QTL Mapping for Phosphorus Efficiency and Morphological Traits at Seedling and Maturity Stages in Wheat

Unraveling the Mechanisms of Efficient Phosphorus Utilization in Popcorn (Zea mays L. var. everta): Insights from Proteomic and Metabolite Analysis

The expansion of agriculture and the need for sustainable practices drives breeders to develop plant varieties better adapted to abiotic stress such as nutrient deficiency, which negatively impacts yields. Phosphorus (P) is crucial for photosynthesis and plant growth, but its availability in the soil is often limited, hampering crop development. In this study, we examined the response of two popcorn inbred lines, L80 and P7, which have been characterized previously as P-use inefficient and P-use efficient, respectively, under low (stress) and high P (control) availability. Physiological measurements, proteomic analysis, and metabolite assays were performed to unravel the physiological and molecular responses associated with the efficient use of P in popcorn. We observed significant differences in protein abundances in response to the P supply between the two inbred lines. A total of 421 differentially expressed proteins (DEPs) were observed in L80 and 436 DEPs in P7. These proteins were involved in photosynthesis, protein biosynthesis, biosynthesis of secondary metabolites, and energy metabolism. In addition, flavonoids accumulated in higher abundance in P7. Our results help us understand the major components of P utilization in popcorn, providing new insights for popcorn molecular breeding programs.

Regulation of root growth and elongation in wheat

Currently, the control of rhizosphere selection on farms has been applied to achieve enhancements in phenotype, extending from improvements in single root characteristics to the dynamic nature of entire crop systems. Several specific signals, regulatory elements, and mechanisms that regulate the initiation, morphogenesis, and growth of new lateral or adventitious root species have been identified, but much more work remains. Today, phenotyping technology drives the development of root traits. Available models for simulation can support all phenotyping decisions (root trait improvement). The detection and use of markers for quantitative trait loci (QTLs) are effective for enhancing selection efficiency and increasing reproductive genetic gains. Furthermore, QTLs may help wheat breeders select the appropriate roots for efficient nutrient acquisition. Single-nucleotide polymorphisms (SNPs) or alignment of sequences can only be helpful when they are associated with phenotypic variation for root development and elongation. Here, we focus on major root development processes and detail important new insights recently generated regarding the wheat genome. The first part of this review paper discusses the root morphology, apical meristem, transcriptional control, auxin distribution, phenotyping of the root system, and simulation models. In the second part, the molecular genetics of the wheat root system, SNPs, TFs, and QTLs related to root development as well as genome editing (GE) techniques for the improvement of root traits in wheat are discussed. Finally, we address the effect of omics strategies on root biomass production and summarize existing knowledge of the main molecular mechanisms involved in wheat root development and elongation.

QTL Mapping and Candidate Gene Identifying for N, P, and K Use Efficiency at the Maturity Stages in Wheat

Nitrogen (N), phosphorus (P), and potassium (K) are the three most important mineral nutrients for crop growth and development. We previously constructed a genetic map of unigenes (UG-Map) based on their physical positions using a RIL population derived from the cross of "TN18 × LM6" (TL-RILs). In this study, a total of 18 traits related to mineral use efficiency (MUE) of N/P/K were investigated under three growing seasons using TL-RILs. A total of 54 stable QTLs were detected, distributed across 19 chromosomes except for 3A and 5B. There were 50 QTLs associated with only one trait, and the other four QTLs were associated with two traits. A total of 73 candidate genes for stable QTLs were identified. Of these, 50 candidate genes were annotated in Chinese Spring (CS) RefSeq v1.1. The average number of candidate genes per QTL was 1.35, with 45 QTLs containing only one candidate gene and nine QTLs containing two or more candidate genes. The candidate gene TraesCS6D02G132100 (TaPTR gene) for QGnc-6D-3306 belongs to the NPF (NRT1/PTR) gene family. We speculate that the TaPTR gene should regulate the GNC trait.

QTL Mapping of Agronomic and Physiological Traits at the Seedling and Maturity Stages under Different Nitrogen Treatments in Barley

Nitrogen (N) stress seriously constrains barley (Hordeum vulgare L.) production globally by influencing its growth and development. In this study, we used a recombinant inbred line (RIL) population of 121 crosses between the variety Baudin and the wild barley accession CN4027 to detect QTL for 27 traits at the seedling stage in hydroponic culture trials and 12 traits at the maturity stage in field trials both under two N treatments, aiming to uncover favorable alleles for N tolerance in wild barley. In total, eight stable QTL and seven QTL clusters were detected. Among them, the stable QTL Qtgw.sau-2H located in a 0.46 cM interval on the chromosome arm 2HL was a novel QTL specific for low N. Notably, Clusters C4 and C7 contained QTL for traits at both the seedling and maturity stages. In addition, four stable QTLs in Cluster C4 were identified. Furthermore, a gene (HORVU2Hr1G080990.1) related to grain protein in the interval of Qtgw.sau-2H was predicted. Correlation analysis and QTL mapping showed that different N treatments significantly affected agronomic and physiological traits at the seedling and maturity stages. These results provide valuable information for understanding N tolerance as well as breeding and utilizing the loci of interest in barley.

QTL cluster analysis and marker development for kernel traits based on DArT markers in spring bread wheat (Triticum aestivum L.)

