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

Identifying the physiological traits associated with DNA marker using genome wide association in wheat under heat stress

Heat stress poses a significant environmental challenge that profoundly impacts wheat productivity. It disrupts vital physiological processes such as photosynthesis, by impeding the functionality of the photosynthetic apparatus and compromising plasma membrane stability, thereby detrimentally affecting grain development in wheat. The scarcity of identified marker trait associations pertinent to thermotolerance presents a formidable obstacle in the development of marker-assisted selection strategies against heat stress. To address this, wheat accessions were systematically exposed to both normal and heat stress conditions and phenotypic data were collected on physiological traits including proline content, canopy temperature depression, cell membrane injury, photosynthetic rate, transpiration rate (at vegetative and reproductive stage and 'stay-green'. Principal component analysis elucidated the most significant contributors being proline content, transpiration rate, and canopy temperature depression, which exhibited a synergistic relationship with grain yield. Remarkably, cluster analysis delineated the wheat accessions into four discrete groups based on physiological attributes. Moreover, to explore the relationship between physiological traits and DNA markers, 158 wheat accessions were genotyped with 186 SSRs. Allelic frequency and polymorphic information content value were found to be highest on genome A (4.94 and 0.688), chromosome 1A (5.00 and 0.712), and marker Xgwm44 (13.0 and 0.916). Population structure, principal coordinate analysis and cluster analysis also partitioned the wheat accessions into four subpopulations based on genotypic data, highlighting their genetic homogeneity. Population diversity and presence of linkage disequilibrium established the suitability of population for association mapping. Additionally, linkage disequilibrium decay was most pronounced within a 15-20 cM region on chromosome 1A. Association mapping revealed highly significant marker trait associations at Bonferroni correction P < 0.00027. Markers Xwmc418 (located on chromosome 3D) and Xgwm233 (chromosome 7A) demonstrated associations with transpiration rate, while marker Xgwm494 (chromosome 3A) exhibited an association with photosynthetic rates at both vegetative and reproductive stages under heat stress conditions. Additionally, markers Xwmc201 (chromosome 6A) and Xcfa2129 (chromosome 1A) displayed robust associations with canopy temperature depression, while markers Xbarc163 (chromosome 4B) and Xbarc49 (chromosome 5A) were strongly associated with cell membrane injury at both stages. Notably, marker Xbarc49 (chromosome 5A) exhibited a significant association with the 'stay-green' trait under heat stress conditions. These results offers the potential utility in marker-assisted selection, gene pyramiding and genomic selection models to predict performance of wheat accession under heat stress conditions.

Genome-wide association studies dissect low-phosphorus stress response genes underling field and seedling traits in maize

Phosphorus (P) is an essential element for plant growth, and its deficiency can cause decreased crop yield. This study systematically evaluated the low-phosphate (Pi) response traits in a large population at maturity and seedling stages, and explored candidate genes and their interrelationships with specific traits. The results revealed a greater sensitivity of seedling maize to low-Pi stress compared to that at maturity stage. The phenotypic response patterns to low-Pi stress at different stages were independent. Chlorophyll content was found to be a potential indicator for screening low-Pi-tolerant materials in the field. A total of 2900 and 1446 significantly associated genes at the maturity and seedling stages were identified, respectively. Among these genes, 972 were uniquely associated with maturity traits, while 330 were specifically detected at the seedling stage under low-Pi stress. Moreover, 768 and 733 genes were specifically associated with index values (low-Pi trait/normal-Pi trait) at maturity and seedling stage, respectively. Genetic network diagrams showed that the low-Pi response gene Zm00001d022226 was specifically associated with multiple primary P-related traits under low-Pi conditions. A total of 963 out of 2966 genes specifically associated with traits under low-Pi conditions or index values were found to be induced by low-Pi stress. Notably, ZmSPX4.1 and ZmSPX2 were sharply up-regulated in response to low-Pi stress across different lines or tissues. These findings advance our understanding of maize's response to low-Pi stress at different developmental stages, shedding light on the genes and pathways implicated in this response.

