Combined analysis of metabolome and transcriptome of wheat kernels reveals constitutive defense mechanism against maize weevils.

Sitophilus zeamais (maize weevil) is one of the most destructive pests that seriously affects the quantity and quality of wheat (Triticum aestivum L.). However, little is known about the constitutive defense mechanism of wheat kernels against maize weevils. In this study, we obtained a highly resistant variety RIL-116 and a highly susceptible variety after two years of screening. The morphological observations and germination rates of wheat kernels after feeding ad libitum showed that the degree of infection in RIL-116 was far less than that in RIL-72. The combined analysis of metabolome and transcriptome of RIL-116 and RIL-72 wheat kernels revealed differentially accumulated metabolites were mainly enriched in flavonoids biosynthesis-related pathway, followed by glyoxylate and dicarboxylate metabolism, and benzoxazinoid biosynthesis. Several flavonoids metabolites were significantly up-accumulated in resistant variety RIL-116. In addition, the expression of structural genes and transcription factors (TFs) related to flavonoids biosynthesis were up-regulated to varying degrees in RIL-116 than RIL-72. Taken together, these results indicated that the biosynthesis and accumulation of flavonoids contributes the most to wheat kernels defense against maize weevils. This study not only provides insights into the constitutive defense mechanism of wheat kernels against maize weevils, but may also play an important role in the breeding of resistant varieties.

Different adaptive patterns of wheat with different drought tolerance under drought stresses and rehydration revealed by integrated metabolomic and transcriptomic analysis.

Wheat as a staple food crop is enduring ever-frequent intermittent and changing drought with the climate change. It is of great significance to highlight the adaptive approaches under such variable conditions at multiple levels to provide a comprehensive understanding of drought tolerance and facilitate the genetic breeding of wheat. Therefore, three wheat lines with different drought tolerance (drought-tolerant mutant Mu > common wheat CK > drought susceptible mutant mu) were analyzed under moderate and severe drought stresses as well as rehydration. Samples were subjected to transcriptomic and metabolomic profiling in combination with physiological and biochemical determination. The moderate drought stress rendered 198 and 115 differentially expressed metabolites (DEMs) in CK and Mu, respectively. The severe drought stress rendered 166, 151 and 137 DEMs in CK, Mu and mu, respectively. The rehydration rendered 150 and 127 DEMs in CK and Mu. 12,557 and 10,402 differentially expressed genes (DEGs) were identified for CK and Mu under moderate drought stress, respectively. 9,893, 7,924, and 9,387 DEGs were identified for CK, Mu, and mu under severe drought stress, respectively. 13,874 and 14,839 were identified in CK and Mu under rehydration, respectively. Metabolomics results showed that amino acid was the most differentially expressed metabolites, followed by phenolic acids. Flavonoids played an important role in drought tolerance. Most enriched pathways under drought included biosynthesis of secondary metabolites, metabolic pathways and photosynthesis. Metabolites and genes involved in osmotic regulation, antioxidase activities, and ABA signaling were more enriched in Mu than in CK and mu. Various drought-responsive genes and metabolites in Mu showed different trends with those in CK and mu. Increased amino acids biosynthetic capability and ROS scavenging ability resulted from higher antioxidase activities and increased flavonoids may be the mechanisms underlying the drought tolerance characteristic of Mu. Recovery from reversible ROS damage and rapid amino acid biosynthesis may contribute to the rapid recovery of Mu. The present study provides new insights for mechanisms of wheat under complex drought conditions.

Transcription-associated metabolomic profiling reveals the critical role of frost tolerance in wheat.