Genetic dissection of yield component traits including kernel characteristics is essential for the continuous improvement in wheat yield. In the present study, one recombinant inbred line (RIL) F₆ population derived from a cross between Avocet and Chilero was used to evaluate the phenotypes of kernel traits of thousand-kernel weight (TKW), kernel length (KL), and kernel width (KW) in four environments at three experimental stations during the 2018-2020 wheat growing seasons. The high-density genetic linkage map was constructed with the diversity arrays technology (DArT) markers and the inclusive composite interval mapping (ICIM) method to identify the quantitative trait loci (QTLs) for TKW, KL, and KW. A total of 48 QTLs for three traits were identified in the RIL population on the 21 chromosomes besides 2A, 4D, and 5B, accounting for 3.00%-33.85% of the phenotypic variances. Based on the physical positions of each QTL, nine stable QTL clusters were identified in the RILs, and among these QTL clusters, TaTKW-1A was tightly linked to the DArT marker interval 3950546-1213099, explaining 10.31%-33.85% of the phenotypic variances. A total of 347 high-confidence genes were identified in a 34.74-Mb physical interval. TraesCS1A02G045300 and TraesCS1A02G058400 were among the putative candidate genes associated with kernel traits, and they were expressed during grain development. Moreover, we also developed high-throughput kompetitive allele-specific PCR (KASP) markers of TaTKW-1A, validated in a natural population of 114 wheat varieties. The study provides a basis for cloning the functional genes underlying the QTL for kernel traits and a practical and accurate marker for molecular breeding.

Multi-omics revolution to promote plant breeding efficiency

Crop production is the primary goal of agricultural activities, which is always taken into consideration. However, global agricultural systems are coming under increasing pressure from the rising food demand of the rapidly growing world population and changing climate. To address these issues, improving high-yield and climate-resilient related-traits in crop breeding is an effective strategy. In recent years, advances in omics techniques, including genomics, transcriptomics, proteomics, and metabolomics, paved the way for accelerating plant/crop breeding to cope with the changing climate and enhance food production. Optimized omics and phenotypic plasticity platform integration, exploited by evolving machine learning algorithms will aid in the development of biological interpretations for complex crop traits. The precise and progressive assembly of desire alleles using precise genome editing approaches and enhanced breeding strategies would enable future crops to excel in combating the changing climates. Furthermore, plant breeding and genetic engineering ensures an exclusive approach to developing nutrient sufficient and climate-resilient crops, the productivity of which can sustainably and adequately meet the world's food, nutrition, and energy needs. This review provides an overview of how the integration of omics approaches could be exploited to select crop varieties with desired traits.

Genome-wide association studies reveal putative QTLs for physiological traits under contrasting phosphorous conditions in wheat (Triticum aestivum L.)

A Genome-wide association (GWAS) study was conducted for phosphorous (P)-use responsive physiological traits in bread wheat at the seedling stage under contrasting P regimes. A panel of 158 diverse advanced breeding lines and released varieties, and a set of 10,800 filtered single nucleotide polymorphism (SNP) markers were used to study marker-trait associations over the eight shoot traits. Principle component analysis separated the two environments (P regimes) because of the differential response of the traits indicating the essentiality of the separate breeding programmes for each environment. Significant variations for genotypic, environmental, and genotype × environment (GEI) effects were observed for all the traits in the combined analysis of variance with moderately high broad sense heritability traits (0.50–0.73). With the different algorithms of association mapping viz., BLINK, FarmCPU, and MLM, 38 unique QTLs under non-limiting P (NLP) and 45 QTLs for limiting P (LP) conditions for various shoot traits were identified. Some of these QTLs were captured by all three algorithms. Interestingly, a Q.iari.dt.sdw.1 on chromosome 1D was found to explain the significant variations in three important physiological traits under non-limiting phosphorus (NLP) conditions. We identified the putative candidate genes for QTLs namely Q.iari.dt.chl.1, Q.iari.dt.sdw.16, Q.iari.dt.sdw.9 and Q.iari.dt.tpc.1 which are potentially involved in the mechanism regulating phosphorus use efficiency through improved P absorption due to improved root architectural traits and better mobilization such as sulfotransferase involved in postembryonic root development, WALLS ARE THIN1 (WAT1), a plant-specific protein that facilitates auxin export; lectin receptor-like kinase essentially involved in plant development, stress response during germination and lateral root development and F-box component of the SKP-Cullin-F box E3 ubiquitin ligase complex and strigolactone signal perception. Expression profiling of putative genes located in identified genomic regions against the wheat expression atlas revealed their significance based on the expression of these genes for stress response and growth development processes in wheat. Our results thus provide an important insight into understanding the genetic basis for improving PUE under phosphorus stress conditions and can shape the future breeding programme by developing and integrating molecular markers for these difficult-to-score important traits.

Prospects of genetics and breeding for low-phosphate tolerance: an integrated approach from soil to cell

Improving phosphorus (P) crop nutrition has emerged as a key factor toward achieving a more resilient and sustainable agriculture. P is an essential nutrient for plant development and reproduction, and phosphate (Pi)-based fertilizers represent one of the pillars that sustain food production systems. To meet the global food demand, the challenge for modern agriculture is to increase food production and improve food quality in a sustainable way by significantly optimizing Pi fertilizer use efficiency. The development of genetically improved crops with higher Pi uptake and Pi-use efficiency and higher adaptability to environments with low-Pi availability will play a crucial role toward this end. In this review, we summarize the current understanding of Pi nutrition and the regulation of Pi-starvation responses in plants, and provide new perspectives on how to harness the ample repertoire of genetic mechanisms behind these adaptive responses for crop improvement. We discuss on the potential of implementing more integrative, versatile, and effective strategies by incorporating systems biology approaches and tools such as genome editing and synthetic biology. These strategies will be invaluable for producing high-yielding crops that require reduced Pi fertilizer inputs and to develop a more sustainable global agriculture.

