Identification of favorable alleles in the <Emphasis Type="Italic">non</Emphasis>-<Emphasis Type="Italic">yellow coloring 1</Emphasis> gene by association mapping in maize

Association mapping was conducted to explore favorable alleles of the chlorophyll-related non-yellow coloring 1 (NYC1) gene under light and dark using an association panel of 146 maize inbred lines. A total of 14 polymorphic sites were identified to be significantly associated with at least one of the chlorophyll-related traits at the seedling stage. Four single nucleotide polymorphisms (SNPs) (S320, S2951, S3901, and S3355) from the NYC1 gene were respectively strongly associated with chlorophyll b (chlb), the ratio of chlorophyll a to chlorophyll b (chl_ratio), chlorophyll a degradation (chla_deg), and total chlorophyll degradation (total_chl_deg). SNPs S320 (C/A) in exon 1, and S2951 (A/G) in intron 8 was related to chlb, with 6.01 and 8.89% of phenotypic variation under light treatment, respectively. Under dark treatment, SNP S3901 (C/T), located in 3′ untranslated region (3′UTR), was associated with chl_ratio, explaining 7.01% of the observed phenotypic variation, whereas SNP S3355 (C/G) in intron 9 explained 6.48 and 5.18% of phenotypic variations in chla_deg and total_chl_deg, respectively. Taken together, these results indicated that the NYC1 gene plays an important role in chlorophyll content and other related traits, and different sites act on chlorophyll metabolism under different light intensities in maize seedlings. Furthermore, these findings improve our understanding of the genetic basis of chlorophyll metabolism under different light conditions.     

QTL mapping and analysis of epistatic interactions for grain yield and yield-related traits in <Emphasis Type="Italic">Triticum turgidum</Emphasis> L. var. <Emphasis Type="Italic">durum</Emphasis>

A quantitative trait loci (QTL) analysis of grain yield and yield-related traits was performed on 93 durum wheat recombinant inbred lines derived from the cross UC1113 × Kofa. The mapping population and parental lines were analyzed considering 19 traits assessed in different Argentine environments, namely grain yield, heading date, flowering time, plant height, biomass per plant, and spikelet number per ear, among others. A total of 224 QTL with logarithm of odds ratio (LOD) ≥ 3 and 47 additional QTL with LOD > 2.0 were detected. These QTL were clustered in 35 regions with overlapping QTL, and 12 genomic regions were associated with only one phenotypic trait. The regions with the highest number of multi-trait and stable QTL were 3BS.1, 3BS.2, 2BS.1, 1BL.1, 3AL.1, 1AS, and 4AL.3. The effects of epistatic QTL and QTL × environment interactions were also analyzed. QTL putatively located at major gene loci (Rht, Vrn, Eps, and Ppd) as well as additional major/minor QTL involved in the complex genetic basis of yield-related traits expressed in Argentine environments were identified. Interestingly, the 3AL.1 region was found to increase yield without altering grain quality or crop phenology.     

Development and application of a molecular marker for TMV resistance based on <Emphasis Type="Italic">N</Emphasis> gene in tobacco (<Emphasis Type="Italic">Nicotiana tabacum</Emphasis>)

Tobacco mosaic virus (TMV) caused serious loss in yield and quality of tobacco every year. It is a long-term goal to improve the tobacco resistance against TMV by tobacco breeding. N gene was the firstly reported TMV-resistant gene, which showed resistance against all Tobamoviruses except the Ob stain and belonged to the toll-interleukin-1 receptor/nucleotide-binding site/leucine-rich repeat class of plant resistance (R) genes. At present, N gene had already been widely used in tobacco conventional breeding, but there is rare available molecular maker used in marker-assisted selection of TMV resistance. In this study, we designed a pair of primers that specific amplify N gene fragment based on the sequence of N gene intron III, named N-marker. Then, we identified TMV resistance by two selecting methods, PCR with N-marker and inoculated with the TMV-C strain. Results from the two method showed that (1) 13 varieties among 67 tobacco varieties displayed hypersensitive reaction when inoculated with the TMV-C strain, also contained N gene fragments screened by PCR with N-marker; (2) 105 strains of 200 BC1 strains showed resistance against TMV when inoculated with TMV-C strain, meanwhile, 103 of the 105 strains contained N gene fragment verified by PCR with N-marker. Therefore, the N-marker is reliable for high throughput screening of germplasm resources and tobacco breeding materials in selection of N-mediated TMV resistance. Our study not only developed a molecular marker for tobacco breeding, but also identified new germplasm resources that are resistant to TMV.     