BACKGROUND: Low temperature is a crucial stress factor of wheat (Triticum aestivum L.) and adversely impacts on plant growth and grain yield. Multi-million tons of grain production are lost annually because crops lack the resistance to survive in winter. Particularlly, winter wheat yields was severely damaged under extreme cold conditions. However, studies about the transcriptional and metabolic mechanisms underlying cold stresses in wheat are limited so far. RESULTS: In this study, 14,466 differentially expressed genes (DEGs) were obtained between wild-type and cold-sensitive mutants, of which 5278 DEGs were acquired after cold treatment. 88 differential accumulated metabolites (DAMs) were detected, including P-coumaroyl putrescine of alkaloids, D-proline betaine of mino acids and derivativ, Chlorogenic acid of the Phenolic acids. The comprehensive analysis of metabolomics and transcriptome showed that the cold resistance of wheat was closely related to 13 metabolites and 14 key enzymes in the flavonol biosynthesis pathway. The 7 enhanced energy metabolites and 8 up-regulation key enzymes were also compactly involved in the sucrose and amino acid biosynthesis pathway. Moreover, quantitative real-time PCR (qRT-PCR) revealed that twelve key genes were differentially expressed under cold, indicating that candidate genes POD, Tacr7, UGTs, and GSTU6 which were related to cold resistance of wheat. CONCLUSIONS: In this study, we obtained the differentially expressed genes and differential accumulated metabolites in wheat under cold stress. Using the DEGs and DAMs, we plotted regulatory pathway maps of the flavonol biosynthesis pathway, sucrose and amino acid biosynthesis pathway related to cold resistance of wheat. It was found that candidate genes POD, Tacr7, UGTs and GSTU6 are related to cold resistance of wheat. This study provided valuable molecular information and new genetic engineering clues for the further study on plant resistance to cold stress.

Identification and characterization of QTL for spike morphological traits, plant height and heading date derived from the D genome of natural and resynthetic allohexaploid wheat.

KEY MESSAGE: QHd.cau-7D.1 for heading date was delimited into the physical interval of approximately 17.38 Mb harboring three CONSTANS-like zinc finger genes. Spike morphological traits, plant height and heading date play important roles in yield improvement of wheat. To reveal the genetic factors that controlling spike morphological traits, plant height and heading date on the D genome, we conducted analysis of quantitative traits locus (QTL) using 198 F7:8 recombinant inbred lines (RILs) derived from a cross between the common wheat TAA10 and resynthesized allohexaploid wheat XX329 with similar AABB genomes. A total of 23 environmentally stable QTL on the D sub-genome for spike length (SL), fertile spikelet number per spike (FSN), sterile spikelet number per spike (SSN), total spikelet number per spike (TSN), spike compactness (SC), plant height (PHT) and heading date (HD) were detected, among which eight appeared to be novel QTL. Furthermore, QHd.cau-7D.1 and QPht.cau-7D.2 shared identical confidence interval and were delimited into the physical interval of approximately 17.38 Mb with 145 annotated genes, including three CONSTANS-like zinc finger genes (TraesCS7D02G209000, TraesCS7D02G213000 and TraesCS7D02G220300). This study will help elucidate the molecular mechanism of the seven traits (SL, FSN, SSN, TSN, SC, PHT and HD) and provide a potentially valuable resource for genetic improvement.

Stress granule-associated TaMBF1c confers thermotolerance through regulating specific mRNA translation in wheat (Triticum aestivum).

Heat stress is a major limiting factor for global wheat production and causes dramatic yield loss worldwide. The TaMBF1c gene is upregulated in response to heat stress in wheat. Understanding the molecular mechanisms associated with heat stress responses will pave the way to improve wheat thermotolerance. Through CRISPR/Cas9-based gene editing, polysome profiling coupled with RNA-sequencing analysis, and protein-protein interactions, we show that TaMBF1c conferred heat response via regulating a specific gene translation in wheat. The results showed that TaMBF1c is evolutionarily conserved in diploid, tetraploid and hexaploid wheat species, and its knockdown and knockout lines show increased heat sensitivity. TaMBF1c is colocalized with the stress granule complex and interacts with TaG3BP. TaMBF1c affects the translation efficiency of a subset of heat responsive genes, which are significantly enriched in the 'sequence-specific DNA binding' term. Moreover, gene expression network analysis demonstrated that TaMBF1c is closely associated with the translation of heat shock proteins. Our findings reveal a contribution of TaMBF1c in regulating the heat stress response via the translation process, and provide a new target for improving heat tolerance in wheat breeding programs.

Proteome and transcriptome analyses of wheat near isogenic lines identifies key proteins and genes of wheat bread quality.