ATP-dependent DNA helicase (TaDHL), a Novel Reduced-Height (Rht) Gene in Wheat

In wheat, a series of dwarf and semi-dwarf plant varieties have been developed and utilized worldwide since the 1960s and caused the ‘Green Revolution’. To date, 25 reduced-height (Rht) genes have been identified, but only several genes for plant height (PH) have been isolated previously. In this study, we identified a candidate gene, ATP-dependent DNA helicase (TaDHL-7B), for PH via QTL mapping and genome-wide association study (GWAS) methods. We knocked out this gene using the CRISPR/Cas9 system in variety ‘Fielder’. Two homozygous mutant genotypes, AAbbDD (−5 bp) and AAbbDD (−1 bp), were obtained in the T2 generation. The PH values of AAbbDD (−5 bp) and AAbbDD (−1 bp) were significantly reduced compared with the wild-type (WT, ‘Fielder’), indicating that TaDHL-7B is a novel Rht gene that controls the PH. This is the first time that a PH gene of wheat has been isolated with a non-hormone pathway, providing a new insight into the genetic control of PH. The TaDHL gene reduced the PH without a yield penalty. It could be used to improve the lodging resistance and yield in wheat breeding programs.

Role of Wheat Phosphorus Starvation Tolerance 1 Genes in Phosphorus Acquisition and Root Architecture

The wheat plant requires elevated phosphorus levels for its normal growth and yield, but continuously depleting non-renewable phosphorus reserves in the soil is one of the biggest challenges in agricultural production worldwide. The Phosphorus Starvation Tolerance 1 (PSTOL1) gene has been reported to play a key role in efficient P uptake, deeper rooting, and high yield in rice. However, the function of the PSTOL1 gene in wheat is still unclear. In this study, a total of 22 PSTOL1 orthologs were identified in the wheat genome, and found that wheat PSTOL1 orthologs are unevenly distributed on chromosomes, and these genes were under strong purifying selection. Under different phosphorus regimes, wheat PSTOL1 genes showed differential expression patterns in different tissues. These results strengthen the classification of Pakistan-13 as a P-efficient cultivar and Shafaq-06 as a P-inefficient cultivar. Phenotypic characterization demonstrated that Pakistan-13 wheat cultivar has significantly increased P uptake, root length, root volume, and root surface area compared to Shafaq-06. Some wheat PSTOL1 orthologs are co-localized with phosphorus starvation’s related quantitative trait loci (QTLs), suggesting their potential role in phosphorus use efficiency. Altogether, these results highlight the role of the wheat PSTOL1 genes in wheat P uptake, root architecture, and efficient plant growth. This comprehensive study will be helpful for devising sustainable strategies for wheat crop production and adaptation to phosphorus insufficiency.

Comparison of different selection traits for identification of phosphorus use efficient lines in mungbean

Phosphorus (P) is one of the major constraints for crop growth and development, owing to low availability and least mobility in many tropical soil conditions. Categorization of existing germplasm under P deficient conditions is a prerequisite for the selection and development of P efficient genotypes in the mungbean. In the present investigation, 36 diverse genotypes were categorized for phosphorus use efficiency traits using four different techniques for identification of phosphorus use efficient mungbean genotypes. The studied genotypes were categorized for P efficiency based on efficiency, responsiveness, and stress tolerance score of genotypes under normal and low P conditions. The mean values of traits, root dry mass, root to shoot ratio, and P utilization efficiency are significantly higher under low P conditions indicating the high responsiveness of traits to P deficiency. The presence of significant interaction between genotypes and P treatment indicates the evaluated genotypes were significantly affected by P treatment for studied traits. The total P uptake showed significant and positive correlations with root dry mass, shoot dry mass, total dry mass,and P concentration under both P regimes. Out of the four techniques used for the categorization of genotypes for P efficiency, three techniques revealed that the genotype PUSA 1333, followed by Pusa Vishal, PUSA 1031, and Pusa Ratna is efficient. The categorization based on stress tolerance score is the finest way to study variation and for the selection of contrasting genotypes for P efficiency. The identified P efficient genotypes would be valuable resources for genetic enhancement of P use efficiency in mungbean breeding.