Resistance screening of breeding lines and commercial tomato cultivars for <Emphasis Type="Italic">Meloidogyne incognita</Emphasis> and <Emphasis Type="Italic">M. javanica</Emphasis> populations (Nematoda) from Ethiopia

Soil and root samples were collected from major tomato growing areas of Ethiopia during the 2012/2013 growing season to identify root-knot nematode problems. DNA-based and isozyme techniques revealed that Meloidogyne incognita and M. javanica were the predominant Meloidogyne species across the sampled areas. The aggressiveness of different populations of these species was assessed on tomato cultivars Marmande and Moneymaker. The two most aggressive populations of each species were selected and further tested on 33 tomato genotypes. The resistance screening and mechanism of resistance was performed after inoculation with 100 freshly hatched (<24 h) second-stage juveniles (J2). Eight weeks after inoculation the number of egg masses produced on each cultivar was assessed. For the resistance mechanism study, J2 penetration and their subsequent development inside the tomato roots were examined at 1, 2, 4 and 6 weeks after inoculation. On both cultivars Marmande and Moneymaker all M. incognita and M. javanica populations formed a high number of egg masses indicating highly aggressive behaviour. Populations from ‘Jittu’ and ‘Babile’ for M. incognita and ‘Jittu’ and ‘Koka’ for M. javanica were selected as most aggressive. None of the 33 tomato genotypes were immune for these M. incognita and M. javanica populations. However, several tomato genotypes were found to have a significant effect on the number of egg masses produced indicating possible resistance. For M. javanica populations there were more plants from cultivars or breeding lines on which no egg masses were found compared to M. incognita populations. The lowest number of egg masses for both populations of M. incognita was produced on cultivars Bridget40, Galilea, and Irma while for M. javanica it was on Assila, Eden, Galilea, Tisey, CLN-2366A, CLN-2366B and CLN-2366C. Tomato genotypes, time (weeks after inoculation) and their interaction were significant sources of variation for J2 penetration and their subsequent development inside the tomato roots. Differential penetration was found in breeding lines such as CLN-2366A, CLN-2366B and CLN-2366C, but many of the selected tomato genotypes resistance for the tested M. incognita and M. javanica populations were expressed by delayed nematode development. Therefore, developing a simple screening technique to be used by local farmers or extension workers is crucial to facilitate selection of a suitable cultivar.     

Induced expression of selected plant defence related genes in pot azalea, <Emphasis Type="Italic">Rhododendron simsii</Emphasis> hybrid

A set of putative marker genes to study plant defense responses against Polyphagotarsonemus latus, a key pest in the production of Rhododendron simsii hybrids, was selected and validated. Genes belonged to the biosynthetic pathway of phytohormones jasmonic acid (JA) (RsLOX, RsAOS, RsAOC, RsOPR3 and RsJMT) and salicylic acid (SA) (RsPAL and RsICS). Furthermore, RsPPO, a putative marker gene for oxidative stress response was successfully cloned from R. simsii. A CTAB-based extraction protocol was optimized to assure excellent RNA quality for subsequent RT-qPCR analysis. The RT-qPCR protocol was extensively tested and RsRG7 and RsRG14 were selected as reference genes from a geNorm pilot study. Validation of the marker genes was done after application with elicitors [methyl jasmonate (MeJA), coronatine, β-aminobutyric acid and acibenzolar-Smethyl] or wounding. Both 100 μM MeJA and 0.1 μM coronatine had a significant effect on the expression of all marker genes. Foliar application of MeJA on the shoots resulted in a significantly earlier response when compared to root application and subsequent sampling of the shoots. Expression patterns after MeJA treatment were generally the same in six R. simsii genotypes: ‘Nordlicht’, ‘Elien’, ‘Aiko Pink’, ‘Michelle Marie’, ‘Mevrouw Gerard Kint’ and ‘Sachsenstern’. Wounding resulted in the same expression patterns as MeJA treatment except for RsJMT. None of the genotypes showed a significant induction of the latter gene 6 h upon wounding. Findings of these experiments indicated that the tolerant genotype ‘Elien’ has low basal expression levels of RsPPO. This might be the first step towards the breeding of mite-tolerant genotypes.     

Digestive Enzyme Activity during Larval Development of Black Snook,Centropomus nigrescens

Black snook, Centropomus nigrescens, have been identified as a promising candidate for aquaculture although, like many of the Centropomid species, high mortality associated with early larval stages presents a significant bottleneck to their commercialization. The digestive capacity of black snook larvae throughout the first 37 d after hatch (d.a.h.) was evaluated by quantifying digestive enzyme activities using biochemical techniques. Results showed that black snook larvae have alkaline proteases at hatching, which are known to be important during the first days of feeding for digestion. Toward the end of the study, acid proteases concentration increased (37 d.a.h.). Enzymes for lipid digestion, pancreatic lipase and bile salt‐activated lipase, were already present in the larvae before exogenous feeding commenced, and their activity increased with age and growth (length). Intracellular digestion, measured as the activity of leucine‐alanine peptidase, was high early on (5 d.a.h.) and decreased as development progressed (next 32 d). In contrast, alkaline phosphatase activity was lowest at first feeding and subsequently increased with age. Overall patterns in enzyme activity suggest the possibility of live feed weaning before 32 d.a.h. if artificial diets can be properly balanced.     

