, a density of 180 × 104 plants ha−1 showed the best plant height, tiller number per plant, yield, and lodging rate; for sweet sorghum, a density of 7 × 104 plants/ha showed the best plant height, yield, and lodging rate. High-density planting of triticale (180, 260, 320 × 104 plants/ha) and sweet sorghum (7, 8, 9 × 104 plants/ha) was associated with high counts of bacteria, Actinomycetes, and salt-tolerant Actinomycetes. However, planting density had no significant effect on the counts of fungi or salt-tolerant bacteria. Redundancy Discriminant Analysis (RDA) showed that plant height, yield, lodging rate, bacteria, salt-tolerant bacteria, Actinomycetes, and salt-tolerant Actinomycetes were negatively correlated with soil salinity, while tiller number per plant and stem thickness were positively correlated with soil salinity. In conclusion, a rotation system of triticale and sweet sorghum with planting densities of 180 × 104 and 7 × 104 plants/ha, respectively was established to improve and make full use of saline soil.

Resequencing of sweetpotato germplasm resources reveals key loci associated with multiple agronomic traits.

Sweetpotato is an important crop that exhibits hexaploidy and high heterozygosity, which limits gene mining for important agronomic traits. Here, 314 sweetpotato germplasm resources were deeply resequenced, and 4 599 509 SNPs and 846 654 InDels were generated, among which 196 124 SNPs were nonsynonymous and 9690 InDels were frameshifted. Based on the Indels, genome-wide marker primers were designed, and 3219 of 40 366 primer pairs were selected to construct the core InDel marker set. The molecular ID of 104 sweetpotato samples verified the availability of these primers. The sweetpotato population structures were then assessed through multiple approaches using SNPs, and diverse approaches demonstrated that population stratification was not obvious for most Chinese germplasm resources. As many as 20 important agronomic traits were evaluated, and a genome-wide association study was conducted on these traits. A total of 19 high-confidence loci were detected in both models. These loci included several candidate genes, such as IbMYB1, IbZEP1, and IbYABBY1, which might be involved in anthocyanin metabolism, carotenoid metabolism, and leaf morphogenesis, respectively. Among them, IbZEP1 and IbYABBY1 were first reported in sweetpotato. The variants in the promoter and the expression levels of IbZEP1 were significantly correlated with flesh color (orange or not orange) in sweetpotato. The expression levels of IbYABBY1 were also correlated with leaf shape. These results will assist in genetic and breeding studies in sweetpotato.

Identification of QTLs associated with multiple agronomic traits in Sorghum

Identification of QTLs associated with multiple agronomic traits in Sorghum

Genome-Wide Identification and Analysis of Ariadne Gene Family Reveal Its Genetic Effects on Agronomic Traits of Brassica napus.

E3 ligases promote protein ubiquitination and degradation, which regulate every aspect of eukaryotic life. The Ariadne (ARI) proteins of RBR (ring between ring fingers) protein subfamily has been discovered as a group of potential E3 ubiquitin ligases. Only a few available research studies show their role in plant adaptations processes against the external environment. Presently, the functions of ARI proteins are largely unknown in plants. Therefore, in this study, we performed genome-wide analysis to identify the ARI gene family and explore their potential importance in B. napus. A total of 39 ARI genes were identified in the B. napus genome and were classified into three subfamilies (A, B and C) based on phylogenetic analysis. The protein–protein interaction networks and enrichment analysis indicated that BnARI genes could be involved in endoreduplication, DNA repair, proteasome assembly, ubiquitination, protein kinase activity and stress adaptation. The transcriptome data analysis in various tissues provided us an indication of some BnARI genes’ functional importance in tissue development. We also identified potential BnARI genes that were significantly responsive towards the abiotic stresses. Furthermore, eight BnARI genes were identified as candidate genes for multiple agronomic traits through association mapping analysis in B. napus; among them, BnaA02g12100D, which is the ortholog of AtARI8, was significantly associated with ten agronomic traits. This study provided useful information on BnARI genes, which could aid targeted functional research and genetic improvement for breeding in B. napus.

Multiplex precision gene editing by a surrogate prime editor in rice

Multiplex precision gene editing by a surrogate prime editor in rice

A new gain-of-function OsGS2/GRF4 allele generated by CRISPR/Cas9 genome editing increases rice grain size and yield

Grain size is one of the most important factors affecting rice grain quality and yield, and attracts great attention from molecular biologists and breeders. In this study, we engineered a CRISPR/Cas9 system targeting the miR396 recognition site of the rice GS2 gene, which encodes growth-regulating factor 4 (OsGRF4) and regulates multiple agronomic traits including grain size, grain quality, nitrogen use efficiency, abiotic stress response, and seed shattering. In contrast to most previous genome editing efforts in which indel mutations were chosen to obtain null mutants, a mutant named GS2E carrying an in-frame 6-bp deletion and 1-bp substitution within the miR396-targeted sequence was identified. GS2E plants showed increased expression of GS2 in consistent with impaired repression by miR396. As expected, the gain-of-function GS2E mutant exhibited multiple beneficial traits including increased grain size and yield and bigger grain length/width ratio. Thousand grain weight and grain yield per plant of GS2E plants were increased by 23.5% and 10.4%, respectively. These improved traits were passed to hybrids in a semi-dominant way, suggesting that the new GS2E allele has great potential in rice improvement. Taken together, we report new GS2 germplasm and describe a novel gene-editing strategy that can be widely employed to improve grain size and yield in rice. This trait-improvement strategy could be applied to other genes containing miRNA target sites, in particular the conserved miR396-GRF/GIF module that governs plant growth, development and environmental response.