Deciphering the change in root system architectural traits under limiting and non-limiting phosphorus in Indian bread wheat germplasm

The root system architectures (RSAs) largely decide the phosphorus use efficiency (PUE) of plants by influencing the phosphorus uptake. Very limited information is available on wheat's RSAs and their deciding factors affecting phosphorus uptake efficiency (PupE) due to difficulties in adopting scoring values used for evaluating root traits. Based on our earlier research experience on nitrogen uptake efficiency screening under, hydroponics and soil-filled pot conditions, a comprehensive study on 182 Indian bread wheat genotypes was carried out under hydroponics with limited P (LP) and non-limiting P (NLP) conditions. The findings revealed a significant genetic variation, root traits correlation, and moderate to high heritability for RSAs traits namely primary root length (PRL), total root length (TRL), total root surface area (TSA), root average diameter (RAD), total root volume (TRV), total root tips (TRT) and total root forks (TRF). In LP, the expressions of TRL, TRV, TSA, TRT and TRF were enhanced while PRL and RAD were diminished. An almost similar pattern of correlations among the RSAs was also observed in both conditions except for RAD. RAD exhibited significant negative correlations with PRL, TRL, TSA, TRT and TRF under LP (r = -0.45, r = -0.35, r = -0.16, r = -0.30, and r = -0.28 respectively). The subclass of TRL, TSA, TRV and TRT representing the 0-0.5 mm diameter had a higher root distribution percentage in LP than NLP. Comparatively wide range of H' value i.e. 0.43 to 0.97 in LP than NLP indicates that expression pattern of these traits are highly influenced by the level of P. In which, RAD (0.43) expression was reduced in LP, and expressions of TRF (0.91) and TSA (0.97) were significantly enhanced. The principal component analysis for grouping of traits and genotypes over LP and NLP revealed a high PC1 score indicating the presence of non-crossover interactions. Based on the comprehensive P response index value (CPRI value), the top five highly P efficient wheat genotypes namely BW 181, BW 103, BW 104, BW 143 and BW 66, were identified. Considering the future need for developing resource-efficient wheat varieties, these genotypes would serve as valuable genetic sources for improving P efficiency in wheat cultivars. This set of genotypes would also help in understanding the genetic architecture of a complex trait like P use efficiency.

Proteome characterization of two contrasting soybean genotypes in response to different phosphorus treatments

Phosphorus (P) is an essential element for the growth and development of plants. Soybean (Glycine max) is an important food crop that is grown worldwide. Soybean yield is significantly affected by P deficiency in the soil. To investigate the molecular factors that determine the response and tolerance at low-P in soybean, we conducted a comparative proteomics study of a genotype with low-P tolerance (Liaodou 13, L13) and a genotype with low-P sensitivity (Tiefeng 3, T3) in a paper culture experiment with three P treatments, i.e. P-free (0 mmol·L-1), low-P (0.05 mmol·L-1) and normal-P (0.5 mmol·L-1). A total of 4126 proteins were identified in roots of the two genotypes. Increased numbers of differentially expressed proteins (DEPs) were obtained from low-P to P-free conditions compared to the normal-P treatment. All DEPs obtained in L13 (660) were upregulated in response to P deficiency, while most DEPs detected in T3 (133) were downregulated under P deficiency. Important metabolic pathways such as oxidative phosphorylation, glutathione metabolism and carbon metabolism were suppressed in T3, which could have affected the survival of the plants in P-limited soil. In contrast, L13 increased the metabolic activity in the 2-oxocarboxylic acid metabolism, carbon metabolism, glycolysis, biosynthesis of amino acids, pentose phosphatase, oxidative phosphorylation, other types of O-glycan biosynthesis and riboflavin metabolic pathways in order to maintain normal plant growth under P deficiency. Three key proteins I1KW20 (prohibitins), I1K3U8 (alpha-amylase inhibitors) and C6SZ93 (alpha-amylase inhibitors) were suggested as potential biomarkers for screening soybean genotypes with low-P tolerance. Overall, this study provides new insights into the response and tolerance to P deficiency in soybean.

Population structure and genome-wide association studies in bread wheat for phosphorus efficiency traits using 35 K Wheat Breeder's Affymetrix array

Soil bioavailability of phosphorus (P) is a major concern for crop productivity worldwide. As phosphatic fertilizers are a non-renewable resource associated with economic and environmental issues so, the sustainable option is to develop P use efficient crop varieties. We phenotyped 82 diverse wheat (Triticum aestivum L.) accessions in soil and hydroponics at low and sufficient P. To identify the genic regions for P efficiency traits, the accessions were genotyped using the 35 K-SNP array and genome-wide association study (GWAS) was performed. The high-quality SNPs across the genomes were evenly distributed with polymorphic information content values varying between 0.090 and 0.375. Structure analysis revealed three subpopulations (C1, C2, C3) and the phenotypic responses of these subpopulations were assessed for P efficiency traits. The C2 subpopulation showed the highest genetic variance and heritability values for numerous agronomically important traits as well as strong correlation under both P levels in soil and hydroponics. GWAS revealed 78 marker-trait associations (MTAs) but only 35 MTAs passed Bonferroni Correction. A total of 297 candidate genes were identified for these MTAs and their annotation suggested their involvement in several biological process. Out of 35, nine (9) MTAs were controlling polygenic trait (two controlling four traits, one controlling three traits and six controlling two traits). These multi-trait MTAs (each controlling two or more than two correlated traits) could be utilized for improving bread wheat to tolerate low P stress through marker-assisted selection (MAS).

QTL mapping of root traits in wheat under different phosphorus levels using hydroponic culture

Background

Phosphorus (P) is an important in ensuring plant morphogenesis and grain quality, therefore an efficient root system is crucial for P-uptake. Identification of useful loci for root morphological and P uptake related traits at seedling stage is important for wheat breeding. The aims of this study were to evaluate phenotypic diversity of Yangmai 16/Zhongmai 895 derived doubled haploid (DH) population for root system architecture (RSA) and biomass related traits (BRT) in different P treatments at seedling stage using hydroponic culture, and to identify QTL using 660 K SNP array based high-density genetic map.