The regulation of wheat protein quality is a highly complex biological process involving multiple metabolic pathways. To reveal new insights into the regulatory pathways of wheat glutenin synthesis, we used the grain-filling period wheat grains of the near-isogenic lines NIL-723 and NIL-1010, which have large differences in quality, to perform a combined transcriptome and proteome analysis. Compared with NIL-1010, NIL-723 had 1287 transcripts and 355 proteins with significantly different abundances. Certain key significantly enriched pathway were identified, and wheat quality was associated with alanine, aspartate and glutamate metabolism, nitrogen metabolism and alpha-linolenic acid metabolism. Differentially expressed proteins (DEPs) or Differentially expressed genes (DEGs) in amino acid synthesis pathways were upregulated primarily in the glycine (Gly), methionine (Met), threonine (Thr), glutamic acid (Glu), proline (proC), cysteine (Cys), and arginine (Arg) synthesis and downregulated in the tryptophan (trpE), leucine (leuC), citrulline (argE), and ornithine (argE) synthesis. Furthermore, to elucidate changes in glutenin in the grain synthesis pathway, we plotted a regulatory pathway map and found that DEGs and DEPs in ribosomes (RPL5) and the ER (HSPA5, HYOU1, PDIA3, PDIA1, Sec24, and Sec31) may play key roles in regulating glutenin synthesis. The transcriptional validation of some of the differentially expressed proteins through real-time quantitative PCR analysis further validated the transcriptome and proteomic results.

Genome-wide association study identifies QTL for thousand grain weight in winter wheat under normal- and late-sown stressed environments.

KEY MESSAGE: GWAS identified stable loci for TGW and stress tolerance in winter wheat based on two sowing conditions, which will provide opportunities for developing new cultivars with high yield and yield stability. Wheat is an important food crop widely cultivated in the world. Breeding new varieties with high yields and superior adaptability is the main goal of modern wheat breeding program. In order to determine the marker-trait associations (MATs), a set of 688 diverse winter wheat accessions were subjected to genome-wide association study (GWAS) using the wheat 90K array. Field trials under normal-sown (NS) and late-sown (LS) conditions were conducted for thousand grain weight (TGW) and stress susceptibility index (SSI) at three different sites across two consecutive years. A total of 179 (NS) and 158 (LS) MATs corresponded with TGW; of these, 16 and 6 stable MATs for TGWNS and TGWLS were identified on chromosomes 1B, 2B, 3A, 3B, 5A, 5B, 5D, 6B, and 7D across at least three environments. Notably, a QTL hot spot controlling TGW under NS and LS conditions was found on chromosome 5A (140-142 cM). Moreover, 8 of 228 stable MATs on chromosomes 4B, 5A, and 5D for SSI were detected. A haplotype block associated with TGW and SSI was located on chromosome 5A at 91 cM, nearby the vernalization gene VRN-A1. Additionally, analysis of wheat varieties from the different eras revealed that the grain weight and stress tolerance are not improved concurrently. Overall, our results provide promising alleles controlling grain weight and stress tolerance (particularly for thermotolerance) for wheat breeders, which can be used in marker-assisted selection for improving grain yield and yield stability in wheat.

Gene co-expression network analysis to identify critical modules and candidate genes of drought-resistance in wheat.

AIM: To establish a gene co-expression network for identifying principal modules and hub genes that are associated with drought resistance mechanisms, analyzing their mechanisms, and exploring candidate genes. METHODS AND FINDINGS: 42 data sets including PRJNA380841 and PRJNA369686 were used to construct the co-expression network through weighted gene co-expression network analysis (WGCNA). A total of 1,896,897,901 (284.30 Gb) clean reads and 35,021 differentially expressed genes (DEGs) were obtained from 42 samples. Functional enrichment analysis indicated that photosynthesis, DNA replication, glycolysis/gluconeogenesis, starch and sucrose metabolism, arginine and proline metabolism, and cell cycle were significantly influenced by drought stress. Furthermore, the DEGs with similar expression patterns, detected by K-means clustering, were grouped into 29 clusters. Genes involved in the modules, such as dark turquoise, yellow, and brown, were found to be appreciably linked with drought resistance. Twelve central, greatly correlated genes in stage-specific modules were subsequently confirmed and validated at the transcription levels, including TraesCS7D01G417600.1 (PP2C), TraesCS5B01G565300.1 (ERF), TraesCS4A01G068200.1 (HSP), TraesCS2D01G033200.1 (HSP90), TraesCS6B01G425300.1 (RBD), TraesCS7A01G499200.1 (P450), TraesCS4A01G118400.1 (MYB), TraesCS2B01G415500.1 (STK), TraesCS1A01G129300.1 (MYB), TraesCS2D01G326900.1 (ALDH), TraesCS3D01G227400.1 (WRKY), and TraesCS3B01G144800.1 (GT). CONCLUSIONS: Analyzing the response of wheat to drought stress during different growth stages, we have detected three modules and 12 hub genes that are associated with drought resistance mechanisms, and five of those genes are newly identified for drought resistance. The references provided by these modules will promote the understanding of the drought-resistance mechanism. In addition, the candidate genes can be used as a basis of transgenic or molecular marker-assisted selection for improving the drought resistance and increasing the yields of wheat.

