Crop mixtures: does niche complementarity hold for belowground resources? An experimental test using rice genotypic pairs

Aims

A growing body of research supports the feasibility of biocrust rehabilitation. Identifying populations of key species that are amenable to cultivation and that are resilient in rehabilitation contexts would advance the efficacy of these technologies. Here we investigate the growth and stress response of the cosmopolitan biocrust moss, Syntrichia ruralis.

Methods

We sampled populations of S. ruralis along a precipitation seasonality gradient from the Colorado Plateau ecoregion of the western United States. We cultivated these populations in an experiment manipulating duration of hydration periods on a weekly cycle. We then treated greenhouse grown materials with brief, stressful watering events, measuring how many events they could survive.

Results

All populations grew at an accelerated rate compared to growth in a natural setting, at least doubling biomass in five months. Increasing duration of hydration periods led to more growth in all but one population. Volunteer biocrust algae and cyanobacteria developed during cultivation, and differed among populations. Greenhouse grown mosses differed in their response to stressful watering, with the most susceptible populations dying at half the number events compared to the most tolerant.

Conclusions

These findings argue for informed selection and deployment of Syntrichia ruralis populations for soil rehabilitation.

     

Prevalence of cytomegalovirus infection and its role in total immunoglobulin pattern in Iranian patients with different subtypes of multiple sclerosis

Multiple sclerosis (MS) is the most common autoimmune disease characterized by multifocal areas of inflammatory demyelination within the central nervous system. Cytomegalovirus (CMV) has a complex pathobiology and in most cases is simply asymptomatic. There is some recent controversy over the role of CMV in the pathology of MS. The aim of this study was to evaluate active CMV infection and its effect on the humoral immunity in patients with MS. Serum, plasma, peripheral blood mononuclear cells (PBMCs), saliva and urine collected from MS patients (n=78) and healthy subjects (n=123) were screened for the presence of anti-CMV antibodies and CMV-DNA by nephelometric and PCR methods. Concentrations of total antibodies in MS subtypes were measured using both nephelometric and enzyme linked fluorescent assay (ELFA) techniques. The results extend the observation of an increased frequency of CMV-DNA in patients, in contrast with controls (p<0.001). Furthermore, systemic CMV infections were found in 25.5% of patients and only 3.2% of controls (p<0.001). There was significant difference in the titers of anti-CMV IgG and total IgE in patient and controls (P<0.001). These results support the hypothesis that CMV may contribute to MS thought to establish systemic infection process and induce immune response.     

Positional cloning of the rice male sterility gene ms-IR36, widely used in the inter-crossing phase of recurrent selection schemes

The monogenetic recessive male-sterile gene ms-IR36 is widely used to facilitate the inter-crossing phase of recurrent selection in rice (Oryza sativa), but its segregation within the progeny disturbs other breeding phases. Marker-assisted early identification of msms and Msms seedlings would help overcome this drawback. Using successively bulked segregant analysis and large F2 populations, we mapped the ms-IR36 gene to a 33-kb region on the short arm of chromosome 2 that includes 10 candidate genes. Sequencing of these candidates together with checking rice genome annotations and expression databases allowed the target to be narrowed down to one candidate gene already isolated and characterized as the tapetum degeneration retardation (TDR) gene and reported to be involved in tapetal programmed cell death. Comparison of the sequence of the TDR gene between male-sterile (MS) and male-fertile (MF) IR36 plants detected one non-synonymous nucleotide substitution affecting the active domain of the encoded protein. Perfect co-segregation was observed between polymorphism at this nucleotide (SNP) and the MS/MF phenotype of 946 F2 plants. Spatial modelling of the active domain of the candidate protein reinforced the candidate status of the only SNP identified. Histological characterization of anther development in MS IR36 revealed defects identical to the ones observed in mutants used for the isolation and characterization of the TDR gene: delayed/non-degradation of tapetum tissue and collapse of the haploid microspores. We concluded that ms-IR36 corresponded to the TDR gene with a different mutation from the earlier one described in the same gene. No significant linkage drag was associated with ms-IR36. A SNP-based marker that enables simple early identification of MS plants and MF plants with the Msms genotype was designed.     

Genome-Wide Association Mapping of Root Traits in a Japonica Rice Panel

Rice is a crop prone to drought stress in upland and rainfed lowland ecosystems. A deep root system is recognized as the best drought avoidance mechanism. Genome-wide association mapping offers higher resolution for locating quantitative trait loci (QTLs) than QTL mapping in biparental populations. We performed an association mapping study for root traits using a panel of 167 japonica accessions, mostly of tropical origin. The panel was genotyped at an average density of one marker per 22.5 kb using genotyping by sequencing technology. The linkage disequilibrium in the panel was high (r²>0.6, on average, for 20 kb mean distances between markers). The plants were grown in transparent 50 cm × 20 cm × 2 cm Plexiglas nailboard sandwiches filled with 1.5 mm glass beads through which a nutrient solution was circulated. Root system architecture and biomass traits were measured in 30-day-old plants. The panel showed a moderate to high diversity in the various traits, particularly for deep (below 30 cm depth) root mass and the number of deep roots. Association analyses were conducted using a mixed model involving both population structure and kinship to control for false positives. Nineteen associations were significant at P<1e-05, and 78 were significant at P<1e-04. The greatest numbers of significant associations were detected for deep root mass and the number of deep roots, whereas no significant associations were found for total root biomass or deep root proportion. Because several QTLs for different traits were co-localized, 51 unique loci were detected; several co-localized with meta-QTLs for root traits, but none co-localized with rice genes known to be involved in root growth. Several likely candidate genes were found in close proximity to these loci. Additional work is necessary to assess whether these markers are relevant in other backgrounds and whether the genes identified are robust candidates.     