Results

All traits showed significant variations among the DH lines with high heritabilities (0.76 to 0.91) and high correlations (r = 0.59 to 0.98) among all traits. Inclusive composite interval mapping (ICIM) identified 34 QTL with 4.64–20.41% of the phenotypic variances individually, and the log of odds (LOD) values ranging from 2.59 to 10.43. Seven QTL clusters (C1 to C7) were mapped on chromosomes 3DL, 4BS, 4DS, 6BL, 7AS, 7AL and 7BL, cluster C5 on chromosome 7AS (AX-109955164 - AX-109445593) with pleiotropic effect played key role in modulating root length (RL), root tips number (RTN) and root surface area (ROSA) under low P condition, with the favorable allele from Zhongmai 895.

Conclusions

This study carried out an imaging pipeline-based rapid phenotyping of RSA and BRT traits in hydroponic culture. It is an efficient approach for screening of large populations under different nutrient conditions. Four QTL on chromosomes 6BL (2) and 7AL (2) identified in low P treatment showed positive additive effects contributed by Zhongmai 895, indicating that Zhongmai 895 could be used as parent for P-deficient breeding. The most stable QTL QRRS.caas-4DS for ratio of root to shoot dry weight (RRS) harbored the stable genetic region with high phenotypic effect, and QTL clusters on 7A might be used for speedy selection of genotypes for P-uptake. SNPs closely linked to QTLs and clusters could be used to improve nutrient-use efficiency.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07425-4.

Identification of genetic factors controlling phosphorus utilization efficiency in wheat by genome-wide association study with principal component analysis

Despite the economic importance of P utilization efficiency, information on genetic factors underlying this trait remains elusive. To address that, we performed a genome-wide association study in a spring wheat diversity panel ranging from landraces to elite varieties. We evaluated the phenotype variation for P utilization efficiency in controlled conditions and genotype variation using wheat 90 K SNP array. Phenotype variables were transformed into a smaller set of uncorrelated principal components that captured the most important variation data. We identified two significant loci associated with both P utilization efficiency and the 1st principal component on chromosomes 3A and 4A: qPE1-3A and qPE2-4A. Annotation of genes at these loci revealed 53 wheat genes, among which 6 were identified in significantly enriched pathways. The expression pattern of these 6 genes indicated that TraesCS4A02G481800, involved in pyruvate metabolism and TCA cycle, had a significantly higher expression in the P efficient variety under limited P conditions. Further characterization of these loci and candidate genes can help stimulate P utilization efficiency in wheat.

Genome-Wide Association Analysis for Phosphorus Use Efficiency Traits in Mungbean (Vigna radiata L. Wilczek) Using Genotyping by Sequencing Approach

Mungbean (Vigna radiata L. Wilczek) is an annual grain legume crop affected by low availability of phosphorus. Phosphorus deficiency mainly affects the growth and development of plants along with changes in root morphology and increase in root-to-shoot ratio. Deciphering the genetic basis of phosphorus use efficiency (PUE) traits can benefit our understanding of mungbean tolerance to low-phosphorus condition. To address this issue, 144 diverse mungbean genotypes were evaluated for 12 PUE traits under hydroponics with optimum- and low-phosphorus levels. The broad sense heritability of traits ranged from 0.63 to 0.92 and 0.58 to 0.92 under optimum- and low-phosphorus conditions, respectively. This study, reports for the first time such a large number of genome wide Single nucleotide polymorphisms (SNPs) (76,160) in mungbean. Further, genome wide association study was conducted using 55,634 SNPs obtained by genotyping-by-sequencing method. The results indicated that total 136 SNPs shared by both GLM and MLM models were associated with tested PUE traits under different phosphorus regimes. We have identified SNPs with highest p value (-log10(p)) for some traits like, TLA and RDW with p value (-log10(p)) of more than 6.0 at LP/OP and OP condition. We have identified nine SNPs (three for TLA and six for RDW trait) which was found to be present in chromosomes 8, 4, and 7. One SNP present in Vradi07g06230 gene contains zinc finger CCCH domain. In total, 71 protein coding genes were identified, of which 13 genes were found to be putative candidate genes controlling PUE by regulating nutrient uptake and root architectural development pathways in mungbean. Moreover, we identified three potential candidate genes VRADI11G08340, VRADI01G05520, and VRADI04G10750 with missense SNPs in coding sequence region, which results in significant variation in protein structure at tertiary level. The identified SNPs and candidate genes provide the essential information for genetic studies and marker-assisted breeding program for improving low-phosphorus tolerance in mungbean.

Novel QTL Conferring Phosphorus Acquisition and Utilization Efficiencies in Barley

Phosphorus (P) deficiency in agricultural soil is a major constraint for crop production and increasing P acquisition efficiency (PAE) of plants is considered as one of the most cost-effective solutions for yield increase. The objective of this study was to detect quantitative trait loci (QTL) controlling (PAE) and P utilization efficiency (PUE) in barley under applied (+P) and non-applied P (-P) conditions. Based on the analysis of a recombinant inbred lines (RILs) population derived from a cross between a malting barley variety and a wild barley accession, 17 QTL controlling PAE, PUE and yield traits were detected. The phenotypic variation explained by each of these QTL ranges from 11.0 to 24.7%. Significant correlation was detected between most of P-related traits and yield traits. Five QTL clusters were identified on four different chromosomes (1H, 3H, 5H, and 7H). Two of the QTL clusters, located on chromosome 1H (for GPUP/PUP) and 7H (for SPUE/SPC), respectively, are novel. Fourteen genes located in the interval harboring the major QTL were identified as candidates associated with P efficiency. The stable QTL for PAE, PUE and yield-related traits could be important for breeding P-efficient barley varieties.

