Genetic dissection of pre‐anthesis sub‐phase durations during the reproductive spike development of wheat

Flowering time is an important factor affecting grain yield in wheat. In this study, we divided reproductive spike development into eight sub‐phases. These sub‐phases have the potential to be delicately manipulated to increase grain yield. We measured 36 traits with regard to sub‐phase durations, determined three grain yield‐related traits in eight field environments and mapped 15 696 single nucleotide polymorphism (SNP, based on 90k Infinium chip and 35k Affymetrix chip) markers in 210 wheat genotypes. Phenotypic and genetic associations between grain yield traits and sub‐phase durations showed significant consistency (Mantel test; r = 0.5377, P < 0.001). The shared quantitative trait loci (QTLs) revealed by the genome‐wide association study suggested a close association between grain yield and sub‐phase duration, which may be attributed to effects on spikelet initiation/spikelet number (double ridge to terminal spikelet stage, DR‐TS) and assimilate accumulation (green anther to anthesis stage, GA‐AN). Moreover, we observed that the photoperiod‐sensitivity allele at the Ppd‐D1 locus on chromosome 2D markedly extended all sub‐phase durations, which may contribute to its positive effects on grain yield traits. The dwarfing allele at the Rht‐D1 (chromosome 4D) locus altered the sub‐phase duration and displayed positive effects on grain yield traits. Data for 30 selected genotypes (from among the original 210 genotypes) in the field displayed a close association with that from the greenhouse. Most importantly, this study demonstrated specific connections to grain yield in narrower time windows (i.e. the eight sub‐phases), rather than the entire stem elongation phase as a whole.     

Gene editing of the wheat homologs of TONNEAU1‐recruiting motif encoding gene affects grain shape and weight in wheat

Grain size and weight are important components of a suite of yield‐related traits in crops. Here, we showed that the CRISPR‐Cas9 gene editing of TaGW7, a homolog of rice OsGW7 encoding a TONNEAU1‐recruiting motif (TRM) protein, affects grain shape and weight in allohexaploid wheat. By editing the TaGW7 homoeologs in the B and D genomes, we showed that mutations in either of the two or both genomes increased the grain width and weight but reduced the grain length. The effect sizes of mutations in the TaGW7 gene homoeologs coincided with the relative levels of their expression in the B and D genomes. The effects of gene editing on grain morphology and weight traits were dosage dependent with the double‐copy mutant showing larger effect than the respective single copy mutants. The TaGW7‐centered gene co‐expression network indicated that this gene is involved in the pathways regulating cell division and organ growth, also confirmed by the cellular co‐localization of TaGW7 with α‐ and β‐tubulin proteins, the building blocks of microtubule arrays. The analyses of exome capture data in tetraploid domesticated and wild emmer, and hexaploid wheat revealed the loss of diversity around TaGW7‐associated with domestication selection, suggesting that TaGW7 is likely to play an important role in the evolution of yield component traits in wheat. Our study showed how integrating CRISPR‐Cas9 system with cross‐species comparison can help to uncover the function of a gene fixed in wheat for allelic variants targeted by domestication selection and select targets for engineering new gene variants for crop improvement.     

TaDA1, a conserved negative regulator of kernel size,has an additive effect with TaGW2 in common wheat (Triticum aestivum L.)

Kernel size is an important trait determining cereal yields. In this study, we cloned and characterized TaDA1, a conserved negative regulator of kernel size in wheat (Triticum aestivum). The overexpression of TaDA1 decreased the size and weight of wheat kernels, while its down‐regulation using RNA interference (RNAi) had the opposite effect. Three TaDA1‐A haplotypes were identified in Chinese wheat core collections, and a haplotype association analysis showed that TaDA1‐A‐HapI was significantly correlated with the production of larger kernels and higher kernel weights in modern Chinese cultivars. The haplotype effect resulted from a difference in TaDA1‐A expression levels between genotypes, with TaDA1‐A‐HapI resulting in lower TaDA1‐A expression levels. This favourable haplotype was found having been positively selected during wheat breeding over the last century. Furthermore, we demonstrated that TaDA1‐A physically interacts with TaGW2‐B. The additive effects of TaDA1‐A and TaGW2‐B on kernel weight were confirmed not only by the phenotypic enhancement arising from the simultaneous down‐regulation of TaDA1 and TaGW2 expression, but also by the combinational haplotype effects estimated from multi‐environment field data from 348 wheat cultivars. A comparative proteome analysis of developing transgenic and wild‐type grains indicated that TaDA1 and TaGW2 are involved in partially overlapping but relatively independent protein regulatory networks. Thus, we have identified an important gene controlling kernel size in wheat and determined its interaction with other genes regulating kernel weight, which could have beneficial applications in wheat breeding.     

