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

Key message

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.

Abstract

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.

     

Strong increase of durum wheat iron and zinc content by field-inoculation with arbuscular mycorrhizal fungi at different soil nitrogen availabilities

Background and aims

The changes in the characteristics of Panicum virgatum, an exotic invasive species, after invading various plant communities on the Loess Plateau in China and the main soil nutrient factors in these communities closely associated with invasion remain unclear.

Methods

A pot culture experiment was carried out to simulate the changes in photosynthesis, biomass, and biomass allocation in P. virgatum and to identify the main soil nutrient factors in various soils collected from local plant communities. P. virgatum was grown in soils collected from communities of P. virgatum (PS treatment), Setaria viridis (SS treatment), Bothriochloa ischaemum (BS treatment), and Artemisia sacrorum (AS treatment) and in a mixed soil from the communities of S. viridis, B. ischaemum, and A. sacrorum (MS treatment).

Results

Photosynthesis in P. virgatum differed significantly among the soil treatments. Net photosynthetic rate, stomatal conductance, and photochemical efficiency (Fv/Fm) were highest in PS, whereas single-photon avalanche diode values were highest in PS and SS. The variation of biomass differed significantly in different tissues of P. virgatum in the treatments. Leaf and stem biomasses were highest in PS and SS, and root biomass was highest in PS and MS. Total biomass differed significantly among the treatments, except between BS and MS. Both the leaf to total and stem to total biomass ratios were highest in AS and SS, but the root to total biomass ratio was lowest in these two treatments. A constrained redundancy analysis and a path analysis suggested that the water-soluble nitrate-nitrogen (W-NN) concentration of the soil could significantly affect photosynthesis, biomass, and biomass allocation in P. virgatum.

Conclusions

Photosynthesis, biomass, and biomass allocation in P. virgatum differed significantly when grown in soils from different local plant communities on the Loess Plateau. The soil W-NN concentration in these local plant communities likely has a large impact on the invasive success of P. virgatum.

     

Responses of litter decomposition and nutrient release rate to water and nitrogen addition differed among three plant species dominated in a semi-arid grassland

Background and aims

Precipitation and nitrogen (N) deposition are predicted to increase in northern China. The present paper aimed to better understand how different dominant species in semi-arid grasslands in this region vary in their litter decomposition and nutrient release responses to increases in precipitation and N deposition.

Methods

Above-ground litter of three dominant species (two grasses, Agropyron cristatum and Stipa krylovii, and one forb, Artemisia frigida) was collected from areas without experimental treatments in a semi-arid grassland in Inner Mongolia. Litter decomposition was studied over three years to determine the effects of water and N addition on litter decomposition rate and nutrient dynamics.

Results

Litter mass loss and nutrient release were faster for the forb species than for the two grasses during decomposition. Both water and N addition increased litter mass loss of the grass A. cristatum, while the treatments showed no impacts on that of the forb A. frigida. Supplemental N had time-dependent, positive effects on litter mass loss of the grass S. krylovii. During the three-year decomposition study, the release of N from litter was inhibited by N addition for the three species, and it was promoted by water addition for the two grasses. Across all treatments, N and potassium (K) were released from the litter of all three species, whereas calcium (Ca) was accumulated. Phosphorus (P) and magnesium (Mg) were released from the forb litter but accumulated in the grass litter after three years of decomposition.

Conclusions

Our findings revealed that the litter decomposition response to water and N supplementation differed among dominant plant species in a semi-arid grassland, indicating that changes in dominant plant species induced by projected increases in precipitation and N deposition are likely to affect litter decomposition, nutrient cycling, and further biogeochemical cycles in this grassland. The asynchronous nutrient release of different species’ litter found in the present study highlights the complexity of nutrient replenishment from litter decomposition in the temperate steppe under scenarios of enhancing precipitation and N deposition.