Improved chloroplast Pi allocation helps sustain electron transfer to enhance photosynthetic low-phosphorus tolerance of wheat

Phosphorus (P) deficit limits high wheat (Triticum aestivum L.) yields. Breeding low-P-tolerant cultivars is vital for sustainable agriculture and food security, but the low-P adaptation mechanisms are largely not understood. Two wheat cultivars, ND2419 (low-P-tolerant) and ZM366 (low-P-sensitive) were used in this study. They were grown under hydroponic conditions with low-P (0.015 mM) or normal-P (1 mM). Low-P suppressed biomass accumulation and net photosynthetic rate (A) in both cultivars, whereas ND2419 was relatively less suppressed. Intercellular CO2 concentration did not decrease with the decline of stomatal conductance. Additionally, maximum electron transfer rate (Jmax) decreased sooner than maximum carboxylation rate (Vcmax). Results indicate that impeded electron transfer is directly responsible for decreased A. Under low-P, ND2419 exhibited greater PSII functionality (potential activity (Fv/Fo), maximum quantum efficiency (Fv/Fm), photochemical quenching (qL) and non-photochemical quenching (NPQ) required for electron transfer than ZM366, resulting more ATP for Rubisco activation. Furthermore, ND2419 maintained higher chloroplast Pi concentrations by enhancing chloroplast Pi allocation, compared with ZM366. Overall, the low-P-tolerant cultivar sustained electron transfer under low-P by enhancing chloroplast Pi allocation, allowing more ATP synthesis for Rubisco activation, ultimately presenting stronger photosynthesis capacities. The improved chloroplasts Pi allocation may provide new insights into improve low-P tolerance.

Identification of structural variations related to drought tolerance in wheat (Triticum aestivum L.)

Structural variations are common in plant genomes, affecting meiotic recombination and distorted segregation in wheat. And presence/absence variations can significantly affect drought tolerance in wheat. Drought is a major abiotic stress limiting wheat production. Common wheat has a complex genome with three sub-genomes, which host large numbers of structural variations (SVs). SVs play critical roles in understanding the genetic contributions of plant domestication and phenotypic plasticity, but little is known about their genomic characteristics and their effects on drought tolerance. In the present study, high-resolution karyotypes of 180 doubled haploids (DHs) were developed. Signal polymorphisms between the parents involved with 8 presence-absence variations (PAVs) of tandem repeats (TR) distributed on the 7 (2A, 4A, 5A, 7A, 3B, 7B, and 2D) of 21 chromosomes. Among them, PAV on chromosome 2D showed distorted segregation, others transmit normal conforming to a 1:1 segregation ration in the population; and a PAVs recombination occurred on chromosome 2A. Association analysis of PAV and phenotypic traits under different water regimes, we found PAVs on chromosomes 4A, 5A, and 7B showed negative effect on grain length (GL) and grain width (GW); PAV.7A had opposite effect on grain thickness (GT) and spike length (SL), with the effect on traits differing under different water regimes. PAVs on linkage group 2A, 4A, 7A, 2D, and 7B associated with the drought tolerance coefficients (DTCs), and significant negative effect on drought resistance values (D values) were detected in PAV.7B. Additionally, quantitative trait loci (QTL) associated with phenotypic traits using the 90 K SNP array showed QTL for DTCs and grain-related traits in chromosomes 4A, and 5A, 3B were co-localized in differential regions of PAVs. These PAVs can cause the differentiation of the target region of SNP and could be used for genetic improvement of agronomic traits under drought stress via marker-assisted selection (MAS) breeding.

