Genetics and molecular mapping of the naked grains in hexaploid oat

Avena sativa L. subsp. nudisativa has the ability to produce naked grains. Genetic studies on the naked trait of oat began over a century ago, but the genetic and molecular factors associated with the expression of this trait have not been fully clarified. The objectives of this study were to evaluate the naked trait in two oat populations of recombinant inbred lines (RILs), to determine the number of genes, to estimate the heritability, and to map genomic regions associated with the naked trait in hexaploid oat. Parental lines and RILs of each population were screened for the naked trait from plants grown in the field over a 2 year period. Based on the phenotypic data, the oat RILs were classed as naked, partially naked, partially hulled and hulled. In both populations and years, a great number of RILs showed variable expressivity for the naked trait. The genetic analysis indicated the action of a major gene (N1) with the action of modifying genes controlling the formation of naked grains. The results of the estimate of heritability show that environmental conditions do not have a great influence in determining the naked trait. The quantitative trait loci analysis detected a genomic region with a large effect on the naked trait that explained more than 50% of the phenotypic variation. Further studies are needed to validate the use of these molecular markers to assist breeding programs to select high quality and stable naked oat cultivars.     

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.     

Characterization of common bean wild populations for their in situ conservation in Northwestern Argentina

In situ conservation of wild species is a method of conservation that allows keeping populations in their natural environments, and set the strategies for maintaining the natural populations. The Active Bank of Northwestern Argentina (BANOA) is in charge of the in situ conservation of wild populations of common bean (Phaseolus vulgaris L.) in Northwestern Argentina (NOA), and has an ex situ collection of 401 landraces and 221 wild accessions from the NOA. We evaluated the phenotypic diversity of 68 common bean wild populations from the NOA both in protected and unprotected areas, finding a moderate variation among them. Ten phenotypic reproductive characteristics related to pod and seed displayed significant differences in the analysis of variance; these traits together with the seed weight were the basis for the multivariate analysis. The cluster analysis ordered the populations in 12 groups but trends in geographical distribution or phenotypical variation were not recognized. For the conservation in situ of the wild bean populations, their diversity should be considered. Two types of populations can be highlighted: (i) candidates for in situ conservation in order to preserve the novel variation generated by convergence with cultivated sympatric germplasm (populations 433, 437, 471, 509, 513 and 517) and (ii) those whose phenotype represents clearly the wild status and should be preserved in situ as such in their current status (populations 480, 495, 496, 525 and 533).     

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.     

Evaluation of carbon sources,gelling agents,growth hormones and additives for efficient callus induction and plant regeneration in Indian wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.) genotypes using mature embryos

Various factors affecting in vitro regeneration like different carbon sources, different gelling agents, and growth additives were assessed comprehensively for callus induction and plant regeneration for five Indian wheat cultivars using mature embryos as the explants for the first time. The tissue culture responses of cultivars WH-1105, HD-2967, and PBW-343 have not been reported earlier. Besides, the effect of different concentrations of the cytokinin, zeatin has also been optimized. Using the optimized factors, the efficiency of five different varieties, i.e., HD 2967, C 306, RAJ 3765, WH 1105, and PBW 343 was evaluated for regeneration. Modified MS basal medium containing dicamba reduced precocious germination of the embryo and induced embryogenic callus more efficiently. Removal of embryogenic calli from non-regenerable structures during early callus phase improved plant regeneration. These calli on zeatin (1.0 mgl^-1) and dicamba (0.1 mgl^-1) containing medium showed the highest regeneration frequency (98%) with a maximum of 8-9 shoots per calli. Maltose had the maximum callusing and regeneration percentage than other carbon sources. Various gelling agents did not have any significant difference on the regeneration. Of all the varieties, C-306 and HD-2967 were found to be more regenerative and can be used in transformation experiments.     

Three AFLP markers tightly linked to the genic male sterility <Emphasis Type="Italic">ms</Emphasis><Subscript><Emphasis Type="Italic">3</Emphasis></Subscript> gene in chili pepper (<Emphasis Type="Italic">Capsicum annuum</Emphasis> L.) and conversion to a CAPS marker

Genic male sterility (GMS) has long been used as a tool for hybrid seed production in chili pepper (Capsicum annuum L.). We developed DNA markers linked to the GMS ms ₃ gene in a segregating population using bulked segregant analysis (BSA) and amplified fragment length polymorphism (AFLP) techniques. The segregating population was subjected to BSA-AFLP with 512 primer combinations. Three AFLP markers (Eagg/Mccc₂₇₆, Eagc/Mctt₁₇₈, and Ecag/Mtgc₂₀₄) were identified as tightly linked to the ms ₃ locus. Among them, we converted the AFLP marker Ecag/Mtgc₂₀₄ to the cleavage amplified polymorphic sequence (CAPS) marker, named GMS3-CAPS, based on sequencing analysis of internal and flanking regions for the markers between male-fertile and sterile plants. This marker will be useful for pepper breeding using the GMS system.     