A quantitative trait locus GW6 controls rice grain size and yield through the gibberellin pathway

Grain size is one of the essential components determining rice yield and is a target for both domestication and artificial breeding. Gibberellins (GAs) are diterpenoid phytohormones that influence diverse aspects of plant growth and development. Several quantitative trait loci (QTLs) have been identified that control grain size through phytohormone regulation. However, little is known about the role of GAs in the control of grain size. Here we report the cloning and characterization of a QTL, GW6 (GRAIN WIDTH 6), which encodes a GA‐regulated GAST family protein and positively regulates grain width and weight. GW6 is highly expressed in the young panicle and increases grain width by promoting cell expansion in the spikelet hull. Knockout of GW6 exhibits reduced grain size and weight, whereas overexpression of GW6 results in increased grain size and weight. GW6 is induced by GA and its knockout downregulates the expression of GA biosynthesis genes and decreases GA content in the young panicle. We found that a natural variation in the cis element CAAT‐box in the promoter of GW6 is associated with its expression level and grain width and weight. Furthermore, introduction of GW6 to Oryza indica variety HJX74 can lead to a 10.44% increase in rice grain yield, indicating that GW6 has great potential to improve grain yield in rice.     

NADH‐dependent glutamate synthase plays a crucial role in assimilating ammonium in the Arabidopsis root

Plant roots under nitrogen deficient conditions with access to both ammonium and nitrate ions, will take up ammonium first. This preference for ammonium rather than nitrate emphasizes the importance of ammonium assimilation machinery in roots. Glutamine synthetase (GS) and glutamate synthase (GOGAT) catalyze the conversion of ammonium and 2‐oxoglutarate to glutamine and glutamate. Higher plants have two GOGAT species, ferredoxin‐dependent glutamate synthase (Fd‐GOGAT) and nicotinamide adenine dinucleotide (NADH)‐GOGAT. While Fd‐GOGAT participates in the assimilation of ammonium, which is derived from photorespiration in leaves, NADH‐GOGAT is highly expressed in roots and its importance needs to be elucidated. While ammonium as a minor nitrogen form in most soils is directly taken up, nitrate as the major nitrogen source needs to be converted to ammonium prior to uptake. The aim of this study was to investigate and quantify the contribution of NADH‐GOGAT to the ammonium assimilation in Arabidopsis (Arabidopsis thaliana Columbia) roots. Quantitative real‐time polymerase chain reaction (PCR) and protein gel blot analysis showed an accumulation of NADH‐GOGAT in response to ammonium supplied to the roots. In addition the localization of NADH‐GOGAT and Fd‐GOGAT did not fully overlap. Promoter–β‐glucuronidase (GUS) fusion analysis and immunohistochemistry showed that NADH‐GOGAT was highly accumulated in non‐green tissue like vascular bundles, shoot apical meristem, pollen, stigma and roots. Reverse genetic approaches suggested a reduction in glutamate production and biomass accumulation in NADH‐GOGAT transfer DNA (T‐DNA) insertion lines under normal CO₂ condition. The data emphasize the importance of NADH‐GOGAT in the ammonium assimilation in Arabidopsis roots.     