Phenotypic and genetic variation in phosphorus-deficiency-tolerance traits in Chinese wheat landraces

BACKGROUND

Phosphorus deficiency is a major limiting factors for affecting crop production globally. To understand the genetic variation of phosphorus-deficiency-tolerance, a total of 15 seedling traits were evaluated among 707 Chinese wheat landraces under application of phosphorus (AP) and non-application of phosphorus (NP). A total of 18,594 single-nucleotide polymorphisms and 38,678 diversity arrays technology sequencing markers were used to detect marker-trait associations under AP and NP.

RESULTS

Top ten genotypes with extremely tolerance and bottommost ten genotypes with extremely sensitivity were selected from 707 Chinese wheat landraces for future breeding and genetic analysis. A total of 55 significant markers (81 marker-trait associations) for 13 traits by both CMLM and SUPER method. These were distributed on chromosomes 1A, 1B, 2A, 2B, 2D, 3A, 4B, 5A, 5B, 6A, 6B, 6D, 7A and 7B. Considering the linkage disequilibrium decay distance, 25 and 12 quantitative trait loci (QTL) were detected under AP and NP, respectively (9 QTL were specific to NP).

CONCLUSIONS

The extremely tolerant landraces could be used for breeding phosphorus-deficiency-tolerant cultivars. The QTL could be useful in wheat breeding through marker-assisted selection. Our findings provide new insight into the genetic analysis of P-deficiency-tolerance, and will be helpful for breeding P-deficiency-tolerant cultivars.

Genome-wide identification and expression analysis of YTH domain-containing RNA-binding protein family in common wheat

BACKGROUND

N6-Methyladenosine (m6A) is the most widespread RNA modification that plays roles in the regulation of genes and genome stability. YT521-B homology (YTH) domain-containing RNA-binding proteins are important RNA binding proteins that affect the fate of m6A-containing RNA by binding m6A. Little is known about the YTH genes in common wheat (Triticum aestivum L.), one of the most important crops for humans.

RESULTS

A total of 39 TaYTH genes were identified in common wheat, which are comprised of 13 homologous triads, and could be mapped in 18 out of the 21 chromosomes. A phylogenetic analysis revealed that the TaYTHs could be divided into two groups: YTHDF (TaDF) and YTHDC (TaDC). The TaYTHs in the same group share similar motif distributions and domain organizations, which indicates functional similarity between the closely related TaYTHs. The TaDF proteins share only one domain, which is the YTH domain. In contrast, the TaDCs possess three C3H1-type zinc finger repeats at their N-termini in addition to their central YTH domain. In TaDFs, the predicated aromatic cage pocket that binds the methylysine residue of m6A is composed of tryptophan, tryptophan, and tryptophan (WWW). In contrast, the aromatic cage pocket in the TaDCs is composed of tryptophan, tryptophan, and tyrosine (WWY). In addition to the general aspartic acid or asparagine residue used to form a hydrogen bond with N¹ of m6A, histidine might be utilized in some TaDFb proteins. An analysis of the expression using both online RNA-Seq data and quantitative real-time PCR verification revealed that the TaDFa and TaDFb genes are highly expressed in various tissues/organs compared with that of TaDFcs and TaDCs. In addition, the expression of the TaYTH genes is changed in response to various abiotic stresses.

CONCLUSIONS

In this study, we identified 39 TaYTH genes from common wheat. The phylogenetic structure, chromosome distribution, and patterns of expression of these genes and their protein structures were analyzed. Our results provide a foundation for the functional analysis of TaYTHs in the future.

Genetic analysis and fine mapping of phosphorus efficiency locus 1 (PE1) in soybean

KEY MESSAGE

PE1 is a valuable locus synergistically regulating both P acquisition and utilization efficiency. Phosphorus (P) is required for crop production, particularly for soybean, due to its high protein and oil contents, and large demands for P in biological nitrogen fixation. Therefore, enhancing P efficiency is a practical and important target for soybean-breeding programs; however, the genetic mechanisms are still unclear. Previously, we identified a phosphorus efficiency locus 1 (PE1) in soybean through field evaluation. Here, fine mapping of PE1 was conducted in field using an expanded RIL population containing 168 F9:11 families derived from the same parents, BX10 and BD2. A high-resolution genetic map covering a 67.39 cM genetic region in a ~ 20.1 M physical region was constructed using 117 bin markers from chromosome 11, and scaffolds-21 and -32. The results revealed that PE1 was comprised of 15 QTLs for 11 of 18 tested traits, all of which could be detected under both P-deficient and P-sufficient conditions. Through map-based cloning, PE1 was further delimited to a 200-kb region located on scaffold-32, where 16 candidate genes were predicted for the PE1 locus. A set of NILs were also evaluated in P-deficient field conditions, with the results that P content and grain yield were 27.9% and 74.8% higher, respectively, and 25.4% more P was allocated to reproductive tissues in #pe1 than in #PE1 plants. The results herein suggest that PE1 is a valuable locus underlying both P absorption and utilization efficiency, which may be directly applicable in breeding programs seeking to develop elite P-efficient soybean varieties.