Comprehensive sequence and expression profile analysis of the phosphate transporter gene family in soybean

The family of phosphate transporters (PHTs) mediates the uptake and translocation of Pi inside the plants. However, little is known about transporters in soybean. Therefore, Searched the Genome Database for Soybean, 57 GmPHTs family members were identified in soybean, Phylogenetic analysis suggested that members of the PHTs gene family can be divided into six clades. Collinearity analysis revealed that most of the GmPHT genes shared syntenic relationships with PHTs members in Arabidopsis thaliana and that large segment duplication played a major driving force for GmPHTs evolution in addition to tandem duplication. Further analysis of the promoter revealed that light-responsive elements and abiotic stress-responsive elements were widely distributed within the promoter regions of GmPHT genes. Based on RNA-seq data, GmPHTs showed different expression patterns in roots and leaves of soybean treated with long-term low phosphorus and short-term low phosphorus, in addition, the expression levels of GmPHT genes can be regulated by drought stresses, it was implied that the induced expression of GmPHTs could promote phosphorus uptake and transport in soybean and thus adapt to low phosphorus and drought stress, which is the first step dissection of Pi transport system and probably refers to new roles of PHTs genes in soybean.

A major quantitative trait locus for wheat total root length associated with precipitation distribution

Optimizing root system architecture (RSA) allows crops to better capture water and nutrients and adapt to harsh environment. Parental reproductive environment (PRE) has been reported to significantly affect growth and development throughout the life cycle of the next generation. In this study, 10 RSA-related traits were evaluated in seedling stage from five independent hydroponic tests using seeds harvested from five different PREs. Based on the Wheat55K SNP array-based genetic map, quantitative trait loci (QTL) for these traits were detected in a recombinant inbred line population. Twenty-eight putative QTL for RSA-related traits were detected, covering thirteen chromosomal regions. A major QTL, QTrl.sicau-2SY-4D for total root length (TRL), which was likely independent of PREs, explained 15.81-38.48% of phenotypic variations and was located at 14.96-19.59 Mb on chromosome arm 4DS. Interestingly, it showed pleiotropic effects on TRL, root area, root volume, root forks, root dry weight, and shoot dry weight. The functional marker KASP-Rht-D1 for Rht-D1 was used to genotype 2SY population and remapping QTL for TRL showed that QTrl.sicau-2SY-4D was not linked to Rht-D1. The kompetitive allele-specific PCR (KASP) marker, KASP-AX-110527441 linked to this major QTL, was developed and used to successfully validate its effect in three different genetic populations. Further analysis suggested that the positive allele at QTrl.sicau-2SY-4D was mainly utilized in wheat breeding of northwest China where precipitation was significantly lower, indicating that wheat requires longer TRL to capture water and nutrients in arid or semi-arid regions due to deficient precipitation. Additionally, four genes (TraesCS4D03G0059800, TraesCS4D03G0057800, TraesCS4D03G0064000, and TraesCS4D03G0064400) possibly related to root development were predicted in physical interval of QTrl.sicau-2SY-4D. Taken together, these results enrich our understanding on the genetic basis of RSA and provide a potentially valuable TRL QTL for wheat breeding.

Deep polygenic neural network for predicting and identifying yield-associated genes in Indonesian rice accessions

As the fourth most populous country in the world, Indonesia must increase the annual rice production rate to achieve national food security by 2050. One possible solution comes from the nanoscopic level: a genetic variant called Single Nucleotide Polymorphism (SNP), which can express significant yield-associated genes. The prior benchmark of this study utilized a statistical genetics model where no SNP position information and attention mechanism were involved. Hence, we developed a novel deep polygenic neural network, named the NucleoNet model, to address these obstacles. The NucleoNets were constructed with the combination of prominent components that include positional SNP encoding, the context vector, wide models, Elastic Net, and Shannon’s entropy loss. This polygenic modeling obtained up to 2.779 of Mean Squared Error (MSE) with 47.156% of Symmetric Mean Absolute Percentage Error (SMAPE), while revealing 15 new important SNPs. Furthermore, the NucleoNets reduced the MSE score up to 32.28% compared to the Ordinary Least Squares (OLS) model. Through the ablation study, we learned that the combination of Xavier distribution for weights initialization and Normal distribution for biases initialization sparked more various important SNPs throughout 12 chromosomes. Our findings confirmed that the NucleoNet model was successfully outperformed the OLS model and identified important SNPs to Indonesian rice yields.