Altered expression of the PTR/NRT1 homologue OsPTR9 affects nitrogen utilization efficiency,growth and grain yield in rice

The plant PTR/NRT1 (peptide transporter/nitrate transporter 1) gene family comprises di/tripeptide and low‐affinity nitrate transporters; some members also recognize other substrates such as carboxylates, phytohormones (auxin and abscisic acid), or defence compounds (glucosinolates). Little is known about the members of this gene family in rice (Oryza sativa L.). Here, we report the influence of altered OsPTR9 expression on nitrogen utilization efficiency, growth, and grain yield. OsPTR9 expression is regulated by exogenous nitrogen and by the day‐night cycle. Elevated expression of OsPTR9 in transgenic rice plants resulted in enhanced ammonium uptake, promotion of lateral root formation and increased grain yield. On the other hand, down‐regulation of OsPTR9 in a T‐DNA insertion line (osptr9) and in OsPTR9‐RNAi rice plants had the opposite effect. These results suggest that OsPTR9 might hold potential for improving nitrogen utilization efficiency and grain yield in rice breeding.     

Arbuscular mycorrhiza influences carbon‐use efficiency and grain yield of wheat grown under pre‐ and post‐anthesis salinity stress

• Soil salinity severely affects and constrains crop production worldwide. Salinity causes osmotic and ionic stress, inhibiting gas exchange and photosynthesis, ultimately impairing plant growth and development. Arbuscular mycorrhiza (AM) have been shown to maintain light and carbon use efficiency under stress, possibly providing a tool to improve salinity tolerance of the host plants. Thus, it was hypothesized that AM will contribute to improved growth and yield under stress conditions.
• Wheat plants (Triticum aestivum L.) were grown with (AMF+) or without (AMF?) arbuscular mycorrhizal fungi (AMF) inoculation. Plants were subjected to salinity stress (200 mm NaCl) either at pre‐ or post‐anthesis or at both stages. Growth and yield components, leaf chlorophyll content as well as gas exchange parameters and AMF colonization were analysed.
• AM plants exhibited a higher rate of net photosynthesis and stomatal conductance and lower intrinsic water use efficiency. Furthermore, AM wheat plants subjected to salinity stress at both pre‐anthesis and post‐anthesis maintained higher grain yield than non‐AM salinity‐stressed plants.
• These results suggest that AMF inoculation mitigates the negative effects of salinity stress by influencing carbon use efficiency and maintaining higher grain yield under stress.

     

“Ecological Armageddon” – more evidence for the drastic decline in insect numbers

The efficient use of nitrogen by crops can minimise environmental risks and maximise returns to farmers. Under organic farming systems, this can be achieved by adjusting the fertilisation management and/or using genetic variability. Seven durum wheat (Triticum durum) cultivars and three emmer (Triticum dicoccum) cultivars were assessed under an organic farming system over a non‐consecutive 4‐year period (2005–11) in Foggia (southern Italy). The objectives were to investigate the agronomic and qualitative characteristics, and to evaluate the agronomic efficiency and adaptability according to three N fertilisation levels (0, 40, 80 kg N ha^?1). A split‐plot design was used, with three replications in each year. Nine traits were investigated: heading time, plant height, seed yield, number of spikes m^?2, harvest index, specific weight, 1000‐seed weight, and protein and gluten contents. Increasing N to 80 kg ha^?1 increased plant height (+7.3%), seed yield (+22.1%), spike density (+16.6%), and protein (+9.8%) and gluten (+2.1%) contents. The emmer genotypes and the oldest durum wheat ‘Cappelli’ showed the highest protein and gluten contents (mean, 13.9%, 11.2%, respectively). The maximum N agronomic efficiency [AE(N)] and N recovery efficiency [RE(N)] were seen for the modern durum wheat cultivars under 40 kg ha^?1 N treatment: ‘Duilio’, ‘Iride’ and ‘Varano’. The significant correlation between AE(N) and RE(N) and the year of release of the durum wheat cultivars (r = 0.53, P < 0.05, F = 4.7 for AE(N) and r = 0.57, P < 0.01, F = 5.7 for RE(N), respectively; n = 14) showed that the genetic breeding of this species for high grain yield is associated with an increase in the efficiency of N fertiliser use under organic farming. The highly significant effect for the Genotype × Environment interaction (F = 18.1, P < 0.001) of seed yield indicate the possibility to select for stable genotypes across environments. Based on the additive main effects and multiplicative interaction analysis, and the yield stability index, the varieties ‘Iride’ and ‘Varano’ show high‐stability responses and good seed yields under all N fertiliser treatments. Therefore, these varieties can be recommended for organic farming systems in Mediterranean areas.