The Hot QTL Locations for Potassium, Calcium, and Magnesium Nutrition and Agronomic Traits at Seedling and Maturity Stages of Wheat under Different Potassium Treatments

Potassium (K) is one of the most important mineral nutrients for wheat. In this study, the effects of low K (LK) treatments and the quantitative trait loci (QTLs) for K, calcium (Ca), and magnesium (Mg) use efficiency traits, both at the seedling and maturity stages of wheat, were investigated. The set of “Tainong 18 × Linmai 6” recombinant inbred lines (RILs) were used to identify the QTLs under different K treatments using hydroponic culture and field trials. The majority of K concentrations and content-related traits at seedling and maturity stages decreased with reduced K supply, but the K use efficiency-related traits increased. In contrast, with reduced K supply, the contents of Ca and Mg increased, while the Ca and Mg use efficiency decreased. A total of 217 QTLs for seedling traits and 89 QTLs for adult traits were detected. Four relatively high-frequency QTLs (RHF-QTLs) and 18 QTL clusters (colocation of QTLs for more than two traits) were detected. Eight clusters were detected for K-, Ca-, and Mg-related traits simultaneously. This means that these traits might be controlled by the same QTL. In addition, we highlight that 4B might be an important chromosome regulating the nutrition of K, Ca, and Mg in wheat. The 4B chromosome and four hot QTL clusters, which located 45 QTLs, might be important potential targets for further investigation.

Phosphorus acquisition efficiency and phosphorus remobilization mediate genotype-specific differences in shoot phosphorus content in grapevine

Crop productivity is limited by phosphorus (P) and this will probably increase in the future. Rootstocks offer a means to increase the sustainability and nutrient efficiency of agriculture. It is known that rootstocks alter petiole P concentrations in grapevine. The objective of this work was to determine which functional processes are involved in genotype-specific differences in scion P content by quantifying P uptake, P remobilization from the reserves in the cutting and P allocation within the plant in three grapevine genotypes. Cuttings of two American rootstocks and one European scion variety were grown in sand and irrigated with a nutrient solution containing either high P (0.6 mM) or low P (0 mM). The high P solution was labelled with 32P throughout the experiment. The grapevine genotypes studied show variation in the inhibition of shoot and root biomass in response to low P supply, and P supply also affected shoot, but not root, P concentrations. Genotype-specific differences in total P content were related to differences in P acquisition and utilization efficiencies (PAE and PUE, respectively). Phosphorus allocation within the plant was not affected by genotype or P supply. The rootstock genotype known to confer high petiole P content in the vineyard was associated with a high PAE under high P, and a high PUE under low P. This suggests that the petiole P concentrations in the vineyard are related to genotype-specific differences in PAE and PUE, and that these traits could be used for rootstock selection programmes in the future.

Quantitative trait locus analysis of adventitious and lateral root morphology of barley grown at low and high P

Barley (Hordeum vulgare L) may alter its root morphology to improve P acquisition efficiency under low-P (LP) stress. This research studied the variations in adventitious and lateral root morphological traits of barley and mapped their quantitative trait loci (QTLs) under LP and high P (HP). The recombinant inbred lines were derived from the F1 population of a cross between CN4027 and Baudin. Two experiments aimed to identify QTLs related to adventitious and lateral root morphological traits under LP and HP. The length, surface area and volume of adventitious and lateral roots were measured. Under HP, Baudin had larger root morphology, especially lateral root morphology, than CN4027. LP stress induced lateral root growth but inhibited adventitious root growth. Nineteen QTLs for root morphological traits were detected. These QTLs clustered within four regions (Cl-2H, Cl-3H, Cl-4H and Cl-7H) on chromosomes 2H, 3H, 4H and 7H, with corresponding contributions of 12.0-42.9%. Some QTLs are linked with the QTLs for P efficiency detected previously, demonstrating the role of root morphological traits in P efficiency. The Cl-2H region was identified in the interval bPb3927665-bPb3265744 on chromosome 2H and had major effects on lateral root growth, especially under LP. Lateral root length and surface area increased when alleles from Baudin were present at the QTLs in Cl-2H. This study demonstrated the patterns of growth among root types and the role of lateral roots in barley's adaption to LP stress. The QTL clusters, especially Cl-2H, may offer clues for fine mapping and map-based cloning.

Utilization of a Wheat55K SNP Array for Mapping of Major QTL for Temporal Expression of the Tiller Number

Maximum tiller number and productive tiller number are important traits for wheat grain yield, but research involving the temporal expression of tiller number at different quantitative trait loci (QTL) levels is limited. In the present study, a population set of 371 recombined inbred lines derived from a cross between Chuan-Nong18 and T1208 was used to construct a high-density genetic map using a Wheat55K SNP Array and to perform dynamic QTL analysis of the tiller number at four growth stages. A high-density genetic map containing 11,583 SNP markers and 59 SSR markers that spanned 4,513.95 cM and was distributed across 21 wheat chromosomes was constructed. A total of 28 single environmental QTL were identified in the recombined inbred lines population, and among these, seven QTL were stable and used for multi-environmental and dynamic analysis. These QTL were mapped to chromosomes 2D, 4A, 4D, 5A, 5D, and 7D, respectively. Each QTL explained 1.63-21.22% of the observed phenotypic variation, with an additive effect from -20.51 to 11.59. Dynamic analysis showed that cqTN-2D.2 can be detected at four growth stages of tillering, explaining 4.92-17.16% of the observed phenotypic variations and spanning 13.71 Mb (AX-109283238-AX-110544009: 82189047-95895626) according to the physical location of the flanking markers. The effects of the stable QTL were validated in the recombined inbred lines population, and the beneficial alleles could be utilized in future marker-assisted selection. Several candidate genes for MTN and PTN were predicted. The results provide a better understanding of the QTL selectively expressing the control of tiller number and will facilitate future map-based cloning. 9.17% SNP markers showed best hits to the Chinese Spring contigs. It was indicated that Wheat55K Array was efficient and valid to construct a high-density wheat genetic map.