Global Identification of White Lupin lncRNAs Reveals Their Role in Cluster Roots under Phosphorus Deficiency

Phosphorus (P) deficiency heterogeneously affected plant nutritional status and physiological performance, ultimately leading to a severe yield reduction. A few putative long non-coding RNAs (lncRNAs) responding to P-starvation in the model crops Arabidopsis thaliana and Oryza sativa have been characterized. White lupin (Lupinus albus) is of prime importance, and is a legume with increasing agronomic value as a protein crop as it exhibits extreme tolerance to nutrient deficiency, particularly P deficiency. Despite its adapted nature to P deficiency, nothing is known about low P-induced lncRNAs in white lupin roots. To address this issue, we identified 39,840 mRNA and 2028 lncRNAs in the eight developmental stages of white lupin root (S0-S7 and lateral root, LR) grown under P deficiency. From these 2028 lncRNAs, 1564 were intergenic and 464 natural antisense intergenic transcript (NAT) lncRNAs. We further predicted six potential targets of miRNAs with twelve lncRNAs, which may regulate P-deficiency-related processes. Moreover, the weighted gene co-expression network analysis (WGCNA) revealed seven modules that were correlated with the expression pattern of lncRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed 606 GO terms and 27 different pathways including signal transduction, energy synthesis, detoxification, and Pi transport. In addition, we screened 13 putative lncRNAs that showed a distinct expression pattern in each root, indicating their role in the P deficiency regulatory network. Therefore, white lupin may be a reference legume to characterize P-deficiency-responsive novel lncRNAs, which would highlight the role of lncRNAs in the regulation of plant responses to P deficiency.

Genome-Wide Association Study of Grain Number in Common Wheat From Shanxi Under Different Water Regimes

Water availability is a crucial environmental factor on grain number in wheat, which is one of the important yield-related traits. In this study, a diverse panel of 282 wheat accessions were phenotyped for grain number per spike (GNS), spikelet number (SN), basal sterile spikelet number (BSSN), and apical sterile spikelet number (ASSN) under different water regimes across two growing seasons. Correlation analysis showed that GNS is significantly correlated with both SN and BSSN under two water regimes. A total of 9,793 single nucleotide polymorphism (SNP) markers from the 15 K wheat array were employed for genome-wide association study (GWAS). A total of 77 significant marker-trait associations (MTAs) for investigated traits as well as 8 MTAs for drought tolerance coefficient (DTC) were identified using the mixed linear model. Favored alleles for breeding were inferred according to their estimated effects on GNS, based on the mean difference of varieties. Frequency changes in favored alleles associated with GNS in modern varieties indicate there is still considerable genetic potential for their use as markers for genome selection of GNS in wheat breeding.

Comparative Transcriptome Analysis Revealed the Key Genes Regulating Ascorbic Acid Synthesis in Actinidia

Actinidia (kiwifruit) is known as ‘the king of vitamin C’ due to its rich ascorbic acid (AsA) concentration, which makes it an important model for studying the regulation of AsA metabolism. Herein, transcriptomic analysis was employed to identify candidate genes that regulate AsA synthesis in Actinidia species with 100-fold variations in fruit AsA content (A. latifolia and A. rufa). Approximately 1.16 billion high-quality reads were generated, and an average of 66.68% of the data was uniquely aligned against the reference genome. AsA-associated DEGs that predominately respond to abiotic signals, and secondary metabolic pathways were identified. The key candidate genes, for instance, GDP-L-galactose phosphorylase-3 (GGP3), were explored according to integrated analysis of the weighted gene co-expression network and L-galactose pathway. Transgenic kiwifruit plants were generated, and the leaves of GGP3 (OE-GGP3) overexpressing lines had AsA contents 2.0- to 6.4-fold higher than those of the wild type. Transcriptomic analysis of transgenic kiwifruit lines was further implemented to identify 20 potential downstream target genes and understand GGP3-regulated cellular processes. As a result, two transcription factors (AcESE3 and AcMYBR) were selected to carry out yeast two-hybrid and BiFC assays, which verified that there were obvious AcESE3–AcMYBR and AcESE3–AcGGP3 protein–protein interactions. This study provides insight into the mechanism of AsA synthesis and provides candidate factors and genes involved in AsA accumulation in kiwifruit.