Dissection and validation of a QTL cluster linked to Rht-B1 locus controlling grain weight in common wheat (Triticum aestivum L.) using near-isogenic lines.

KEY MESSAGE: This study dissected and validated a QTL cluster associated with thousand grain weight on chromosome 4B using multiple near-isogenic lines in common wheat. Grain size and weight are crucial components of wheat yield. Previously, we identified a QTL cluster for thousand grain weight (TGW) on chromosome 4B using the Nongda3338 (ND3338)/Jingdong6 (JD6) doubled haploid population. Here, near-isogenic lines (NILs) in the ND3338 background were developed to dissect and validate the QTL cluster. Based on six independent BC3F3:4 heterogeneous inbred families, the 4B QTL cluster was divided into two linked QTL intervals (designated 4B.1 and 4B.2 QTL). For the 4B.1 QTL, the Rht-B1 gene, of which Rht-B1b allele reduces plant height (PH) by 21.18-29.34 cm (34.34-53.71%), was demonstrated to be the most likely candidate gene with pleiotropic effects on grain size and TGW. For the 4B.2 QTL, the NILJD6 consistently showed an increase in TGW of 3.51-7.68 g (8.84-22.77%) compared with NILND3338 across different field trials, along with a significant increase in PH of 2.26-6.71 cm (3.92-12.01%). Moreover, both QTL intervals had a larger effect on grain width than on grain length. Additionally, the first significant difference in 100-grain fresh weight and 100-grain dry weight between the NIL pairs of the 4B.1 QTL interval (Rht-B1) was observed at 6 days after pollination (DAP), while the differences were first visible at 30 DAP for the 4B.2 QTL interval. Collectively, our work provides a new example of QTL dissection for grain weight in wheat and lays a foundation for further map-based cloning of the major QTL that have potential applications in wheat molecular breeding for high yield.

Pleiotropic QTL influencing spikelet number and heading date in common wheat (Triticum aestivum L.).

KEY MESSAGE: Three pleiotropic QTL regions associated with spikelet number and heading date were identified, with FT-A1 considered the candidate gene for QTspn/Hd.cau-7A. Spikelet number traits and heading date (HD) play key roles in yield improvement of wheat and its wide adaptation to different environments. Here, we used a Recombinant Inbred Lines population derived from a cross between Yi5029 (5029) and Nongda4332 (4332) to construct a high-density genetic linkage map and identify quantitative trait loci (QTL) associated with total spikelet number per spike (TSPN), fertile spikelet number per spike (FSPN), sterile spikelet number per spike (SSPN) and HD. A total of 22 environmentally stable QTL for TSPN, FSPN, SSPN and HD were identified. Notably, three pleiotropic QTL regions for TSPN and HD were detected on chromosomes 2A, 7A and 7D. The QTL associated with TSPN and HD on chromosome 7AS was designated QTspn/Hd.cau-7A. Furthermore, the candidate gene FT-A1 located in the region of QTspn/Hd.cau-7A had a single-nucleotide polymorphism (T-G) within the third exon, which might be the cause of diversity in spikelet number and HD between the two parents. Additionally, we developed a semi-thermal asymmetric reverse PCR (STARP) marker to analyze the geographical distribution and evolution of FT-A1 (T or G) alleles. This study contributes to our understanding of the molecular mechanisms of the four traits (TSPN, FSPN, SSPN and HD) and provides further insights into the genetic relationship between spikelet number traits and HD in wheat.

Dissection of genetic factors underlying grain size and fine mapping of QTgw.cau-7D in common wheat (Triticum aestivum L.).