A multi-method approach to delineate and validate migratory corridors

Context

Managers are faced with numerous methods for delineating wildlife movement corridors, and often must make decisions with limited data. Delineated corridors should be robust to different data and models.

Objectives

We present a multi-method approach for delineating and validating wildlife corridors using multiple data sources, which can be used conserve landscape connectivity. We used this approach to delineate and validate migration corridors for wildebeest (Connochaetes taurinus) in the Tarangire Ecosystem of northern Tanzania.

Methods

We used two types of locational data (distance sampling detections and GPS collar locations), and three modeling methods (negative binomial regression, logistic regression, and Maxent), to generate resource selection functions (RSFs) and define resistance surfaces. We compared two corridor detection algorithms (cost-distance and circuit theory), to delineate corridors. We validated corridors by comparing random and wildebeest locations that fell within corridors, and cross-validated by data type.

Results

Both data types produced similar RSFs. Wildebeest consistently selected migration habitat in flatter terrain farther from human settlements. Validation indicated three of the combinations of data type, modeling, and corridor detection algorithms (detection data with Maxent modeling, GPS collar data with logistic regression modeling, and GPS collar data with Maxent modeling, all using cost-distance) far outperformed the other seven. We merged the predictive corridors from these three data-method combinations to reveal habitat with highest probability of use.

Conclusions

The use of multiple methods ensures that planning is able to prioritize conservation of migration corridors based on all available information.

     

Participatory mapping of landscape values in a Pan-European perspective

Context

Human–nature interactions are reflected in the values people assign to landscapes. These values shape our understanding and actions as landscape co-creators, and need to be taken into account to achieve an integrated management of the landscape that involves civil society.

Objectives

The aim of this research was to increase the current knowledge on the most and least common landscape values perceived by local stakeholders, the patterns in the spatial distribution of values, and their connection to different socio-economic backgrounds and landscape characteristics across Europe.

Methods

The research consisted of a cross-site comparison study on how landscape values are perceived in six areas of Europe using Public Participation GIS surveys. Answers were analysed combining contingency tables, spatial autocorrelation and bivariate correlation methods, kernel densities, land cover ratios, and viewshed analyses. Results were discussed in the light of findings derived from other European participatory mapping studies.

Results

We identified shared patterns in the perception of landscape values across Europe. Recreation, aesthetics, and social fulfilment were the most common values. Landscape values showed common spatial patterns mainly related to accessibility and the presence of water, settlements, and cultural heritage. However, respondents in each study site had their own preferences connected to the intrinsic characteristics of the local landscape and culture.

Conclusions

The results encourage land planners and researchers to approach landscape values in relation to socio-cultural and bio-physical land characteristics comprehensibly, acknowledging the complexity in the relationship between people’s perception and the landscape, to foster more effective and inclusive landscape management strategies.

     

CRISPR-Cas Technology in Plant Science

CRISPR-Cas technology has raised considerable interest among plant scientists, both in basic science and in plant breeding. Presently, the generation of random mutations at a predetermined site of the genome is well mastered, just like the targeted insertion of transgenes, although both remain restricted to species or genotypes amenable for plant transformation. On the other hand, true genome editing, i.e. the deliberate replacement of one or several nucleotides of the genome in a predetermined fashion, is limited to some rather particular examples that generally concern genes allowing positive selection, for example tolerance to herbicides. Therefore, further technological developments are necessary to fully exploit the potential of genome editing in enlarging the gene pool beyond the natural variability available in a given species. In principle, the technology can be applied to any quality related, agronomical or ecological trait, under the condition of upstream knowledge on the genes to be targeted and the precise modifications necessary to improve alleles. Published proof of concepts concern a wide range of agronomical traits, the most frequent being disease resistance, herbicide tolerance and the biochemical composition of harvested products. The regulatory status of the plants obtained by CRISPR-Cas technology raises numerous questions, in particular with regard to the plants that carry in their genomes the punctual modifications caused by the presence of the Cas9 nuclease but not the nuclease itself. Without clarification by the competent authorities, CRISPR-Cas technology would continue to be a powerful tool in functional genomics, but its potential in plant breeding would remain untapped.