Physiological responses and transcriptomic changes reveal the mechanisms underlying adaptation of Stylosanthes guianensis to phosphorus deficiency

BACKGROUND

Phosphorus (P) is an essential macronutrient for plant growth that participates in a series of biological processes. Thus, P deficiency limits crop growth and yield. Although Stylosanthes guianensis (stylo) is an important tropical legume that displays adaptation to low phosphate (Pi) availability, its adaptive mechanisms remain largely unknown.

RESULTS

In this study, differences in low-P stress tolerance were investigated using two stylo cultivars ('RY2' and 'RY5') that were grown in hydroponics. Results showed that cultivar RY2 was better adapted to Pi starvation than RY5, as reflected by lower values of relative decrease rates of growth parameters than RY5 at low-P stress, especially for the reduction of shoot and root dry weight. Furthermore, RY2 exhibited higher P acquisition efficiency than RY5 under the same P treatment, although P utilization efficiency was similar between the two cultivars. In addition, better root growth performance and higher leaf and root APase activities were observed with RY2 compared to RY5. Subsequent RNA-seq analysis revealed 8,348 genes that were differentially expressed under P deficient and sufficient conditions in RY2 roots, with many Pi starvation regulated genes associated with P metabolic process, protein modification process, transport and other metabolic processes. A group of differentially expressed genes (DEGs) involved in Pi uptake and Pi homeostasis were identified, such as genes encoding Pi transporter (PT), purple acid phosphatase (PAP), and multidrug and toxin extrusion (MATE). Furthermore, a variety of genes related to transcription factors and regulators involved in Pi signaling, including genes belonging to the PHOSPHATE STARVATION RESPONSE 1-like (PHR1), WRKY and the SYG1/PHO81/XPR1 (SPX) domain, were also regulated by P deficiency in stylo roots.

CONCLUSIONS

This study reveals the possible mechanisms underlying the adaptation of stylo to P deficiency. The low-P tolerance in stylo is probably manifested through regulation of root growth, Pi acquisition and cellular Pi homeostasis as well as Pi signaling pathway. The identified genes involved in low-P tolerance can be potentially used to design the breeding strategy for developing P-efficient stylo cultivars to grow on acid soils in the tropics.

Genome-Wide Association Study of Kernel Traits in Aegilops tauschii

Aegilops tauschii is the diploid progenitor of the D subgenome of hexaploid wheat (Triticum aestivum L.). Here, the phenotypic data of kernel length (KL), kernel width (KW), kernel volume (KV), kernel surface area (KSA), kernel width to length ratio (KWL), and hundred-kernel weight (HKW) for 223 A. tauschii accessions were gathered across three continuous years. Based on population structure analysis, 223 A. tauschii were divided into two subpopulations, namely T-group (mainly included A. tauschii ssp. tauschii accessions) and S-group (mainly included A. tauschii ssp. strangulata). Classifications based on cluster analysis were highly consistent with the population structure results. Meanwhile, the extent of linkage disequilibrium decay distance (r² = 0.5) was about 110 kb and 290 kb for T-group and S-group, respectively. Furthermore, a genome-wide association analysis was performed on these kernel traits using 6,723 single nucleotide polymorphism (SNP) markers. Sixty-six significant markers, distributed on all seven chromosomes, were identified using a mixed linear model explaining 4.82–13.36% of the phenotypic variations. Among them, 15, 28, 22, 14, 21, and 13 SNPs were identified for KL, KW, KV, KSA, KWL, and HKW, respectively. Moreover, six candidate genes that may control kernel traits were identified (AET2Gv20774800, AET4Gv20799000, AET5Gv20005900, AET5Gv20084100, AET7Gv20644900, and AET5Gv21111700). The transfer of beneficial genes from A. tauschii to wheat using marker-assisted selection will broaden the wheat D subgenome improve the efficiency of breeding.