Simultaneous Improvement of Grain Yield and Quality through Manipulating Two Type C G Protein Gamma Subunits in Rice.

Heterotrimeric G protein signaling is an evolutionarily conserved mechanism in diverse organisms that mediates intracellular responses to external stimuli. In rice, the G proteins are involved in the regulation of multiple important agronomic traits. In this paper, we present our finding that two type C G protein gamma subunits, DEP1 and GS3, antagonistically regulated grain yield and grain quality. The DEP1 gene editing we conducted, significantly increased the grain number per panicle but had a negative impact on taste value, texture properties, and chalkiness-related traits. The GS3 gene editing decreased grain number per panicle but significantly increased grain length. In addition, the GS3 gene-edited plants showed improved taste value, appearance, texture properties, and Rapid Visco Analyser (RVA) profiles. To combine the advantages of both gs3 and dep1, we conducted a molecular design breeding at the GS3 locus of a “super rice” variety, SN265, which has a truncated dep1 allele with erect panicle architecture, high-yield performance, and which is of mediocre eating quality. The elongated grain size of the sn265/gs3 gene-edited plants further increased the grain yield. More importantly, the texture properties and RVA profiles were significantly improved, and the taste quality was enhanced. Beyond showcasing the combined function of dep1 and gs3, this paper presents a strategy for the simultaneous improvement of rice grain yield and quality through manipulating two type C G protein gamma subunits in rice.

A Study on Genotype-by-Environment Interaction Analysis for Agronomic Traits of Maize Genotypes Across Huang-Huai-Hai Region in China

Facing the trend of increasing population, how to increase maize grain yield is a very important issue to ensure food security. In this study, 28 nationally approved maize hybrids were evaluated across 24 different climatic conditions for two consecutive years (2018–2019). The purpose of this study was to select high-yield with stable genotypes and identify important agronomic traits for maize breeding program improvement. The results of this study showed that the genotype ╳ environment interaction effects of the 12 evaluated agronomic traits was highly significant (P < 0.001). We introduced a novel multi-trait genotype-ideotype distance index (MGIDI) to select genotypes based on multiple agronomic traits. The selection process exhibited by this method is unique and easy to understand, so the MGIDI index will have more and more important applications in future multi-environment trials (METs) research. The genotypes selected by the MGIDI index were G22, G10, G12 and G1 as the high yielding and stable genotypes. The parents of these selected genotypes have the ability to play a greater role as the basic germplasm in the breeding process. A new form of genotype (G) main effects and genotype (G) -by-environment (E) interaction (GGE) technician, genotype*yield*trait (GYT) biplot, based on multiple traits for genotypes selection was also applied in this study. The GYT biplot ranked genotypes by combining grain yield with other evaluated agronomic traits, and displayed the distribution of their traits, namely strengths and weaknesses.

Evaluation of drought tolerance in different genotypes of foxtail millet during the entire growth period

AbstractDrought significantly affects foxtail millet [Setaria italica (L.) Beauv.] yield, and its adverse effects can be mitigated via genetic improvement to generate drought‐tolerant varieties. This study aimed to screen drought‐tolerant materials and genes in foxtail millet germplasm resources to improve the efficiency of breeding for drought tolerance. A field experiment was conducted in a randomized incomplete block design (α‐lattice design) and repeated thrice with 30 foxtail millet genotypes treated under drought stress or normal water supply (control) for 2 yr. The agronomic traits and drought tolerance coefficient (DC) of each genotype were assessed during the entire growth period. The soil water environment and genotype significantly affected the indices. Moreover, the interaction between genotype and soil water environment significantly affected the growth traits of foxtail millet. A genotype plus genotype × environment interaction (GGE) biplot revealed mixed correlations among the DC indices. Various indices had different effects on the drought tolerance of foxtail millet. The drought tolerance performance and evaluation indices of foxtail millet were ranked according to the distance from the “ideal” drought tolerance genotype and index. The drought tolerance was classified into five categories according to the comprehensive evaluation index (D‐value) cluster analysis. Discriminant analysis showed that the plant height and spike weight could be used as indices for identifying drought tolerance identification in foxtail millet. The GGE biplot results were consistent with the results based on the D‐value. Therefore, multiple agronomic traits combined with D‐value as an evaluation parameter can effectively and accurately identify drought‐tolerant foxtail millet.

A study on genotype × environment interactions for the multiple traits of maize hybrids in China

AbstractThe correct interpretation of the adaptability and stability of maize (Zea mays L.) hybrids in different ecological environments is very important for plant breeders. Additive main effect and multiplicative interaction model and genotype main effects and genotype × environment interaction biplot are the two most popular methods in the analysis of genotype × environment interaction in multienvironment trials. We conducted an experiment designed to examine and evaluate the adaptability and stability of four agronomic traits of 19 tested maize genotypes in two consecutive growth cycles across seven provinces including 37 locations using a randomized completely block design with three replicates. The combined ANOVA for all traits showed that the effect of genotype, environment, and genotype × environment interaction were significant at 0.1% probability levels. In order to evaluate multiple agronomic traits more accurately, multitrait stability index (MTSI) as an emerging selection method based on mean performance and stability was adopted. Agronomic trait grain yield (GY) was positively correlated with grain weight per ear and growth period. In addition, it was also found that GY and bar tip length showed obvious negative correlation. The MTSI is very helpful for breeders who hope to select mean performance and stability based on a variety of agronomic traits because it provides a convenient selection process while taking into account the relevant results of the traits.