Analysis of rice blast resistance gene <Emphasis Type="Italic">Pi</Emphasis>-<Emphasis Type="Italic">z</Emphasis> in rice germplasm using pathogenicity assays and DNA markers

The Pi-z gene in rice confers resistance to a wide range of races of the rice blast fungus, Magnaporthe oryzae. The objective of this study was to characterize Pi-z in 111 rice germplasm accessions using DNA markers and pathogenicity assays. The existence of Pi-z in rice germplasm was detected by using four simple sequence repeat (SSR) markers (RM527, AP4791, AP5659-1, AP5659-5) closely linked to Pi-z, and was verified using pathogenicity assays with an avirulent strain (IE1k) and two virulent races (IB33 and IB49). Among 111 germplasm accessions evaluated, 73 were found to contain the Pi-z gene using both SSR markers and pathogenicity assays. The remaining 38 germplasm accessions were found to be inconsistent in their responses to the blast races IB33, IEIk and IB49 with expected SSR marker alleles, suggesting the presence of unexpected SSR alleles and additional R gene(s). These characterized germplasm can be used for genetic studies and marker-assisted breeding for improving blast resistance in rice.     

Establishment of a comprehensive indicator system for the assessment of biodiversity and ecosystem services

Context

Common indicators are needed to monitor biodiversity loss and the implications for the sustainable provision of ecosystem services (ES). A plethora of different sets of indicators may hinder the identification of major endpoints for large-scale assessments of biodiversity and ecosystem services (BES).

Objectives

We aim to describe the main challenges of indicators for BES assessment and provide suggestions for establishing a comprehensive indicator system.

Methods

An extensive literature review was conducted in this study. We review the main challenges of indicators for BES assessment and propose corresponding improvements from our perspectives of theory and practical applications.

Results

The main theoretical challenges of existing indicators include inconsistent definitions and classifications of ES, misunderstanding of linkages among biodiversity, ecosystem structure, functions and services, and practical problems relate to such issues as indicator representativeness, data availability, and uncertainty. Our suggested improvements include clarifying the main terms, concepts and classification of indicators, establishing a robust conceptual framework with clear interactions among different components and indicators, selecting indicators based on ecosystem properties, streaming existing data into one platform, and strengthening validation of proxies. The steps for constructing a comprehensive indicator system for BES assessment are summarized.

Conclusions

Clear definitions of key terms are indispensable to classify indicators and construct a conceptual framework. Improved understanding of the relations among indicators of biodiversity, ecosystem functions, and ES across multiple scales can guide the development of the indicator system. The integrated indicator system is an important tool for BES assessment to support decision making for sustainable development.

     

The genetic diversity associated with seed proteins in a collection of Spanish underground vetches (<Emphasis Type="Italic">Vicia sativa</Emphasis> L. subsp. <Emphasis Type="Italic">amphicarpa</Emphasis> (Dorthes) Asch. et Graebn.)

The characterization of plant genetic resources is the first step towards improving their use. The Spanish Plant Genetic Resources Centre, which belongs to the National Institute for Agricultural and Food Technology Research (CRF-INIA), conserves accessions of wild underground vetches collected in Spain. In the present work, 26 underground vetch accessions were characterized in terms of their seed storage proteins (separated by SDS-PAGE) as a means of assessing the genetic variation of these plants and their agronomic value. Vicia sativa cv. Vereda was used as control. A total of 54 bands were detected, of which 49 were polymorphic. Fifty eight different electrophoretic patterns were observed in total. Protein bands were scored in terms of their presence (1) or absence (0) for all the seeds studied, and two matrices constructed, one with all the bands present in each accession, the other with the different patterns for each accession. Dendrograms based on the Jaccard similarity index and the UPGMA clustering method were produced from these matrices, and the degree of genetic variation between and within accessions was calculated. The groups obtained were compared with the chromosome number for each accession. The results reflect the great diversity of underground vetch seed storage proteins. The aerial and underground seeds of 16 accessions were then analysed separately. In some cases, the aerial and underground flowers of the same plant produced different proteins.     

Inheritance of red foliage in flowering dogwood (<Emphasis Type="Italic">Cornus florida</Emphasis> L.)

Flowering dogwood (Cornus florida L.) is an ornamental tree valued for its showy white, pink, or red spring bract display and red fall color. A “pseudo” F₂ flowering dogwood population was recently developed from a honeybee mediated cross of ‘Cherokee Brave’ × ‘Appalachian Spring’. The foliage color of 94 “pseudo” F₂ plants segregated into green- and red- leaved phenotypes and was visually rated for color on five spring dates over 3 years (2007–2009). Chi-square analyses of observed segregation of phenotypes indicated that a complementary gene interaction form of epistasis controls foliage color with a 9:7 two gene ratio. We propose the symbols rl ₁ and rl ₂ for the genes controlling this trait.