Accuracy of Genomic Selection in a Rice Synthetic Population Developed for Recurrent Selection Breeding

Genomic selection (GS) is a promising strategy for enhancing genetic gain. We investigated the accuracy of genomic estimated breeding values (GEBV) in four inter-related synthetic populations that underwent several cycles of recurrent selection in an upland rice-breeding program. A total of 343 S_2:4 lines extracted from those populations were phenotyped for flowering time, plant height, grain yield and panicle weight, and genotyped with an average density of one marker per 44.8 kb. The relative effect of the linkage disequilibrium (LD) and minor allele frequency (MAF) thresholds for selecting markers, the relative size of the training population (TP) and of the validation population (VP), the selected trait and the genomic prediction models (frequentist and Bayesian) on the accuracy of GEBVs was investigated in 540 cross validation experiments with 100 replicates. The effect of kinship between the training and validation populations was tested in an additional set of 840 cross validation experiments with a single genomic prediction model. LD was high (average r² = 0.59 at 25 kb) and decreased slowly, distribution of allele frequencies at individual loci was markedly skewed toward unbalanced frequencies (MAF average value 15.2% and median 9.6%), and differentiation between the four synthetic populations was low (F_ST ≤0.06). The accuracy of GEBV across all cross validation experiments ranged from 0.12 to 0.54 with an average of 0.30. Significant differences in accuracy were observed among the different levels of each factor investigated. Phenotypic traits had the biggest effect, and the size of the incidence matrix had the smallest. Significant first degree interaction was observed for GEBV accuracy between traits and all the other factors studied, and between prediction models and LD, MAF and composition of the TP. The potential of GS to accelerate genetic gain and breeding options to increase the accuracy of predictions are discussed.     

Detecting selection along environmental gradients: analysis of eight methods and their effectiveness for outbreeding and selfing populations

Thanks to genome‐scale diversity data, present‐day studies can provide a detailed view of how natural and cultivated species adapt to their environment and particularly to environmental gradients. However, due to their sensitivity, up‐to‐date studies might be more sensitive to undocumented demographic effects such as the pattern of migration and the reproduction regime. In this study, we provide guidelines for the use of popular or recently developed statistical methods to detect footprints of selection. We simulated 100 populations along a selective gradient and explored different migration models, sampling schemes and rates of self‐fertilization. We investigated the power and robustness of eight methods to detect loci potentially under selection: three designed to detect genotype–environment correlations and five designed to detect adaptive differentiation (based on F_ST or similar measures). We show that genotype–environment correlation methods have substantially more power to detect selection than differentiation‐based methods but that they generally suffer from high rates of false positives. This effect is exacerbated whenever allele frequencies are correlated, either between populations or within populations. Our results suggest that, when the underlying genetic structure of the data is unknown, a number of robust methods are preferable. Moreover, in the simulated scenario we used, sampling many populations led to better results than sampling many individuals per population. Finally, care should be taken when using methods to identify genotype–environment correlations without correcting for allele frequency autocorrelation because of the risk of spurious signals due to allele frequency correlations between populations.     

Effect of Organic Zinc,Manganese, Copper,and Selenium Chelates on Colostrum Production and Reproductive and Lameness Indices in Adequately Supplemented Holstein Cows

The current study aimed to investigate if different sources of supplemental zinc (Zn), manganese (Mn), copper (Cu), and selenium (Se) fed to dry and lactating dairy cows affect reproductive performance, lameness status, and colostrum production. The experiment was carried out on 60 multiparous non-lactating Holstein cows in a commercial dairy herd. The cows received randomly mineral mixtures in three treatment groups containing inorganic, 25% organic–75% inorganic, or 50% organic–50% inorganic forms of Zn, Mn, Cu, and Se starting from approximately 3 weeks prior to calving up to 90 days postpartum. Supplements were included in rations and fed twice a day. Reproductive parameters including days to first service, days to first estrus, service per conception, and conception rate were investigated. After parturition, colostrum production, composition, and immunoglobulin G₁ concentration were determined. Lameness, as an indicator of trace minerals deficiency, was evaluated in a five-score scale. The source of mineral supplement only numerically improved the assessed parameters excluding colostrum fat, protein, and ash percent. The organic form of supplements did not significantly affect reproductive performance, lameness score, or colostrum production.     

Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations

Genotyping by sequencing (GBS) is the latest application of next-generation sequencing protocols for the purposes of discovering and genotyping SNPs in a variety of crop species and populations. Unlike other high-density genotyping technologies which have mainly been applied to general interest “reference” genomes, the low cost of GBS makes it an attractive means of saturating mapping and breeding populations with a high density of SNP markers. One barrier to the widespread use of GBS has been the difficulty of the bioinformatics analysis as the approach is accompanied by a high number of erroneous SNP calls which are not easily diagnosed or corrected. In this study, we use a 384-plex GBS protocol to add 30,984 markers to an indica (IR64) × japonica (Azucena) mapping population consisting of 176 recombinant inbred lines of rice (Oryza sativa) and we release our imputation and error correction pipeline to address initial GBS data sparsity and error, and streamline the process of adding SNPs to RIL populations. Using the final imputed and corrected dataset of 30,984 markers, we were able to map recombination hot and cold spots and regions of segregation distortion across the genome with a high degree of accuracy, thus identifying regions of the genome containing putative sterility loci. We mapped QTL for leaf width and aluminum tolerance, and were able to identify additional QTL for both phenotypes when using the full set of 30,984 SNPs that were not identified using a subset of only 1,464 SNPs, including a previously unreported QTL for aluminum tolerance located directly within a recombination hotspot on chromosome 1. These results suggest that adding a high density of SNP markers to a mapping or breeding population through GBS has a great value for numerous applications in rice breeding and genetics research.