KEY MESSAGE: Thirty environmentally stable QTL controlling grain size and/or plant height were identified, among which QTgw.cau-7D was delimited into the physical interval of approximately 4.4 Mb. Grain size and plant height (PHT) are important agronomic traits in wheat breeding. To dissect the genetic basis of these traits, we conducted a quantitative trait locus (QTL) analysis using recombinant inbred lines (RILs). In total, 30 environmentally stable QTL for thousand grain weight (TGW), grain length (GL), grain width (GW) and PHT were detected. Notably, one major pleiotropic QTL on chromosome arm 3DS explained the highest phenotypic variance for TGW, GL and PHT, and two stable QTL (QGw.cau-4B and QGw.cau-7D) on chromosome arms 4BS and 7DS contributed greater effects for GW. Furthermore, the stable QTL controlling grain size (QTgw.cau-7D and QGw.cau-7D) were delimited into the physical interval of approximately 4.4 Mb harboring 56 annotated genes. The elite NILs of QTgw.cau-7D increased TGW by 12.79-21.75% and GW by 4.10-8.47% across all three environments. Collectively, these results provide further insight into the genetic basis of TGW, GL, GW and PHT, and the fine-mapped QTgw.cau-7D will be an attractive target for positional cloning and marker-assisted selection in wheat breeding programs.

Correction to: Dissection of two quantitative trait loci with pleiotropic effects on plant height and spike length linked in coupling phase on the short arm of chromosome 2D of common wheat (Triticum aestivum L.).

Theoretical and Applied Genetics.

Fine mapping and candidate gene analysis of a QTL associated with leaf rolling index on chromosome 4 of maize (Zea mays L.).

KEY MESSAGE: One QTL qLRI4 controlling leaf rolling index on chromosome 4 was finely mapped, and ZmOCL5, a member of the HD-Zip class IV genes, is likely a candidate. Leaf rolling is an important agronomic trait related to plant architecture that can change the light condition and photosynthetic efficiency of the population. Here, we isolated one EMS-induced mutant in Chang7-2 background with extreme abaxial rolling leaf, named abrl1. Histological analysis showed that the increased number and area of bulliform cells may contribute to abaxial rolling leaf in abrl1. The F2 and F2:3 populations derived from Wu9086 with flat leaves and abrl1 were developed to map abrl1. Non-Mendelian segregation of phenotypic variation was observed in these populations and five genomic regions controlling the leaf rolling index (LRI) were identified, which could be due to the phenotypic difference between Chang7-2 and Wu9086. Moreover, one major QTL qLRI4 on chromosome 4 was further validated and finely mapped to a genetic interval between InDel13 and InDel10, with a physical distance of approximately 277 kb using NIL populations, among which one 602-bp insertion was identified in the promoter region of HD-Zip class IV gene Zm00001d049443 (named as ZmOCL5) of abrl1 compared with wild-type Chang7-2. Remarkably, the 602-bp InDel was associated with LRI in an F2 population developed by crossing abrl1 mutant and its wild-type. In addition, the 602-bp insertion increased ZmOCL5 promoter activity and expression. Haplotype analysis demonstrated that the 602-bp insertion was a rare mutation event. Taken together, we propose that the rolled leaf in the abrl1 mutant may be partially attributed to the 602-bp insertion, which may be an attractive target for the genetic improvement of LRI in maize.

Dissection of two quantitative trait loci with pleiotropic effects on plant height and spike length linked in coupling phase on the short arm of chromosome 2D of common wheat (Triticum aestivum L.).

KEY MESSAGE: Two QTL with pleiotropic effects on plant height and spike length linked in coupling phase on chromosome 2DS were dissected, and diagnostic marker for each QTL was developed. Plant height (PHT) is a crucial trait related to plant architecture and yield potential, and dissection of its underlying genetic basis would help to improve the efficiency of designed breeding in wheat. Here, two quantitative trait loci (QTL) linked in coupling phase on the short arm of chromosome 2D with pleiotropic effects on PHT and spike length, QPht/Sl.cau-2D.1 and QPht/Sl.cau-2D.2, were separated and characterized. QPht/Sl.cau-2D.1 is a novel QTL located between SNP makers BS00022234_51 and BobWhite_rep_c63957_1472. QPht/Sl.cau-2D.2 is mapped between two SSR markers, SSR-2062 and Xgwm484, which are located on the same genomic interval as Rht8. Moreover, the diagnostic marker tightly linked with each QTL was developed for the haplotype analysis using diverse panels of wheat accessions. The frequency of the height-reduced allele of QPht/Sl.cau-2D.1 is much lower than that of QPht/Sl.cau-2D.2, suggesting that this novel QTL may be an attractive target for genetic improvement. Consistent with a previous study of Rht8, a significant difference in cell length was observed between the NILs of QPht/Sl.cau-2D.2. By contrast, there was no difference in cell length between NILs of QPht/Sl.cau-2D.1, indicating that the underlying molecular mechanism for these two QTL may be different. Collectively, these data provide a new example of QTL dissection, and the developed diagnostic markers will be useful in marker-assisted pyramiding of QPht/Sl.cau-2D.1 and/or QPht/Sl.cau-2D.2 with the other genes in wheat breeding.