Shallower Root Spatial Distribution Induced by Phosphorus Deficiency Contributes to Topsoil Foraging and Low Phosphorus Adaption in Sugarcane (Saccharum officinarum L.)

Low phosphorus (P) availability in acid soils is one of the main limiting factors in sugarcane (Saccharum officinarum L.) production. Reconstruction of the root system architecture (RSA) is a vital mechanism for crop low P adaption, while the RSA of sugarcane has not been studied in detail because of its complex root system. In this study, reconstruction of the RSA and its relationship with P acquisition were investigated in a P-efficient sugarcane genotype ROC22 (R22) and two P-inefficient genotypes Yunzhe 03-103 (YZ) and Japan 2 (JP). An efficient dynamic observation room was developed to monitor the spatiotemporal alternation of sugarcane root length density (RLD) and root distribution in soil with heterogeneous P locations. The sugarcane RSA was reconstructed under P deficiency, and R22 had an earlier response than YZ and JP and presented an obvious feature of root shallowness. Compared with the normal P condition, the shallow RLD was increased by 112% in R22 under P deficiency while decreased by 26% in YZ and not modified in JP. Meanwhile, R22 exhibited a shallower root distribution than YZ and JP under P deficiency, supported by 51 and 24% greater shallow RLD, and 96 and 67% greater shallow root weight, respectively. The ratio of shallow RLD to total RLD in R22 was 91% greater than YZ, and the ratio of shallow root weight to total root weight in R22 was greater than that of YZ and JP by 94 and 30%, respectively. As a result, R22 had a higher shoot P accumulation than YZ and JP, which thereby increased the relative leaf sheath inorganic P concentration (RLPC) by 47 and 56%, relative shoot biomass (RSB) by 36 and 33%, and relative cane weight (RCW) by 31 and 36%, compared with YZ and JP under P deficiency, respectively. We verified the reliability and efficiency of a dynamic observation room and demonstrated that a shallower root distribution contributed to improving topsoil foraging, P acquisition, and low P adaption under P deficiency in sugarcane. Therefore, a shallower root distribution merits consideration as an evaluation trait for breeding P efficient sugarcane genotypes and genetic improvement.

Multi-Locus Genome-Wide Association Study of Four Yield-Related Traits in Chinese Wheat Landraces

Wheat (Triticum aestivum L.) is one of the most important crops in the world. Here, four yield-related traits, namely, spike length, spikelets number, tillers number, and thousand-kernel weight, were evaluated in 272 Chinese wheat landraces in multiple environments. Five multi-locus genome-wide association studies (FASTmrEMMA, ISIS EN-BLASSO, mrMLM, pKWmEB, and pLARmEB) were performed using 172,711 single-nucleotide polymorphisms (SNPs) to identify yield-related quantitative trait loci (QTL). A total of 27 robust QTL were identified by more than three models. Nine of these QTL were consistent with those in previous studies. The remaining 18 QTL may be novel. We identified a major QTL, QTkw.sicau-4B, with up to 18.78% of phenotypic variation explained. The developed kompetitive allele-specific polymerase chain reaction marker for QTkw.sicau-4B was validated in two recombinant inbred line populations with an average phenotypic difference of 16.07%. After combined homologous function annotation and expression analysis, TraesCS4B01G272300 was the most likely candidate gene for QTkw.sicau-4B. Our findings provide new insights into the genetic basis of yield-related traits and offer valuable QTL to breed wheat cultivars via marker-assisted selection.