Characterization of QTLs for Root Traits of Wheat Grown under Different Nitrogen and Phosphorus Supply Levels

Root is important in acquiring nutrients from soils. Developing marker-assisted selection for wheat root traits can help wheat breeders to select roots desirable for efficient acquisition of nutrients. A recombinant inbred line (RIL) population derived from wheat varieties Xiaoyan 54 and Jing 411 was used to detect QTLs for maximum root length and root dry weight (RDW) under control, low nitrogen and low phosphorus conditions in hydrophobic culture (HC). We totally detected 17 QTLs for the investigated root traits located at 13 loci on 11 chromosomes. These loci differentially expressed under different nutrient supplying levels. The RILs simultaneously harboring positive alleles or negative alleles of the most significant three QTLs for RDW, qRDW.CK-2A, qRDW.CK-2D, and qRDW.CK-3B, were selected for soil column culture (SC) trial to verify the effects of these QTLs under soil conditions. The RILs pyramiding the positive alleles not only had significantly higher shoot dry weight, RDW, nitrogen and phosphorus uptake in all the three treatments of the HC trial, but also had significantly higher RDW distribution in both the top- and sub-soils in the SC trial than those pyramiding the negative alleles. These results suggested that QTL analysis based on hydroponic culture can provide useful information for molecular design of wheat with large and deep root system.

QTL mapping of root traits in phosphorus-deficient soils reveals important genomic regions for improving NDVI and grain yield in barley

Major QTLs for root rhizosheath size are not correlated with grain yield or yield response to phosphorus. Important QTLs were found to improve phosphorus efficiency. Root traits are important for phosphorus (P) acquisition, but they are often difficult to characterize and their breeding values are seldom assessed under field conditions. This has shed doubts on using seedling-based criteria of root traits to select and breed for P efficiency. Eight root traits were assessed under controlled conditions in a barley doubled-haploid population in soils differing in P levels. The population was also phenotyped for grain yield, normalized difference vegetation index (NDVI), grain P uptake and P utilization efficiency at maturity (PutE_GY) under field conditions. Several quantitative traits loci (QTLs) from the root screening and the field trials were co-incident. QTLs for root rhizosheath size and root diameter explained the highest phenotypic variation in comparison to QTLs for other root traits. Shared QTLs were found between root diameter and grain yield, and total root length and PutE_GY. A common major QTL for rhizosheath size and NDVI was mapped to the HvMATE gene marker on chromosome 4H. Collocations between major QTLs for NDVI and grain yield were detected on chromosomes 6H and 7H. When results from BIP and MET were combined, QTLs detected for grain yield were also those QTLs found for NDVI. QTLs qGY5H, qGY6H and qGY7Hb on 7H were robust QTLs in improving P efficiency. A selection of multiple loci may be needed to optimize the breeding outcomes due to the QTL x Environment interaction. We suggest that rhizosheath size alone is not a reliable trait to predict P efficiency or grain yield.

Identification of putative QTLs for seedling stage phosphorus starvation response in finger millet (Eleusine coracana L. Gaertn.) by association mapping and cross species synteny analysis

A germplasm assembly of 128 finger millet genotypes from 18 countries was evaluated for seedling-stage phosphorus (P) responses by growing them in P sufficient (Psuf) and P deficient (Pdef) treatments. Majority of the genotypes showed adaptive responses to low P condition. Based on phenotype behaviour using the best linear unbiased predictors for each trait, genotypes were classified into, P responsive, low P tolerant and P non-responsive types. Based on the overall phenotype performance under Pdef, 10 genotypes were identified as low P tolerants. The low P tolerant genotypes were characterised by increased shoot and root length and increased root hair induction with longer root hairs under Pdef, than under Psuf. Association mapping of P response traits using mixed linear models revealed four quantitative trait loci (QTLs). Two QTLs (qLRDW.1 and qLRDW.2) for low P response affecting root dry weight explained over 10% phenotypic variation. In silico synteny analysis across grass genomes for these QTLs identified putative candidate genes such as Ser-Thr kinase and transcription factors such as WRKY and basic helix-loop-helix (bHLH). The QTLs for response under Psuf were mapped for traits such as shoot dry weight (qHSDW.1) and root length (qHRL.1). Putative associations of these QTLs over the syntenous regions on the grass genomes revealed proximity to cytochrome P450, phosphate transporter and pectin methylesterase inhibitor (PMEI) genes. This is the first report of the extent of phenotypic variability for P response in finger millet genotypes during seedling-stage, along with the QTLs and putative candidate genes associated with P starvation tolerance.