Dissection of two quantitative trait loci with pleiotropic effects on plant height and spike length linked in coupling phase on the short arm of chromosome 2D of common wheat (Triticum aestivum L.).

KEY MESSAGE: Two QTL with pleiotropic effects on plant height and spike length linked in coupling phase on chromosome 2DS were dissected, and diagnostic marker for each QTL was developed. Plant height (PHT) is a crucial trait related to plant architecture and yield potential, and dissection of its underlying genetic basis would help to improve the efficiency of designed breeding in wheat. Here, two quantitative trait loci (QTL) linked in coupling phase on the short arm of chromosome 2D with pleiotropic effects on PHT and spike length, QPht/Sl.cau-2D.1 and QPht/Sl.cau-2D.2, were separated and characterized. QPht/Sl.cau-2D.1 is a novel QTL located between SNP makers BS00022234_51 and BobWhite_rep_c63957_1472. QPht/Sl.cau-2D.2 is mapped between two SSR markers, SSR-2062 and Xgwm484, which are located on the same genomic interval as Rht8. Moreover, the diagnostic marker tightly linked with each QTL was developed for the haplotype analysis using diverse panels of wheat accessions. The frequency of the height-reduced allele of QPht/Sl.cau-2D.1 is much lower than that of QPht/Sl.cau-2D.2, suggesting that this novel QTL may be an attractive target for genetic improvement. Consistent with a previous study of Rht8, a significant difference in cell length was observed between the NILs of QPht/Sl.cau-2D.2. By contrast, there was no difference in cell length between NILs of QPht/Sl.cau-2D.1, indicating that the underlying molecular mechanism for these two QTL may be different. Collectively, these data provide a new example of QTL dissection, and the developed diagnostic markers will be useful in marker-assisted pyramiding of QPht/Sl.cau-2D.1 and/or QPht/Sl.cau-2D.2 with the other genes in wheat breeding.

Unconventional splicing of wheat TabZIP60 confers heat tolerance in transgenic Arabidopsis.

Conditions that disrupt protein folding, such as heat stress, can overwhelm the capacity of cells to fold proteins, thus causing endoplasmic reticulum (ER) stress. In Arabidopsis thaliana and other plants, inositol-requiring enzyme-1 mediated unconventional splicing of bZIP60 plays a crucial role in the heat and ER stress responses. However, little is known about this pathway in wheat (Triticum aestivum), especially its importance in heat tolerance. Here, we found that heat stress induced upregulation and unconventional splicing of TabZIP60 occurred in wheat seedlings. Constitutive expression of the spliced form of TabZIP60 (TabZIP60s) enhanced heat tolerance in Arabidopsis, but overexpression of the unspliced form (TabZIP60u) did not. RNA-sequencing analysis revealed ER stress related genes involved in heat responses in TabZIP60s-overexpression transgenic Arabidopsis. Chromatin immunoprecipitation-qPCR showed that TabZIP60s directly binds to 17 target genes including AtbZIP60. Also, the 26S proteasome pathway post-translationally regulates TabZIP60s levels during heat stress responses. Our findings suggest that unconventional splicing of TabZIP60 could contribute to heat tolerance in transgenic plants by modulating the expression of ER stress-related genes.

Three genomes differentially contribute to the seedling lateral root number in allohexaploid wheat: evidence from phenotype evolution and gene expression.