     

Comparative Genomics and Synteny Analysis of <Emphasis Type="BoldItalic">KCS17</Emphasis>-<Emphasis Type="BoldItalic">KCS18</Emphasis> Cluster Across Different Genomes and Sub-genomes of Brassicaceae for Analysis of Its Evolutionary History

Comparative genomics-based synteny analysis has proved to be an effective strategy to understand evolution of genomic regions spanning a single gene (micro-unit) to large segments encompassing hundreds of kilobases to megabases. Brassicaceae is in a unique position to contribute to understanding genome and trait evolution through comparative genomics because whole genome sequences from as many as nine species have been completed and are available for analysis. In the present work, we compared genomic loci surrounding the KCS17-KCS18 cluster across these nine genomes. KCS18 or FAE 1 gene encodes beta-ketoacyl synthase, (β-KCS) a membrane-bound enzyme that catalyses the key rate-limiting step during synthesis of VLCFAs such as erucic acid (C22) present in seed oil in Brassicaceae by elongating carbon chain from C18 to C22; knowledge on role of KCS17 in plant development is however lacking. Synteny across the genomic segments harbouring FAE1 showed variable levels of gene retention ranging between 26% (Arabidopsis thaliana and Brassica napus C03) and 89% (between A. thaliana and Brassica rapa A01), and gene density ranged between 1 gene/2.86 kb and 1 gene/4.88 kb. Interestingly, in diploid Brassica species, FAE1 was retained in only one of the sub-genomes in spite of the presence of three sub-genomes created as a result of genome triplication; in contrast, FAE1 was present at three loci, with four copies in Camellina sativa which is also known to have experienced a recent genome triplication revealing contrasting fates upon duplication. The organization of KCS17 and KCS18 as head-to-tail cluster was conserved across most of the species, except the C genome containing Brassicas, namely B. oleracea and B. napus, where disruptions because of other genes were observed. Even in the conserved blocks, the distance between KCS17 and KCS18 varied; the functional implication of the organization of KCS17-KCS18 as a cluster vis-à-vis fatty acid biosynthesis needs to be dissected, as the cis-regulatory region is expected to be present in the intergenic space. Phylogenetic analysis of KCS gene family along with KCS17-KCS18 from members of Brassicaceae reveals their ancestral relationship with KCS8-KCS9 block. Further comparative functional analysis between KCS8, KCS9, KCS16, KCS17 and KCS18 across evolutionary time-scale will be required to understand the conservation or diversification of roles of these members of KCS family in fatty acid biosynthesis during course of evolution.     

Time-resolved infrared spectroscopy in the study of photosynthetic systems

Time-resolved (TR) infrared (IR) spectroscopy in the nanosecond to second timescale has been extensively used, in the last 30 years, in the study of photosynthetic systems. Interesting results have also been obtained at lower time resolution (minutes or even hours). In this review, we first describe the used techniques—dispersive IR, laser diode IR, rapid-scan Fourier transform (FT)IR, step-scan FTIR—underlying the advantages and disadvantages of each of them. Then, the main TR-IR results obtained so far in the investigation of photosynthetic reactions (in reaction centers, in light-harvesting systems, but also in entire membranes or even in living organisms) are presented. Finally, after the general conclusions, the perspectives in the field of TR-IR applied to photosynthesis are described.     

The Psilostomidae Looss, 1900 (<Emphasis Type="Italic">sensu stricto</Emphasis>) (Digenea: Echinostomatoidea): description of three new genera and a key to the genera of the family

Three new psilostomid genera, Byrdtrema n. g., Longisaccus n. g. and Macracetabulum n. g., each with a single species, are described from ducks, Aix sponsa (L.) and Bucephala albeola (L.) in North America. Byrdtrema n. g. and Macracetabulum n. g. possess a bipartite seminal vesicle and share this character with four psilostomid genera, Grysoma Byrd, Bogitsh & Maples, 1961, Neopsilotrema Kudlai, Pulis, Kostadinova & Tkach, 2016, Psilostomum Looss, 1899 and Psilotornus Byrd & Prestwood, 1969. Byrdtrema n. g. differs from Macracetabulum n. g. in the shape of the body (elongate vs elongate-oval); the position of the ventral sucker (in first third of body vs just pre-equatorial); the shorter forebody; as well as in the smaller size of the eggs in relation to body length. Both new genera differ from (i) Grysoma by the nature of the vitellarium (large, compact follicles with small vitelline cells vs weakly defined follicles with large vitelline cells, respectively) and the smaller size of the eggs in relation to body length; (ii) Psilostomum in the posterior extend of the cirrus-sac in relation to ventral sucker (slightly posterior vs more posterior), the location of the genital pore (at the level of oesophagus vs just postbifurcal), the shorter length of uterine and longer post-testicular fields in relation to body length, and the anterior limits of vitellarium (at the level of ventral sucker vs posterior to ventral sucker); (iii) Psilotornus by the presence of a muscular pharynx (vs absent or rudimentary) and the location of the cirrus-sac (antero-dorsal to ventral sucker or more posterior vs entirely anterior to ventral sucker) and ovary (in hindbody vs in forebody). Byrdtrema n. g. differs from Neopsilotrema in the shape of the body (elongate vs subspherical to elongate-oval) and ventral sucker (elongate-oval vs subspherical to transversely oval), the shorter forebody and smaller eggs in relation to body length. Macracetabulum n. g. differs from Neopsilotrema by the shape of the ventral sucker (elongate-oval vs subspherical to transversely oval), the anterior limits of vitellarium (level of middle of ventral sucker vs level of intestinal bifurcation or anterior testis); and the slightly smaller size of eggs in relation to body length. Among the psilostomid genera, Longisaccus n. g. shows close affinities to Psilochasmus Lühe, 1909 in the presence of the long cirrus-sac and tubular internal seminal vesicle but can be clearly distinguished from the latter by the absence of the retractile tail-like process. In combination with molecular data, the above differences justify the recognition of three new genera. A key to the genera of the Psilostomidae is provided.     