Common wheat is an allohexaploid (BBAADD) that originated from the hybridization and polyploidization of the diploid Aegilops tauschii (DD) with the allotetraploid Triticum turgidum (BBAA). Phenotypic changes often arise with the formation and evolution of allopolyploid wheat, but little is known about the evolution of root traits in different wheat species with varying ploidy levels. Here, we reported that the lateral root number on the primary root (LRNPR) of synthetic and natural allohexaploid wheats (BBAADD) is significantly higher than that of their allotetraploid (BBAA) and diploid (AA and SS) progenitors, but is much lower than that of their diploid (DD) progenitors. The expression of the wheat gene TaLBD16, an ortholog of the Arabidopsis LATERAL ORGAN BOUNDARIES-DOMAIN16/ASYMMETRIC LEAVES2-LIKE18 (LBD16), which is involved in lateral root development in Arabidopsis, was positively correlated with the LRNPR in diploid and allopolyploid wheats. In natural and synthetic allohexaploid wheats, the transcript of the TaLBD16 from the D genome (TaLBD16-D) was relatively more abundant compared with TaLBD16-A and TaLBD16-B. Consistent with the observed variation in LRNPR, the divergence in the expression of TaLBD16 homoeologous genes occurred before the formation of polyploidy wheat. Collectively, our observations indicate that the D genome played a crucial role in the increased lateral root number of allohexaploid wheats compared with their allotetraploid progenitors, and that TaLBD16-D was one of the key genes involved in the formation of lateral root number during wheat evolution.

Transcriptome analysis reveals potential mechanisms for different grain size between natural and resynthesized allohexaploid wheats with near-identical AABB genomes.

BACKGROUND: Common wheat is a typical allohexaploid species (AABBDD) derived from the interspecific crossing between allotetraploid wheat (AABB) and Aegilops tauschii (DD). Wide variation in grain size and shape observed among Aegilops tauschii can be retained in synthetic allohexaploid wheats, but the underlying mechanism remains enigmatic. Here, the natural and resynthesized allohexaploid wheats with near-identical AB genomes and different D genomes (TAA10 and XX329) were employed for analysis. RESULTS: Significant differences in grain size and weight between TAA10 and XX329 were observed at the early stages of development, which could be mainly attributed to the higher growth rates of the pericarp and endosperm cells in XX329 compared to TAA10. Furthermore, comparative transcriptome analysis identified that 8891 of 69,711 unigenes (12.75%) were differentially expressed between grains at 6 days after pollination (DAP) of TAA10 and XX329, including 5314 up-regulated and 3577 down-regulated genes in XX329 compared to TAA10. The MapMan functional annotation and enrichment analysis revealed that the differentially expressed genes were significantly enriched in categories of cell wall, carbohydrate and hormone metabolism. Notably, consistent with the up-regulation of sucrose synthase genes in resynthesized relative to natural allohexaploid wheat, the resynthesized allohexaploid wheat accumulated much higher contents of glucose and fructose in 6-DAP grains than those of the natural allohexaploid wheat. CONCLUSIONS: These data indicated that the genetic variation of the D genome induced drastic alterations of gene expression in grains of the natural and resynthesized allohexaploid wheats, which may contribute to the observed differences in grain size and weight.

Identification and characterization of a high kernel weight mutant induced by gamma radiation in wheat (Triticum aestivum L.).

BACKGROUND: Inducing mutations are considered to be an effective way to create novel genetic variations and hence novel agronomical traits in wheat. This study was conducted to assess the genetic differences between Shi4185 and its mutant line Fu4185, produced by gamma radiation with larger grain, and to identify quantitative trait loci (QTLs) for thousand kernel weight (TKW). RESULTS: Phenotypic analysis revealed that the TKW of Fu4185 was much higher than that of Shi4185 under five different environments. At the genomic level, 110 of 2019 (5.4%) simple sequence repeats (SSR) markers showed polymorphism between Shi4185 and Fu4185. Notably, 30% (33 out of 110) polymorphic SSR markers were located on the D-genome, which was higher than the percentage of polymorphisms among natural allohexaploid wheat genotypes, indicating that mutations induced by gamma radiation could be a potential resource to enrich the genetic diversity of wheat D-genome. Moreover, one QTL, QTkw.cau-5D, located on chromosome 5DL, with Fu4185 contributing favorable alleles, was detected under different environments, especially under high temperature conditions. CONCLUSIONS: QTkw.cau-5D is an environmental stable QTL, which may be a desired target for genetic improvement of wheat kernel weight.