<Emphasis Type="Italic">Lobocapillaria austropacifica</Emphasis> n. g., n. sp. (Nematoda: Capillariidae) from the obtuse barracuda <Emphasis Type="Italic">Sphyraena obtusata</Emphasis> Cuvier (Sphyraenidae,Perciformes) off eastern Australia

Based on light and scanning electron microscopical studies, a new nematode parasite, Lobocapillaria austropacifica n. sp. (Capillariidae), is described from the gall-bladder of the marine fish (obtuse barracuda) Sphyraena obtusata Cuvier (Perciformes: Sphyraenidae) from off the eastern Pacific coast of Australia, for which a new genus Lobocapillaria n. g. is established. This new genus is mainly characterised by a single row of stichocytes, the presence of two large, conspicuously elongated lateral caudal lobes and a pair of subventral papillae at their base in males, a flat spicule distended laterally towards its proximal end and provided with superficial rough transverse grooves, a spicular canal and a very long, aspinose spicular sheath with a conspicuous expansion near its proximal end when evaginated. Capillaria sphyraeni Parukhin, 1971 is transferred to Lobocapillaria as L. sphyreni (Parukhin, 1971) n. comb. A key to capillariid genera containing species parasitic in fishes is provided.     

Filling the gaps in the classification of the Digenea Carus, 1863: systematic position of the Proterodiplostomidae Dubois, 1936 within the superfamily Diplostomoidea Poirier, 1886, inferred from nuclear and mitochondrial DNA sequences

The Diplostomida Olson, Cribb, Tkach, Bray & Littlewood, 2003 is the less diverse order of the two orders within the subclass Digenea Carus, 1863 and is currently classified into three superfamilies, i.e. Brachylaimoidea Joyeux & Foley, 1930, Diplostomoidea Poirier, 1886, and Schistosomatoidea Stiles & Hassall, 1898. Although the suprageneric-level relationships have been elucidated with the use of molecular markers, the lack of representation of some groups obscure the phylogenetic relationships among families, rendering the classification unstable. Here, we tested the phylogenetic position of the family Proterodiplostomidae Dubois, 1936 based on partial 28S rDNA and complete 18S rDNA sequences for Crocodilicola pseudostoma (Willemoes-Suhm, 1870), a crocodile parasite that has been found as a progenetic metacercaria parasitising the pale catfish Rhamdia guatemalensis (Günther) in Mexico and in other siluruforms in the Neotropics. We augmented the representation of the species, genera and families within the Diplostomida, including mostly representatives of the superfamily Diplostomoidea, and assembled a dataset that contains 49 species for the 28S rRNA gene, and 45 species for the 18S rRNA gene. Additionally, we explored the phylogenetic signal of the mitochondrial gene cox1 in reconstructing the phylogenetic relationships of selected members of the superfamily. Our analyses showed that the family Proterodiplostomidae is the sister taxon to the paraphyletic Diplostomidae Poirier, 1886 and Strigeidae Railliet, 1919, with Cyathocotylidae Mühling, 1898 + Brauninidae Wolf, 1903 as their sister group. Analysis of concatenated 18S + 28S sequences revealed the Liolopidae Odhner, 1912 as the basal group of the superfamily Diplostomoidea, although analyses of independent datasets showed that the position of this family remains uncertain. Analysis based on cox1 unequivocally resolved the Proterodiplostomidae as the sister taxon to the Diplostomidae and Strigeidae, although the Cyathocotylidae was nested in a different clade, along with brachylaimoids and schistosomatoids.